Introduction. Overview of STN Express 6.0. System Requirements

Transcription

1 STN Express with Discover! 6.0 User Guide for Windows Version 6.0 April, 2001 Copyright Ó 2001 American Chemical Society All rights reserved.

2 1 Introduction Introduction 1 1 Overview of STN Express 6.0 STN Express with Discover! is a fully integrated software package designed to easily and efficiently search scientific and technical databases online through STN as well as other online hosts. It includes: a wizard interface for logon setup, selecting databases, conducting searches, displaying or analyzing results, creating and editing alerts, and much more, without having to know the STN command language easy retrieval of data for hyperlinked CAS Registry Numbers, patent numbers, and other information post-processing options for creating reports and tables from transcripts easy access to Web services through your Web browser easy structure-drawing and searching on STN fragmentation code generation from query structures for searching in World Patent Index convenient access to the STN command-line interface. System Requirements STN Express 6.0 with Discover! requires: Computer: an Intel 486 processor or compatible; a Pentium is recommended Connection to STN: a local modem, networked modem, or a TCP/IP (Internet) connection that supports the telnet protocol Operating System: Microsoft Windows 95, 98, Me, NT 3.51, NT 4.0 or 2000 Memory: 32 MB of RAM; 64MB is recommended Hard Drive: 16 MB or more of free hard disk space Monitor: VGA color monitor compatible with Windows, 800X600 minimum screen resolution Mouse: a mouse, trackball, or similar pointing device Printer: high-quality graphics printer, e.g., laser or inkjet Internet: a web browser and Internet connection for those features that provide links to the World Wide Web

3 1 2 Introduction Help You have the following options for STN Express help: select an option from the Help menu on the Main Menu bar press F1 or click the Help buttons for context-sensitive help. Technical Support For technical assistance, please consult Appendix I, Troubleshooting, in your User Guide or visit on the World Wide Web. If you continue to experience problems, contact your Help Desk by or telephone. To send , you may go to the STN Express Help menu, select Request Help, and then choose your STN Service Center to open your application. North America (and areas not in Japan or Europe) CAS 2540 Olentangy River Road P.O. Box 3012 Columbus, OH USA Phone: (North America) (worldwide) Fax: [email protected] WWW: Japan Japan Science and Technology Corporation (JST) 5-3 Yonbancho Chiyoda-ku Tokyo Japan Phone: (03) Telefax: (03) [email protected] WWW: Japan Association for International Chemical Information (JAICI) Nakai Building Honkomagome, Bunkyo-ku Tokyo 113, Japan Phone: (03) Fax: (03) [email protected] WWW:

4 Introduction 1 3 Europe STN International c/o FIZ Karlsruhe P.O. Box 2465 D Karlsruhe Germany Phone: / Fax: / [email protected] WWW: About this User Guide The user guide covers both the basic and the advanced features of STN Express with Discover! 6.0. You should be familiar with your Windows operating system. If you are not, you may refer to your owner s guide for detailed information on your system. Items that you select, e.g., STN Express buttons or menu options, are presented in bold type. Information intended for you to type or titles of publications or chapters are presented in italics.

5 2 Installation and Main Menu 2 1 Installation and Main Menu Installation This chapter covers the following topics Installing from CD-ROM Upgrading to STN Express 6.0 with Discover! Installing Adobe Acrobat Reader Installing QuickTime Opening STN Express with Discover! Main Menu and Toolbar For information on Network Installation, refer to Appendix G. Network Installation, of your electronic STN Express with Discover! User Guide or the ReadMe.txt file. Installing from CD-ROM 1. Insert the STN Express with Discover! CD-ROM into the CD-ROM drive to start the STN Express setup program. If the setup program does not automatically start, double-click the CD-ROM icon to open it and then double-click setup.exe. 2. Install STN Express with Discover! dialog box is displayed.

6 2 2 Installation and Main Menu Select any or all of the following in the Setup Options: Copy Software to HD - to install the STN Express with Discover! software Softcopy documentation - to install the electronic STN Express User Guide Start Menu Item - to create a Windows Start Menu item for STN Express Select the appropriate Setup Type: Single User - to install STN Express with Discover! to your local hard drive Network User - see your Network Administrator for details Network Server - for information, refer to Appendix G, Network Installation in the STN Express User Guide or click the View ReadMe button to view the ReadMe.txt file. Click Install STN Express with Discover!. Respond to the prompts to complete installation. Upgrading to STN Express Insert the STN Express with Discover! CD-ROM into the CD-ROM drive to start the STN Express setup program. 2. Choose your setup options and select Single User from the Setup Type. 3. Click Install STN Express. Because you have an existing copy of STN Express, its current location is placed in the dialog box as the default. Click Yes to overwrite your existing copy of STN Express. Note that only files provided by your previous STN Express installation programs are overwritten. Any structures, scripts, transcripts, and logon setups that you have created are retained. 4. Respond to the prompts to complete installation. Installing Adobe Acrobat Reader The STN Express with Discover! User Guide is a PDF file. You will need Adobe Acrobat Reader to view the User Guide. To install the Acrobat Reader 4 from the STN Express with Discover! CD-ROM, follow these steps: 1. Insert the STN Express with Discover! CD-ROM into the CD-ROM drive. 2. Click the Install Adobe Acrobat Reader button. 3. Respond to the prompts to complete the installation.

7 Installation and Main Menu 2 3 Installing QuickTime QuickTime 4 software is needed to display JPEG (.jpg) and GIF (.gif) images that can be downloaded in some STN files. 1. Insert the STN Express with Discover! CD-ROM into the CD-ROM drive. 2. Click the Install QuickTime button. 3. Respond to the prompts to complete the installation. Opening STN Express with Discover! To open STN Express with Discover! 1. Launch STN Express with Discover! from the Windows Start menu. By default, an entry has been made under Programs. 2. When STN Express with Discover! is open, the STN Express Main Menu & Toolbar are displayed. Main Menu The Main Menu contains the following menus: File Logon Query Results Setup Web Help File menu File menu item Edit Text File Exit STN Express Function Edit a text file, such as a script Close the STN Express application and all associated applications

8 2 4 Installation and Main Menu Logon menu The Logon! allows you to connect to an online service via a logon setup. There are no sub-menus to Logon!. Query menu The Query menu provides commands to build, edit, or use chemical structure queries, command files, predefined search strategies, and WPI fragmentation code strategies. For details, refer to Chapters 6-9. Query menu item Prepare Structure Query Prepare Command File Check Command File Edit WPI Strategy Generate WPI Strategy Print WPI Strategy Include WPI Other Code Concepts Function Open a new Standard structure drawing window. Open a file to create a script of commands for your online session. Refer to Appendix C for details. Check a script for errors. Edit an existing Derwent WPI fragmentation code strategy. Refer to Chapter 8 for information. Generate a WPI fragmentation code strategy for a WPI query structure. Refer to Chapter 8 for information. Print a WPI fragmentation code search strategy. Select Other Code Concepts to include when generating a WPI fragmentation code strategy. Refer to Chapter 8 for more information.

9 Installation and Main Menu 2 5 Results menu Results Menu Item Browse Transcript Print Transcript Edit Transcript Export Transcript Accounting Table Tool Report Tool Predefined Report Open Function Open (display) a transcript in Browse mode. Print one or more transcripts. Edit the text portion of a.trn transcript. Export a transcript to a new RTF file. Create a cost report for STN online sessions. Refer to Chapter 12 for more information. Create a table from search results in transcript. Create a custom report from search results in transcripts. Create a predefined report from patent search results in transcripts. Open the Trnscrpt folder to browse transcripts, reports, and tables Setup menu Setup Menu Item STN Setup Wizard Connections Preferences Save Configuration Restore Saved Configuration Function Create an automated logon setup. Create or modify a logon setup configuration for an online host. Customize Preferences. Refer to Appendix A for information on General and STN Online and Results Preferences. Refer to Chapter 6 for information on Structure Drawing preferences. Save all logon setups. Restore all logon setups to the last saved configuration.

10 2 6 Installation and Main Menu Web menu Web Menu Item STN Columbus STN Karlsruhe STN Tokyo Function Link web browser to STN Columbus services. Link web browser to STN Karlsruhe services. Link web browser to STN Tokyo services. Help menu Help Menu Item Index Using Help View STN Express User Guide About STN Express Function Obtain an index of help for STN Express. Find out how to use Windows help. Open the STN Express User Guide in your Adobe Acrobat Reader. View copyright and version information.

11 Installation and Main Menu 2 7 Main Toolbar The Toolbar is used to quickly open the STN Express applications. Tool Button Name Setup Logon Prepare Query Browse Transcript Print Transcript Table Tool Custom Report Tool Predefined Report Edit Transcript Preferences Help Exit Function Create logon setups Log onto an online service Open a structure drawing window Open transcript and other files Print transcript and other files Create tables from transcript search results Create custom reports from transcripts Create a patent report from transcripts using a predefined template Open a transcript file for editing Set preferences Display a list of help topics. Quit the STN Express applications.

12 2 8 Installation and Main Menu Customizing the Toolbar To replace a button or gap on the Toolbar, follow these steps: 1. Right click on a button or in an empty space on the toolbar. 2. The STN Express Toolbar Preferences dialog box is displayed. Click Next.

13 Installation and Main Menu Click the Next button until the icon for the desired tool appears. Click OK to complete the action and select the button. 4. The new button appears on the toolbar.

14 2 10 Installation and Main Menu To remove a tool button from the Toolbar, follow these steps: 1. Right-click on the tool button that you want to remove. 2. Click OK in the STN Express Toolbar Preferences dialog box.

15 3 STN Logon Setup STN Logon Setup 3 1 Your online connection and logon information are required each time you connect to STN or another online host. This information, e.g., the telephone number your modem will dial, or the Internet address of the host, is stored in a logon setup. For the latest logon setup information, visit This chapter includes description and examples of the following topics on STN logon setups: Internet setup with STN Setup Wizard Manual modem setup Customizing for academic accounts Setup Definition Values Managing setups Internet Setup with STN Setup Wizard If you do not have any logon setups, the STN Setup wizard starts when you launch STN Express. You may also access the wizard via the Setup menu. Click the Before I Begin button on the opening page for details of how to use the wizard.

16 3 2 STN Logon Setup Follow these steps: 1. Select the STN Service Center for your account and confirm your STN Logon Port. For commercial accounts, X is usually correct. For other accounts, consult the materials supplied with your STN login ID. Click Next. 2. Select the middle radio button to specify an Internet connection to STN.

17 STN Logon Setup Give your new logon setup a name by which you will remember it. If you choose, type your STN login ID and password to save them in the setup. Click Finish. Manual Modem Setup 1. Click on the STN Express Toolbar. 2. The STN Setup dialog box is displayed. Click New to create a new setup.

18 3 4 STN Logon Setup 3. The Setup Definition dialog box is displayed. Enter or select the following information: type a name in Setup Name select your STN Service Center, e.g., STN-Columbus, from the Host Name pull-down menu type your Login ID and password (optional) if you do not want to be prompted for them at login select your modem or appropriate communication option in Connect Via for the Logon Method, select the appropriate telecommunications network or Directdial from the Standard list. Some telecommunications networks require additional information, i.e., Network User Address, Network User ID, Network User Password. If required, a Network Logon section is added into this dialog box. Enter the appropriate information. In the Primary Phone # box, type the telephone number appropriate for your Logon Method select Standard as the Logoff Method Click OK. If you entered your password, you are prompted to re-enter it for verification. After you re-enter it, click OK.

19 STN Logon Setup Click Save to save this setup to your hard disk. Click OK to return to the STN Express Main Menu & Toolbar. Customizing for Academic Accounts If you have an academic account, you need to change: STN Port in logon setup Account Preferences

20 3 6 STN Logon Setup Changing STN Port with STN Setup Wizard If you are using the STN Setup Wizard, replace the Logon Port of X with the appropriate academic account port for your area. Contact your STN account administrator or your STN Service Center for this information.

21 STN Logon Setup 3 7 Changing STN Port in a Manual Logon Setup 1. Click on the STN Express Toolbar. Highlight the setup you want to modify. Click Modify. The setup Definition dialog box is displayed. Click the Host Settings tab. 2. Replace the STN Port of X with the appropriate academic port for your area.

22 3 8 STN Logon Setup Changing Account Preferences for academic accounts To customize Account Preferences for academic accounts, follow these steps: 1. Click Setup from the Main Menu. Select Preferences and then STN Online and Results. 2. Click on the Account tab of Preferences. In the STN Account Type box, select the type of account you have and its features: Commercial (Full access) - default setting Full Academic - if you have access to STN files under your academic program FIZ Academic - if you have access to FIZ discounted files only CAS & FIZ Academic - if you have access only to CAS and FIZ files under your academic program BEILSTEIN subscriber - if you have a Beilstein subscription GMELIN subscriber - if you have a GMELIN subscription DERWENT subscriber - if you have a DERWENT subscription Under Property Data Databases, select the property databases that the Discover! wizards are authorized to access. Click OK.

23 STN Logon Setup 3 9 Setup Definition Values The Setup Definition dialog box opens when you click New or Modify buttons in the STN Setup dialog. This dialog box contains the logon setup s settings, including the name of the online host and the details about how to connect to the host. Setup name The Setup Name identifies a specific setup. The name must be 20 characters or fewer and can include any combination of letters, numbers, special characters, and spaces. Suggested setup names would help identify the host, e.g., STN, and the connection method, e.g., Internet. Host name The Host Name identifies the online host that you want to access in this setup. Select the STN Service Centers for your account from the Host Name pop-up menu Login ID Type your STN login ID in the Login ID box. Entering a login ID at this time is optional. If you do not enter it here, you will be prompted to enter it when you log on to STN. Password Enter your STN password in the Password. For security, an asterisk is displayed for each password character you type. Your password is stored in the express.ini file in an encrypted form. Entering a password at this time is optional. If you do not enter it here, you will be prompted to enter it when you log on to STN. Path Select Path 1 to define the first communication path to STN. Select Paths 2-4, as needed, to define alternate communication paths. When STN Express tries to connect to STN, it first uses Path 1. If Path 1 fails to connect, STN Express tries the next path until the connection is made or there are no more paths to try.

24 3 10 STN Logon Setup Host Settings Select the Host Settings tab to see settings that are specific to STN. Many of the settings are critically important and cannot be changed. Click a in the Command Window box to cause STN Express with Discover! to open a Command Window when you log on to STN. The Command Window can be turned off and on while you are logged on. Click a in the Close Window at logoff box to tell STN Express with Discover! to close the session window after you log off. If you prefer to view cost information, scroll back through your session for any reason, or capture a transcript after you log off, do not select this option. Up to five commands may be entered in the Execute at first Host Prompt window. The first command is sent when the first => prompt is received, and the remaining commands are sent, one at a time, with each succeeding arrow prompt. By default, a carriage return is sent after each line. The keyword NOCR may be added as the last word on the last line that you enter to indicate that this line is to be displayed in the STN Online and Results window, but not sent. This allows you to enter data after the defined character string, before it is sent.

25 STN Logon Setup 3 11 The STN Port is X by default and is a appropriate for commercial accounts. Change it to the port letter appropriate for you account if necessary. The Graphics option specifies whether chemical structure diagrams will be displayed in a transcript. Uncheck the Graphics box if you do not want to display structure graphics. Connect via Select a communication method from the Connect via pulldown menu to connect to the online host you selected. The method that you choose controls the information that is required in the Communication Settings section. This is described further in the Communications Settings section, later in this chapter. Connect via options are: Winsock (Internet) - select if your network software supports Windows Sockets and Telnet from your PC (most do). When selected, the Host Name or IP Address, Port, and Echo fields are displayed. Enter the host name or host address, if different from the default (rare). Set Echo to No if you do not want STN Express with Discover! to echo characters as they are typed. The Port setting of 23 (Standard Telnet) in most cases should not be changed. Dial-Up Networking - STN Express with Discover! lists all connections defined in Windows Dial-Up Networking. Dial-Up Networking connections are most commonly used to define connections to the Internet via an Internet Service Provider (ISP). When you log on to STN, STN Express with Discover! will attempt to use the Standard Windows interface to Dial-Up Networking (in WININET.DLL). You will be prompted to connect to your ISP as needed. NOTE: Winsock is the underlying connection type for this option. Modem - STN Express with Discover! lists all modems installed in the Windows Modems Control Panel. This option eliminates the need to set many of the modem options, because this information is obtained directly from Windows. Most users will only need to specify a phone number for this option. NOTE: If you cannot make a connection using this method, try using COM port option. COM1, COM2, COM3, or COM4 - select to connect via a serial port, e.g., to a modem, terminal server, or host system.

26 3 12 STN Logon Setup Standard logon Use a Standard Logon Method to connect to STN via one of the supported networks. To use a standard logon procedure, click the radio button next to Standard in the Logon Method section and select one of the supported networks from the pulldown menu. STN Express with Discover! automatically inserts the scripts to connect to STN through the selected network. For example, if a setup is defined to connect to STN-Karlsruhe via Datex- P, STN Express with Discover! selects several scripts from the Scripts folder: a script that sends dial commands to a modem a script that connects to STN-K via the Datex-P network. a script that logs on to STN. The scripts use the values in the logon setup, such as dial method, phone number, and NUA, to make the connection and log you in. Standard logoff Click the radio button next to Standard in the Setup Definition dialog box to tell STN Express with Discover! to use the discnct script to disconnect the communication path. This script handles most connections, including those made through a modem and via Winsock. If STN Express with Discover! does not correctly disconnect the communication path, you will need to define a custom logoff. Network Logon The Network Logon section in the Setup Definition dialog box is displayed when STN Express with Discover! recognizes that the Connect via option you selected requires information to make the network connection to STN. You may need to enter any of the following values: NUA (Network User Address) - the address of the host on the network you selected. The value may be a character string, e.g., stnc, or a numerical string, e.g., NUI (Network User Identifier) - a character string that identifies the user to the network. Some networks require this. NUP (Network User Password) - a password to confirm the identity of the user on the network. Some networks require this. To keep the NUP entry secure, only asterisks are displayed when you type this value. It is stored in the express.ini file in encrypted form. To confirm your NUP, you are prompted to re-enter the password after you select OK in the Setup Definition dialog box. STN Express with Discover! provides the NUA values for a limited number of networks. If an NUA is not available, an error message is displayed when you try to use the setup. If this occurs, return to the Setup Definition dialog box. Then select the path that failed and fill in the NUA and related fields.

27 STN Logon Setup 3 13 Communications Settings The Communications Settings section of the Setup Definition dialog box contains the communication parameters used by STN Express with Discover! to connect to a host. The available settings are based on your selection in the Connect via pulldown menu. Settings for Winsock (Internet) and dial-up networking setups An example logon setup for STN-Karlsruhe using the Internet is shown: The Communications Settings for STN logon setups when Connect via is Winsock (Internet) or a Dial-Up Networking item are Host Name or IP Address - the name or address of the STN computer to which STN Express will connect. For example, the name of the STN-Karlsruhe computer is stnk.fiz-karlsruhe.de and its address is These values are provided automatically when you select an STN Service Center from the Host Name list. If you must connect to STN through a telnet gateway, enter the name or IP address of the gateway and see Appendix F for more information. Port - the TCP/IP port number for telnet (Winsock) connections. The default is 23, and you should change this only if your organization has a firewall that uses a different port for the telnet protocol.

28 3 14 STN Logon Setup Echo the duplex setting that specifies whether to echo characters as they are typed. If you cannot see the characters you are typing or if you see two characters for every one that you type, try changing the Echo selection. Settings for modem setups When the name of a modem is selected in Connect via, the following settings are available in STN Express. To view and change the modem s other communications settings, use the Windows Modems Control Panel. Echo the duplex setting that specifies whether to echo characters as they are typed. If you cannot see the characters you are typing or if you see two characters for every one that you type, try changing the Echo selection. Break Length - the duration of a Break signal sent by STN Express with Discover! through a serial (modem) connection. The duration ranges from 10 to 2000 milliseconds; the default is 500. If STN does not recognize the Break signal, you may need to increase this value. If the Break signal disconnects you from your network, you may need to decrease this value. Dial - the type of dialing to be used: Tone, Pulse (rotary), or Manual. If Manual is specified, STN Express with Discover! issues a message and waits for you to manually dial the telephone. Primary Phone # - the telephone number for the network provider you selected. Secondary Phone # - an alternate telephone number for your network provider that is used if the primary phone number fails to connect.

29 STN Logon Setup 3 15 Settings for COM Port setups Here is an example logon setup for STN-Columbus using a COM port: When the COM port to which your modem is attached is selected in Connect via, the following settings are available in STN Express. Echo - the duplex setting that specifies whether to echo characters as they are typed. If you cannot see the characters you are typing or if you see two characters for every one that you type, try changing the Echo selection. Break Length - the duration of a Break signal sent by STN Express with Discover! through a serial (modem) connection. The duration ranges from 10 to 2000 milliseconds; the default is 500. If STN does not recognize the Break signal, you may need to increase this value. If the Break signal disconnects you from your network, you may need to decrease this value. Speed (bps) - the serial port speed used to connect to your modem. The speed may range from 300 to bits per second. Select the highest speed that your modem supports.

30 3 16 STN Logon Setup Flow Control - the type of flow control, e.g., None, Software (XON/XOFF), Hardware (RTS/CTS), to be used. Flow Control is used to prevent the overflow and loss of data from an online host. Hardware is the default and should be used in most cases. Data loss may occur if this setting is not synchronized with your modem s settings. Data bits, Stop bits, and Parity - select to identify the number of data bits in each byte sent or received, the minimum number of bits sent after each byte, and the parity. 8, 1.0, and NONE are nearly always the best choices and are the defaults. Use 7, 1.0, and EVEN when the maximum modem speed is lower than 9600 baud. Dial - the type of dialing to be used: Tone, Pulse (rotary), or Manual. If Manual is specified, STN Express with Discover! issues a message and waits for you to manually dial the telephone. Primary Phone # - the telephone number for the network provider you selected. Secondary Phone # - an alternate telephone number for your network provider that is used if the primary phone number fails to connect. Advanced (Communications Settings) The Advanced option in the Communications Settings section of the Setup Definition dialog box is used to provide information used by three different features of STN Express with Discover!. They are: connecting to STN through a telnet gateway, firewall, or proxy server. Refer to Appendix F for details. sending an initialization string to a modem sending a character string instead of a standard Break command

31 Click the Advanced button to open the Advanced dialog box. STN Logon Setup 3 17 Enter the appropriate information. Click OK when all specifications are entered. Or click Cancel to cancel all the specifications. Modem Configuration Enter values in the Modem Configuration section to define an Initialization String for the modem. If you specify a value in this field, the string is sent to the modem before the dial command is issued, and a response of OK is expected. See your modem manual for details about modem commands and options. NOTE: Not recommended if you have selected the name of your modem from the Connect via list. The Phone # field in the Modem Configuration section normally displays the value of the Primary Phone # for this path. For the special case when the phone number fields in the Communication Settings area are not available, e.g., for Winsock connections to a network modem pool, use this field to specify a telephone number. Other Enter the appropriate value in the Break sequence text box to define a character string that you want STN Express with Discover! to use as a Break indication to an online host. This value is needed only for systems that do not support a standard Break.

32 3 18 STN Logon Setup Custom Logon Use custom logon when STN Express does not support the network you choose, i.e., if the telecommunications network you use to connect to STN is not in the Logon Method Standard list. A custom logon method is also appropriate if you must use a combination of supported networks. A custom logon requires you to select scripts to tell STN Express with Discover! how to connect to STN. Scripts typically are used to execute a step in the logon process. For example, one script might have the modem dial a telephone number and connect to a telecommunications and network a second script may connect to STN through that network. Always use the STNLOGON script to log on to STN. You may also write your own script to connect through an unsupported network. For information on writing scripts, refer to Appendix C, Script Language. To create a custom logon procedure, click the radio button next to Custom in the Logon Method section. Then click the Configure button. The Custom Logon dialog box is displayed. The Scripts Folder box displays a list of scripts from either the User or Standard scripts folder. The Standard scripts folder corresponds to the Predefined Scripts folder in General Preferences. The User scripts folder corresponds to the User Scripts folder in General Preferences. The Selected script list box displays the scripts that have been selected for this custom logon setup. The scripts will be executed in the order shown as part of the connect and logon process. To change the order of the scripts in the Selected script list, select a script and click the up ( ) or down ( ) arrow to move the script name one position at a time.

33 STN Logon Setup 3 19 To add a script to the logon procedure, select (highlight) a script in the Scripts Folder list. Then click the Copy>> button to copy the script to the Selected script list. Click the Watch Me button to insert the watchme.sc script into the Selected script list window. The watchme.sc script can be used more than once in the Selected script list. For more information, refer to the Watch Me section later in this chapter. Click the Delete button to delete a script from the Selected script list. Click the View button to display the actual script for a script name that you select from the Scripts Folder window. Click OK to when you have completed your entries to the Selected script list window and to return to the Setup Definition dialog box. The scripts you selected are displayed in the Custom Logon Script List box. Watch Me For some custom logon methods, a custom-written script is needed. You may write the script yourself, but it may be more efficient to let Watch Me write it for you. The Watch Me function creates a script by recording the commands that you enter from the keyboard and the network s responses when you log on to a network. STN Express with Discover! begins the Watch Me function when it finds the script named watchme.sc as the name of the script that it is ready to execute. After watchme.sc is found, you are prompted to enter the name of the new script that is to be created. (After Watch Me has finished, watchme.sc is replaced with the new script in the Custom Logon Script List.) A dialog box with two buttons, Stop and Cancel is displayed. An STN Express with Discover! script is created in this window and is generated from the commands entered from the keyboard and from the prompts received from the host system. The script continues to be created until you click Stop. STN Express with Discover! continues executing the next script listed in the Selected scripts list window located in the Custom Logon dialog box. The next time you log on using this setup, your newly created script will run, executing the commands recorded during the Watch Me function. Click Cancel, at any time, to cancel the Watch Me function without creating the new script.

34 3 20 STN Logon Setup Custom logoff Use a custom logoff procedure when the method to disconnect from an online host is not successful or is not supported by the standard logoff method. The Logoff Method section in the Setup Definition dialog box defines how STN Express with Discover! will disconnect the communications path when you log off from an online host. When you log off, STN Express with Discover! scans the output from the host system looking for the logoff messages defined under the Host Settings tab in the Setup Definition dialog box. When it locates a message, STN Express with Discover! knows that is has logged off of the remote system. It then disconnects the communication path using the method defined in this section. If the communication path is not disconnected correctly, you may get a Communication Port In Use error when you try to use a program that requires the use of a communication port. The steps for defining a custom logoff are nearly identical to that for defining a custom logon. Refer to Custom Logon in this chapter for details. Managing Setups Open the STN Setup dialog box by clicking the Setup button in the main toolbar or by clicking Setup Connections.

35 STN Logon Setup 3 21 Modifying a setup To modify an existing logon setup, select a setup from the Setup Names list in the STN Setup dialog box. Then click Modify. The Setup Definition dialog box is displayed, as well as the values you selected for this setup. Change any value. Then click OK to accept the changes or Cancel to cancel the changes. You are returned to the STN Setup dialog box. To save your changes, click Save. To test your changes before saving, or to use those changes for only that STN Express session, click OK. You will be prompted to save the configuration when you exit STN Express with Discover!. If you do not want to continue using these changes in subsequent sessions, click NO when prompted. Copying a setup To make a copy of a setup, select a setup from the Setup Names list in the STN Setup dialog box. Then click Duplicate. An Enter new name dialog box is displayed. Type a new name. Then click OK. The new setup is listed in the STN Setup dialog box. Select the new setup and click Save. Then click OK. You can modify a copied setup to efficiently create a new setup. Deleting a setup To delete a setup, select a setup from the Setup Names list in the STN Setup dialog box. Then click Delete. A STN Setup dialog box is displayed that asks you to confirm the deletion. Click Yes to delete the setup or No to cancel the request. If you click Yes, the setup is removed from the list displayed in the STN Setup dialog box. Password protecting setups The Password Options section in the STN Setup dialog box allows you to password protect access to your STN Setup dialog box. Click in the Password Protected check box in the Password Options section. Then click Set Password. The Password Protect dialog box is displayed. The password is not displayed. Therefore typing it twice confirms that you have entered it correctly. Click OK. You are returned to the STN Setup dialog box. If the Password Protected option is enabled, you are prompted to enter this password when you access Setup. Your password is required only once per STN Express with Discover! session.

36 3 22 STN Logon Setup Changing setup password To change an existing setup password, click the Set Password button in the Password Options section of STN Setup dialog box. The Password Protect dialog box is displayed. Type your current password in the Old Password text box. Then type your new password in the New Password text box. Reenter your new password in the Retype New Password text box. Then click OK. You are returned to the STN Setup dialog box. Disabling setup password To disable your setup password, click in the Password Protected check box located in the Password Options section of the STN Setup dialog box. The is removed. A password is no longer required when entering the STN Setup dialog box.

37 4 Online Session on STN Online Session on STN 4 1 Overview This chapter covers the following topics: Connecting to STN Capturing transcript STN Online and Results window Toolbar STN Online and Results window Status Bar Using the Online menu Entering commands Managing transcripts while online Viewing downloaded images Searching STN with the Discover! wizards Connecting to STN 1. Click Logon on the STN Express Main Menu or the Toolbar. 2. The Select Logon Settings dialog box is displayed, if you have more than one setup. If you have only one setup created, this dialog box is not displayed. Select a setup name and click OK.

38 4 2 Online Session on STN Capturing Transcript The Capture Session dialog box is displayed at login. To capture your online session as a transcript, type a name for the session in the File name text box and click Open. The default type format is *.trn. Select another file type, e.g., RTF (Rich Text Format) if you want your transcript captured in Rich Text Format. Refer to the Appendix A. Preferences for information on how to change the default file type for capturing transcripts. Click Cancel to continue the logon process with no transcript. If you choose the name for an existing transcript, a message is displayed asking if you want to append or overwrite the existing transcript. You may also cancel session capture.

39 Online Session on STN 4 3 STN Online and Results Window When the connection to STN is completed, the STN arrow prompt (=>) is displayed in the STN Online and Results window. Online interaction with STN occurs in the STN Online and Results window. The STN Online and Results window contains: Content the Menu bar the Toolbar the text area for entering commands the Status Bar

40 4 4 Online Session on STN Toolbar The Toolbar displays buttons for quick access to tools and menu options. You can display the name and function for a particular button. Hover the cursor over the button to have its function displayed in the Status Bar. The tool buttons include: Begin a new online session (Logon) Open transcript Edit transcript Turn off transcript capture Print Copy the selected area to the clipboard Paste the clipboard content to the screen Report Tool

41 Online Session on STN 4 5 Table Tool Predefined Report Tool Scroll to previous command in the session Scroll forward to next command in the session Upload structure query Activate the Command Window Run Command File Send break to online host Hyperlink all CAS Registry Numbers while connected to STN Send Logoff command to online host Force Send-Click, enter your command and press Enter Switch to STN Structure Drawing Set STN Online and Results Preferences View online help documents or request help by

42 4 6 Online Session on STN You may easily customize the Toolbar by removing or adding tool buttons. Adding tool buttons to the Toolbar To add a tool button, follow these steps: 1. Right-click in the space on the toolbar where you want to add a button. The Toolbar Preferences dialog box appears. The option Remove button or gap from toolbar is always the initial option. Click Next. 2. Click Next to view the buttons one at a time. Continue to click Next until you see the desired button.

43 3. Click OK to choose the displayed button for the toolbar. Online Session on STN The new button is displayed on the toolbar in the slot you have selected. Removing tool buttons from the Toolbar To remove a tool button or a gap from the toolbar, follow these steps: 1. Right-click on the button that you want to remove. 2. In the Toolbar Preferences dialog box, click OK. The tool button that you have selected is now removed from the Toolbar.

44 4 8 Online Session on STN Status Bar The Status Bar is located at the bottom of the STN Online and Results window. Status Bar Item Discover! Transcript File Name INS/OVR Hold On/Hold Off Print Off/Print On Online Running timer Function Displays a pop-up menu for the Discover! wizards Displays the directory path and the file name for your transcript. If you are not capturing a transcript, click on transcript to start capture. Displays the current STN file. Click this box to display a pop-up menu with recently entered files or to select From a List of files. Click this box to change from the insert or overwrite mode for entering text. Toggle to Hold On to stop the screen from continuously scrolling. Toggle to Hold Off to resume scrolling. Print On activates slave printing of information on the terminal window. Print Off turns off printing. Indicates an active session; the green color indicates ready and red indicates busy. Offline indicates terminated communication. Displays the total amount of time you have been connected in your online session. For information on how you can customize the Status Bar, refer to Appendix A. Preferences.

45 Online Session on STN 4 9 Using the Online Menu Only the non-greyed options in the Online menu are available while you are connected to STN.

46 4 10 Online Session on STN Online menu option Recall Command Use Pagination Mode/ Use Continuous Scroll Show Text Structures/ Show Graphics Structures Suppress Screen Display/ Restore Screen Display Send Break Prompt Override Terminal Mode Kermit Send Kermit Receive Logoff Logoff Hold Command Window Function Recall the last command you typed online. You may use this command repeatedly to recall prior commands from the same session, or to edit a line to create a new command. Use the Up Arrow/Down Arrow keys as shortcuts. Toggle to control the scrolling of your online display data. Pagination Mode holds a screen temporarily. To continue displaying the next screen, click the Hold On box in the Status bar. Toggle to display text or graphics structures. Toggle to control the output display in a terminal window. Suppress Screen Display prevents STN Express from updating the window with new data; this increases the speed at which you may capture results. Send a break to interrupt a host system process. Moves your cursor to the line directly below the prompt and makes STN Express ready to accept a typed command. Use to change terminal emulation if you want to access non-stn hosts. Upload text or binary files using the Kermit protocol. Download a file from a host system. Disconnect from an online host. Disconnect from STN temporarily. Open a separate window for entering commands to your online host.

47 Online Session on STN 4 11 Entering Commands You may enter STN commands in the following ways: by typing them at an arrow prompt (=>) in the text area of the STN Online and Results window by using the Command Window by using scripts Entering commands in the Command Window In the STN Online and Results window you can create a separate window for entering commands by typing them or by inserting the contents of a file. To open a Command Window, select Command Window from the Online menu or the tool button from the STN Online and Results toolbar. To enter commands in the Command Window: 1. Keep this button from the right toolbar of the Command Window in the locked position. In the locked mode, you can type a series of commands and edit them. 2. To send the commands in the Command Window to STN, use the buttons from the right toolbar of the Command Window: Button Function To send one command line at a time To send multiple command lines.

48 4 12 Online Session on STN Inserting a command file into Command Window To insert the contents of another file (with commands): 1. Click the Open button, located on the left toolbar 2. Open a command file name in the dialog box to insert the contents of the command file into the Command Window. Saving the content of the Command Window Click the Save button located on the left toolbar in the Command Window to save the contents of the Command Window to a file. Clearing the content of the Command Window To clear the contents of the Command Window, click the Clear button located on the left toolbar in the Command File Window. Using scripts STN Express includes a script language that lets you automate online tasks. Refer to Appendix C for information about the script language. The Query menu in the STN Online and Results window online provides options for using scripts. Option Prepare Command File Check Command File Run Command File Function Create a script of commands for entering in your online session. Refer to Appendix C for information on the script language. Check a script for errors. Execute a previously prepared script.

49 Online Session on STN 4 13 Using Predefined Search Strategies STN Express provides a number of predefined search strategies that you can use or edit. To access the predefined search strategies, select Use Predefined Search Strategy from the Query menu. Managing Transcripts While Online While you are connected to STN, the Results menu offers the following options for managing transcripts in a toggle mode. Option Capture Session Print Session Start New Page Edit Transcript Function Capture text and graphics of your online session to a file. Print the session as it occurs (slave mode). Insert a page break into the transcript or a slave print. Edit the text of an existing (already created) transcript file. Refer to Chapter 10 for information.

50 4 14 Online Session on STN Viewing Downloaded Images Some STN files include technical drawings, chemical structures, trademarks, complete pages of publications, and other graphical images. These images are different from chemical structure diagrams in, for example, the Registry file because each image is downloaded into a separate file. Downloaded images may be in one of three file formats: Image Format TIFF JPEG GIF File Extension.tif.jpg.gif When you display records on STN using display formats that include images, STN Express automatically downloads the images to your PC. The files are named according to the name of your transcript, a sequential number, and the appropriate extension for the image type. For example, if your transcript is named silane.trn, the first TIFF image downloaded is named silane001.tif. If the next image is a GIF image, it is named silane002.gif. If you are not capturing a transcript, the image files are named IMAGE001.TIF, etc. When you browse a transcript offline, you have the option of viewing all the downloaded images in the context of your transcript. Viewing JPEG and GIF Images Online JPEG and GIF are common image file formats. Use your own image or graphics software to view individual JPEG and GIF images. QuickTime TM is provided with the STN Express 6.0 software to allow you to view JPEG and GIF images in transcripts, reports, and tables.

51 Online Session on STN 4 15 Viewing TIFF images online To view a TIFF Image while online, select View TIFF image from the File menu or click the View TIFF Image button from the STN Online and Results Toolbar. A TIFF File dialog box is displayed. Select a file name and click Open. The image is displayed in the TIFF File Display window.

52 4 16 Online Session on STN View menu options The View menu in the TIFF File Display window provides a number of options for viewing the TIFF images. Option Zoom In Zoom Out Function Enlarge the size of the image Reduce the size of the image Rotate Change the orientation of the image, 90 degrees, clockwise Flip Horizontal Flip Vertical Display the image 180 degrees opposite its horizontal axis Display the image 180 degrees opposite its vertical axis

53 Online Session on STN 4 17 File menu options The File menu in the TIFF File Display window contains the following options for displaying and printing images. Option Open Previous Image Next Image Print Print Setup Exit Function View the image View the preceding image in a series View the next image in a series Print the image. The size of the printed image is determined by the zoom setting; zoom in for a larger printed image, zoom out for a smaller printed image. Modify the printer setup Exit the TIFF File Display

54 4 18 Online Session on STN Mode menu options You may also use the Mode menu to change the display of the images. Searching STN with Discover! Wizards STN Express with Discover! enables you to use wizards, rather than type commands, for some functions. Click the Discover! button at the bottom of the STN Online and Results window to see the Discover! wizards menu. Discover! menu

55 Online Session on STN 4 19 Searching hyperlinked data with Discover! To make it easy to retrieve data automatically, various items in STN search results are hyperlinked by default, such as the following: CAS Registry Numbers Patent numbers OS (Other Source) field Full-text options. For example, the hyperlinking of CAS Registry Numbers makes it easy to obtain additional data. Simply click on the hyperlinked CAS Registry Number. A pop-up menu is displayed. Select an option from the pop-up menu. STN Express with Discover! enters the appropriate files, conducts searches, and returns the requested substance data. STN Express with Discover! even remembers the last CAS Registry Number that you have selected. When you right-click, a pop-up menu displays again, showing you the previously selected CAS Registry Number. ANALYZE wizard While you are connected to STN, you may also use the ANALYZE wizard to display the analyzed fields from search results as a histogram. Follow these steps. 1. Click the Discover! button. Select Analyze Answers from the Discover! menu.

56 4 20 Online Session on STN 2. The ANALYZE wizard is invoked. Click Next. 3. Highlight the answer set for analyzing. Click Next.

57 Online Session on STN Select the field to analyze. Click Analyze. 5. Select the range of terms to analyze. Click Display.

58 4 22 Online Session on STN 6. The analyzed results are displayed as a histogram. To display the answers from the histogram, click on one of the boxes on the left and click the Display these answers button. To print the histogram, click the Print button. To save the histogram, click Save As. 7. If you click Save As, the Select Analyze Results File dialog box is displayed. Enter the name for the saved file and select the format, e.g., Excel Files.

59 Online Session on STN The saved results are displayed as a bar graph in Microsoft Excel.

60 5 Using non-stn Hosts Using non-stn Hosts 5 1 Overview In addition to STN, STN Express with Discover! provides automatic logon and other features for the following supported online hosts: DIMDI Datastar Dialog EINS NLM Ovid Questel Orbit STN Express also lets you define host settings for other, unsupported online hosts so that automatic features will function. In addition, manual emulation, with no automatic features, can be used to connect to any computer or online host. This chapter covers the following topics: Logon setups for supported non-stn hosts Logon setups for other hosts Online session on non-stn hosts Refer to Chapter 3 for information about logon setups for STN and general information about managing setups. Refer to Chapter 4 for information on online session on STN.

61 5 2 Using non-stn Hosts Logon Setup for Supported non-stn Hosts To create a new logon setup for a supported host, click the Setup button on the STN Express Toolbar or click the Setup menu and select Connections. The STN Setup dialog box opens. Click New to open the Setup Definition dialog box. Creating a logon setup Basic logon setup values Setup Name The Setup Name identifies a specific setup. The name must be 20 characters or fewer and can include any combination of letters, numbers, special characters, and spaces. Suggested setup names help identify the host (Questel, in this example) and communication path (COM1), e.g., Questel via modem. Host Name The Host Name identifies the online host that you want to access in this setup. Login ID Enter your login ID for the online host you selected in the Login ID text box. Entering a login ID at this time is optional. If you do not enter it here, you will be prompted to enter it when you log on to the host Password Enter your host password in the Password box. For security, an asterisk is displayed for each password character you type. Your password is stored in the express.ini file in an encrypted form. Entering a password at this time is optional. If you do not enter it here, you will be prompted to enter when you log on to the host. Path Tabs Select Path 1 to define the communication path to reach the online host you selected. Select Paths 2-4, as needed, to define alternate communication paths to the online host. When STN Express tries to

62 Using non-stn Hosts 5 3 connect to the host, it first uses Path 1. If Path 1 fails to connect, STN Express tries the next path until the connection is made or there are no more paths to try. + Only Path 1 is available when the Host Name is set to Manual Emulation. The Host Settings tab, to the right of the Path tabs, contains settings that are specific to the selected online host. Usually these settings do not need to be changed. Refer to the Host Settings section later in this chapter for details. Connect via Select a communication method from the Connect via pulldown menu to connect to the online host you selected. The method that you choose controls the information that is required in the Communication Settings section. This is described further in the Advanced Communications Settings section, later in this chapter. Connect via options are: Winsock (Internet) - select if your network software supports Windows Sockets and Telnet from your PC (most do). When selected, the Host Name or IP Address, Port, and Echo fields are displayed. Overwrite the host name or host address, if different from the default (rare). Set Echo to No if you do not want STN Express with Discover! to echo characters as they are typed. The Port setting of 23 (Standard Telnet) in most cases should not be changed. Dial-Up Networking - STN Express with Discover! lists all connections defined in Windows Dial-Up Networking. Dial-Up Networking connections are most commonly used to define connections to the Internet via an Internet Service Provider (ISP). STN Express with Discover! will then attempt to use the Standard Windows interface to Dial-Up Networking (in WININET.DLL) when a logon is attempted. You will be prompted to connect to your ISP as needed. NOTE: Winsock is the underlying connection type for this option. Modem - STN Express with Discover! lists all modems installed in the Windows Modems Control Panel. This option eliminates the need to set many of the modem options, because this information is obtained directly from Windows. Most users will only need to specify a phone number for this option. NOTE: If you cannot make a connection using this method, try using a COM Port option. COM1, COM2, COM3, or COM4 - select to connect via a serial port, e.g., to a modem, terminal server, host system.

63 5 4 Using non-stn Hosts Standard Logon and Logoff methods The logon method includes connecting to the online host and logging on to the host. Use a Standard Logon Method to connect to a supported host system via one of the supported networks. Use a Custom Logon Method when you connect via an unsupported network and when you log on to an unsupported host. A custom logon method is also needed for certain combinations of supported networks, such as when a network modem pool is reachable by a Winsock connection. See Custom Logon and Logoff later in this chapter for details. Standard Logon To use a standard logon procedure, click the radio button next to Standard in the Logon Method section and select one of the supported networks from the pulldown menu. STN Express with Discover! automatically inserts the scripts necessary to connect to the network and the host you selected, and also inserts the values that the scripts require. Modify these values, as needed. For example, if a setup is defined to connect to DIMDI host via Tymnet, using a tone or pulse modem, STN Express with Discover! selects several scripts from the Scripts folder including the following: a script that sends dial commands to a modem a script that connects to DIMDI via the Tymnet telecommunications network a script that logs on to DIMDI + If you are connecting via a gateway or firewall that requires a separate logon, see Settings for Winsock (Internet) Setup for Supported non-stn Hosts later in this chapter and Appendix F. Standard Logoff Click the radio button next to Standard in the Setup Definition dialog box to tell STN Express with Discover! to use the discnct script to disconnect the communication path. This script handles most connections, including those made through a modem and via Winsock. If STN Express with Discover! does not correctly disconnect the communication path, you will need to define a custom logoff. See Custom Logon and Logoff later in this chapter for more information.

64 Using non-stn Hosts 5 5 Network Logon The Network Logon section in the Setup Definition dialog box is displayed when STN Express with Discover! recognizes that the Host Name and Connect via combination you selected require information to make the network connection. You may need to enter any of the following values: NUA (Network User Address) - the address of the host on the network you selected. The value may be a character string, e.g., stnc, or a numerical string, e.g., NUI (Network User Identifier) - a character string that identifies the user to the network. Some networks require this. NUP (Network User Password) - a password to confirm the identity of the user on the network. Some networks require this. To keep the NUP entry secure, only asterisks are displayed when you type this value. It is stored in the express.ini file in encrypted form. To confirm your NUP, you are prompted to re-enter the password after you select OK from the Setup Definition dialog box. STN Express with Discover! provides default NUA values for a limited number of combinations of hosts and networks. If a default value is not available for the combination you have selected, an error message is displayed when you try to use the setup. If this occurs, return to the Setup Definition dialog box. Then select the path that failed and fill in the NUA field. Settings for Winsock (Internet) setup for supported non-stn hosts When Connect via is Winsock or a Dial-up Networking item, settings specfic to Internet TCP/IP connections are available. The settings are Host Name or IP Address - the name or address of the host computer to which STN Express will connect. For example dialog.com or These values are provided automatically for supported online hosts. If you must connect to the host through a telnet gateway, enter the name or IP address of the gateway and see Appendix F for more information. Port - the TCP/IP port number for telnet (Winsock) connections. The default is 23, and you should change this only if your organization has a firewall that uses a different port for the telnet protocol. Echo - the duplex setting that specifies whether to echo characters as they are typed. If you cannot see the characters you are typing or if you see two characters for every one that you type, try changing the Echo selection.

65 5 6 Using non-stn Hosts Modem settings for supported non-stn hosts When a modem or COM port is selected in the Connect via list, the Communications Settings section of the Setup Definition dialog box contains modem communication parameters. The following settings are available: Echo - the duplex setting that specifies whether to echo characters as they are typed. If you cannot see the characters you are typing or if you see two characters for every one that you type, try changing the Echo selection. Break Length - the duration of a Break signal sent by STN Express with Discover! through a serial (modem) connection. The duration ranges from 10 to 2000 milliseconds; the default is 500. If the online host does not recognize the Break signal, you may need to increase this value. If the Break command disconnects you from your network, you may need to decrease this value. Dial - the type of dialing to be used: Tone, Pulse (rotary), or Manual. If Manual is specified, STN Express with Discover! issues a message and waits for you to manually dial the telephone. Primary Phone # - the telephone number for the network provider you selected. Secondary Phone # - an alternate telephone number for the network provider, used if the primary phone number fails to connect. Use the Windows Modems Control panel to change other communication settings.

66 Using non-stn Hosts 5 7 Connect via COM port settings The following settings are available: Echo - specifies whether to echo characters as they are typed. If you cannot see the characters you are typing or if you see two characters for every one that you type, try changing the Echo selection. Break Length - the duration of a Break signal sent by STN Express with Discover! through a serial (modem) connection. The duration ranges from 10 to 2000 milliseconds; the default is 500. If the online host does not recognize the Break signal, you may need to increase this value. If the Break command disconnects you from your network, you may need to decrease this value Speed (bps) - the serial port speed used to connect to your modem. The speed may range from 300 to bits per second. If your modem s maximum speed is not listed, select next higher speed. Flow Control the method of synchronizing communications between the PC, modem, and online host. Flow Control is used to prevent the overflow and loss of data from an online host. Hardware is the default and should be used in most cases. Data loss may occur if this setting is not synchronized with your modem s settings. Data bits, Stop bits, and Parity - data transfer settings. Data bits 8, Stop bits 1.0, and Parity NONE are nearly always the best choices and are the defaults. Use 7, 1.0, and EVEN when the maximum modem speed is lower than 9600 baud.

67 5 8 Using non-stn Hosts Dial - the type of dialing to be used: Tone, Pulse (rotary), or Manual. If Manual is specified, STN Express with Discover! issues a message and waits for you to manually dial the telephone. Primary Phone # - the primary telephone number for the network provider Secondary Phone # - an alternate telephone number for the network provider. Advanced Communication Settings The Advanced option in the Communications Settings section of the Setup Definition dialog box is used to provide information used by three distinct features of STN Express with Discover!. They are: Connecting to an online host through a telnet gateway, firewall, or proxy server. Refer to Appendix F for details. Sending an initialization string to a modem Sending a character string instead of a standard Break command Advanced dialog box Click the Advanced button to open the Advanced dialog box. Enter the appropriate information. Click OK when all specifications are entered. Or click Cancel to cancel all changes.

68 Using non-stn Hosts 5 9 Advanced dialog box values Modem Configuration Enter values in the Modem Configuration section to define an Initialization String for the modem. If you specify a value in this field, the string is sent to the modem before the dial command is issued, and a response of OK is expected. See your modem manual for details about modem commands and options. NOTE: Not recommended if you have selected the name of your modem from the Connect via list. The Phone # box in the Modem Configuration section normally displays the value of the Primary Phone # for this path. For the special case when the phone number fields in the Communication Settings area are not available, e.g., for Winsock connections to a network modem pool, use this field to specify a telephone number. Other Enter the appropriate value in the Break sequence text box to define a character string that you want STN Express with Discover! to use as a break indication to an online host. This value is needed only for systems that do not support a standard break. Host Settings Select the Host Settings tab to see settings that are specific to the selected online host. Some of the settings enable features such as automatic logon to the host. + Fields in the Host Settings tab are unique to the host that you select. + The Host Settings tab is not available when you select Manual Emulation from the Host Name pulldown menu. Host Prompts The Host Prompts window may list up to five prompts issued by the host you select. STN Express with Discover! uses this information to determine when the host is ready to receive the next command. This supports several STN Express with Discover! features, such as the Command Window and command line recall while you are logged on. STN Express with Discover! provides default values in the fields for the online hosts in the Host Name list. For STN hosts, these default values cannot be changed. For other hosts, these default values can be changed, although caution is advised.

69 5 10 Using non-stn Hosts When searching for a host prompt, STN Express with Discover! looks for an exact match with one of these strings, including blanks and control characters. The search begins with the last character received from the host and works backward for the length of the string. The following conventions are used to represent special characters in these strings: # - any string of digits, e.g., 102, or the # character - Blank (represented by a space) [M - Carriage return [Q - Control Q (XON) character [J - Line feed [[ - One left square bracket ( [ ) Logoff Messages The Logoff Messages window lists up to five text strings that are issued by the host at logoff. STN Express with Discover! uses this information to determine when the session with the host has ended. When this happens, the processing defined in the Logoff Method section of the Setup Definition dialog box is executed and your connection is closed. STN Express with Discover! provides default values in the Logoff Messages window for the host listed in the Host Name field. For STN hosts, these default values cannot be changed. For other hosts, these default values can be changed, although caution is advised. STN Express with Discover! looks for an exact match with one of the Logoff Messages strings to any of the data received from the host. This match includes looking for any trailing blanks. Matching of control characters is not supported. Command Window Click a Ö in the Command Window box to enable STN Express with Discover! to open a Command Window when you log on to a host. The Command Window can also be turned off and on while logged on to an online host. Click a Ö in the Close Window at logoff box to tell STN Express with Discover! to close the session window after you log off the host. If you prefer to scroll back through your session or capture a transcript after you log off, do not select this option. Highlight ON Sequence Enter a character string in the Highlight ON Sequence text box to tell STN Express with Discover! how the host system will indicate hit term highlighting during an online session and when browsing a transcript. The string you enter must be unique as highlighting is indicated at any point where this term appears. Matching of control characters is not currently supported.

70 Using non-stn Hosts 5 11 Highlight OFF Sequence Enter a character string in the Highlight OFF Sequence text box to tell STN Express with Discover! how the host system will indicate the end of a highlighted term. Matching of control characters is not currently supported. Execute at first Host Prompt window Up to five commands may be entered in the Execute at first Host Prompt window. The first command is sent when the first host prompt is received, and the remaining commands are sent, one at a time, with each succeeding the host prompt. By default, a carriage return is sent after each line. The keyword NOCR may be added as the last word on the last line that you enter to indicate that this line is to be displayed in the STN Online and Results window, but not sent. This allows you to enter data after the defined character string, before it is sent. Choice of Service and Language options The Choice of Service and Language options are displayed only if you have selected Questel from the Host Name pulldown menu. The Choice of Service value should be from 1 to 6 characters in length and is sent at the first Questel prompt. The language you enter is the language in which you want to interact with Questel. + For the Markush DARC service, the language is not set automatically at logon because of the time required to do this. However, the script Qst_op.sc, located in the Scripts folder, can be run after logging on to set the language and other options used by this service. If you access this feature frequently, copy the Qst_op.sc script to the User Scripts folder to access it more easily. See Appendix C, for instructions on running an STN Express with Discover! script. Logon Setups for Other Hosts To create a setup for a host that is not currently supported by STN Express with Discover!, either select Manual Emulation or Other from the Host Name pulldown menu in the Setup Definition dialog box. Select the Manual Emulation host name to create a setup that does not use any of the automatic features, e.g., automatic logon, host prompt recognition, special handling of host highlighting characters, of STN Express with Discover!. When selected, STN Express with Discover! requires only values in the Communications Settings section of the STN Setup dialog box.

71 5 12 Using non-stn Hosts Manual Emulation Use the Manual Emulation mode to bypass the automatic features of STN Express with Discover!. In this case, STN Express with Discover! only allows for terminal emulation, without automatic dialing, automatic logon, etc. To create a Manual Emulation setup: 1. Type a name in the Setup Name text box 2. Select Manual Emulation from the Host Name pulldown menu 3. Select the appropriate connection method from the Connect via pulldown menu 4. Modify the values for the Communications Settings if necessary 5. Click OK. Other as host name Select the host name Other to create a setup for a host that is not in the Host Name list. A Custom Logon Method is required. You may click the Host Settings tab to define the host prompts, logoff messages, and highlight characters. Use the Other mode to create a setup that supports some of the automatic features of STN Express with Discover!. However, you must provide a script for logging on to the host, and you must provide the values needed in the Host Settings tab of the Setup Definition dialog box. To create a setup for another host: 1. Type a name in the Setup Name text box 2. Select Other from the Host Name pulldown menu 3. Click the radio button next to Custom in the Logon Method section. Then click Configure. 4. Click the Watch Me button to create a script for logging on the host system. Then click OK. 5. Click the Host Settings tab and fill in the Host Prompts fields If you leave the Host Prompts fields blank, you will be able to interact with the host, but features such as the Command Window will not work. 6. Optionally, fill in the values in the Logoff Messages field on the Host Settings tab If you do not add a message to the Logoff Messages fields, STN Express with Discover! may not disconnect the session after logoff. You can disconnect the session manually by selecting Drop DTR from the Online menu or by closing the window that contains the online session. 7. Optionally, fill in the values in the Highlight ON Sequence and Highlight OFF Sequence text fields 8. Click OK.

72 Using non-stn Hosts 5 13 Custom Logon and Logoff Use custom logon and logoff methods when STN Express does not support the telecommunications network or online host you choose. If you write your own logon or logoff scripts, review the Predefined Setup Variables section in Appendix C. Script Language. A custom logon requires you to select scripts to tell STN Express with Discover! how to connect to your network and host. Scripts typically are used to execute a step in the logon process. For example, one script might have the modem dial a telephone number and connect to a network; a second script may connect through the network; a third script may log on to the host. Custom Logon To create a custom logon procedure, click the radio button next to Custom in the Logon Method section. Then click the Configure button. The Custom Logon dialog box is displayed. The Scripts Folder box displays a list of scripts from either the User or Standard Scripts folder. The Standard scripts folder corresponds to the Predefined Scripts folder in General Preferences. The User scripts folder corresponds to the User Scripts folder in General Preferences. The Selected script list box displays the scripts that have been selected for this custom logon setup. The scripts will be executed in the order shown as part of the connect and logon process. To change the order of the scripts in the Selected script list, select a script and click the up (s) or down (t) arrow to move the script name one position at a time. To add a script to the logon procedure, select (highlight) a script in the Scripts Folder list. Then click the Copy>> button to copy the script to the Selected script list. Click the Watch Me button to insert the watchme.sc script into the Selected script list window. The watchme.sc script can be used more than once in the Selected script list. For more information, refer to the Watch Me section later in this chapter. Click the Delete button to delete a script from the Selected script list. Click the View button to display the actual script for a script name that you select from the Scripts Folder window. Click OK to when you have completed your entries to the Selected script list window and to return to the Setup Definition dialog box. The scripts you selected are displayed in the Custom Logon Script List box.

73 5 14 Using non-stn Hosts Custom Logoff Use a custom logoff procedure when the method to disconnect from an online host is not successful or is not supported by the standard logoff method. The Logoff Method section in the Setup Definition dialog box defines how STN Express with Discover! will disconnect the communications path when you log off from an online host. When you log off, STN Express with Discover! scans the output from the host system looking for the logoff messages defined under the Host Settings tab in the Setup Definition dialog box. When it locates a message, STN Express with Discover! knows that is has logged off of the remote system. It then disconnects the communication path using the method defined in this section. + If the communication path is not disconnected correctly, you may get a Communication Port In Use error when you try to use a program that requires the use of a communication port. The steps for defining a custom logoff are nearly identical to that for defining a custom logon. Refer to Custom Logon in this chapter for details. Online Session on non-stn Hosts The STN Express with Discover! STN Online and Results menus vary with the online host that is used. Because STN Express with Discover! is specifically designed for STN, more online features and commands are available when connecting to STN. Basic features, such as capturing a transcript and sending a break to interrupt the host, are available for any online host. The File and Edit menus function the same for all online services. The Online and Terminal menus provide similar commands for controlling your online or terminal session. The Query menu provides commands to take advantage of special features while online to STN or Questel. These include uploading structure queries, running command files (including WPI strategies), and using predefined search strategies. The Results menu is used to capture items displayed in the terminal window to a file. Use these files to browse, print, edit, or export.

74 Using non-stn Hosts 5 15 Terminal menu The Terminal menu is available if you are connected to a vendor other than the seven non-stn hosts supported by STN Express with Discover! and when you are logged on through manual emulation.

75 5 16 Using non-stn Hosts Terminal menu options Option Use Pagination Mode Use Continuous Scroll Mode Suppress Screen Display Send Break (Ctrl+B) Prompt Override (Ctrl+Enter) Terminal Mode VT320 Settings VT320 Keyboard Setup Terminal Parameters Result Pause after displaying a window full of information. Click Hold On in the status bar to display the next page. Display information from the online host continuously, without pausing. Stop the display of information in the STN Online and Results window. Even when transcript capture is on, no information is saved in the transcript file when Suppress Screen Display is selected. Send a break signal to the online host to interrupt a command or another function If STN Express does not recognize a host prompt, it will not let you type a command. Use Prompt Override to let you type. Specify the terminal emulation mode. See Terminal Mode later in this chapter for more information. Specify terminal settings when using VT320 terminal emulation. See VT320 Settings later in this chapter for details. Specify the keyboard configuration when using VT320 terminal emulation. See VT320 Keyboard later in this chapter for details. Select communications settings for certain types of modem connections. Refer to the Setup Terminal Parameters section later in this chapter for more information.

76 Terminal menu options (continued) Option Kermit Send Kermit Receive Logoff Execute Script Watch Me Drop DTR Raise DTR Command Window Result Using non-stn Hosts 5 17 Upload a file to an online host. STN Express can send text or binary files. Kermit protocol is used with the timeout interval of 10 and the packet size of 94. Download a text or binary file from the online host. A packet size of 4000 is recommended. This option is not available for Manual Emulation or for setups defined using the Other host name. Run a script written in the STN Express script language. For information, refer to Appendix C, Script Language. STN Express with Discover! records all activities from your online session into a script file. The Watch Me menu item is a toggle switch. Set the modem s Data Terminal Ready circuit to OFF. Set the modem s Data Terminal Ready signal to ON. Open a box at the bottom of your online window that can be used to type commands and other functions. The Command Window is available for all hosts, but you must define the host prompts in the logon setup (Host Settings tab) for all features of the command window to work properly.

77 5 18 Using non-stn Hosts Terminal Mode Options Three terminal emulation modes are available: TTY Tek41xx VT320 The Terminal Emulation modes interpret escape sequences in the data stream. These direct the receiving terminal either to perform a particular operation or to interpret characters. An escape sequence is one or more characters that are transmitted to define a specific control function. When STN Express with Discover! receives characters from a remote host, the selected terminal mode interprets them accordingly. + The Hold On/Hold Off and Capture commands function in all three emulation modes. TTY mode TTY is the default terminal mode. It supports a number of STN-specific escape sequences.

78 Using non-stn Hosts 5 19 Tek41xx mode STN Express with Discover! supports the basic Tektronix 4100 sequences. The graphics operations are supported with line vectors and text. Advanced graphics features such as Graphtext rotation, pixel copying, rectangle filling, and others are not supported. The Tek41xx emulation is based on a 1024 by 768 coordinate system. If this exceeds the screen dimensions of your display, you may lose some definition when mapping the coordinate system. Maximizing the STN Online and Results window is advised. Although standard Tek4100 escape sequences for printing are not supported by STN Express with Discover!, you may capture the data to a transcript file to print later. If the current transcript file is SESSION.TRN, the TEK data are captured to the file SESSION.TEK. This file may be browsed or printed in the normal manner. Three basic modes support this emulation. Switching between these modes is performed transparently and automatically by escape sequences that are sent by the host. 1. Alpha Mode - When your terminal is in the Alpha Mode, it interprets received characters and displays ASCII characters. When the cursor reaches the bottom of the display screen, the display scrolls to allow you to view the incoming data. 2. Vector Mode - When your terminal is in the Vector Mode, the incoming characters are interpreted as a series of XY coordinate positions. The emulator moves the current graphics position to the first XY position and draws lines (vectors) to any subsequent positions. Graphics are displayed at the XY positions. 3. GIN Mode - When your emulator receives the ENABLE 4010 GIN command from its host, it displays a cross-hair cursor. Position the cursor at the required location and then press a key or click your mouse button. The emulator sends a 4010 GIN REPORT. This escape sequence contains details of the key pressed and the current cursor position. It is typical for the host to have previously entered the Vector Mode to draw the input screen with text. Options are displayed at set locations on the screen. The host application can map the GIN REPORT key/ coordinate combination to carry out specific actions.

79 5 20 Using non-stn Hosts VT320 mode STN Express with Discover! supports limited DEC VT320 terminal functions. It supports basic 80 or 132 column mode with 24 lines. It does not support printing, selective erase, soft character sets, user-defined keys, or the 25th status line. The cursor position (line and column) is displayed on the STN Online and Results status bar. Although printing is using VT320 escape sequences is not supported, standard STN Express with Discover! print features are available. Save your data to a transcript and print the transcript file or use the Print Selected option on the File menu while online. When you are in the VT320 Mode, VT320 Settings and the VT320 Keyboard options are enabled in the Terminal menu. VT320 Settings Select VT320 Settings from the Terminal menu to change specific display options. The Terminal Settings dialog box is displayed. Number of Columns - sets the terminal width to either 80 or 132 columns. The default is 80. Some VT320 applications can operate in either 80 or 132 column mode. Terminal Modes - includes the following terminal options: Line Wrap - if selected, received characters are automatically wrapped onto the next line. If not selected, characters received after the last allowable character on a line overwrite existing characters. Local Echo - if selected, keyboard characters are displayed on the screen and sent to the host. The host does not need to echo the characters. If not selected, the host is responsible for sending the characters back to the terminal for display. Auto-repeat - if selected, you may hold a key and that key is sent repeatedly to the host. If not selected, only one character is sent to the host each time a key is pressed.

80 Using non-stn Hosts 5 21 Backspace - determines which character to send the host when the backspace key is pressed. Select BS to send a backspace character (8) to the host. Or, select DEL to send a delete character (127) to the host. End of line - determines which character to send the host when the carriage return key is pressed. CR sends only a carriage return character, and CR/L sends a carriage return followed by a linefeed. Control - select 8bit to obtain faster control sequences. The data path to the host must recognize 8-bit characters. If problems occur, select 7bit. All hosts recognize 7-bit characters. After you change one or more options, click OK to save and use the settings. VT320 Keyboard Select VT320 Keyboard to change keyboard options. The Keyboard dialog box is displayed. Keypad - determines which character to send the host when a key on the numeric keypad is pressed. Select Numeric to transmit the actual character you press, i.e., number, comma, plus sign. Select Application to transmit a standard sequence of characters to the host. These characters are not user-definable. Cursor Keys - select Normal to send standard ANSI cursor sequences. Select Application to send an application sequence of characters to the host. Cursor - select Blanked to hide the cursor. Select Visible to show the cursor. Cursor Type - select Block or Underline cursor style. After you change one or more options, click OK to save and use them.

81 5 22 Using non-stn Hosts Setup Terminal Parameters Setup Terminal Parameters is active only when the logon setup Host Name is Manual or Other and a COM port is selected in Connect via. A Communications Settings for Terminal Emulation dialog box is displayed. Change the settings to meet your communication needs. When you have modified your communications settings, click OK to save and use the settings.

82 Structure Queries Structure Queries Structure queries may be built in the STN Express with Discover! Structure Drawing program. Structures may be drawn as Standard, Specinfo, WPI, and Questel structure types. The basic structure-building techniques are discussed in this chapter and are applicable to all structure types, including reaction queries. Chemical structures may be built offline. This is the best economic approach as no connect time or online costs are incurred as you construct the query. Simply draw the structure. Then during an online session, upload the query by selecting Upload Structure Query from the Query menu. For extensive documentation and training on structure searching strategies, contact your Customer Service representative. Launching Structure Drawing Select Prepare Structure Query from the Query menu or click the Prepare Query button on your Toolbar. The Structure Drawing program opens, along with a new Untitled Standard window.

83 6 2 Structure Queries The Structure Drawing window includes its own Structure Drawing menu bar. These menus contain the commands and subcommands to access structure drawing tools. It also contains toolbars and a tool palette that give quick access to drawing tools, atoms, and bonds. Atoms & Bonds Toolbar The Atoms & Bonds Toolbar provides quick and easy access to common atoms and bonds. If atoms or bonds that you need are not located here, access the Draw menu in Structure Drawing. The term atom is frequently used in this User Guide to refer to atoms, variables, shortcuts, G-groups, and the points of attachment for G-group fragments. Current Atom Box Common Atoms Current Bond Box Common Bonds Reset Atom/Bond The Current Atom Box The Current Atom box displays the symbol of the current atom that is being used. This symbol is inserted into the ring or chain that you draw. The default atom is C, carbon. Right-click in the Current Atom box to display the Atom Selection dialog box. Type a new atom in the Symbol text box or use the scroll bar to locate the atom you need.

84 Structure Queries 6 3 Then click Single Use to insert the selected atom one time. Click Multiple Use to insert the atom more than once and retain it as your default. Click a in the Exclude box to exclude the selected atom from retrieved substances during an online search. Click Cancel to cancel the Atom Selection request. You may also left-click in the Current Atom box to display either the Periodic Table dialog box, the Atom Selection dialog box, or the List dialog box. These dialog boxes are used to select atoms for single or multiple use in a structure drawing. The dialog box that displays depends on the selection in the Drawing section of your Structure Drawing Preferences. Refer to The Preferences! Menu section, later in this chapter, for more details. The Common Atoms The Common Atoms are icons for those atoms that are most frequently used in structure drawing. Single-click an atom icon to insert it into a structure once. After you insert the atom, the previous default atom is reset in the Current Atom box. Double-click an atom icon to insert it into a structure more than once and to retain it as your atom default. You may customize the Common Atoms to include the atoms you most commonly use. To do so, right-click on an atom that you want to replace. The Atom Selection dialog box is displayed. Locate and click the atom you want to insert on the palette. Then click OK. The atom you selected permanently replaces the atom that was previously in that position. The Current Bond Box The Current Bond Box displays the bonds that you are currently inserting into your structure. To select another bond, click in the Current Bond box. The Bond Selection dialog box is displayed. The radio button of the current bond is selected. To choose a different bond, click the radio button next to that bond.

85 6 4 Structure Queries Then click Multiple Use to insert the bond more than once and to retain it as your default selection. Click Single Use to insert the bond once. After you insert the bond, the previous default bond is reset in the Current Bond box. Or click Cancel to cancel the request. The Common Bonds The Common Bonds are the bonds you most often used in structure drawing. If a common bond is your current default, it is highlighted and is also displayed in your Current Bond box. By default, the single bond and the double bond appear in the palette. Single-click the Single bond or the Double bond to insert it into your structure once. After you insert the bond, the previous default bond is reset in the Current Bond box. Or double -click the Single bond or Double bond to insert it into your structure more than once and to retain it as your default bond. Click on the Current Bond box to display the Bond Selection dialog box. Select a different bond by clicking the appropriate radio button. Click Multiple Use or Single Use. Refer to the previous section for more details. To customize one of the common bonds, right-click on either existing common bond. The Bond Selection dialog box is displayed. Select a bond and click OK. The bond you select becomes a common bond. Reset Atom/Bond Defaults Click the Reset Atom/Bond button to quickly return to the STN Express with Discover! Structure Drawing atom and bond defaults. The atom default is C, carbon, and the bond default is a single bond. You may also press the Spacebar to reset the atom/bond defaults. Toolbar (Function Keys & Menu Shortcuts) The Toolbar provides quick and easy access to common file functions and to menu shortcuts. These tools are also located in various menus within Structure Drawing.

86 Structure Queries 6 5 Customizing the Toolbar You may customize this toolbar by right-clicking on any button shown or in a vacant button position. This displays the Structure Drawing Toolbar Preferences dialog box. A tool button is displayed along with a description of its function in the Description section of the dialog box. If you right-click on a specific button or a specific vacancy (toolbar gap), click OK to replace the button or gap. Or, click Next to display the next button. When you locate a button you want to insert in the button position that you clicked, click OK. Or, click Cancel to cancel this request. You may also click Previous to backtrack to a button you already viewed. You may also customize the position of the Toolbar by left-clicking a gap on the tool bar. A selection box is displayed. Drag your cursor over a selection to highlight it. Then click to select that option. The positions include: Vertical/Horizontal - select to display the Toolbar horizontally, above the Structure Drawing window Double Line/Single Line - select to display the Toolbar in a single line or a double line Close - select to close the Toolbar If you close the Toolbar, you must access the Layout tab of Structure Drawing Preferences and then click Visible in the Toolbar section to display it. You may also customize Toolbar positioning in the Layout option of Structure Drawing Preferences.

87 6 6 Structure Queries List of Toolbar Buttons Toolbar Button Description Open a new Standard STN structure drawing window Open a new SpecInfo STN structure drawing window Open a new WPI STN structure drawing window Open a new Questel structure drawing window Save the current structure Save the current structure with a new name Open existing structure drawing queries Display the carbon atoms as C, dots, or angles Toggle the Query Attribute pop-up display, i.e., point your cursor on any item in a query and its attributes are described Print the current structure query Set Structure Drawing Preferences Verify the query s attributes Cut the selected structure or structure fragment and place it on the clipboard Copy the selected structure or structure fragment and place it on the clipboard Paste the clipboard contents into the current structure query Fuse two structures or structure fragments together Undo the last action Center the structure in the Structure Drawing window

88 Structure Queries 6 7 Toolbar Button Description Display the Shortcut menu, which contains shortcuts to insert one or more times in your query Display the Variable Selection menu, which contains a variable to insert one or more times in your query Toggle the use of the reaction drawing mode Toggle the use of the Functional Group drawing mode Show Structure Drawing Help Analyze the structure query and suggest filters View existing filters Return to original application Fast return to main program View the existing Functional Group command file Switch to STN Terminal Emulation mode and logon to an online vendor

89 6 8 Structure Queries Tool Palette The Tool Palette provides the tools used to create or modify structure queries. The Reaction and the Functional Group drawing tools are located on the Tool Palette and are activated when you click the RXN button or the FG button on the Toolbar. Pencil Tool Ring Tool Chain Tool Eraser Tool Selection Tool Lasso Tool Text Tool Reaction Arrow Tool Reaction Role Tool Reaction Site Tool Atom Mapping Tool Functional Group Tool OR Tool for Functional Groups - draw atoms/bonds using the current atom/bond - draw 3-15 member ring systems - draw 1-30 member chains - delete objects in the structure query - select (highlight) objects in the structure query - select (grab) objects in the structure to move - add text to your screen (not searched) - set up a chemical reaction between structures - specify the roles of the participants in a reaction - specify which bonds change in a reaction - specify correspondence between atoms in reactant and product - add functional groups in a query for CASREACT on STN - link functional groups with an OR operator Customizing the Tool Palette You may customize the position of the Tool Palette by left-clicking the open position in the tool palette. A small selection box is displayed. Drag your cursor over a selection to highlight it. Then click to select that option. The positions include: Horizontal/Vertical - select to display the Tool Palette horizontally, above the Structure Drawing window Double Line/Single Line - select to display the Tool Palette in a single line or a double line Close - select to close the Tool Palette If you close the Tool Palette, you must access the Layout option of Structure Drawing Preferences and then click Visible from the Palette section to display it. You may also customize Tool Palette positioning in the Layout option of Structure Drawing Preferences.

90 Structure Queries 6 9 Pencil Tool The Pencil tool is used to place or change atoms or bonds. Click the Pencil tool to activate the pencil to draw atoms and bonds with the current atom/bond. When you click the Pencil tool, the cursor changes to resemble a pencil. To draw one node bonded to another node: 1. Place the pencil where you want the first node to appear. 2. Press and hold the mouse button and drag the cursor to the point where you want the second node. Release the mouse button. When placing a carbon atom (the default atom), the display of the carbon is determined by a setting in the Drawing options of your Structure Drawing Preferences. Settings include C, dot, or angle. To change the display of carbons for a specific instance, select Carbons from the Display menu. To change a node: 1. Click a common atom from the Common Atoms Palette, select Atom, Shortcut, Variables, or G-groups from the Draw menu, click in the Current Atom box to select an atom, or right-click in the Current Atom box to type an atom, shortcut, variable, or G- group. 2. Place the pencil tip on the node that you want to change. An A appears inside the pencil when the pencil tip is on a node. Click and the node changes to the current atom. To change an existing bond: 1. Click a bond from the Common Bonds Palette to select a single or a double bond. Or, display the Bond Selection dialog box by selecting Bond from the Draw menu or clicking in the Current Bond box. If you display the Bond Selection dialog box, click the radio button next to the bond that you want and then click Multiple Use or Single Use. 2. Place the pencil tip on the bond that you want to change. A line appears inside the pencil when the pencil tip is on a bond. Click and the bond changes to the current bond.

91 6 10 Structure Queries Ring Tool The Ring tool is used to draw 3-15 membered rings. When you click the Ring tool, the Ring Description dialog box is displayed. Type a number from 3 to 15 to specify the size of the ring you want to draw or type a ring system. You may also select the ring size or ring system that you want from the scrolling list. A 6-membered ring is the default. You may also select one of the common rings by clicking the ring icon that you want. To draw a ring: 1. Type a ring size/ring system and click OK or click a ring icon. The cursor changes to a 6-membered ring. 2. Place the ring cursor where you want to insert the ring and click. The ring appears in the Structure Drawing window. When drawing SPECINFO queries, the rings with alternating double and single bonds are drawn with special aromatic bonds. Shortcut: To quickly set the Ring tool to the default 6-membered ring, right-click on the Ring tool. Shortcut: In the drawing area, left-click to place the ring with all single bonds. Right-click to place the ring with alternating single and double bonds. For example, left-click for cyclohexane and right-click for benzene.

92 Structure Queries 6 11 Spiro Rings To draw a spiro ring system, i.e., two rings that share a single common node, create the first ring. Then center the + in the ring cursor directly on the node to be shared. Then click. Cyclohexane Ring Two Cyclohexane Rings in a Spiro Ring System Fused Rings To draw two rings that are fused together, i.e., two rings that share a common bond, center the + in the ring cursor on the middle of the bond to be shared and click. Cyclohexane Ring Two fused Cyclohexane Rings Ring Systems Type a shorthand ring system description in the Ring Description box or select a ring system from the scrolling list. A shorthand ring system description includes the number of nodes in each ring in the system. By default, rings are fused to one another from left to right, e.g., 65 indicates a 6-membered ring fused to a 5-membered ring with the 5-membered ring on the right. Ring sizes of 4 through 6 are allowed. Optional U (Up) and D (Down) indicators modify the direction of ring fusion. U moves the location of the fused bond up (counter-clockwise) one bond. D moves the location of the fused bond down one bond. Additional fusion continues in the new direction until the direction is changed. Direction indicators are not allowed when the shorthand includes a ring of size 4. For example, type 66U6D5 for the steroid ring system.

93 6 12 Structure Queries Then click OK and left-click in the drawing area. Chain Tool The Chain tool is used to draw chains of lengths ranging from 1 to 30 atoms. When you click the Chain tool, the Chain Length dialog box is displayed. The default chain length is 1. Type a number from 1 to 30 or select a number from the scrollable list. Then click OK. Your cursor changes to resemble a chain. To draw a chain, place the chain arrowhead where you want it to appear and click your mouse button. The chain is inserted into your structure drawing. To insert a chain of a different size, click the Chain tool again. Enter a new chain length in the Chain Length dialog box. Click OK. You may attach a chain to another chain or to a ring by placing the arrowhead of the chain cursor where you want to attach the chain. Then click your mouse button. STN Express with Discover! attempts to position the chain logically. If the chain could overwrite another atom, an error message is displayed and the chain is not placed. Shortcut: To quickly choose a chain length of 1, right-click the Chain tool on the Tool Palette. Then place your cursor in the drawing area. Left-click to place the chain.

94 Structure Queries 6 13 Eraser Tool The Eraser tool is used to delete an atom or bond from your structure. When you click the Eraser tool, the cursor changes to resemble a pencil eraser. To use the Eraser tool, click its icon. To remove an atom, position the tip of the eraser on an atom. An A appears in the pencil section of the eraser when the cursor is on an atom. Click and the atom and any bonds attached to it are removed. To remove a bond, position the tip of the eraser on a bond. A line appears in the pencil section of the eraser when the cursor is on a bond. Click and the bond is removed. To cause the atoms at the ends of the bond to be removed also, select Delete Atoms with Bonds on the Drawing tab of Structure Drawing Preferences. Selection Tool The Selection tool is used to select individual atoms, bonds, or structure fragments or entire structures. Selected items may be cut, copied, deleted, or assigned attributes. If a shortcut is selected, you may reverse it, if applicable. When you select the Selection tool, the cursor changes to resemble its icon. To select a structure or a structure fragment, position the Selection tool cursor to the top-left point of the structure. Press and hold your mouse button while you drag the mouse in a direction where the structure is included in a rectangular box. Then release your mouse button and the entire structure or structure fragment is selected. To select a single bond or node, place the Selection tool cursor on the middle of a bond or on a node. Then click. The bond or node is highlighted with the color specified in your Structure Drawing Preferences. Refer to the Colors/Fonts Structure Drawing Preferences section, in this chapter, for more details. To select more than one item, press the Shift key and click simultaneously while using the Selection tool. This is useful for selecting several nodes and bonds that do not fit within a single rectangle.

95 6 14 Structure Queries Lasso Tool The Lasso tool is used to select a structure or segments of a structure in a free-hand mode. Once selected, you may move, cut, copy, or delete it. To lasso (select) an object, click the Lasso tool. The cursor changes to resemble a lasso. Press and hold your mouse button and drag the lasso cursor around the structure. A line appears around the structure fragment as you drag the cursor. Release the mouse button when the entire fragment is enclosed (lassoed). To move the lassoed structure fragment, place the lasso cursor inside the lassoed area. The cursor changes to a hand. Press and hold your mouse button while dragging it to a new location. Release the button and the selected fragment is redrawn in the new location. To remove the lassoed structure fragment, select Cut or Clear from the Edit menu or press your Delete key. The selected fragment is removed from the structure. If you select Cut, the structure fragment is removed and placed on your clipboard. To place a copy of the structure fragment on your clipboard, select Copy from the Edit menu. The selected fragment is now in the structure and on your clipboard. To lasso a single node, align the point of the lasso tail on the node. An A is displayed inside the lasso cursor when it is touching a node. Click to select the node. The node is enclosed in a small box. You may move, copy, cut, or delete a single node just as you would a structure. Text Tool The Text tool is used to add nonsearchable text or labels to your structure drawings. When you select the Text tool, the cursor changes to resemble an I-beam. To enter text or labels to your structure, click the Text tool. Position the cursor where you want the text to appear and click. Type the text. To add text in a different area, reposition your cursor and click. Text is displayed in the system font you are using. To change the text font, select Preferences from the Structure Drawing Main Menu bar or click the Preferences button if it is on the Structure Drawing Toolbar. Then click the Colors/Fonts tab. Deselect the Text Font=Atom Font box and then click the Text Font button. A Font dialog box is displayed. Change the font as desired. To delete text, click the Selection or the Lasso tool. Then select the text. Press the Backspace key or select Cut from the Edit menu. You may also use the Eraser tool to remove each block of text. To relocate text, click the Lasso tool. Select the text you wish to move. Then drag the selection to a new location.

96 Structure Queries 6 15 Structure Drawing Main Menu Bar The Structure Drawing Main Menu Bar provides the tools necessary to create a substance, Markush, or reaction query. Keyboard shortcuts are available for some commands. They are displayed on the menus to the right of the commands. Commands that are grayed are not available for the current application. The File Menu The File menu provides basic structure file and window management commands. New The New command provides four subcommands to open a new, Untitled structure drawing window for the following structure formats: Standard SpecInfo WPI Questel Open (Ctrl+O) The Open command opens an existing structure that was previously saved. When you select the Open command, a list of saved files is displayed in the Open Query dialog box. Highlight a file name to see its structure query within this dialog box and to identify what format, e.g., Standard, it was saved in. If this is the structure file you want to open, click Open. Note that you may open several different file types, e.g., MDL molfiles, DARC, by clicking the Files of type pop-up menu. You may convert a saved file to a new format by clicking the radio button next to a format listed in the Convert to section of the dialog box. Converted structures are opened in a new Untitled window. The original structure retains its original format.

97 6 16 Structure Queries When importing an MDL rxnfile to STN, i.e., MDL STN, change the *.mol to *.rxn in the Open File Name text box. Refer to Appendix E, MDL Molfile Conversion Assumptions, for more details. Different version of ISIS/DRAW have different instructions for copying structures to the clipboard to import to STN Express with Discover!. Refer to your ISIS/DRAW documentation for more details. Open File Types File Example Applications Format Extension That Create the Format STN Express Structure Query.str STN Express Chemical Exchange Format.cxf SciFinder DARC.drc Generic DARC MDL Molfile.mol ISIS/Draw, ChemDraw, ChemWindow SMD.smd ChemDraw Alchemy.alc Alchemy Close The Close command closes the current structure query. If you close a structure query before you save it, you are prompted to save. Browse Browse allows you to quickly view all of the structure queries you have saved in your default folder, i.e., the folder you defined in General Preferences (the folders command is located in the Setup menu on the STN Express Main Menu bar). When you select Browse, the Browsing dialog box is displayed. You may view each saved query at your pace by clicking Next or you can view them in a continuous fashion by clicking Continuous. You may modify a structure by clicking Edit.

98 Structure Queries 6 17 Save (Ctrl+S) Select Save to save a structure query to the directory of your choice. After entering a file name and selecting a file type, click OK. A Saving dialog box is displayed. Click a in a box adjacent to an item in black text. Verify Query is selected by default and is recommended to catch any drawing errors before you search online. See the Query Verification section, later in this chapter, for more details. If G-group orientation and Verify Reaction Specifications are active and are not selected, the query can only be Saved Unsearchable. These options must be selected, if available, before you upload a query to an online session. Save As Save As allows you to save a structure with a new file name and a new standard file type, e.g., DARC, MDL Molfile, or picture file type, e.g., TIFF, Metafile. Save As File Types File Example Applications Format Extension That Read the Format STN Express Structure Query.str STN Express Chemical Exchange Format.cxf SciFinder DARC.drc Generic DARC MDL Molfile.mol ISIS/Draw, ChemDraw, ChemWindows SMD.smd ChemDraw SMILES.smi Daylight s software PCX image.pcx Paint Shop Windows Metafile image.wmf Microsoft Word TIFF image.tif Microsoft Word

99 6 18 Structure Queries Page Setup Page Setup allows you to set page settings for printing. Print (Ctrl+P) The Print command prints the current structure. Exit This command ends your structure drawing session. The Edit Menu The Edit menu provides standard editing commands.

100 Structure Queries 6 19 Draw Menu for Structure Drawing The Draw menu provides commands to help you create structure drawings. Some of the commands have shortcuts, e.g., left-clicking the Current Bond box to display the Bond Selection dialog box. Bond Select Bond to display the Bond Selection dialog box. Click Single Use to insert the bond once. After inserting the bond, the default returns to the previous bond. Click Multiple Use to insert the bond and retain it as your default. Click Cancel to cancel the request. Atom Select Atom to display the Dialog Box, Periodic Table, or List of atoms. The dialog box that displays is the one selected in the Drawing tab of your Structure Drawing Preferences. If the Periodic Table is displayed, the atom that is the current default is highlighted and some of its atomic and physical properties are displayed as well. Click an atomic symbol to select a different atom. It will become highlighted and its atomic and physical properties will display. Click Multiple Use to insert the atom more than once and to retain it as your default node. Click Single Use to insert the atom once. Or click Cancel to cancel the request. If the Dialog Box is selected, the atoms are displayed in a window. Click the radio button next to the atom you want. Then click Multiple Use to insert the atom and to retain it as your default node. Click Single Use to insert the atom once. Or click Cancel to cancel the request.

101 6 20 Structure Queries If List is selected, the atoms are available in a scrollable list. Scroll to an atom and select it or type an atom in the Symbol text box. Then click Multiple Use to insert the atom and to retain it as your default selection. Click Single Use to insert the atom once. Or click Cancel to cancel the request. Shortcut Select Shortcut to display the Shortcuts dialog box. This dialog box displays all available shortcuts for common chemical moieties. Click the radio button next to the shortcut you want. Then click Multiple Use to insert the shortcut and to retain it as your default selection. Click Single Use to insert the shortcut once. Or click Cancel to cancel the request. A shortcut with a small box next to its radio button indicates a Reversible Shortcut. If you select a Reversible Shortcut and you wish to reverse its orientation after inserting it in a structure, select the shortcut with the Selection tool and then choose Reverse Shortcut from the Display menu. Shortcuts differ for Questel structure queries. Variables Select Variables to display the Variable Selection dialog box. This dialog box provides a list of the available variable nodes you may insert in a structure. Click the radio button next to the variable you want. Then click Multiple Use to insert the variable and to retain it as your default selection. Click Single Use to insert the variable once. Or click Cancel to cancel the request. The X, M, and Id variables may be excluded from a postion in a query by clicking the Exclude checkbox.

102 Structure Queries 6 21 Variable Points of Attachments Select Variable Points of Attachment (VPA) to choose multiple possible sites of attachment for a node on a single ring or a ring system. For example, use VPA to search for pyridines with a chlorine attached at the 2- or 3-position. To use VPA: 1. Build a ring or a ring system and build the substituent as a separate fragment. In the example, draw the pyridine ring and a chlorine atom. 2. Click the Selection tool and select the node (Cl in the example) that may attach to the ring or ring system. Also, select the atoms in the ring where the node may attach. Hold the Shift key to select multiple items in your structure window. 3. Select Variable Points of Attachment from the Draw menu. STN Express with Discover! draws a connection from the attaching node to the center of the ring or ring system.

103 6 22 Structure Queries The allowable points of attachment on the ring are shown as dotted lines to each ring position. To toggle the display of these attachments, select Show VPA from the Display menu. Using G-groups (Ctrl+G) Use G-groups to search for structures that have more than one allowable value at a node, e.g., use a G-group to search for a benzene with an N, O, S, or methyl attached to a given position. Using G-groups reduces the need to create multiple structures. G-group definitions can include atoms, shortcuts, variables (STN only), other G- groups, or fragments. When using fragments, you must draw the fragment and point of attachment first. Then define a new G-group value or modify an existing one. G-Groups must contain between 2 and 20 items. To use a G-group, select G-groups from the Draw menu. The G- Group Definitions dialog box is displayed. Select a G-group. Click Single Use or Multiple Use. Place the Pencil tool cursor on the atom you want to replace with the G-group and click. The G-group is represented as G1 (or G2, G3, etc.). Changing a G-group Definition: Select G-groups from the Draw menu to modify a G-group definition. Select a previously defined G- group from the list. Click Modify. The G-group Definitions dialog box is displayed. Select atoms, shortcuts, variables, G-groups, and/or fragments to modify. Click each item that you want to deselect and/or click new items to add to the definition. Click OK to complete the modification. Then click Save.

104 Structure Queries 6 23 Defining a New G-group Select G-groups from the Draw menu to display a G-group Definitions dialog box. Click New. The Define New G-Group dialog box is displayed. The first G-group defined is labeled G1. Up to 20 G-groups can be defined and each G-group is numbered consecutively, i.e., G1, G2, G3, G20. Click Atoms, Shortcuts, Variables, G-groups, and/or Fragments to define the members of the G-group. Atoms, Shortcuts, Variables (STN only): When you click the Atoms, Shortcuts, or Variables button to use in a G-group, the appropriate dialog box is displayed. Select nodes to include in your G-group. The selections are listed next to the G-group name, e.g., G1. G-groups: When you click G-groups, you may add a previously defined G-group to a new G-group. To add a G-group, select a G-group from the G-Groups Definitions dialog box. This is only available if you have previously defined a G-group. Questel structures may nest G-groups only 3 levels deeper than the main drawing level, may use a G-group only once, and require you to create another identical G-group if you want to use the same one more than once.

105 6 24 Structure Queries Fragments: To include a fragment as a G-group: 1. Draw your primary structure and the fragment(s) you wish to include in the G-group definition. 2. Define the Points of Attachment for each fragment. Select G-groups from the Draw menu. point of attachment. Click Multiple Use. is displayed in the Current Atom box. No more than two points of attachment are permitted on a fragment. Select the atoms in your fragment that will be the points of attachment to your primary structure. will display next to the atoms you selected. 3. Define a G-group containing a fragment and use it in a structure. Select G-groups from the Draw menu. Click New to display the Define New G-Group dialog box. Then click Fragments. The G-group Fragments dialog box is displayed.

106 Structure Queries 6 25 To select all fragments that have defined points of attachment, click Include All Fragments. A is inserted in the Include This Fragment check box. Click OK. The G-group definition is shown in the Define New G-Group dialog box. You can also pre-select fragments to include in your G-group definitions by clicking them with the Selection tool. Then click the Include Preselected Fragments button in the G- group Fragments dialog box to include them. Click Save to create your G-group and return to the G-Group Definitions dialog box. Click Single Use or Multiple Use. You are returned to your structure query. Click the atom you want to replace with the G-group. 4. Click Save from the File menu to save the structure. If the fragments contain two points of attachment, the G-group orientation option is active and ed in the Saving dialog box. 5. G-group Orientation When two points of attachment exist in a fragment that is part of a G-group and the G-group orientation is ed, the Fragment Orientation dialog box is displayed. Specify the placement of the fragment relative to the other atoms in the primary structure. You must perform fragment orientation to create a searchable structure for STN or Questel. G-group orientation is performed during Fragmentation Code generation for WPI structures. In the Fragment Orientation dialog box, click Show Fragment to show how the fragment s points of attachment are numbered. Click Show Structure to see how the G-group is attached within the structure. The G-group and a connecting atom are highlighted. Select the fragment s point of attachment number that corresponds to the highlighted node in the structure. Click Select to continue saving the structure. You must select an orientation for single-atom fragments if they have two points of attachment.

107 6 26 Structure Queries [ ]m-n (Repeating Groups) Use the [ ]m-n command to insert a repeating group into your structure query. To create a repeating group: 1. Draw a structure that will contain the repeating group. 2. Click the Selection tool and select the nodes that are to become members of a repeating group. Refer to the Selection Tool section for details on selecting multiple items. There must be two attachments to the repeating group that are not part of the repeating group. 3. Select [ ]m-n from the Draw menu to define the selected nodes as a repeating group. The Repeating Group Range dialog box is displayed. Type the numerical range for the group to repeat (0-20 times). The group is bracketed and subscripted with the repeating range entered.

108 Structure Queries 6 27 Delete [ ]m-n Delete [ ]m-n is used to remove a repeating group from a structure. To delete a group: 1. Click the Selection tool. Select an atom in the repeating group that you want to delete. 2. Select Delete [ ]m-n from the Draw menu to delete the repeating group definition. The atoms in the repeating groups are not deleted. Only the brackets and repeating range are deleted. Chain Superatoms Select Chain Superatoms to insert a chain superatom into a WPI structure query only. When you select this command, the Chain Superatoms dialog box is displayed. Click the radio button next to one of the chain superatoms. Then click Single Use or Multiple Use. Insert the chain superatom at the desired location in your structure. Refer to Chapter 8, WPI Fragmentation Codes, for more details. Ring Superatoms Select Ring Superatoms to insert a ring superatom into a WPI structure query only. When you select this command, the Ring Superatoms dialog box is displayed. Click the radio button next to one of the ring superatoms. Then click Single Use or Multiple Use. Insert the ring superatom at the desired location in your structure. Refer to Chapter 8, WPI Fragmentation Codes, for more details. Other Superatoms Select Other Superatoms to insert a superatom other than a chain or a ring superatom into a WPI structure query only. When you select this command, the Other Superatoms dialog box is displayed. Click the radio button next to one of the other superatoms. Then click Single Use or Multiple Use. Insert the other superatom at the desired location in your structure. Refer to Chapter 8, WPI Fragmentation Codes, for more details.

109 6 28 Structure Queries Square Brackets Select Square Brackets to insert brackets around a structure or a structure fragment. This is useful when you want to include the structure or structure fragment in a word processing application to reference it. To enclose a structure or structure fragment, select Square Brackets from the Draw menu. Your cursor changes to resemble two square brackets. Click and drag the cursor so that the dashed rectangle includes the structure to be enclosed. A Brackets dialog box is displayed after you release the mouse button. Type a number from 1 to 99 in the Text box, i.e., a reference number. Click the radio button next to Back or Front to place the number after the right-most bracket or before the left-most bracket. Click OK. Brackets do not affect search results. To delete a set of brackets, use the Eraser tool. Fuse Fragment Fuse Fragment is used to join two fragments at a node or a bond. To use this command: 1. Click the Selection tool and select the node or bond in the fragment that you want to fuse. 2. Select Fuse Fragment from the Draw menu or click the Fuse Fragment button if it is located on your Structure Drawing Toolbar. The cursor changes to two facing arrows. 3. Place the cursor at the node or bond of the other fragment that you are fusing to the first fragment and click. The fragments become fused together. Depending on the the positions of the nodes and bonds in the two fragments, more than one node and bond can be fused.

110 Structure Queries 6 29 Template! Menu for Structure Drawing The Template! menu contains a collection of predefined structures to use when building a structure query. STN Express with Discover! contains a variety of templates in the Templates directory. You may also draw your own structures and save them as templates. To insert a template into your Structure Drawing window, click Template from the Structure Drawing Main Menu bar. The Open Template dialog box is displayed and lists the templates by their file names. Select a template file by clicking a template file name in the scrollable file name box. The structure is shown in the lower right hand corner of the dialog box. Then click Open. Three types of templates are included with STN Express with Discover!. They are the.std (Standard) extension, the.ste (Stereo) extension, and the.spe (SPECINFO) extension. Standard and stereo templates are in the \template\standard directory while SPECINFO templates are stored in the \template\specinfo directory. The structure for the template you selected is displayed in the Template dialog box and the Selection tool is activated. Select the entire structure or a structure fragment and then click OK. The Template dialog box disappears and you are returned to the Structure Drawing environment. Click to insert the selected structure. QueryDef Menu for Structure Drawing The QueryDef menu is used to define very specific and precise attributes in your structure query, e.g., an STN ring system to be isolated as opposed to isolated or embedded. To set an attribute for a structure, click the Selection or Lasso tool. Select one or more nodes in the fragment to define. Then select a command from the QueryDef menu. Select the attributes from the resulting dialog box. Click OK. Shortcut: To set attribute values on a single atom or bond, right-click on that object and select the desired attribute from the pulldown menu.

111 6 30 Structure Queries Ring Isolation Ring Isolation is used to select a ring system specification for a selected ring. First select the entire ring system or any nodes in it. Then select Ring Isolation from the QueryDef menu. The Ring Isolation dialog box displays. Shortcut: right-click on a node and select Ring Isolation. Click the radio button next to the selection you want. The selections include: Isolated/Embedded: This setting retrieves search results with the selected ring system either isolated or embedded in a larger ring system. This is the default and will retrieve the most answers. Isolated: This setting retrieves only search results that have no additional ring fusion to the selected ring system. Additional chain substitution is allowed at nodes in the ring. Mixture: Structure Drawing activates this choice to remind you that you have selected rings or ring systems that have a mixture of Ring Isolation settings. You may not select this choice yourself. Click OK. Bond Characteristics Bond Characteristics is used to set a bond type and a bond value for one or more bonds in a structure query. Select the bonds to be modified. Select Bond Characteristics from the QueryDef menu. The Bond Characteristics dialog box is displayed and includes options to set the Bond Type (ring or chain) and the Bond Value (bond order, e.g., single or double). Shortcut: right-click on a bond. Click the radio button next to the Bond Type and Bond Value that you want. Click the Bond Types button to select a bond default for single or multiple use. Then click OK. The bond types and bond values include: Bond Types Chain: Search results include structures containing only the selected bonds in a chain. This is the default type for drawn chain bonds. You cannot alter the bond type of bonds drawn in rings. Ring/Chain: Search results include structures containing the selected bonds in either rings or chains. Nodes on either side of a bond set to ring/chain are set to ring or chain. Ring: Search results include substances containing the specified bonds in rings. This is the default type for ring bonds. You may change a chain bond to a ring bond, but you cannot alter a bond within a drawn ring. The nodes on either side of the new ring bond are also set to ring. Mixture: Structure Drawing activates this choice to remind you that you have selected bonds that have a mixture of bond types. You may not select this choice yourself.

112 Structure Queries 6 31 Bond Values Exact/Normalized: Search results match answers either with the exact bond value drawn or with normalized bonds in the corresponding position. Using these bonds ensures maximum recall without sacrificing precision. Exact: Search results exactly match the bond value drawn. This is the default value for carbon-carbon bonds in chains and most bonds in isolated rings. Normalized: Search results only match answers with corresponding normalized bonds. This is the default for even-numbered rings and ring systems with alternating single and double bonds all the way around the cyclic path and for tautomeric bonds. Unspecified: Search results have any bond value for a bond with this value. This is selected when the selected bond has a value of Unspecified, but is grayed because it is not user-selectable in this dialog box. Select Bond from the Draw menu to change bonds to Unspecified. Mixture: Structure Drawing activates this choice to remind you that you have selected bonds that have a mixture of bond values. You may not select this choice yourself. Click OK. Node Characteristics Node Characteristics is used to set an attribute for one or more nodes in a structure query. Select the nodes. Then select Node Characteristics from the QueryDef menu. The Node Characteristics dialog box is displayed. Shortcut: right-click on a node and select Node Characteristics. Click the radio button next to the attribute you want. They include: Chain: This setting retrieves search results that include structures with the selected node in a chain. This is the default for nodes drawn in chains. This characteristic may not be applied to a node in a ring. Ring: This setting retrieves search results that have the selected node in a ring. This is the default for ring nodes. You may change a chain node to ring, but you cannot change a ring node to chain. Changing node characteristics of atoms on both ends of a bond does NOT change the bond type. Ring/Chain: This setting retrieves search results that have the selected node(s) in either a chain or a ring. Mixture: Structure Drawing activates this choice to remind you that you have selected nodes that have a mixture of node characteristics. You may not select this choice yourself. Click OK. Changing the node characteristics changes all selected nodes regardless of their previous setting.

113 6 32 Structure Queries Hydrogen Attachments Hydrogen Attachments is used to specify the number of hydrogens attached to selected nodes in a structure query. Select the nodes. Select Hydrogen Attachments from the QueryDef menu. The Hydrogen Attachments dialog box is displayed. Shortcut: right-click on a node and select Hydrogen Attachments. Select the radio button next to the value you want. Any: This setting retrieves search results that include structures with any number of hydrogen attachments at the selected node, including none. This is the default setting for all nodes. Specific: This setting allows you to specify the number of hydrogens allowed to attach to a selected node. You may specify the exact or minimum number. Type a number from 0 to 99. Exact: This setting retrieves search results that include only structures with exactly the specified number of hydrogens attached to the selected node(s). Minimum: This setting retrieves search results that include only structures with at least the specified number of hydrogens attached to the selected node. Alternately, you could draw the hydrogens on the node directly using the Pencil or Chain tool. Mixture: Structure Drawing activates this choice to remind you that you have selected nodes that have a mixture of hydrogen attachments. You may not select this choice yourself. The value for hydrogen attachments must include the count of hydrogen atoms drawn as attachments to the node. If the value for hydrogen attachments is less than the count of hydrogens attached to a node, a warning comes up during Save. Changing the number of hydrogen attachments changes all selected nodes regardless of their previous setting. Click OK.

114 Structure Queries 6 33 Non-H Attachments Non-H Attachments is used to specify the degree of substitution for one or more selected node(s) in a structure query. Select the nodes. Select Non-H Attachments from the QueryDef menu. The Non Hydrogen Attachments dialog box is displayed. Shortcut: right-click on a node and select Non-H Attachments. Select the radio button next to an attribute in the Non Hydrogen Attachments dialog box. Any: This setting retrieves search results that include structures with substitution of any number of ring or chain non-hydrogen connections at the selected node(s). This is the default setting for all nodes. Specific: This setting allows you to specify the number and type of non-hydrogen connections allowed to attach to a selected node. You may specify the exact or minimum number. Type a number from 1 to 16. You may specify that the bond(s) to the attached node(s) be Chain, Ring, or Ring/Chain. Click OK. Exact: This setting retrieves search results that include structures with only the exact number of Non-H connections for the specified type (chain, ring, or ring/chain) attached to the selected node(s). Minimum: This setting retrieves search results that include structures only with at least the specified number for Non-H connections of the specified type (chain, ring, or ring/chain) attached to the selected node. Maximum: This setting retrieves search results that include structures with only no more than the specified number of non-hydrogen connections of the specified type (chain, ring, or ring/chain) attached to the selected node(s). Mixture: Structure Drawing activates this choice to remind you that you have selected a mixture of non-hydrogen attachments. You may not select this choice yourself. Chain: This setting defines that the bond(s) to the attached node(s) must be chain. Ring: This setting defines that the bond(s) to the attached node(s) must be ring. Ring/Chain: This setting defines that the bond(s) to the attached node(s) may be ring or a chain.

115 6 34 Structure Queries Other Attributes Other Attributes is used to set a charge, valency, and isotope attributes for ONE node in a structure. Select the node. Select Other Attributes from the QueryDef menu. The Other Node Attributes dialog box is displayed. Shortcut: right-click on a node and select Other Attributes. Select the appropriate option from the following: Charge: The default charge is Any, which retrieves answers with both charged and uncharged atoms at the selected node. Other settings include Any+, Any-, or a specific number in the range from -30 to +30. Scroll the Charge box to select a numeric charge. Valency: The default valency setting is Any, which retrieves answers with any valency on the selected node. Other settings include Abnormal or a specific number in the range from 1 to 16. Valency is equal to the total number of bonds to a node, plus the absolute value of any charge on the selected node. Isotope: The default isotope setting is Any, which retrieves answers with any isotope value, including none, for the selected node. Other settings include Abnormal or a specific number. Specified numbers may be in the range from 1 to 255. Generic Definition Generic Definition is used to change a default setting for selected generic nodes, i.e., Ak, Cb, Cy, Hy. Select a generic node in the drawing area. Then select Generic Definition from the QueryDef menu. The Generic Definition dialog box is displayed and provides options for Saturation, Type of Chain, Number of Hetero Atoms, Type of Ring System, and Number of Carbon Atoms. Shortcut: right-click on a generic group node. Only generic definitions applicable to the selected generic node are active.

116 Structure Queries 6 35 Click the radio buttons next to the selections you want. Options include: Saturation: A generic group is saturated when all of the bonds between the atoms of the group are single exact bonds. The generic group is unsaturated when there is at least one double exact, triple, or normalized bond in the group. The default setting is Any. Type of Chain: A generic group is linear when all of the atoms within the group have one or two attachments to other atoms in the group. A generic group is branched when at least one atom within the group has more than two attachments to other atoms in the group. The default setting is Any. Number of Hetero Atoms: A hetero atom is defined as a noncarbon atom. Some generic groups may have one or more hetero atom. The default setting is Any. Type of Ring System: A ring is monocyclic when only one bond must be broken to change the ring to a chain. For polycyclic rings, two or more bonds must be broken to change the ring system to a chain. The default setting is Any. Number of Carbon Atoms: Selected generic groups may have fewer than 7 carbon atoms or 7 or more carbon atoms. The default setting is Any. Click OK. Markush Attributes Markush Attributes affect search results only in the MARPAT and MARPATPREV Files. Markush Attributes is used to change the default setting for one or more selected nodes. Select the nodes. Select Markush Attributes from the QueryDef menu. The Markush Attributes dialog box is displayed and provides options for Match Level and Element Count Level. Shortcut: right-click on a generic group node. Click the radio buttons next to the selections you want. The default may be changed, for rings or chains separately, on the Chemistry tab of your Structure Drawing Preferences.

117 6 36 Structure Queries Match Level (MLEVEL) Options Class - searches for structure matches at either the generic group or the atom level. This is the initial default setting for chain nodes. Atom - limits the search to structure matches at the atom level. This is the initial default setting for ring nodes. Any - searches for matched structures at any level, including generic R groups Mixed - Structure Drawing activates this choice to remind you that you have selected nodes that have a mixture of match levels. You may not select this choice yourself. Changing the match level changes all selected nodes regardless of their previous setting. Element Count Level Options Limited - requires an Element Count to be explicitly stated on matching generic nodes in answers. The box is gray if the nodes you select have both Limited and Unlimited values. After selecting your choices for either Match Level or Element Count Level, click OK. Element Count Element Count is used to limit the types and numbers of elements in generic groups or to limit the types of Markush retrievals for your query. To use this command, select one or more generic nodes in your structure. Then select Element Count from the QueryDef menu. The Element Count dialog box is displayed. Shortcut: right-click on a generic group node. Choose the elements that you wish to limit in your query. Select Exact, Range, Minimum, or Maximum. Click Add to apply the Element Count to selected nodes. Click Remove to remove the Element Count from selected nodes. Click OK to return to structure building. If multiple nodes are selected, only the Limited box is available unless all of the nodes are generic groups with the same element count definitions. The elements available for selection depend upon the generic group selected. Click in the Limited box to match generic groups that explicitly meet your Element Count specifications. If the Limited box is not clicked, generic groups that merely imply your Element Count specification will be matched.

118 Structure Queries 6 37 Delocalized Charge Delocalized Charge is used to change the default setting for selected nodes. Select the nodes. Selected nodes MUST be adjacent. Then select Delocalized Charge from the QueryDef menu. The Delocalized Charge dialog box is displayed and provides a scrollable list of delocalized charge values. Select a delocalized charge from the scrollable list. Options include: Any: Retrieves substances with or without a delocalized charge. This is the default. Specific Numbers: Select a specific number between 5+ and 5- or a specific number range to include Any+, i.e., from 1+ to 5+, or Any-, i.e., from 5- to 1-. After selecting a delocalized charge value, click OK. Stereochemistry Refer to the Stereo Searching section, at the end of this chapter for details on this command. Free Sites The Free Sites command is applicable only when creating WPI and Questel structures. Free Sites is used to change the default setting for one or more selected node. Select the nodes. Select Free Sites from the QueryDef menu. The Free Sites dialog box is displayed and provides a scrollable list of free site values. Select a value from the scrollable list. The default, None, retrieves search results containing the normal valency of the atom with hydrogen attachments only. You may also specify a maximum value, between 1 and 9, for nonhydrogen attachments acceptable to the selected nodes. Bond types are not considered. Click OK.

119 6 38 Structure Queries Review Functional Group STN Commands Review Functional Group STN Commands allows you to review the STN command file that represents a saved Functional Group structure query. The command file displays the list of search refinement filters that have been saved for the query. To use this command, select Review Functional Group STN Commands from the QueryDef menu. The command file is displayed in the stnedit dialog box. After you have reviewed the commands, click OK. For more details about functional groups, refer to Chapter 7, Reaction Queries. Query Verification Query Verification is used to review the attributes of your current structure query. To use this command, select Query Verification from the QueryDef menu. The Query Verification dialog box is displayed. Click the radio button next to All, the default, to review all attributes. Or click the radio button adjacent to Select to choose specific attributes to review. If you choose Select, you may quickly select attributes in a category by clicking the appropriate button, e.g., Rings. Otherwise, click a in each attribute you want to review. You may also examine each attribute in a structure query by clicking the Query Attribute button on the Toolbar. Refer to the Toolbar section earlier in this chapter for more details. Click OK. STN Express with Discover! displays small dialogs describing these attributes and their locations in your structure.

120 Structure Queries 6 39 Display Menu in Structure Drawing Carbons The Display menu commands affect the appearance or orientation of your current structure. Use this option to change the display of individual carbon atoms for the purpose of documentation or presentation. Search results are not affected. First select the carbon atoms that you want to change using the Selection tool. Then select one of the three display options available from the Carbons command in the Display menu. The selected carbons are changed to your specification. To change the display of all carbon atoms, click the Carbon Atom Display button on your Toolbar or change the setting in the Drawing section of your Structure Drawing Preferences. Stereo Select Stereo to label selected nodes as d, l, dl, +, -, +/-, R, S, RS,., :, ::, or RAC. This is for display only and does not affect your search results. Stereo labels can be deleted using the Eraser tool and moved using the Lasso tool. Show/Hide VPA (STN structures only) Show Node Numbers (N) Select Show VPA to toggle the display of hidden bonds with Variable Points of Attachment. Select Show Node Numbers to toggle between showing the node symbols, e.g., O, Me, X, or their node numbers. Ring Circles Select Ring Circles to toggle between displaying benzene rings with a circle in the middle or with alternating single and double bonds. Show Reactions Select Show Reactions to display reaction information such as Reaction Roles, Reaction Sites, and Reaction Mapping and to activate the reaction drawing tools.

121 6 40 Structure Queries Show Query Attributes Select Show Query Attributes to launch the query attribute viewer for displaying attribute information for a node or bond at the cursor position. Smooth (Ctrl+E) Select Smooth to straighten and align structure components, e.g., freehand drawn rings. Sometimes STN Express with Discover! is unable to smooth some structures and, in these cases, will display an informational message. Also, structures may be smoothed in a way that you do not like. If so, select Undo from the Edit menu to restore the structure. Expand (>) Select Expand to enlarge and center your structure drawing. Use the scroll bars to view a drawing that is off the screen. Contract (<) Select Contract to reduce and center your structure drawing. Reverse Shortcut Select Reverse Shortcut to display a shortcut in the opposite orientation. This command is available only after you have selected a shortcut that is reversible in your structure. Rotate Select a fragment using the Lasso tool or the Selection tool. Then select Rotate. The cursor changes to indicate the direction and point of rotation. Drag the cursor as the fragment rotates about its center. Flip fragment horizontal (L) Select Flip fragment horizontal to flip a structure left or right. To flip a fragment, position the cursor on an atom on the vertical axis line where the structure will be flipped and click.

122 Structure Queries 6 41 Flip fragment vertical (U) Select Flip fragment vertical to flip a structure up or down. To flip a fragment, position the cursor on an atom on the horizontal axis line where the structure will be flipped and click. Show Grid Select Show Grid to display a drawing grid in your Structure Drawing window. The structure is displayed on top of the grid. Refer to the Drawing section of Structure Drawing Preferences to modify the default spacing between grid lines. Snap to Grid Select Snap to Grid to place selected nodes on the nearest grid position. Refer to the Drawing section of (Structure Drawing) Preferences to modify the default spacing between grid positions. If no nodes are selected, all nodes in the drawing area are snapped to the grid. Snap to Compass Select Snap to Compass to snap selected bonds to the nearest compass position. Refer to the Drawing section of (Structure Drawing) Preferences to modify the default spacing between compass intervals. If no bonds are selected, all bonds in the drawing area are snapped to the nearest compass angle.

123 6 42 Structure Queries Preferences! Menu in Structure Drawing The Preferences! menu is used to customize your Structure Drawing environment. Click the Preferences! menu to display the Preferences dialog box. Six tabs are available to customize structure drawing. They are Chemistry, Layout, Save Time, Warnings, Colors/Fonts, and Drawing. Click a tab to modify preferences. Chemistry Click the Chemistry tab to modify defaults for chemistry-related attributes in Structure Drawing. Click the check box or the radio button to toggle one of the following options on or off. Show VPA - select to display right attachment points associated with VPA (Variable Points of Attachment). Deselect to hide attachment points associated with VPA. This can also be changed by clicking the Display menu from the Structure Drawing Main Menu bar. Limited - select to set the default for the Markush element count level. This may also be changed for any given node with the Markush Attributes command or the Element Count command in the QueryDef menu from the Structure Drawing Main Menu bar. Use Bond Algorithm - allows you to bypass the Structure Drawing bond algorithm that automatically sets the bond value for optimal retrievals. This creates all bonds as Exact/Normalized unless you manually change them. Some queries can be created only with the Bond Algorithm turned off. Show Reactions - select to activate reaction drawing mode by default.

124 Structure Queries 6 43 Markush Match Level Defaults - select to set defaults for Ring Nodes and Chain Nodes when creating Markush structures. The defaults may be overridden while in Structure Drawing. Methyl Display - choose to display methyl groups as CH3 or Me Then click OK. Your changes take effect immediately. Click Cancel to cancel the changes. Layout Click the Layout tab to modify display of the Structure Drawing tool palette, toolbar, status bar, and tool tips. Palette Click a in the check boxes to customize the display of the (Tool) Palette. More than one option may be selected. Options include: Horizontal - select to display the Palette horizontally, above the Structure Drawing window Visible - select to display the Palette Single Line - select to display the Palette in a single line or a double line Some Layout changes may not take affect until after STN Structure Drawing is restarted. Toolbar Click a in the check boxes to customize the display of the Toolbar. More than one option may be selected. Options include: Horizontal - select to display the Toolbar horizontally, above the Structure Drawing window Visible - select to display the Toolbar Single Line - select to display the Toolbar in a single line or a double line

125 6 44 Structure Queries Status Bar Click a in the check boxes to customize the display of the Status Bar. More than one option may be selected. Options include: Clock - select to display the current date and time Menu Help - select to display help text for all buttons on the Toolbar and the Tool Palette Mol Formula - select to display a saturated molecular formula Tool Tips - select to see information about a tool button when the cursor is positioned on a button Then click OK to accept all changes. Or click Cancel to cancel the changes. Save Time Click the Save Time tab to customize the features shown in the dialog box below. Autosave (Seconds) - automatically saves a query being drawn at the time interval specified. Untitled queries are prompted for a name, followed by the standard Save options. If you choose to cancel this option, you are prompted again, after the specified number of seconds, following the next change to the query. Initial Save Dialog Box Checkbox states - click a in the following check boxes to set the initial value at save time. These values can be changed at save time, if desired. Query Verify - display the Query Verification dialog box when you save a structure query G-group Orientation - prompts you to specify fragment orientation for G-groups containing fragments with two or more points of attachment Refine Using Structure Filters - Select to refine your structure query using structure filters

126 Structure Queries 6 45 Advanced Save all Chain Atoms as Ring/Chain - set all chain atoms to Ring/Chain when saved Save all Chain Bonds as Ring/Chain - set all chain bonds to Ring/Chain when saved Save all Terminal Atoms as Ring/Chain - set all terminal chain atoms to Ring/Chain when saved Select Chain Atoms/Nodes to be saved as Ring/Chain - manually select atoms and/or bonds to be saved as Ring/ Chain Click OK after setting the options. Click Cancel to cancel the changes. Warnings Click the Warnings tab to disable or enable warning messages in Structure Drawing. To disable messages, select them by clicking anywhere on the line that contains each message. Then click Disable. An X appears to the left of each disabled message. To disable all messages quickly, click the Select All button. Then click Disable. To re-enable messages, select them by clicking anywhere on the line that contains the disabled message. Then click Enable. To re-enable all messages quickly, click the Select All button. Then click Enable.

127 6 46 Structure Queries If you do not see a message of interest, use the scroll bar to find it. Or type words in the Search For > text box. Then click Search For >. If a message is found containing the words, it is automatically scrolled to and highlighted. Click OK after setting the options. Click Cancel to cancel any changes. Colors/Fonts Click the Colors/Fonts tab to customize the colors of Bonds, Atoms, Selections, Attributes, Text, and Reactions and to customize the fonts for atom symbols and text. To change the color of any item, click the appropriate radio button. Then click one of the 16 color boxes. The change is shown in the sample structure displayed in the box on the right. To change the font for both the atom symbols and the text, click a in the Text Font=Atom Font box (selected by default). Then click the Atom Font button. A Font dialog box is displayed. You may change the font and point sizes. To change the font for the atom symbols or the text, uncheck the Text Font=Atom Font box. Then click the appropriate button, i.e., Atom Font, Text Font. A Font dialog box is displayed. You may change the font and point sizes. Click OK after setting the options. Click Cancel to cancel the changes.

128 Structure Queries 6 47 Drawing Click the Drawing tab to customize the options that affect structures while they are being drawn. You may modify the following: Double Bond Width (Pixels) - specify the distance between double bonds (only takes effect on printing) Pen Width (Pixels) - set the thickness of bonds (only takes effect on printing) Grid Spacing (mm) - specify the default distance between grid lines. The Grid box must be checked for the Grid to be displayed. Compass Interval (deg) - specify the default compass interval. (Note that compass intervals used should be factors of 90 degrees, e.g., 15, 30, otherwise bonds cannot be drawn horizontally and vertically. Bond Length (mm) - set a default bond length which is used for the ring and chain commands and for freehand drawing when the Snap Bonds option is checked. Snap Bonds must be checked to set values for Bond Length. Browse Delay (secs) - set the time between displays when browsing structure queries Depending on your printer, the double bond width and the pen width values may need adjustments. You may change the default for display of carbon atoms from Angles to Dots or C s (carbon atoms). This is also available by clicking the button on the toolbar.

129 6 48 Structure Queries Click a in any of the following items to turn on the feature. These include: Reaction Help (on by default) - display help dialogs when drawing a reaction structure query Grid - turns a grid on that acts as a guide when drawing a structure. The grid line spacing can be changed using the Grid Spacing option. Ring Circles - draw circles inside normalized rings, replacing the alternating single and double bonds. Note that refreshing the screen display is slower when ring circles are displayed. Snap Bonds - specify the bond length to use when drawing rings and chains. Bonds drawn freehand will automatically snap to the nearest compass interval at the bond length that you specify. If this option is unchecked the standard bond length built into the program is used for drawing rings and chains. Bonds drawn in freehand are placed at the length and orientation indicated by the cursor position. Delete Atoms with Bonds - specify that the nodes at either end of a bond are deleted when a bond is deleted Click OK after making changes to the Drawing Preferences. Changes take effect immediately. Or click Cancel to cancel the changes. Building and Searching a Structure Query on STN Follow the steps below to build and search the following structure query. 1. Select Prepare Structure Query from the Query menu or click the Prepare Query button on your STN Express Toolbar. A new Structure Drawing window is displayed. 2. Build your structure using the Structure Drawing tools and menus. a. Click the Ring tool and click the six-membered hexagonal ring with alternating bonds shortcut. Click in the center of your window to place the ring.

130 Structure Queries 6 49 b. Click the Chain tool and type a 2 in the Chain Length box and click OK to draw a 2-length chain. Place the cursor on the lower right node of the ring and click. Draw a 6-Membered Normalized Ring with 2-Atom Chain Attached c. Click the Chain tool again. Accept the default chain length of 1 to draw a 1-length chain. Click on the upper right node of the ring to draw the chain. d. Click the double bond icon on the Atoms & Bonds Toolbar to select a double bond value for single use. The cursor changes to the Pencil tool. Place the Pencil tip on the atom to which you want to attach another atom by a double bond. Press the left mouse button and hold while dragging the Pencil straight down. Release the mouse button to draw a double bond to a single carbon atom. Attach an Atom with a Single Bond (Chain Tool) and another Atom with a Double Bond (Pencil Tool) e. Double click the N icon (nitrogen atom) on the Atoms & Bonds Toolbar to select nitrogen for multiple use. Place it on the top carbon in the ring and click to replace the carbon with a nitrogen. Repeat the process for the bottom carbon in the ring. f. Single click the O icon (oxygen atom) on the Atoms & Bonds Toolbar to select oxygen for single use. Using the Pencil tool, click to place it on the bottom node of the double-bonded chain. Add Nitrogen and Oxygen Nodes

131 6 50 Structure Queries g. Select Shortcut from the Draw menu. Select OH and click Single Use. Position the Pencil cursor on the right most node in the structure and click to replace the carbon with an OH. h. Select Variables from the Draw menu and select X Halogens. Click Single Use. Position the Pencil cursor on the top, right-most node and click to replace the carbon with the halogen variable (X). This completes your structure drawing. Add OH and Halogen Variable (X) Nodes 3. Select Save from the File menu. Type a name, e.g., halopyra, and click Save. Select Verify Query from the Save dialog box. Click Save. Click OK if each attribute is correct. When the query verification completes, you are ready to upload your structure to an online system. 4. Select Exit from the Structure Drawing File menu to return to the Main Menu bar 5. Click the Logon menu to connect to STN, via a logon setup. (Refer to Chapter 4, Setup, if you have not defined your setup.) STN Express with Discover! opens the STN Terminal Emulation window and automatically connects to STN. Type FILE REGISTRY at the arrow prompt (=>) and press Return. 6. Click Upload Structure Query from the Query menu. Click your structure file to upload, e.g., halopyra.str, and click Open. STN Express with Discover! uploads your structure. 7. Type DIS QUE (DISPLAY QUERY) and press Return to see the uploaded structure diagram.

132 Structure Queries Type SEARCH L1 and press Return. Type the defaults at the search type and search scope prompts. When the sample search completes, the number of records found is displayed, as well as the full file search projections. Conduct a Substructure Sample Search (SSS) 9. Type D (DISPLAY) at the arrow prompt and press Return. The first answer from your sample search is displayed. Display First Answer of Sample Search You can also type D SCAN to display answers in random order. D SCAN is a no charge feature that allows you to review answers to confirm that you have the expected results from the query.

133 6 52 Structure Queries 10. Select Logoff or Logoff Hold from the Online menu. Logoff Hold saves your session for 60 minutes with no charge for the hold time. Creating Stereospecific Structures Select Prepare Structure Query from the Query menu or click the Prepare Query button if it is located on the Main Menu Toolbar. Open a new or existing file and build and save the structure below. Structure Example Convert the structure into a chiral structure with the following steps: 1. Select Bond from the Draw menu. Select Stereo from plane. Click Multiple Use to draw more than one Stereo from plane bond. 2. Click the Pencil tool. Click on the bonds that connect the substituents to the ring to make them Stereo. Stereo Structure Example To confirm that the structure is now a stereo structure, select Query Verification from the QueryDef menu. To change the orientation, select the node with the Selection tool. Select Stereochemistry from the QueryDef menu. Click Invert from the Node Attribute list. Click OK.

134 Structure Queries 6 53 Stereochemistry in QueryDef menu Select Stereochemistry from the QueryDef menu to customize your stereospecific structure. The Stereochemistry dialog box is displayed. The Stereochemistry command is most commonly used to specify either Absolute or Relative stereochemistry. The default is Relative. Relative searches are broader than Absolute searches because relative stereochemistry allows retrieval of both possible enantiomers. When performing a relative Stereo Search, your answers may be either absolute or relative. The answer record for each substance states whether the substance s stereochemistry is relative or absolute. An Absolute Stereo Search limits your answers to the single enantiomer that you have drawn in your query. Absolute structure searches reduce the number of retrieved records because your search is more precise. Also, you may want to set the stereochemistry to Absolute for any query with a single chiral center.

135 6 54 Structure Queries To search for structures with double bond geometry, draw the double bonds with the geometry that you want. Then indicate that the double bond should be searched with stereochemistry by following these steps: 1. Select the bonds 2. Select Stereochemistry from the Query menu 3. Select Stereo under Geometric Bonds in the Stereochemistry dialog box To further customize structures stereospecifically, select from the following options in the Stereochemistry menu. Stereo Set options are used to define different stereo groups within a single structure, e.g., to make the relative stereo of the attachments to one ring independent of the relative stereo of the attachments to another ring. Stereo Sets are typically needed for very complex queries. Please consult the STN Help Desk before using Stereo Sets. Node Attribute options are used to alter stereo structures, e.g., flatten, invert. To use any of these options, select the stereo nodes in your structure using the Selection tool. Select Stereochemistry from the QueryDef menu. Select your options and click OK. A Few Hints 1. The first item drawn in your stereospecific structure is assumed to be the stereo center. This determines the direction of all the stereo bonds in the structure. 2. You cannot distinguish whether a stereo query has Relative or Absolute stereochemistry by its structure diagram. Queries may be checked in STN Express with Discover! by selecting Stereochemistry from the QueryDef menu and checking the default setting. The text for an answer s display record will indicate whether the stereochemistry is Absolute or Relative. 3. When creating double stereo bonds and stereo centers, STN Express with Discover! automatically checks the bond angles, the attachments, the angles of attachments, and the patterns of stereo bonds to ensure that the stereo center is valid. Chiral centers must unambiguously represent a tetrahedron. If any ambiguity exists, an error message is issued. 4. The small end of a wedge stereo bond must be drawn next to the chiral center. To change the direction of a stereo bond, click the right mouse button while on that bond.

136 Structure Queries 6 55 Stereo Structure Building Features The features available in stereo query building are listed in the table below. Stereo Query Building Function STN Express with Discover! Actions Change existing bonds to stereo bonds Select Bond from Draw menu or click Current Bond Box to display Bond Selection dialog box. Select a stereo bond. Create a wedge or dash stereo bond Select Bond from Draw menu or click Current Bond box to display Bond Selection dialog box. Select a wedge or dash stereo bond. Delete stereo aspects of a stereo bond Select Bond from Draw menu or click Current Bond box to display Bond Selection dialog box. Select a new bond value.

137 6 56 Structure Queries Stereo Query Building Function STN Express with Discover! Actions Flatten a stereo bond Select Stereo Mode and choose Stereochemistry from QueryDef menu. Click flatten. Set the stereo default Select bond Select Stereochemistry from QueryDef menu. Select the default option. Reverse stereo bond Place cursor on stereo bond. Click right mouse button on bond. Invert a stereo bond Select Bond from Draw menu or click Current Bond box. Select a different stereo bond. Invert stereo bonds from a chiral center Select stereo node Select Stereochemistry from QueryDef menu. Select Invert option. Make double bond geometric Select double bond in structure Select Stereochemistry from QueryDef menu. Select choice from Geometric Bonds option.

138 Structure Queries 6 57 Stereo Query Building Function STN Express with Discover! Actions Create a Stereo Set Select nodes in structure. Select Stereochemistry from QueryDef menu. Select option from Stereo Set list. Add a node to a Stereo Set Redefine Stereo Set. Delete a node from a Stereo Set Select a node. Select Stereochemistry from QueryDef menu. Select Node Attribute, flatten, or Stereo Set, none. Change the Stereo Set type Select all nodes in set. Select Stereochemistry from QueryDef menu. Choose a Stereo Set option. Invert stereo in all chiral centers Click Select All in Stereochemistry from QueryDef menu. Click Invert. Put all chiral centers into Stereo Sets Click Select All and a Stereo Set choice.

139 6 58 Structure Queries Stereo Query Building Function STN Express with Discover! Actions Delete Stereo at a chiral center Select the node. Select Stereochemistry. Select Flatten under Node Attributes. Delete stereo aspects of a geometric bond Select bond in structure. Select Stereochemistry from QueryDef menu. Click No Stereo from Geometric Bonds list. Delete a specific Stereo Set Select all nodes in the set. Click None from Stereo Set list in Stereochemistry from QueryDef menu. Delete all stereo specifications Select Stereochemistry from QueryDef menu. Click Select All, Flatten from Node list, and/or None from Geometric Bonds list. Delete all Stereo Sets Click Delete Sets in Stereochemistry from QueryDef menu. Delete all geometric specifications Select Stereochemistry from QueryDef menu. Click Select All and No Stereo from Geometric Bonds list.

140 Structure Queries 6 59 Stereo Query Building Function STN Express with Discover! Actions Delete all chiral specifications Select Stereochemistry from QueryDef menu. Click Select All and Flatten from Node list. Check for common errors Select Query Verification from QueryDef menu. Select items to verify. Click OK. Display Stereo Attributes and Stereo Sets Select Query Verification from QueryDef menu. Select items to verify. Click OK.

141 6 60 Structure Queries Keyboard Shortcuts in Structure Drawing STN Express with Discover! supports many of the standard Windows keyboard shortcuts. These shortcuts are listed along with menu commands. The following shortcuts are available in Structure Drawing and are not shown in the menu selections. Shortcut Function Backspace (Shift+Del) A C Edit Clear Preview Match Level (toggle) Chain Tool [ Repeating Groups (Draw menu) D L M N P R T U V Erase Flip Fragment Horizontal Center structure Show Node Numbers (toggle) Repaint Ring Tool Text input mode Flip Fragment Vertical Valency of node at cursor + Positive charge dialog for node at cursor

142 Structure Queries 6 61 Shortcut Function - Negative charge dialog for node at cursor > Scale up (Expand) < Scale down (Contract) Ctrl+G Ctrl+E Right click on bond Space Bar Right click in Current Atom Box Right click atom or bond Right click common atom or bond Right click Ring, or Chain Tool Right click in drawing area with Ring or Chain Tool Left click on Toolbar or a Palette gap Right click on Toolbar Right click Reaction Arrow Right click Text Tool G-Groups Smooth Stereo Bond reversal (in Pencil mode) Reset to C and Single Bond (defaults) Display the Atom Selection box Direct access to attributes Change value of common atom or bond Select the tool and set the default size Insert alternating single and double bonds Change the layout of the Toolbar or Palette Edit the Toolbar Select the tool and the default reaction arrows Display font selection dialog

143 6 62 Structure Queries Creating Structure Queries from Structures in Transcripts STN Express makes it very easy to transform transcript structures into searchable structure queries. Just follow these steps. 1. Select Browse transcript. Open the transcript containing the captured structures that you want to change to searchable structure queries. 2. Highlight the structure diagram in the open transcript. Select Create Query File from the Edit menu. 3. The Create Query File message is displayed. Click OK.

144 Structure Queries In the Structure Queries dialog box, type the name that you want to assign to the structure.

145 6 64 Structure Queries 5. To recall the saved structure, select Prepare Structure Query, select File menu, and Open the saved structure.

146 Reaction Queries Reaction Queries The Structure Drawing environment contains reaction and functional group drawing tools that enable you to draw reaction queries. Reaction queries may include: Structures and roles for the participants A reaction arrow to define the reaction Reaction sites to define the bonds where the reaction takes place Mapping to show the correspondence of atoms in the reactant to the atoms in the product Reactants, reagents, and products are structure searchable in STN reaction files. Catalysts and solvents are not structure searchable. To draw a reaction query, you must first open the Structure Drawing window by clicking on the Prepare Query button on the main toolbar or selecting Prepare Structure Query from the Query menu. Click the Reaction button located on the Toolbar or select Show Reactions from the Display menu. The Structure Drawing window is displayed in Reaction mode and the Reaction Drawing tools are activated. To use Functional Groups, you must click the Functional Group button. This activates the Functional Group and Reaction structure drawing mode drawing tools. Rxn Tool Button Functional Group Button Reaction Drawing Tools Functional Group Tools

147 7 2 Reaction Queries Use the Reaction Drawing tools to create your reaction query. All Structure Drawing tools that are active are available to draw a reaction query. Reaction Arrow Tool Click the Reaction Arrow tool from the Tool Palette to set up a chemical reaction between structures. A Reaction Arrow dialog box is displayed. The first arrow displayed is the default. Click OK to accept the default, or select another reaction arrow and click OK. To draw an arrow, press the mouse button and drag the arrow between the two points where you want the arrow to appear. Release the mouse button. You may continue to draw arrows of the same type. To change arrow types, click the Reaction Arrow tool again. Reaction arrows are not searched. However, if a participant is assigned ANY ROLE at the time you draw an arrow, STN Express with Discover! reassigns the role as PRODUCT or REACTANT/REAGENT based on the direction of the arrow and the proximity of a participant to the arrow s end. Reaction Role Tool The Reaction Role tool is used to specify the roles of the participants in a reaction. To use this tool, click the Reaction Role tool from the Tool Palette. STN Express with Discover! displays a message telling you to select a node in a structure fragment. Click OK. This message is displayed by default. To deactivate all Reaction Drawing help messages, access Preferences in Structure Drawing. Then click the Drawing tab and uncheck Reaction Help.

148 Reaction Queries 7 3 Click a node in the structure fragment whose role you want to define. The Role Specification Selection dialog box is displayed. Select a role. Click OK. The role is displayed under the fragment you selected. You may continue to specify roles for reaction participants by clicking a fragment node, and selecting a role. Reaction Site Tool The Reaction Site tool is used to specify a reaction site label for a specific bond. Labels include: CC - completely changed bond, i.e., the selected bond is either formed or broken PC - partially changed bond, e.g., an exact bond becomes normalized XC - either completely or partially changed bond NC - the bond is unchanged NON - no reaction site specification is declared To use this tool, click the Reaction Site tool from the Tool Palette. STN Express with Discover! displays a message telling you to select a bond in a structure. Click OK. This message is displayed by default. To deactivate all Reaction Drawing help messages, access Preferences in Structure Drawing. Then click the Drawing tab and uncheck Reaction Help. The cursor changes to resemble a spider. Click a bond in the structure fragment you want to define as a reaction site. The Site Specification Selection dialog box is displayed.

149 7 4 Reaction Queries Select one of the options. Click OK. All reaction sites are marked with the Reaction Site tool cursor symbol on the bond. If you select the NON site specification, the cursor symbol is removed from the bond. Atom Mapping Tool The Atom Mapping tool is used to specify a correspondence between atoms in the reactant and atoms in the product. To use this tool, click the Atom Mapping tool from the Tool Palette. A dialog box is displayed. Select either the Manual Mapping or the Automatic Mapping option. The default is Manual Mapping. Click OK. If you select Manual Mapping, STN Express with Discover! displays a message telling you how to use the Manual Mapping. Click OK. This message is displayed by default. To deactivate all Reaction Drawing help messages, access Preferences in Structure Drawing. Then click the Drawing tab and uncheck Reaction Help. To indicate a mapping, press and hold the Shift key and click on an atom in a structure fragment and then on an atom in another fragment. The selected atoms are numbered identically. Continue mapping pairs by clicking on the corresponding atoms. Pairs are numbered sequentially in the order you map them. The elements at both nodes must be the same. Maps may not be assigned to shortcut symbols, Gk nodes, or generic groups. Select one of the options. Click OK.

150 Reaction Queries 7 5 Building and Searching a Reaction Query Follow the steps below to build and search a reaction query. 1. Select Prepare Structure Query from the Query menu or click the Prepare Query button from the Toolbar. 2. Click the RXN button located on the Toolbar. 3. Build the structure shown below using the Structure Drawing tools and menus described in Chapter 6, Structure Queries. Any Role is assigned to all structures in a reaction query until you assign them with the Reaction Arrow tool or the Reaction Role tool. 4. Click the Reaction Arrow tool from the Tool Palette. Accept the default arrow from the Reaction Arrow dialog box and click OK. 5. Draw an arrow from the first structure to the second. 6. The reactions are assigned roles of Reactant/Reagent and Product, respectively. 7. Click the Reaction Role tool from the Tool Palette. Click on a node in the first structure. The Role Specification Selection dialog box is displayed. 8. Select Reactant and click OK.

151 7 6 Reaction Queries 9. Select Save from the File menu or click the Save button if it is located on your Toolbar. Type a name, e.g., reactque.str, and click Save. 10. Query Verification and Verify Reaction Specifications are performed to make sure that the query attributes are set to what you intended and to ensure all reaction specifications are correct. 11. Select Exit from the File menu. 12. Click the Logon menu or click the Logon button from the Toolbar. Select a logon setup. (If you have not yet defined a setup, refer to Chapter 4, Setup.) STN Express with Discover! starts your online session, automatically, and opens a Terminal Emulation window. 13. Type FILE CASREACT, or another reaction file, at an arrow prompt (=>) and press Return. 14. Select Upload Structure Query from the Query menu or click the Upload Query button from the Toolbar. Double-click the structure to upload, reactque.str. STN Express with Discover! displays a dialog box that asks you which file you intend to search. Select Reaction-searchable file to execute the search in CASREACT and to assign a single L-number to the reaction. If you select the other options, each structure in the reaction is assigned a separate L-number. STN Express with Discover! uploads your reaction query, displays a dialog box with the status of the upload, and displays the following message: Uploading reactque.str. 15. Type D QUERY and press Return to see the uploaded reaction query. 16. Type SEARCH L1 RANGE=1996 (RANGE is an STN option) and press Return. Enter the default at the search type prompt. 17. Type D (DISPLAY) and press Return. The default display format, the first hit reaction, and the compressed bibliography for the first answer from your range search are displayed.

152 Reaction Queries 7 7 Structure attributes must be viewed using STN Express query preparation. => SEARCH L1 RANGE=1996 ENTER TYPE OF SEARCH (SSS) OR CSS: SSS RANGE SEARCH INITAITED 12:04:23 SCREENING SCREENING SCREENING SCREENING COMPLETE REACTIONS TO VERIFY FROM 1895 DOCUMENTS 25.9% DONE 4277 VERIFIED 2 HIT RXNS 2 DOCS 42.7% DONE 7055 VERIFIED 11 HIT RXNS 8 DOCS 52.2% DONE 8626 VERIFIED 13 HIT RXNS 10 DOCS 71.6% DONE VERIFIED 22 HIT RXNS 15 DOCS 84.3% DONE VERIFIED 24 HIT RXNS 16 DOCS 100.0% DONE VERIFIED 26 HIT RXNS 18 DOCS SEARCH TIME: L2 18 SEA RAN=(1996) SSS L1 ( 25 REACTIONS) Select Logoff from the Online menu or click the Logoff button from the Toolbar.

153 7 8 Reaction Queries Using Functional Groups To use Functional Groups in a Reaction Query, you must open a new window by selecting New/Standard from the Structure Drawing File menu or clicking the New/Standard button located on the Toolbar. After opening a new Structure Drawing window, click the Functional Group button on the Toolbar. The reaction and the functional group drawing tools, located at the bottom of the Tool Palette, are activated. The Ring and Chain tools become inactive in the Functional Group mode. Selecting a Functional Group To select a functional group, either: 1. Right- or left-click in the Current Atom box The Functional Group Selection dialog box is displayed. Scroll the list to select the Functional Group you want to insert. Then click Multiple Use to insert it more than one time and retain it as your default. Or click Single Use to insert it one time. The functional group you select is placed in the Current Atom box. 2. Click the Functional Group button on the Tool Palette to select a functional group from a predefined list.

154 Reaction Queries 7 9 Select a Functional Group from any scrollable list. The functional group you select is placed in the Current Atom box. Functional Groups selected in this manner can only be placed once. If you want to select a functional group for multiple use, you must right- or left-click in the Current Atom box. See the previous step for details. Placing Functional Groups To place a functional group, click the Pencil tool. Then position the Pencil tool cursor where you want the functional group and click. Continue selecting and placing functional groups until your query is complete. To see the attributes of a functional group right-click on a functional group. Its attributes are displayed in a Functional Group dialog box. Completing a Functional Group Reaction Query To complete the query, click the Reaction Arrow tool from the Tool Palette. Select an arrow from the Reaction Arrow dialog box. Refer to the Reaction Arrow Tool section for more details. Then click the Reaction Role tool to specify the roles of the participants in the functional group query. STN Express with Discover! displays a message telling you to select a node in the appropriate fragment. Click OK. This message is displayed by default. To deactivate all Reaction Drawing help messages, access Preferences in Structure Drawing. Then click the Drawing tab and uncheck Reaction Help.

155 7 10 Reaction Queries The cursor changes to resemble an arrow. Click a functional group. The Functional Group Role Selection dialog box is displayed. Click the radio button next the role you want for the selected functional group. Then click OK. Functional Group searching provides additional role values that are not available for regular reaction searching. Continue assigning roles to the remaining functional groups in the same manner. To see the structure of a functional group, right-click on the functional group name in the Structure Drawing window. The Functional Group dialog box is displayed. The name and the structure of the functional group you clicked is displayed. Click OK to close this box and return to the Structure Drawing window.

156 Reaction Queries 7 11 Combining Functional Groups for Searching To combine functional groups with the OR Boolean operator within a reaction query, click the OR tool from the Tool Palette. Position the cursor close to the functional groups that you want combined. Press your mouse button and drag until a box encloses those functional groups. Then release your mouse button. The functional groups are enclosed in brackets and are OR d together in the reaction query. When you save a functional group reaction query, an STN Command File is also created. Select Review Functional Group STN Commands from the QueryDef menu or click the Review FG button from the Toolbar to display the stnedit dialog box. This identifies the command file that will be used when searching the CASREACT File on STN.

157 7 12 Reaction Queries Saving a Functional Group Reaction Query Save the functional group reaction query by clicking Save from the File menu or by clicking the Save button if it is located on the Toolbar. Type a file name, e.g., fg2, and click Save. Verify Reaction Specifications is performed to ensure all reaction specifications are correct. Searching a Functional Group Query 1. Click the Logon menu or click the Logon button from the Toolbar. Select a logon setup. (If you have not yet defined a setup, refer to Chapter 4, Setup.) STN Express with Discover! automatically starts your online session within a Terminal Emulation window. 2. Type FILE CASREACT, or another reaction file, at an arrow prompt (=>) and press Return. 3. Select Upload Structure Query from the Query menu. Double-click the structure to upload, fg2.str. STN Express with Discover! then uploads the STN FG command file. 4. Type SEARCH L1 and press Return. 5. Type D (DISPLAY) and press Return. => S L1 L NITRO/FG.FORM PRIMARY AMINE/FG.RCT SECONDARY AMINE/FG.RCT 554 NITRO/FG.FORM (L) (PRIMARY AMINE/FG.RCT OR SECONDARY/FG.RCT => D L2 ANSWER 1 OF 554 CASREACT COPYRIGHT 1996 ACS 6. Select Logoff from the Online menu.

158 8 WPI Fragmentation Codes 8 1 WPI Fragmentation Codes The procedures for drawing structures and generating a Fragmentation Code strategy are described. Fragmentation Codes are generated from WPI (World Patents Index) structures for searching in the WPIDS (Derwent subscribers) and the LWPI (the WPI learning file) files on STN. If you frequently use the WPI features in STN Express with Discover! refer to Chapter 3, Main Menu & Toolbar, and to Chapter 6, Structure Queries, for details about modifying the STN Express Toolbar and the Structure Drawing Toolbar to contain WPI-specific buttons. Creating a WPIDS or LWPI Structure Query To draw a WPI structure, open Structure Drawing. Click Prepare Structure Query from the Query menu or click the Prepare Query button on your Toolbar. Select New/WPI from the File menu or click the Open WPI button, if it is located on your Toolbar, to open a new WPI structure drawing window. An Untitled *WPI* window is displayed. You may also open an existing WPI structure by selecting Open from the File menu or clicking an Open button on the Toolbar. Then choose a structure file. The structure is previewed. If the structure is in a format other than WPI, click the WPI radio button from the Convert to list and click Open. Use the structure drawing tools and menus to create your structure query. Refer to Chapter 6, Structure Queries, for information about these tools. WPI Structure Drawing Conventions The following section lists the structure conventions that can be applied to WPI structure drawings. Some conventions differ from those applied in structures drawn for other structure-searchable files, e.g., normalized/ aromatic bonds are not used in WPI structures. For most structures, STN Express with Discover! automatically detects groups that could have more than one possible representation, e.g., tautomeric systems, and generates the correct code. Normalization Aromatic rings, such as benzene, should be drawn with single and double bonds. Normalized bonds are not used when drawing WPI structures.

159 8 2 WPI Fragmentation Codes Tautomeric Structures STN Express with Discover! automatically generates the correct fragmentation codes for tautomeric structures, e.g., keto-enols. If your structure contains a free site, the substitution at this site may result in a tautomeric structure. When you generate the strategy, this option is displayed in the Select Fragments dialog box. Refer to the Generating the Strategy section later in this chapter. The L9 negation code is generated only for quinones and other unambiguous cases. Salts Inorganic Anion + Inorganic Cation Draw these structures as separate ions or with single bonds, e.g., Na + Cl - or Na-Cl Ca 2+ Cl - or Cl-Ca + or Cl-Ca-Cl Organic Anion + Inorganic Cation Draw these structures with bonds between the anion and the cation, e.g., C-CO-O-Na, C-CO-O-Ca + or C-CO-O-Ca-O-CO-C Inorganic Anion + Organic Cation Draw these structures as disconnected ions with a charge, e.g., (CH3)4N + Cl - Inorganic Acid Addition Salts of Organic Base Draw this salt and acid as two separate fragments on the same screen. Do not draw explicit hydrogens, e.g., C-N Cl (methylamine.hcl) Organic Anion + Organic Cation The anion and cation are indexed as two separate records. To search, treat each component as a separate structure. Create two drawings, one for each component. Then, generate two strategies. Combine the hit lists with the AND operator and add the salt code manually.

160 WPI Fragmentation Codes 8 3 Multi-atom Anions Simple Metal Containing Anions Place the charge on the metal atom, e.g., O O Mn O O Simple Non-metal Containing Anions Draw multi-atom anions containing no metals, e.g., sulfate, carbonate, or phosphate, with bonds between the sulfur and the oxygen, or the carbon and the oxygen, or the phosphorus and the oxygen, e.g., O O P O O Zwitterionic or Ampholytic Compounds Zwitterionic or ampholytic compounds are indexed as neutral molecules by shifting a hydrogen from the positive part of the compound to the negative. If this shift is not possible, the positive and negative parts are indexed according to the rules that govern individual acids and bases, e.g., an onium group is indexed as charged and an ionized organic acid is indexed as a free acid. <v5> N + O O S <v6> O Charge Separation Canonical Forms If there are no mobile hydrogen atoms and charges are on adjacent atoms, the bond order is raised and the charge is neutralized, e.g., organic azides R-N=N N notr-n=n + =N - This is not permitted if the bond is a triple bond.

161 8 4 WPI Fragmentation Codes Dative Bonds Dative bonds drawn between two nonmetal atoms are represented by a double bond, e.g., N O Dative bonds are only used between metals and ligands. Refer to the next section, Organometallic Complexes, for more details. Organometallic Complexes Draw all metals and ligands in the same screen. Place the charge on the cations and inorganic anions. Do not place a charge on an organic anions. Neutral ligands are joined to the metal by dative bonds, e.g., Cr Carbonyls Draw carbonyl groups with double or triple bonds, e.g., -C=O or -C O Acetylacetone and Related Complexes Draw acetylacetone and related complexes as two separate fragments. No bonds should be drawn between the metal atom and the acetylacetone group. Therefore, the code for the metal bound to the oxygen of the organic group will not be generated. However, this can be added manually.

162 WPI Fragmentation Codes 8 5 Adjust the valency of the metal atom or apply charge to avoid filling empty valencies with hydrogen atoms, e.g., O V <V2> O O The structure should be drawn in this way because attaching the vanadium to the oxo group would mean that the code for the two oxo groups would not be generated. Metal Phthalocyanines Draw metal phthalocyanine structures with single and double bonds. Attach two of the Nitrogens to the metal using dative bonds, e.g., N N N N M N N N N Metal-Carbon Bonds Draw metal-carbon bonds, where the metal is attached to a specific carbon atom, as single bonds, e.g., C-C-C-C-Li n-butyl lithium For more complex systems, refer to the Organometallic Complexes section in this chapter. Extended Structures Draw extended structures, e.g., zeolites, according to the rules governing salts, e.g., O O - O Na + Si Al - O O

163 8 6 WPI Fragmentation Codes Sugars Input cyclic sugar tautomers in acyclic form. Sugar codes (L8) are not generated automatically for these compounds. Select Include WPI Other Code Concepts from the Query menu to manually select sugar codes. STN Express with Discover! automatically detects structures that may be a sugar and asks you if you want to apply the L8 Negation Code to your strategy during strategy generation. Elements and Alloys Elements that exist in molecular form in the free state are drawn in their normal form, e.g., O=O, F-F. However, you may draw elements as single atoms with the valency set to 0. Otherwise, empty valencies are filled with hydrogen atoms. Alloys are indexed as extended structures and are searched using multifragment representation. The valencies of the metals are set to zero, with no free sites. Quinone Diazides Draw quinone diazides, e.g., diazonium phenoxide, with no charge on the oxygen. Place the charge on the nitrogen. O N + N Hydrogen Atoms Hydrogen atoms should not be drawn except as values in G-groups. Select H as the value of a G-group by clicking on the Atoms button from the G-group definition dialog box. Select Deuterium and Tritium from the Atoms menu. Hydrogen atoms are assumed to fill the empty valencies on atoms. For example, an isolated carbon atom is treated as methane because carbon has a default valency of 4. To increase the number of hydrogen atoms attached to an atom, increase the valency of the atom.

164 WPI Fragmentation Codes 8 7 Constructing Generic Queries Superatoms If you are creating a generic WPI structure query, you may use superatoms, G-groups, and/or Free Sites in your structure drawing. In a WPI format structure, superatoms act as predefined generic groups. They generate codes for all of the groups or atoms covered in the definition. Superatoms include: ACT Actinide (including actinium) AMX Alkali (ne Earth) Metal ARY Aryl-Carbocyclic, optionally fused, containing at least 1 benzene ring A35 Group IIIa-Va Metal - Al, Ga, In, Tl, Ge, Sn, Pb, Sb, Bi CHE Alkenyl, Alkenylene CHK Alkyl, Alkylene CHY Alkynyl, Alkynylene CYC Cycloaliphatic - Carbocyclic, optionally fused HAL Halogen HEA Heterocyclic - Aromatic, Monocyclic (5 or 6 ring atoms) HEF Heterocyclic - Fused, optionally aromatic HEO Heterocyclic - containing metal, halogen or B, Si, P or As HET Heterocyclic - Non-aromatic, Monocyclic LAN Lanthanide (including Lanthanum) MX Metal, any TM1 First series transition metals TM2 Second series transition metals TM3 Third series transition metals TRM Transition Metals excluding Lanthanum TX O, S, Se, Te UX O, S, Se, Te, N ZX B, Si, P, As For example, a structure containing a CHK (alkyl), generates codes for all the possible alkyl chains; a structure containing a HET generates codes to retrieve any monocyclic non-aromatic heterocyclic structures.

165 8 8 WPI Fragmentation Codes Placing Superatoms To place a superatom, follow the steps below. 1. Select Chain Superatoms, Ring Superatoms, or Other Superatoms from the Draw menu. A dialog box is displayed for each respective command. 2. Select a Superatom from the dialog box. Click Single Use to use the superatom once or Multiple Use to change it to your default. The superatom you choose is displayed in the Current Atom box on the Atom & Bond Palette. You may also right-click in the Current Atom box and type a Superatom or select a superatom from the scrollable list in the Atom Selection dialog box. To apply attributes to a superatom, you must: 1. Click the Selection tool located on the Tool Palette. Then select a superatom that is in your structure query. 2. Select Other Attributes from the QueryDef menu. A dialog box is displayed that contains attribute options. This dialog box varies depending on the superatom you selected. You may also right-click on the superatom with the Selection or Pencil tool and select other attributes from the pop-up list. Modify the attributes by clicking an arrow to display the pulldown menu for each attribute and selecting the appropriate menu item. Click OK when attributes are complete. Click Cancel to cancel the changes.

166 WPI Fragmentation Codes 8 9 G-Groups G-Groups may be defined as atoms, shortcuts, superatoms, other G- groups, and/or as multi-atom fragments. You may insert a G-group before or after you define the G-group. Drawing a G-Group Right-click in the Current Atom box, located on the Atom & Bond Palette, to draw a G-group. The Atom Selection dialog box is displayed. Type a G-group, e.g., G1. Click Single Use to use it once or Multiple Use to make it your default. Click the Pencil tool. Place the G-group on a node and click. G-groups can be used more than once, but the values of the G-groups are not permuted with one another. G 1 G 1 G 1 =H,Cl For this example, fragmentation codes are generated for an unsubstituted ring and a dichloro- substituted ring. Refer to the Generating the Strategy section later in this chapter for more details. If you define a G-group as another G-group, the values of the G-groups are permuted. G 1 G 1 =G 2 =H,Cl G 2 Fragmentation codes generated in this example include codes for an unsubstituted ring and a monochloro- and dichloro-substituted compound. G-Groups - Fragments Fragments included in the definition should be drawn on the screen before defining the G-group. The attachment point(s) must be indicated on each fragment. Single atoms with free sites or attributes should be drawn as fragments with 1 or 2 attachment points. To indicate an attachment, you must: 1. Select G-Groups from the Draw menu 2. point of attachment. Click Single Use to indicate one point of attachment or Multiple Use to indicate more than one. 3. Click a node to indicate a point of attachment. symbol is displayed at the node. There is a limit of 20 attachment points per structure.

167 8 10 WPI Fragmentation Codes No G-group orientation of fragments occurs when you save the WPI structure query. The G-group orientation occurs when you generate a Fragmentation Code strategy. See the Orienting Fragments section later in this chapter for more details. G-Groups - Superatoms Draw superatoms as single-node fragments, with attachment points. G-Groups - Nesting Fragments may contain additional G-groups and/or superatoms. Nest up to three levels of G-groups. Examples include: G0 = Ph-G1 G1 = -C-G2,-C=O G2 = -O-G3,-C=O G3 = H,C,Et Notice that the G3 definition cannot contain another G-group because it would exceed the three-level nesting limit. For more information on defining G-groups, refer to Chapter 6, Structure Drawing. Displaying a G-Group You may display a G-group definition by: 1. Selecting G-groups from the Draw menu 2. Selecting Query Verification from the QueryDef menu Select Query Verification from the QueryDef menu to display a G- group definition. Click the radio button next to Select, at the top of the Query Verification screen, to mark those attributes you want to verify. Select Contents in the G-group list. Click OK.

168 WPI Fragmentation Codes 8 11 Free Sites Free sites allow optional substitution on an atom or a superatom. Free sites are not assumed on structures and should be applied if you want to carry out a substructure search. Select an atom or superatom with the Selection tool. Select Free Sites from the QueryDef menu. Enter the number of free sites. The number of free sites determines the maximum number of neighbors (substituents) permitted on that site, regardless of its bond value. For example, -C retrieves: -CH3, -CH2F, -CHO, -CN, etc. -C 2 retrieves: -CH3, -CH2F, -CHF2, -CHO, -CO2H, -CN When you generate a fragmentation code strategy for a structure with free sites, you are prompted for substitution information at each free site. For more information, refer to the Format of Fragmentation Code Strategies section in this chapter. If your structure contains a free site on 2 or more atoms, it is possible that the substituents on these sites may combine to complete a ring. During Fragmentation Code generation, you are asked if this is possible for any pair of free sites in the structure. However, if two free sites are on the same atom in a ring, it is assumed that the substituents do not combine to complete a ring. For example, the structure below, does not retrieve,

169 8 12 WPI Fragmentation Codes You should draw this structure type with a G-group instead of a carbon. The G-group is defined as C with two free sites or CYC, ARY, HET, HEA, HEF, and HEO. The attributes on the heterocyclic superatoms should be substituent attached to carbon. This is the default for all heterocyclic superatoms except HEO. Ph-G1 G1 = C2, CYC, ARY, HEA, HET, HEF, HEO Other Concept Codes When generating a Fragmentation Code strategy, you may include nonstructural or sugar codes in your search. You must save your WPI query to include Other Concept Codes. To use this feature, return to the STN Express Main Menu & Toolbar. Then select Include WPI Other Code Concepts from the Query menu. The Other Code Concept dialog box is displayed. The Other Concept Codes window is blank until you make your selections. Click Select Codes menu in the Other Code Concepts dialog box. Continue to make selections. The selected codes are displayed in the Current Selection and the Codes Selected dialog boxes. The codes you select are combined with the AND operator. AND operation specifies that all of the codes are present in the structure record. Click the AND operator, on the menu bar, to toggle it to the OR operator. OR operation specifies that at least one of the fragmentation codes is present in the structure record. Click Delete Last or Delete All to delete codes from the Codes Selected dialog box. Click Leave OCC to leave this environment. You are returned to the Main Menu bar.

170 WPI Fragmentation Codes 8 13 Click Edit WPI Strategy from the Query menu to edit a strategy. Select a structure query file name. STN Express with Discover! warns you if there is a current strategy that may be overwritten. Generating the Strategy First, exit Structure Drawing. Save and name your structure file if you have not already done so. From the STN Express Main Menu & Toolbar, select Generate WPI Strategy from the Query menu. An Open WPI Structure dialog box is displayed listing the WPI structures. Select a file name to preview the structure. Click a in the Generate RIN codes only box to only generate RINs for your WPI structure. If you selected a non-structural code or sugar code from Include WPI Other Code Concepts, you may include them in your strategy. Click Include OCC. If you did not pre-select one of these codes, the Include OCC button is unavailable. Click OK after completing your selections. Orienting Fragments If fragments contain two attachment points, STN Express with Discover! asks you to specify their orientation. The parent structure is displayed with the G-group. An atom that the G-group is attached to is highlighted. Click the number of the attachment point that you want connected to the highlighted atom. Click Select. Select Show Fragment if you want to view the fragment.

171 8 14 WPI Fragmentation Codes Structures with Free Sites If your structure contains free sites, STN Express with Discover! asks you to restrict the substitution type at each free site. Click the checkmarks out of the boxes that you wish to exclude from your WPI strategy. Then click OK. The Select Fragments dialog box is displayed for each node that has free sites. The choices available for substitution vary with each structure. If there are free sites present, STN Express with Discover! displays a Groups/Codes Included/Excluded From Free Site Substituents dialog box allowing you to restrict the type of substitution in the overall structure. Basic Group Codes The Basic Group Codes dialog box is located on the left side of the Groups/Codes Included/Excluded From Free Site Substituents dialog box. Click a in the Rings Present dialog box to indicate that rings may be present in the structure other than those you have drawn. Then specify which type of ring may be present. These selections affect the basic group codes and multiplier codes included in your strategy. Negation Codes The Negation Codes are located on the right side of the Groups/Codes Included/Excluded From Free Site Substituents dialog box. Notice that every choice is pre-selected, i.e., these groups are assumed to be absent. Click the out of a group box to include the possibility that the group is present, i.e., to broaden the search. Click Deselect All to permit any of these groups in the WPI strategy. Click Select All to exclude all groups from the strategy, i.e., to narrow the search. When you have completed this selection process, click OK. A warning message is displayed informing you that the structure has been modified. You are asked if you want to generate the fragmentation codes. Click Yes to generate the codes.

172 WPI Fragmentation Codes 8 15 Selecting SUBs A series of messages are displayed as the structural codes are processed. When the process completes, a Select Subs dialog box is displayed. A list of Subs (Subheadings) (M0-M6) is displayed. Select the ones you want to search. Then, click OK. Again, a series of messages are displayed as processing continues. When the process completes, a command file is displayed in the editor that lists the fragmentation code strategy. A file name has been assigned and the command file has been saved to disk. Editing the Strategy The Fragmentation Code strategy is displayed as an STN command file. You may display and edit this file, provided you are cautious of the script variables being used. Position the cursor on a code and select Code Definitions from the Utilities menu to see a definition of a fragmentation code. If you have edited the strategy, select Validate Codes from the Utilities menu. Check the fragmentation code strategy list for invalid codes. A warning message is displayed if invalid codes are found. This only detects mistyped codes. It does not check that your strategy was formatted correctly. Select Save from the File menu to save the strategy. Two files are saved. The STN command file using a.sc extension and a strategy control file using a.stg extension. The strategy file contains information linking the file and the STN command file. Printing the Strategy On the main STN Express Menu Bar, select Print WPI Strategy from the Query menu. You may include the WPI structure, the code definitions, the fragmentation code strategy, and the negation code definitions by selecting these options in the Select Data to Print dialog box.

173 8 16 WPI Fragmentation Codes Uploading the Strategy Select STN from the Logon menu to search the fragmentation code strategy. You are automatically logged on to STN using your STN logon setup you created in Chapter 4, Setup. If you did not set up an automatic logon, refer to Chapter 4. When the logon completes, you will see an arrow prompt (=>). Type FILE WPIDS or FILE LWPI at this prompt. Select Run Command file from the Query menu. Type the command file name. This file name ends in.sc. Select Exit from the File menu to return to the Main Menu & Toolbar. You are prompted to save the strategy if you have not previously done so.

174 9 SPECINFO Queries SPECINFO Queries 9 1 The SPECINFO File contains spectral data for a representative section of organic chemistry, including organometallic substances. SPECINFO features five calculation packages that produce different types of spectral data. They are: Calculation Packages CHESS Definition Searches for chemical structures identical or similar to a query structure (structure code similarity search) COUPCAL Estimates coupling constants for a query structure. Calculates and displays NMR-spectroscopic data. EDSPEC Modifies existing spectra or creates new spectra GETSPEC Searches for spectra similar to a query spectrum SPECAL Calculates and displays NMR spectra from a query structure

175 9 2 SPECINFO Queries Creating a SPECINFO Query Select Prepare Structure Query from the Query menu or click the Prepare Query button if it is located on your Structure Drawing Toolbar. Then select New/SPECINFO from the File menu or click the button that opens a new SPECINFO structure drawing window from the Structure Drawing Toolbar. You may also open an existing SPECINFO structure query, by selecting Open from the File menu or by clicking an Open button for SPECINFO queries from the Structure Drawing Toolbar. If you open an existing structure that was created in the Standard, WPI, or Questel format and change it to the SPECINFO format, the structure is automatically converted to a SPECINFO structure. The original structure is retained in its original format and you are prompted to name the SPECINFO query when you save it. Use the commands and tools discussed in Chapter 6, Structure Queries, to draw your SPECINFO structure. The commands that differ from the STN Standard structure query commands are described next. Bond Command in Draw Menu Select Bond from the Draw menu to choose a bond value. You may also left click the Current Bond box from the Atom & Bond Palette to quickly display the Bond Selection dialog box. Three bonds are unique to SPECINFO queries. They include: Aromatic CO (Coordination) CP (Coordination in pi-system) The remaining bonds are equivalent to those in standard STN structure queries. Select a bond and click Single Use to insert the bond one time, or Multiple Use to make it the default bond. The current bond value is displayed in the Current Bond box.

176 SPECINFO Queries 9 3 QueryDef Menu for SPECINFO Queries The commands available in the QueryDef menu are described next. Query Verification is NOT available for SPECINFO structure queries because all attributes are visible in the structure. Other Attributes Select Other Attributes to change the default setting for the charge of a selected node. The default charge setting is 0 (zero). This setting retrieves substances that are both charged and uncharged. Delocalized Charge Select Delocalized Charge to change the delocalized charge default setting for selected nodes. You MUST select at least consecutive two nodes with the Selection tool before selecting this command. In SPECINFO queries, a node may exist in more than one delocalized charge group. The default setting is Any. This setting retrieves substances with or without a delocalized charge group. Searching a SPECINFO Query After you have created your SPECINFO query, save and name the file as you did with STN Standard queries. Refer to Chapter 6, Structure Queries. Select STN from the Logon menu to logon to STN online. When you have connected to STN, type FILE SPECINFO at the arrow prompt (=>). Select Upload Structure Query from the Query menu. Upload the structure you saved. Type RUN followed by the appropriate calculation package name (COUPCAL, SPECAL, or CHESS) and the L-number of the uploaded query. Continue responding to prompts. If you do not know the response, type a question mark (?). An explanation of the valid responses is displayed and you are reprompted for the information.

177 10 Managing Transcripts This chapter describes Managing Transcripts 10 1 browsing transcripts printing transcripts viewing images exporting transcripts as RTF files modifying transcripts with transcript filters customizing highlighting in transcripts combining transcripts editing transcripts with the STN Express editor Browsing Transcripts To browse a captured transcript, follow these steps: 1. Select Browse Transcript from the Results menu on the Main Menu bar, or click Browse Transcript on the toolbar.

178 10 2 Managing Transcripts 2. In the Transcript File dialog box, select a file name from the list and click Open. The Show structure queries option is selected. Deselect this option if you do not want to have structure queries included in the transcript. 3. If your transcript contains downloaded images, i.e., TIFF, GIF, or JPEG images, answer the prompt whether to view them in context. The selected transcript file opens for browsing.

179 Managing Transcripts 10 3 Saving transcripts as RTF files While you are browsing a transcript, you may save it as an RTF (Rich Text Format) file. 1. Select Save As from the File menu. 2. The RTF File dialog box opens with the transcripts listed as.rtf files. Select the transcript and click Save. The saved transcript automatically opens in the program associated with.rtf documents.

180 10 4 Managing Transcripts Printing Transcripts To print a transcript from the Main Menu window, follow these steps. 1. Select Print Transcript from the Results menu or from the Main Menu Toolbar. 2. In the Transcript File dialog box, select the file for printing and click Open. 3. Select the specifications in the Page Layout dialog box and enter any specifications for your printer. Select Print from the File menu to print a transcript from the STN Online and Results window while you are browsing a transcript. Select Print from the STN Online and Results toolbar to start printing immediately.

181 Managing Transcripts 10 5 Viewing Images While you are browsing or printing transcripts, TIFF, GIF, or JPEG downloaded images are displayed in context if you answer Yes to the prompt: In addition, you may display any TIFF images separately from the transcript text. Follow these steps. 1. Select View TIFF image from the File menu.

182 10 6 Managing Transcripts 2. A list of TIFF files is displayed in the TIFF File dialog box. Select the TIFF file you want to display. 3. The TIFF image displays in a separate window.

183 Managing Transcripts 10 7 Exporting Transcripts as RTF Files To export a transcript file to an RTF (Rich Text Format) file, follow these steps: 1. Select Export Transcript from the Results menu. 2. In the Transcript File dialog box, select a file and click Open.

184 10 8 Managing Transcripts 3. In the RTF File dialog box, the transcript name is displayed with the.rtf extension. By default, the file is saved to the default transcripts folder, but you can direct it to any location on your PC. Click Save. The transcript automatically opens in the program associated with RTF files. Modifying Transcripts with Transcript Filters You may easily modify an existing transcript using transcript filters. STN Express offers five predefined filters. You may also define your own filters. To customize your transcript with predefined STN Transcript Filters, follow these steps: 1. Select Browse Transcript and open an existing transcript that you want to modify.

185 2. Select Transcript Filters from the File menu. Managing Transcripts In the Transcript Filters dialog box, type the name of a new transcript. Click Save.

186 10 10 Managing Transcripts 4. In the Specify Filter dialog box, select one of the predefined filters from the Load Filter list. Predefined Filter stn-ans stn-cmd stn-cmdh stn-strs stn-tifs Result a transcript with only answers a transcript with only STN commands a transcript with only STN commands and their results, excluding reactions a transcript with only structure graphics a transcript with only TIFF images 5. Click OK in response to the message confirming that your new transcript has been created successfully. You may also define your own filter. To define your own filter, enter a new name in the Filter name box of the Transcript Filters dialog box. Enter the parameters for the information to remove. Click the Help button for details and examples of how to create customized transcript filters.

187 Managing Transcripts Customizing Highlighting in Transcripts In STN Express you can create a list of terms to be highlighted in a transcript. Follow these steps. 1. Select Browse Transcript to open a transcript. 2. To create a dictionary file with your list of terms, select Edit Dictionary from the Edit menu. 3. In the Dictionary File dialog box, click New to create a new dictionary file.

188 10 12 Managing Transcripts 4. In the Edit Dictionary dialog box, type a term that you want highlighted in your transcript. Click Add to add it to the dictionary file. Continue adding up to ten terms. Terms will be listed in alphabetical order and are not case-sensitive. Click the color in which you want the terms highlighted. Click OK. Save the dictionary file at the next prompt. 5. To apply the dictionary, select Install Dictionary from the Edit menu. In the Dictionary File dialog box, select the dictionary file to apply. Click Open. The selected dictionary file is applied to the current transcript, i.e., the terms that you have added to the dictionary file are now highlighted by displaying them in the color that you have selected.

189 Managing Transcripts Combining Transcripts Follow these steps to merge multiple transcript files into one file. 1. Open any transcript file that you do not want to merge with another. While the transcript file is open, select Combine Transcripts from the File menu. 2. The Combine Transcripts dialog box is displayed. Type a new file name in the File name box. Click Save.

190 10 14 Managing Transcripts 3. The Select Transcripts to combine dialog box is displayed. Select a file that you want to combine and click Copy. The file is moved to the Selected Transcripts box. Select another transcript and click Copy. You may merge as many files as you need. Click OK to create the merged file.

191 Managing Transcripts Editing Transcripts with the STN Express Editor To edit a transcript file with the STN Express editor, follow these steps: 1. Select Edit Transcript from the Results menu or the toolbar. 2. In the Edit Transcript File dialog box, select the transcript file to edit. 3. The stnedit window is displayed. While capturing a transcript as a.trn file, two separate files are created: one contains text and the other contains graphics. Only the text file is displayed when using the Edit Transcript command. However, graphics and TIFF call-out lines are displayed in the appropriate locations. DO NOT modify these lines. In the stnedit window you may use the standard Cut, Copy, and Paste commands, as well as the File, Edit, Search, and Help menus. The Search menu provides commands to find and replace terms in your transcript file. Command in the Search menu Find (Ctrl+F) Find Next (Ctrl+F) Replace (Ctrl+H) Function to find a term in the transcript to find the next occurrence of your term to replace a term in the text with a term of your choice

192 10 16 Managing Transcripts Adding page breaks while editing transcripts You may add page breaks to a transcript while editing. There are two ways to do this. 1. Position the cursor where you want a page break. Press the Ctrl key and the letter L simultaneously. 2. Create a transcript that contains a page break while online by using the Start New Page command from the Results menu. While offline, edit the transcript containing the page break and copy the line to the clipboard. Edit the file to which you want to add the page break and paste the line where you want a page break added. The page break needs to be on a line by itself and left justified. Using an alternative editor Instead of using the stnedit editor, you may choose to use another text editor. To use another editor, enter its path in General Preferences. Refer to Appendix A for information on General Preferences. If you have entered the path of an alternative editor, the file that you choose to edit is opened in that application. While editing a transcript in an alternative editor, you may use the features of that editor. However, because you must save the file as ASCII text, formatting and font assignments are ignored.

193 11 Creating Reports and Tables 11 1 Creating Reports and Tables Overview This chapter provides step-by-step instructions for creating reports or tables with the following STN Express tools: Tool Predefined Report Tool Custom Report Tool Table Tool Function Creates patent reports from transcripts Prepares reports including only desired transcript data and formatting Creates a table of selected data from Search results The following topics are included in this chapter Creating patent reports Creating custom reports Saving reports Creating tables Saving tables Creating Patent Reports Use the Predefined Report Tool to quickly create a formatted patent report from a transcript (.trn or.rtf) file. Only answers from the patent files or patent-containing files, e.g., CAplus, with the PI (Patent Information) field are included in a patent report generated by the Predefined Report Tool. The content and format of the predefined report may not be modified. To create a customized report, use the Custom Report Tool. After creating a transcript, follow these steps to create a predefined patent report.

194 11 2 Creating Reports and Tables Selecting the Predefined Report Tool Click the Predefined Report Tool button on the toolbar of the STN Express Main Menu and the STN Online and Results window. You may also access the tool from the Results menu on the STN Express Main Menu or from the File menu of the STN Online and Results window.

195 Creating Reports and Tables 11 3 Selecting transcript In the Transcript File dialog box, select the transcript file for your patent report. Click Open. Patent report A predefined report is automatically displayed with patent records from your transcript.

196 11 4 Creating Reports and Tables Creating Custom Reports Selecting the Custom Report Tool Click the Custom Report Tool button on the toolbar of the STN Express Main Menu and the STN Online and Results window. You may also access the tool from Results on the STN Express Main Menu or from the File menu of the STN Online and Results window.

197 Creating Reports and Tables 11 5 Report Tool window Custom Report Tool opens the Report Tool window. Select from the buttons on the left side of the Report Tool window.

198 11 6 Creating Reports and Tables Alternatively, use the Next and Back buttons to move sequentially between screens. When selected, each button displays a screen with options for you to choose. Once the transcripts are chosen, you can click buttons for different screens in any order. Button Transcript(s) Template Content Highlighting Cover Page Fields Statistics Function To select one or more transcripts for the report To select a template for the report To define the content of the report To define highlighting in the report To define the content and format of the cover page To select the fields from answers To define the charts for the report The Report Tool window also includes the following buttons on the bottom of the window: Button Save Template Finish Back Next Cancel Function To save a custom template for reports To produce the report once all selections for content and style have been made To go back to a previous screen To select the next screen To cancel the report-generation process

199 Creating Reports and Tables 11 7 Transcript(s) This window is displayed when you select the Report Tool or when you click the Transcript(s) button in the Report Tool Window. The path for the most recently used transcript is displayed by default. Click on the Remove button on the right if you do not want to select this transcript for your report. Click on the Browse to Add button on the right to locate other transcripts. The Transcript File folder opens with a list of transcripts for you to choose. Select the desired transcript and click Open or browse for other file locations. Once you select another transcript, you are returned to the Transcript(s) window for the Report Tool. You may select multiple transcripts for a single report.

200 11 8 Creating Reports and Tables Template When you click on the Template button of the Report Tool, a list of the currently available templates (.prf files) is displayed. Only one predefined template - the patent template - is currently available. If you have defined and saved other report templates, their names are also displayed in this window. The Description box shows a summary of the attributes of the selected template. Report and Table templates display separately. To view both report and table templates, choose the All radio button. A Table template may be used for a report and vice versa, but attributes that are not applicable will be ignored. To locate templates that are not in the default Transcripts folder, clock the Change Folder button and navigate to that location. Click Choose Template to select the highlighted template for this report. If no template is chosen, STN Express sends a prompt for verification. Click Ignore to continue to define a custom report.

201 Creating Reports and Tables 11 9 Content In the Content window you may select parts of the transcript for your report. Click in the appropriate boxes to include this content in your report. When the Report Tool is used again, the previous content selections will be recalled. Highlighting

202 11 10 Creating Reports and Tables The Highlighting screen shows the following options: Highlighting option Highlight Hit Terms Highlight the Following Terms Highlight Terms in this Text File Result if selected Hit-terms are highlighted in red. Select the Format button to change the font and/or the color of highlighting. To remove any hit-term highlighting, deselect this option. Type the terms to be highlighted. Choose Format to change the font and/ or color of highlighting. The highlighted terms may be any terms in your answers. Terms should be separated with commas. Multiword terms between commas will be highlighted only when the entire phrase is present. This feature is case-insensitive. Highlight a list of terms saved in a text file. Browse for a saved file. Choose Format to change the font and/or color of highlighting. Each line of the text file is treated as a phrase. This feature is case-insensitive. When you select Format, the following options are displayed. If you leave blanks in the Font menus, the highlighted text will follow the font definitions from the Fields screen for the field in which it occurs.

203 Creating Reports and Tables Cover page 1. Select STN Express Cover Page if you want to create a cover page for your report. 1. Choose the content of your cover page by selecting from the options on the left, e.g., Title. Note that Title, Prepared By, and For may not be de-selected. 2. Choose if you want to center the Title, Prepared By, and For. If you do not select this option, all elements of the cover page are leftjustified. 3. Select the order of appearance of the selected items on the cover page by highlighting the item and moving it with the up and down buttons. If the centered option, e.g., Title, is selected, you cannot change the order of the Title, Prepared By, and For.

204 11 12 Creating Reports and Tables 4. Click on the tab for each desired selection, e.g., Title, to enter or modify the existing information and default format for the selection. For example, when you click on the Title tab, the default title, consisting of the names of the transcripts, is displayed in the default font and size. You may modify or replace the text and select the Format button to change the font. Other items that are automatically filled include: Prepared by (from User Data in Preferences) Date of Search (from the file-creation date) Strategy (from last DISPLAY HISTORY in transcript) Update Information (from databases entered in transcript) Cost (last cost display in transcript).

205 Creating Reports and Tables Fields When you select the Fields button on the left, you are guided in selecting the fields for your report. The available fields are those found in the transcripts. The fields are listed alphabetically in the Field Name window on the left. A blank Selected Fields window is displayed on the right. Use the buttons in the middle of the screen for selecting the fields: Button Insert Insert All Rename Delete Delete All Function Insert any highlighted fields from the Field Name list into the Selected Fields list Insert all the fields from the Field Name list into the Selected Fields list Rename a highlighted field from the Field Name list Delete any highlighted fields from the Selected Fields list Delete all the fields from the Selected Fields list For example, you might want to use the Insert All button to select all fields, and then use the Delete button to delete any fields that are not desired. You may select multiple fields using the Shift and Ctrl keys.

206 11 14 Creating Reports and Tables You may also change the order of selected fields by using the Change Order buttons on the right. You may change the format of any highlighted fields on the right by clicking on the Change Font button. The information that displays to the right of the Change Font button reflects the properties of the fields in the Selected Fields box. An example of the final selection for a report is shown. Statistics This window is used for defining histograms or pie charts in your report. You may create up to 3 histograms or pie charts from the transcript as part of the report. Choose one field for each histogram or pie chart. You may also choose to display the graphs at the beginning or at the end of your report.

207 Creating Reports and Tables Saving template Click the Save Template button when you want to save the attributes of the current report as a template for future use. In the Saving a Template dialog box enter the name for your template and click Save. Generating report To generate a custom report, click Finish. The report is displayed.

208 11 16 Creating Reports and Tables Editing reports To edit a field in a report, follow these steps: 1. Right-click on the field. 2. Choose Edit Field 3. Make the changes 4. Click OK. Inserting comments in reports To insert a comment for an answer, follow these steps: 1. Right-click on the answer. 2. Choose Edit Record Comments 3. Type the comment. 4. Click OK. Comments are visible on.rep files only, and appear when the mouse is passed over the Answer Selection Box. Saving Reports You may save a report as the following types of files: STN Express report (.rep) file Rich Text Format (.rtf) file HTML (.htm) file Microsoft Excel (.xls) file ASCII (.txt) file. Saving as STN Report files To save a report as an STN Express Report (.rep file), follow these steps: 1. Select Save from the File menu in the STN Online and Results window.

209 Creating Reports and Tables In the Enter Filename dialog box, select the transcript and choose the.rep format for the saved file (.rep is the only type of format available when you use the Save option). Saving reports in RTF, HTML, and XLS formats 1. Select Save As from the File menu to save the report in standard formats: RTF, HTML, or XLS.

210 11 18 Creating Reports and Tables 2. In the Enter Filename dialog box, choose the format for the saved file and enter or modify the file name. Saving marked answers in custom reports 1. Each record in the custom report is preceded by a selection box. Click on the selection box to mark this record for saving.

211 2. Select Save Marked Answers from the File menu. Creating Reports and Tables Another Report window opens, showing only the selected answers. Once you are certain that it contains the answers you desire, save the report by selecting Save As from the File menu and choosing the file format.

212 11 20 Creating Reports and Tables Creating Tables To create tables of data from answers in your transcripts, use the Table Tool. For example, you may create tables with: substance names, molecular formulas, and structures from the Registry file titles, patent assignees, and IPCs from patent records patent numbers, titles, and graphics trademarks and related data from the trademark files EUMAS and DEMAS. Selecting the Table Tool To use the Table Tool, follow this procedure. 1. Click on the Table Tool button. This button is available on the toolbar of the STN Express Main Menu and the STN Online and Results window. You may also access the Table Tool from the Results menu of the STN Express Main Menu or from the File menu of the STN Online and Results window. Table Tool window The Table Tool window is displayed. To create a table from answers in your transcript, select from the buttons on the left side panel of the Table Tool window. When selected, each button displays a window with options for you to choose.

213 Creating Reports and Tables The Table Tool window contains the following buttons for your use: Button Transcript(s) Template Highlighting Cover Page Fields Statistics Function To select transcripts for the table To select a template for the table To define highlighting in the table To define the content and format of the cover page To select the fields (from answers displayed) to include in the table To define the charts The Table Tool window also includes the following buttons (on the bottom of the window): Button Save Template Finish Back Next Cancel Function To save a template for tables To product the table once all selections for content and style have been made To go back to a previous screen To select the next screen To cancel the selections on a screen

214 11 22 Creating Reports and Tables Selecting Table Tool buttons Selecting any of the Table Tool buttons results in the same type of interaction as that produced by the same button of the Report Tool. Refer to the section on Creating Custom Reports in this chapter for details. Fields The following example shows only the Fields screen of the Table Tool followed by an example of a table that was created. Selecting the Row field results in each row being numbered. If you choose Answer for the Selected Fields, answer numbers from search results will be included in the table.

215 Creating Reports and Tables Generating Table Click Finish when you are done. The table is displayed for you to use. Editing tables You may edit tables by editing cells copying cells deleting rows sorting columns Right-click on the cell, row, or column that you want to modify. Select the operation from the displayed menu of options. For example, select Delete row to delete the row. Resizing the columns To resize the columns in the table place your cursor on a column separator when your cursor changes to resemble a ladder, with left-right pointing arrows, hold down the left mouse key and drag the column separator to the desired position release your mouse button

216 11 24 Creating Reports and Tables Saving Tables You may save tables as the following types of files: Excel Files (*.xls) Express Table Files (*.tbl) RTF Files (*rtf) ASCII Text (*.txt) HTML Files (*.htm) Follow these steps: 1. Select Save As from the File menu.

217 Creating Reports and Tables The Enter Filename dialog box is displayed. Enter the name of the file in the File name box. In the Save as type box, choose the type of file for saving.

218 12 Accounting Overview Accounting 12 1 With the Accounting feature of STN Express you can create a report that contains estimated online session costs for your STN sessions. You can customize the report to show what is reported, in what time frame, and how the report looks. In addition, you can easily export the accounting information in various formats, e.g., as an Excel file. STN Express automatically saves accounting information for STN sessions in the file account.dat. Viewing Accounting Reports To view the accounting information, follow these steps: 1. Select Accounting from the Results menu on the Main Menu bar. You may also select the Accounting button your Main Menu Toolbar. if you have added it to

219 12 2 Accounting 2. In the Select Account File dialog box, choose an Account file from your Uscripts folder. The default file name is account.dat. Click Open. 3. Your online accounting is shown in the STN Accounting window. The estimated costs are displayed in a tabular format.

220 Accounting 12 3 To resize the columns in the table place your cursor on a column separator when your cursor changes to resemble a ladder, with left-right pointing arrows, hold down the left mouse key and drag the column separator to the desired position release your mouse button Customizing Accounting Table You can customize the accounting table by: changing the accounting table parameters, e.g., list the fields to include or exclude defining the time span, i.e., the year and months for the report Changing the accounting table parameters 1. In the STN Accounting window, click on Setup and select Report. 2. Customize the parameters in the Report Settings dialog box.

221 12 4 Accounting Parameter Function Field Name Font Column Width Alignment Sort Key Units Selected Fields Choose up to 8 fields (columns) to monitor, including a blank column that can be used for comments, notes, etc. when you export the accounting file Choose from among a variety of fonts, styles, and point size in your report Define the width of the selected field Indicate the placement of text within each column as left justified, right justified, or centered Define the primary and secondary sort fields for sorting cost information Choose the unit of measure for the width of your table Insert, delete, and change the order of selected fields in your table Defining the date range To define the range of dates for your accounting report, follow these steps: 1. In the STN Accounting window, select Date Range from the Setup menu. 2. In the Set Range dialog box, select the year and months for your report.

222 Accounting 12 5 Exporting Accounting Data To export an accounting report, follow these steps: 1. Select Export from the File menu in the STN Accounting window. 2. In the Enter Export Filename dialog box, select or enter the following: the file name to represent the exported file the file format for the exported data, e.g., Excel. Click Save. If you choose the format as Excel Files, the accounting information is displayed as a Microsoft Excel spreadsheet, if you have the software available on your PC.

223 12 6 Accounting Clearing Accounting Data To clear all cost and session information from the accounting file that you have opened, select Clear Data File from the File menu. This feature does not remove the file, but only erases the data. If you would like to save these data for future reference, make a copy of the account.dat file before clearing the data file. An informatory message appears that requests confirmation of the action.

224 Appendix A Types of Preferences Preferences There are three types of Preferences: General STN Online and Results Structure Drawing Preferences A 1 Structure Drawing preferences are described in Chapter 6. Structure Queries. This appendix describes the General and STN Online and Results preferences. In addition, two preferences in the Host Settings window of Setup are noted. Accessing Preferences To access all preferences, click the Preferences tool Menu toolbar or from the Setup menu of the Main Menu. from the Main

225 A 2 Preferences General Preferences General Preferences is used to: customize default folders for use in STN Express with Discover! customize the display of the Main Menu and Toolbar select the language that STN Express and related programs use for the display of menus and buttons specify your own text editor The folders defined here are used by default to save or open a file. You may choose another folder each time you open or save a file. Changing editor In General Preferences you may also designate another editor, rather than the text editor provided within STN Express. This option lets you take advantage of features of other editor packages. Type or paste the complete path to the editor program in the Editor box. If this box is blank, the STN Express built-in editor is used.

226 Preferences A 3 Changing folders To change a folder: Click in the text box of the folder you wish to change and type in the pathname, or Click in the text box of the folder you wish to change. Then doubleclick a folder or drive letter in the folder selection box, located above the Set *Path To button, to select the appropriate folder. Click the Set *Path To button once the desired pathname is displayed. Customizing Main Toolbar You may also customize the display of the Main Menu and Toolbar by clicking the following options: Option selected Toolbar Always on top Minimize on use Tooltips Result Display the toolbar buttons in STN Express (default) Force the Main Menu & Toolbar to remain visible at all times Minimize the Main Menu & Toolbar after accessing an STN Express application Control whether the main Toolbar has tool tips in addition to the text on the buttons Selecting the language You may also select the language that STN Express and related programs use for the display of menus and buttons. To use Japanese you must have a Japanese version of Windows. The language setting takes effect as soon as you click OK. Other STN Express programs that are already running must be restarted before the language is changed.

227 A 4 Preferences STN Online and Results Preferences To access the STN Online and Results preferences, click the Preferences tool on the toolbar of the STN Online and Results window or the Main Menu toolbar. Click one of the tabs to change those preferences. Account In the STN Account Type box, select the type of account you have and its features: Commercial (Full access) - default setting Full Academic - if you have access to STN files under your academic program FIZ Academic - if you have access to FIZ discounted files only CAS & FIZ Academic - if you have access only to CAS and FIZ files under your academic program BEILSTEIN subscriber - if you have a Beilstein subscription GMELIN subscriber - if you have a GMELIN subscription DERWENT subscriber - if you have a DERWENT subscription Under Property Data Databases, select the property databases that the Discover! wizards are authorized to access.

228 Preferences A 5 Function Keys Use the Function Keys tab to define keyboard shortcuts for frequently used text strings. Up to 18 key combinations may be defined, using Shift F1-F9 and Control-Alt F1- F9. To define a Shift Function Key, click the radio button next to Shift. Type a text string in any of the function key boxes. To define a Control-Alt Function Key, click the radio button next to Control-Alt. A new list is displayed. Type a text string in any of the function key boxes. Type [cr] at the end of a line to insert a carriage return after each string.

229 A 6 Preferences Online Use the Online tab to customize your online environment. Click in the box adjacent to the preferences you want to activate. Then click OK.

230 Preferences A 7 Option selected Continuous scrolling Modifiable Queries Use Filters Result Text and graphics scroll without interruption (recommended) Uploaded structure queries may be modified in the STRUCTURE command Automatically upload structure filters when they are available Enable idle time warning Warning message is displayed after Logoff no commands are sent to STN for 15 Logoff Hold minutes File Transfer Long Packets 4000 File Transfer Log Packets Reduce CPU usage when Online Display international characters Logon splash screen frequency once per day Autoload command history into Command Window Faster Kermit downloads of TIFF images and other files (recommended) A log of upload and download (Kermit) activity is created. Select only on request by STN support staff for problem resolution. Puts STN Terminal Emulation into a passive mode that uses less CPU resources when waiting for you to enter data. If this option is not selected, STN Terminal Emulation uses all the idle CPU time on your local system, without degrading performance of your machine. Allows proper display of international characters when you are connected to an online host that supports those characters. This option cannot be used if the connection route to the host computer requires the use of parity. If the data display from your online host appears to be corrupt, turn this option off. If the problem is resolved, then your connection is using parity. STN logon splash screen is displayed once per calendar day Command history for the current session is automatically loaded at the time you open the command window.

231 A 8 Preferences Colors/Fonts/ Scaling Click the Colors/Fonts/Scaling tab to define colors and fonts in your online window or Browse Transcript window or for prints; to scale structure graphics; and modify TIFF viewer scale settings. To change the color of highlighted text or the color of the text you type at a prompt, click the radio button adjacent to Highlight text or Prompt text, respectively. Then click the color that you want. To change the font of text in the online window or browser window or when printing, click the Change button in the Display Font box or the Printer Font box, respectively. A Font dialog box is displayed. You may modify the font and point size. For display fonts, only fixed-width fonts are available. For print fonts, only fixed width printer and True Type fonts are available. Proportional fonts are not available because text does not line up properly when they are used. To change the horizontal or vertical scaling factor for structure graphics, click in the entry box. Enter a new scaling factor. The defaults are 1.0 for both scaling factors. If the two factors are not changed proportionately, vertical or horizontal distortion will occur. To modify the initial scale used by the TIFF Viewer, click the appropriate radio button next to the Full, Half, or Quarter option.

232 Links Preferences A 9

233 A 10 Preferences Option selected Use a single browser for all WWW links Launch a new browser window for each WWW link Override Windows default browser Change to STNGUIDE when jumping to the WWW Full-text links Use secure ChemPort link Return to original file after executing STN links (not Full-text) Enable Links Result Existing browser window is reused, if it is already running. If the browser window is not running, STN Express will launch the browser (default). A new browser window is opened for each WWW link, resulting in multiple open windows. If you have several internet browsers installed, this option allows you to specify the path to the one that you prefer. STN Express with Discover! moves your online session to the STNGUIDE file any time you request a web function. When you are ready to continue your STN session in another file, you have to enter that file. Select the STN service center where you have your account Select for extra security when you click Full-text links; may be selected only for access to ChemPort from STN- Columbus. Return to original file after STN links, except for Full-text, are executed. Selected items are hyperlinked when you are logged on to STN.

234 Preferences A 11 Postprocessing Postprocessing preferences allow you to set preferences related to transcripts.

235 A 12 Preferences Option selected Capture at logon Capture as RTF Confirm Transcript Capture Stop Wrap Abstracts in Export Use fixed-width fonts on non-wrapping fields in reports and tables Enable Full-Text links in reports and exported transcripts Symbol characters Expand abbreviations Launch Excel when saving as Excel Launch Word when saving as RTF Combine Author and Inventor in Reports and Tables Combine Patent Assignees and Corporate Source Autosave Transcript Default Font Result Transcript is automatically captured at logon (default) Transcript is captured in Rich Text Format. Confirmation message is displayed if you stop capture of transcript (default). Text of abstracts is automatically wrapped in RTF transcripts (default). Tabular STN data, e.g., patent family information, line up in reports and tables (default). Full-text links are preserved in reports and RTF transcripts (default). Symbols and special characters, e.g., Greek letters, display as symbols or special characters in reports, tables, and transcripts (default). CAS standard abbreviations are automatically expanded in transcripts, e.g., oxidn. is expanded to oxidation (default). Microsoft Excel (the application associated with.xls files) is launched when a file is saved in Excel format (default). Microsoft Word (the application associated with.rtf files) is launched when a file is saved in RTF (Rich Text Format (default). Combine author and inventor data in reports and tables. Combine patent assignees and corporate source in reports and tables. Transcript is periodically saved for a specified number of minutes, while you are online. Click Change to change the default font for custom reports, tables, and exported transcripts.

236 Preferences A 13 Discover! Option selected Suppress background display of Discover! commands Histogram in Analyze Answers Wizard Edit Alert L-number deletion warning Result STN commands generated by Discover! wizards are not displayed in the session window until the wizard function is completed. When the Analyze Answers wizard of Discover! is used, analyzed results are presented graphically as histograms. Warning is displayed when a deletion of an L-number used in an SDI alert is requested. Return to original file after Online session returns to the original closing a wizard file after a wizard function is completed. Activate uploaded structure queries in Uploaded structure queries are activated in LREGISTRY by default. You may select another structuresearchable file in which to activate uploaded structure queries.

237 A 14 Preferences User data Under this tab, you can enter data that appear on the cover page of reports and tables. This information is also used to identify you when you click Request Help on the Help menu in order to send a message to your STN Service Center.

238 Preferences A 15 Layout Use the Layout tab to customize the layout of your STN Online and Results window. Status bar - select the items to display in the Status Bar located at the bottom of the STN Online and Results window. Show Toolbar - select to show the Toolbar Open Command Window in locked mode - if locked mode is selected, you can enter multiple commands in the Command Window before sending them to the host. If locked mode is not selected, the Command Window opens in Send mode, which sends a command directly to the host when a carriage return is pressed.

239 A 16 Preferences Cost warning Option selected Issue cost warning when requesting all answers using 1- Issue cost warning before display commands exceeding Issue cost warning before search commands exceeding Result Warning is displayed when a Discover! script contains the TOTAL display option requesting a display of all answers from an answer set. A warning is displayed before a Discover! script or a wizard would exceed the cost limit you have set for answer display. A warning is displayed before a Discover! script or a wizard executes a search command that would exceed the cost limit you have set.

240 Preferences A 17 Host Settings Preferences There are two preferences located on the Host Settings window in Setup. Option Command Window Close Window at logoff Result if selected Command Window is opened when you logon to STN. STN Express session window closes after you logoff from STN.

241 Appendix B ALCHEMY ALCHEMY B 1 ALCHEMY 2000 is a powerful molecular graphics and computation tool for your desktop computer. It features high-performance visualization for all types of chemical structures, including proteins, polymers, and small molecules. Features in ALCHEMY 2000 include: Molecular Dynamics - A tool where you can examine the vibrational motion of the molecules as a function of time. You may also monitor distances and angles throughout the run and create dynamic playbacks of results for visual insight. Results are returned in a table format. Note that a wizard is available to lead you through setting up the calculation and data reporting. Conformational Searching - The opportunity to explore conformational spaces of flexible molecules to find global minimum geometries that satisfy specific distance constraints. Searching may be done by specified increments or randomly assigned values in selected dihedrals. Note that a Conformational Search Wizard is available for your convenience. Intermolecular Interactions - Create an energy function describing the interaction of a small molecule at the site of a large molecule and minimize it to determine a geometry for the small molecular at this site. Use the Molecular Interactions Wizard to lead your through this interaction. Internet Helper Application - Use your browser to display molecules when they are downloaded to your machine. Build, analyze, and modify chemical models Energy Minimization - A technique of modifying molecular coordinates to obtain reasonable, low-energy molecular geometries Fitting - A visual comparison of a series of molecules by matching atom pairs in a least-squares fitting routine. The molecular geometries are then compared to superimpose the structures. Twisting - An interactive rotation of parts of a molecule about a bond to change its conformation with real-time display of distances and angles Spacefilling - A depiction of molecular shape by models that display a molecule s surface as defined by its atomic van der Waals radii Ball and Stack Imaging - Depict a molecule as a sphere connected by a slender rod Contact Tripos, Inc. for additional information about ALCHEMY Tripos, Inc South Hanley Road St. Louis, MO Phone: Internet:

242 B 2 ALCHEMY About CONCORD TM CONCORD. Developed by Robert S. Pearlman and associates at the University of Texas, is marketed by Tripos, Inc. CONCORD is a computer program for rapid, automatic generation of high-quality 3D molecular structures. It is capable of generating approximate structures for almost all compounds composed of the organic elements with connectivity between 1 and 4. CONCORD is not intended to provide realistic structures for large molecules with high potential flexibility. For example, octadecane or a polypeptide is created fully extended rather than in coiled conformations. Many CONCORD structures are visually indiscernible from structures optimized by Molecular Mechanics (MM) or Molecular Orbital (MO) energy. CONCORD structures are usually generated in 0.2 to 2 VAX 11/780 CPU seconds. Many energy minimizations take several minutes to several hours of CPU time. Thus, CONCORD represents a compromise between speed and accuracy. Studies indicate the loss in accuracy as very small. Diagnostics are provided for those exceptions. CONCORD structures serve as exceptionally good initial guesses for energy minimization procedures when your application demands such accuracy. Ring Systems A ring system is defined as a set of rings. Each ring in the set contains at least two atoms in common with another ring in the set. An analysis of each ring system determines the general conformation of each ring. The bond and torsion angles are determined by minimizing a strain function. CONCORD can construct mono- and polycyclic planar ring systems, as well as complex, nonplanar, heteroatomic, fused, bridged, spiro, and caged ring systems. A maximum of 200 heavy (non-hydrogen) atoms per molecule is permitted. The Mechanism of Transformation The CONCORD algorithm provides a mechanism for transforming the information contained in a molecule s atomic CONnection table into the atom CoORDinates. Connection tables from the CAS REGISTRY File for organic substances without stereochemistry and standard CAS bond conventions are provided to CONCORD. The resulting coordinates are available to download using STN Express with Discover!. Substances with more than one component or single atom fragments, polymers, coordination compounds, or incompletely defined substances are not processed.

243 ALCHEMY B 3 Energy Configuration By default, CONCORD produces the lowest energy configuration. It is consistent with the connectivity and the stereochemistry of the structure. For example, methylcyclohexane and 2-butene are made in the lowenergy equatorial and E configurations, respectively. Coordinates are unavailable for stereo-specific substances. However, coordinates for chiral substances with no stereochemistry (NS) are specified. These substances are chiral in nature, but are referred to in literature as having no stereochemistry specifications. Structure-Building Algorithm CONCORD s structure-building algorithm is an offspring of the expert and pseudo-molecular mechanics approaches. Decisions regarding bond and torsion angles are based on a set of rules that expert chemists apply. For example, methoxybenzne is made in the plane of a ring, whereas the methyl group in 2,6-dichloromethoxybenzene is oriented perpendicular to the plane of the ring. Other decisions are made through an optimization procedure to minimize the molecular mechanics energy function. Decisions regarding bond lengths are based on a table. A warning message is issued when an approximated bond length is used. Acyclic Substructures The geometry of acyclic substructures is determined by minimizing steric interactions. H-bonding and stereochemical specification calls are exceptions for higher energy isomeric forms. ALCHEMY MOL Files The 3D CONCORD structure downloaded from STN Express with Discover! is contained in an ALCHEMY MOL File. The MOL File contains a complete description of the molecule. The number of atoms, bonds, and charges, as well as the atom types, coordinates, and connectivities are listed. A comment is also included with CONCORD diagnostics, as well as the CAS Registry Number for the substance. A portion of an ALCHEMY MOL File may resemble the following: 16 ATOMS, 15 BONDS 1 C C H The first line in the file represents the number of atoms and the number of bonds in the molecule. Next is a set of lines, one per atom, that provide the atom number, the atom label, and the x, y, and z coordinates of the atom, in angstroms. The atom number is not read by ALCHEMY. The atom label is four characters or fewer.

244 B 4 ALCHEMY The following list of atoms is the bond list, part of which is shown below. The first column in this table is the bond number. It is not readable by ALCHEMY. The next two numbers are the first and second atoms of the bond pair. The last column is a text field describing the bond value, e.g., SINGLE, DOUBLE, TRIPLE, or AROMATIC SINGLE SINGLE SINGLE SINGLE SINGLE The first line indicates that a single bond exists between the first and the second atoms in the previous atom list. The next three lines show that the first atom is also bonded to atoms 3, 4, and 5. The last line indicates that a single bond exists between atoms 5 and 6. STN Express with Discover! may potentially add two more fields to the MOL File it creates, the CAS Registry Number and the CONCORD Diagnostic Message. The CAS Registry Number is considered an optional field. It is always present in files downloaded from STN. The CONCORD Diagnostic Message is also an optional field. Typically, these are not present. If it is present, the message Warning Diagnostic generated by CONCORD is displayed. ALCHEMY 2000 and STN Express with Discover! ALCHEMY 2000 can be used in conjunction with STN Express with Discover!. You can: 1. Search structures created in ALCHEMY on STN by importing them into STN Express with Discover! and uploading to a structure-searchable file 2. Download with STN Express with Discover! 3D CONCORD coordinates, generated by CONCORD, for over 6 million organic compounds from the CAS REGISTRY File for molecular modeling with ALCHEMY 2000 For information about building ALCHEMY structures, refer to your ALCHEMY manual.

245 ALCHEMY B 5 Searching for ALCHEMY Structures on STN ALCHEMY structures are searched on STN as follows: 1. Transfer a connection table for a structure search Select Prepare Structure Query from the Query menu or click the Prepare Query button if it is located on your Main Menu Toolbar. Depending on how you saved your ALCHEMY structure, change the Files of Type setting to Alchemy Molfile or MDL Molfile. Select a file and click Open. Each MOL File contains data, connection tables, and coordinates for a single substance. Refer to your ALCHEMY manual for information on using MOL Files. 2. Edit the ALCHEMY structure in STN Express with Discover! Edit and modify the ALCHEMY structure that was imported to STN Express with Discover!. These structure types are edited and modified like any structure created on STN Express with Discover!. Refer to Chapter 6, Structure Queries, for more information. 3. Upload ALCHEMY structures to STN Upload the imported ALCHEMY structure from STN Express with Discover! to STN to search the STN structure files. Refer to Chapter 6, Structure Queries, for information on structure searching.

246 B 6 ALCHEMY Downloading Answers from STN for Molecular Modeling in ALCHEMY Search the REGISTRY File on STN to retrieve three-dimensional (3D) coordinate data for millions of organic compounds. The data are generated by CONCORD. Download 3D CONCORD data from STN Express with Discover! by using the search answers from the REGISTRY File or by providing Accession Numbers. In REGISTRY, the Accession Number is identical to the CAS Registry Number. Type HELP ACC at an arrow prompt (=>) for information about Accession Numbers in the REGISTRY File or refer to the REGISTRY File Database Summary Sheet for overall file information. Download connection tables for substances that have 3D CONCORD in the REGISTRY File s File Segment (/FS) search field. Use CONCORD/FS to limit your answers to those containing CONCORD data. You may download to a local PC or to a terminal by typing DOWNLOAD ALCHEMY at an arrow prompt (=>). STN Express with Discover! executes Kermit to process the file transfer. Choose a file name with a.mol extension. For example, inititate the following search in the REGISTRY File: => S ATROPIN? AND CONCORD/FS 336 ATROPIN? CONCORD/FS L1 19 ATROPIN? AND CONCORD/FS => D L1 ANSWER 1 OF 19 REGISTRY COPYRIGHT 1996 ACS RN REGISTRY CN Benzeneacetic acid,.alpha.-chloro-, 2-oxo-1-phenyl-2-[(1,2,2,6- tetramethyl-4-piperidinyl)oxy]ethyl ester (9CI) (CA INDEX NAME) OTHER NAMES: CN Eucatropine.alpha. -chlorophenylacetate FS 3D CONCORD MF C25 H30 Cl N O4 SR CA LC STN Files: CA, CAPLUS, TOXLIT, USPATFULL 1 REFERENCES IN FILE CA (1967 TO DATE) 1 REFERENCES IN FILE CAPLUS (1967 TO DATE) => DOWNLOAD ALCHEMY ENTER (L1), L#, ACC OR?:L1 ENTER ANSWER NUMBER OR RANGE (1):1 ENTER HIGHLIGHT OR NOHIGHLIGHT:HIGHLIGHT ENTER FILENAME OR (?):ATROPINE.MOL TEXT DATA WILL BE DOWNLOADED TO ATROPINE.MOL USING CAPTURE START DOWNLOAD (Y):Y

247 Appendix C Script Language Script Language C 1 A script is a text file that contains a set of statements in the Script Language that are executed by STN Express with Discover! The STN Express with Discover! Script Language can be used to create: custom logon procedures custom search strategies procedures to automate repetitive search or display tasks. For example, you may routinely perform a certain subject or author search on STN. Rather than logging on to STN and opening a transcript file to capture search results, searching multiple files, and then logging off and reviewing the transcript, you can use scripts to streamline the process. One script can log you on to STN, another can initiate the searches, and another script can display your answers. Alternatively, one script can perform all three tasks. Because the script runs automatically, without waiting for you to type, you may reduce your online time and costs. Steps in Writing and Running a Script Defining the Task Define what you want to accomplish and the steps required to accomplish the task. For example, suppose you have a list of CAS Registry Numbers (RN) and want to display their records on STN. What steps would you follow? 1. Log on to STN. 2. Enter the Registry file. 3. Display the record for the first RN. 4. Repeat step 3 until finished. 5. Log off STN.

248 C 2 Script Language Translating the Task into Script Statements After you have defined the task, translate the steps into Script Language statements that will accomplish the task. (The statements are listed in detail later in this Appendix.) 1. Log on to STN. The script could log on to STN, but it is often better to separate the logon task from the job the script performs. In this example, log on to STN as usual and then run the script. 2. Enter the Registry file. The STN command to enter the Registry file is FILE REGISTRY. To use an STN command in a script, use the => (arrow prompt) statement: => FILE REGISTRY 3. Display the record for the first Registry Number. To display a record on STN, use the DISPLAY command. Again we use the => statement: => DIS Repeat step 3 until finished. Add more DIS commands 5. Log off STN. End your STN session with the LOGOFF command, again using the => statement: => LOG Y Creating a script To create a script, select Prepare Command File from the Query menu on the STN Express Main Menu. Click New in the Open Script dialog. This opens the STNEdit window with an Untitled text window inside it. Type the following script statements: \* Display CAS RNs in the Registry file on STN. => FILE REGISTRY => DIS => DIS => LOG Y

249 Script Language C 3 Saving the Script To save the script file, select Save from the File menu. Type a name in the File name box and click Save. By default, the script file is saved to the User Scripts folder defined in General Preferences in the Setup menu (on the Main Menu Toolbar). Refer to Appendix A for information about General Preferences. Do not use any name that exists in the Predefined Scripts folder unless you are replacing the functions of that script. Checking the Script for Errors To check the script for syntax errors, go to the Utilities menu in STNEdit and select Check Command File. If errors are found, STNEdit highlights appropriate script lines and displays a message at the bottom of the STNEdit window. To learn the nature of the error, move the mouse pointer over the highlighted part of a line. Correct the error, save the script, and check the script again until no errors are found. Check Command File does not find all errors because some errors cannot be found until the script actually runs. It is not necessary to be logged on to an online host to use Check Command File. Using or Running the Script While you are logged on to STN, Select Run Command File from the Query menu. A Command File dialog box is displayed. Select a script file to run and then click Open. The script runs until it finishes or until an error is found in the script. You may use your own word processor to write a script as long as you save the file in a text-only format. Statements may be entered in upper- or lower-case. A line in a script is limited to 80 characters. However, STN commands can be up to 256 characters in length. To continue a statement on the next line, put a backslash, \, at the end of each line that is continued on the next line. A single script statement can be 140 characters long. Scripts do not require an exact format style as you type in the statements. However, each statement MUST be entered on a new line. It is recommended that you use the style that is shown throughout this appendix. Follow the steps below to begin writing a script. More advanced script examples are included after this section. To ensure that all STN Express features are available while you are online, use the STNLOGON script instead of writing your own commands to logon to STN. Open a new script file by selecting New from the File menu within the STNEdit window. A new, untitled window is displayed.

250 C 4 Script Language Script Language Components The STN Express with Discover! Script Language is a miniature computer programming language. As such, it has many of the same components as other programming languages. The components of the Script Language include: Variables - Temporary storage places for data, or places to store data that can change Character Strings and Numbers Constant, literal text and numeric data File names - Names of transcript or data files on your PC Labels - Identifiers for statements Statements - Instructions to STN Express with Discover! that perform an action. For example, the SEND statement instructs STN Express with Discover! to send a string of characters to an online host or communications device. Operators and Conditions Elements that manipulate and compare pieces of data Syntax requirements - Rules for organizing scripts and typing statements Variables A variable is a name for a place to store information. Specifically, a variable can store a number, a string of characters, a file name, or the result of a search. Use a variable when a specific value is unknown or will change within a script. For example, if you write a script that performs an author search, make the script flexible by using a variable for the author s name instead of typing the author s name in the script. Variables are named with an underscore followed by one to twelve alphanumeric characters. They are considered declared after their first use. Once a variable is declared, the same name may not be used to refer to another variable. Variables are always considered to be of type string (text), except for variables that represent search results (L-numbers). Variables are automatically converted to numbers (integers) when necessary for arithmetic operations or conditions. Attempts to perform arithmetic operations on non-numeric text result in errors when the script is run. To give a variable a value, use an assignment statement, described below, or the \> operator, described at the => statement. See also the # operator, explained under the => statement. Up to 200 variables are permitted within a script. If there are more variables, this is noted when you run the script online rather than when you use Check Command File. Variable values may not exceed 255 characters in length.

251 Script Language C 5 Character Strings Textual data is enclosed in double quotes and can be a string up to 140 characters long. You may continue a string on a new line by typing a backslash, \, at the end of the line. To use the value of a string variable, type the variable along with the text. Place double quotes around the entire string. For example: _s = how to use ECHO This is _s a variable in a string. displays: This is how to use a variable in a string. Variables within strings are replaced by their values, converting integers to text. The # operator, along with a variable, is replaced by the number of answers in the answer set and is converted to text. If you want a variable within a string to be immediately followed by nonblank text, separate the variable name and text with a period. For example, _variable = con ECHO This example string includes _variable.catenated text displays: This example string includes concatenated text Special characters and escape characters within strings include: [CR] [TAB] [BS] [ESC] [BELL] [CTRL-A]...[CTRL-Z] [FF] Carriage return Move to next tab position Backspace Escape Sound bell (beep) Unprintable control characters Formfeed Note that many networks and STN Express with Discover! use control characters in normal operations. As a result, indiscriminate use of control characters may result in lost data, locked sessions, or terminated processes.

252 C 6 Script Language The characters, _, \,, [, and #, have special use within the script language and must be doubled if they are to be used within a string. In other words, to include a [ in a string, use two in a row: ECHO Here is a string with a left bracket\ (i.e., [[) in it. displays Here is a string with a left bracket (i.e., [) in it. A distinction between upper- and lower-case is made when the characters are within a string and the number of spaces between words and letters is not ignored. Numbers The Script Language supports integers; there are no decimals or fractions. Type whole numbers in an ordinary way. For example _var = 42 IF _var < 100 THEN To use a negative number, subtract a positive number from zero: _neg = -1 \* not allowed _neg = 0 1 IF _neg < 0 THEN File Names Enclose file names within angle brackets, < >. All characters within the brackets are taken literally, but underscore characters are not allowed. File names may be included with variables. For example, CAPTURE ON <transcript> \* a literal file name _var = <new script> \* assign a file name \* to a variable EXEC _var \* execute a script \* whose name is in _var CAPTURE OFF <> Labels A label or statement label identifies a line in a script so that other statements can refer to that line. Labels are named similarly to variables except that they begin with character. The following are examples of Refer to the CONTINUE, GOTO, GOSUB statements for examples of how to use labels.

253 Script Language C 7 Statements and Control Constructs The Script Language is composed of keywords and values. Keywords are words that have special meaning in the Script Language. Values are pieces of data in the form of variables, strings, numbers, or file names. A statement has at least one keyword, and some statements have parameters. A parameter is the object of the statement and may be a keyword, a value or a combination of keywords and values. You can sometimes think of statements as having verbs and objects. For example, in the statement GET _author, GET is the verb and _author is the object (parameter). The conventions used to describe the STN Express with Discover! Script Language are: 1. Keywords are shown in upper-case letters, e.g., EXIT. 2. Strings are shown in lower-case letters inside double quotation marks. For example, in the statement SEND string, SEND is a keyword, and string is a string value. You may use a variable wherever you can use a string. 3. Variables are shown in lower-case letters with a preceding underscore. For example, in GET _var1, GET is a keyword, and _var1 represents the name of a variable. 4. Numbers are denoted by lower case letters or words. For example, in the statement PAUSE n n represents a number. 3. Optional parameters are shown inside square brackets. For example, PAUSE n [SECONDS] means the PAUSE statement has a required parameter n, and an optional keyword, SECONDS. Do not type the brackets when you type the parameter or keyword. 4. When there is a choice of parameters or values, the choice are enclosed in braces, and a vertical bar separates the choices. For example, in the statement CAPTURE {ON OFF}, the keyword ON or the keyword OFF follows the CAPTURE keyword. 5. File names are shown within angle brackets, DELETE <file name>. You may use a variable whose value is a file name wherever you can use a file name. 7. Comments are preceded by \* and continue through the ends of their lines. The script processor ignores comments. The statements in the STN Express with Discover! Script Language are listed in alphabetical order.

254 C 8 Script Language Make sure you review the common statements, i.e., SEND, WAIT, =>, :, ECHO, IF, GOTO, and EXIT. => : => [host-command] [\!] [\> _var] (primary prompt statement) : [STN-reply] [\!] [\> _var] (STN secondary prompt statement) The => and : statements are shortcuts for a WAIT/SEND combination. The => command waits for a primary or level 1 prompt, => on STN. The : command waits for a secondary or level 2 prompt, : on STN. For example, => del history \* Send a delete history \* command : y \* and reply to the secondary \* prompt. is equivalent to SEND \* Cause an arrow prompt. WAIT FOR => \* Wait for the arrow prompt SEND del history \* and send a delete command. WAIT FOR : \* Wait for the confirmation \* question SEND y \* and reply. In each case, STN Express waits to receive a command prompt from STN. After receiving the arrow prompt, STN Express sends a delete history command and then waits for a secondary prompt from STN. STN responds with DELETE ALL L# ITEMS? (Y)/N: which STN Express recognizes as a level 2 prompt The => command works for online hosts other than STN. The : command is for STN only. Use the \! option if you want to edit the host command before it is sent (see also the EDIT statement). Use the \> operator to assign the L-number result of the command to a variable. For example, suppose the search command in the following statement produces L2 and 1492 answers: => s acid cow \> _lnum The value of _lnum will be L2. Furthermore, the # operator can be used with _lnum to retrieve the number of answers in an L-number. The statement ECHO _lnum contains #_lnum answers. displays L2 contains 1492 answers.

255 Script Language C 9 Assignment Statement _var = expression Use an assignment statement to assign a value to a variable. First type the name of the variable, then an equal sign (assignment operator), and an expression. An expression can be a variable, a string, a number, a file name, an arithmetic expression, or a function. For example _count = 0 _count = _count + 1 _author = dittmar, p _filename = <rn.txt> BEGIN/END BEGIN/END BEGIN/END forms a block of statements that are treated as a group. A BEGIN/END block usually follows an IF or ONEXIT statement. To use this statement, type BEGIN before the statements you want grouped together. Type END after the statement group. For example, IF (_status = NOT CONNECTED ) BEGIN ECHO DIALING... SEND ATDT WAIT FOR CONNECT CONTINUE FOR 5 SECONDS EXIT ECHO CONNECTED! END This example executes every line between BEGIN and END only if the value of _status is NOT CONNECTED. Otherwise, the script continues after the END statement. BREAK BREAK [n [MILSEC[S]]] The BREAK statement sends a break to the host system. Enter the number, n, as either a variable or an integer. If x is not entered, 750 is the assumed value. For example, BREAK 500 sends a break 500 milliseconds in duration.

256 C 10 Script Language CAPTURE CAPTURE {ON OFF} <[file name [/A]]> The CAPTURE statement turns on or off the capturing of your online session. /A opens the file name in append mode. Entering a file name is optional. If you do not enter a file name, you must still type <>. Typing CAPTURE ON <> prompts you to enter the transcript file name. Typing CAPTURE OFF <> assumes that you want the currently opened transcript file closed. For example, CAPTURE ON <tranfile> ECHO THIS LINE OF TEXT CAPTURE OFF <> results in the line This LINE OF TEXT being placed in a file named tranfile in the Transcripts folder defined in your General Preferences. If the file exists, you may opt to append the file by clicking Append. Click the Save button to replace the file. Once the file is open, the output from your session up to the CAPTURE OFF statement, is placed in the transcript file. Capturing is turned off when STN Express with Discover! receives the CAPTURE OFF <> statement. If an error occurs, the _$filerror system variable is non-zero. CLOSE CLOSE The CLOSE statement closes the currently open file. For example, CLOSE closes the data file that was opened by the OPEN statement. If an error occurs at the end of the file, the _$filerror system variable is non-zero.

257 Script Language C 11 CONTINUE CONTINUE The CONTINUE statement is used to continue processing a script beyond the current SEND, WAIT FOR, and TRYAGAIN statements. For example, SEND X WAIT FOR LOGINID CONTINUE FOR 20 SECONDS SEND _loginid If LOGINID is received from the host, the script continues at the SEND statement. DELETE DELETE <file name> The DELETE statement deletes a specific file. For example, _filename = <oldfile.txt> DELETE _filename deletes the file named OLDFILE.txt. If an error occurs, the _$filerror system variable is non-zero. DROP DTR DROP DTR The DROP DTR statement is used to set the DTR (Data Terminal Ready) circuit to an off state. In some rare situations, you may need to control the DTR setting on your modem. See also RAISE DTR. ECHO ECHO string [NOCR] The ECHO statement is used to display a character string or variable on the screen. The string can be zero or more characters, variables, or both. For example, _var = example _item = ECHO statement. ECHO This is an _var of the NOCR ECHO _item displays This is an example of the ECHO statement on your screen. A carriage return automatically occurs after this statement. To suppress it, use the NOCR keyword.

258 C 12 Script Language When you use the ECHO statement in conjunction with the GET statement, echo a blank line first (carriage return only). Then ECHO a prompt or message. For example, ECHO \*outputs a blank line to the screen ECHO Enter your Password: GET _password HIDDEN EDIT EDIT {ON OFF} The EDIT statement is used to interact with the script processor by pausing the script after each line is sent and displaying a text editing box that allows you to modify the next line before it is processed. The changes made in the text editing box are not saved in the script file. The default is EDIT OFF. For example, => FILE CAPLUS \* This line is sent as typed EDIT ON => S ASPIRIN \* This line can be modified \* before it is sent EDIT OFF => D 1-3 ALL \* This line is sent as-is You may use \! as a shortcut for the EDIT statement. Use \! on the => and : statement lines for STN scripts. This shortcut must occur at the end of a line. EXEC EXEC <file name> The EXEC statement is used to execute another script from within a script. The script file name is required. Scripts may be executed eight levels deep. Variables defined in the calling script are also available for the called script. When the called script completes, processing continues on the line immediately after the EXEC statement in the calling script. For example, _filevar = <SECOND SCRIPT> EXEC _filevar ECHO _filevar has completed processing. executes the script SECOND SCRIPT. Then it returns to the calling script and prints: SECOND SCRIPT has completed processing.

259 Script Language C 13 All scripts that are executed must reside in the User Scripts or Predefined Scripts folder as defined in General Preferences (located in the Setup menu on the Main Menu bar). The User Scripts folder is checked first for the script. If it is not found, the Predefined Scripts folder is checked. If the script is not found in either folder, an error message is displayed. If an error occurs, the _$filerror system variable is non-zero. EXISTS EXISTS <file name> The EXISTS statement tests for the existence of a file, first in the User Scripts and then in the Scripts folder. It sets _$filerror to zero of the file exists and to a nonzero value if the file does not exist. EXIT EXIT The EXIT statement defines a point to leave the script. EXIT has no parameters. An exit is assumed after the last statement in a script. Thus, an EXIT statement is not required in any script. More than one EXIT statement may be used in a script. If an ONEXIT statement exists in a script, the ONEXIT block is executed before exiting. If the ONEXIT statement includes an EXIT statement, an exit occurs immediately when that exit is executed. GET GET _varname [HIDDEN] The GET statement is used to accept input from the keyboard to use in a script. When a GET statement is reached in the script, processing is transferred to the user. A text entry box is displayed in which the user may type a line. Typed items, up to but not including the first carriage return, are placed in _varname. The script then continues at the next statement. All input lines are scanned for a colon (:). If found, GET returns only the characters that follow the colon. If the HIDDEN option is present, the typed characters are not displayed on the screen. For example, ECHO Please enter your password: GET _passwd HIDDEN prompts you for your password. When your password is entered, it is processed but not displayed.

260 C 14 Script Language GOSUB The GOSUB statement is used to branch to a different location in the script with the option of returning to the statement after GOSUB. This statement is useful when an identical set of statements is executed from various points in the script. GOSUB has only one parameter, a label of a set of statements that may reside outside of the normal flow of the script. When GOSUB is reached, processing moves to the indicated label and continues processing until a RETURN statement is reached. The RETURN statement causes processing to continue with the statement following the GOSUB statement. GOSUBs may be nested up to eight levels. For example, ECHO Right before the GOSUB. ECHO Right after the GOSUB. ECHO Within the GOSUB. RETURN displays Right before the GOSUB. Within the GOSUB. Right after the GOSUB. GOTO The GOTO statement is used to continue processing at a line that is not directly after the current line of a script. This statement is useful to redirect processing. GOTO is similar to GOSUB except that there is no option to RETURN unless it is initiated with another GOTO. For example, IF (_var1 = FIRST ) ECHO Value of var1 is not FIRST. ECHO Value of var1 is FIRST EXIT outputs only one of the above ECHOed lines before exiting depending on the value of _var1.

261 Script Language C 15 IF IF (condition) block [ELSE block] The IF statement is used to execute one or more statements based on a certain condition. Conditions are defined later in this Appendix. The IF/ELSE statement forms a construct that decides which statement to execute next. If the condition is true, the statements directly following the IF are executed. If the condition is false, the statements directly following the ELSE are executed. For example, IF (_phoneno = ) BEGIN ECHO Enter phone number: GET _phoneno END ELSE echo Dialing... \* if no telephone number was \* given \* else phone number exists SEND ATDT _phoneno \* single statement as a block Note that the SEND statement is outside of the IF/ELSE construct. It is executed regardless of the condition. ONEXIT ONEXIT block ONEXIT is used to specify a set of statements to execute before leaving a script. The ONEXIT statement may be placed anywhere within a script. It cannot contain a GOTO or RETURN statement. An EXIT statement within an ONEXIT block signifies an EXIT when the EXIT statement is reached. Statements following the EXIT statement in the ONEXIT block are ignored. The block portion of the statement may be entered as one line, or as a set of statements between BEGIN and END. For example, the statements ONEXIT BEGIN ECHO These two lines will always be ECHO executed upon exiting the script. END cause the two lines to be displayed to the screen when you leave the script.

262 C 16 Script Language OPEN OPEN <file name> [ {/R /W} ] The OPEN statement is used to open a new or existing file from within a script. Entering the file names is optional. If no file name is supplied, you are prompted to enter one. The /R option opens the file to read only. The /W option allows both reading and writing in the file. The default option is /W. For example, _error = Command timed out. Error ##36. DELETE <ERROR FILE> OPEN <ERROR FILE> WRITE _error CLOSE places the following message in a file named ERROR FILE : Command timed out. Error #36. If an error occurs, the _$filerror system variable is non-zero. PAGE PAGE The PAGE statement forces output to a new page when printing. PAGE is issued with no parameters and causes output from a captured file to begin at the start of a new page. The statement places a [CTRL]-L in the file. This is the control character sequence to start a new page. PAUSE PAUSE {n [SECOND[S]] [UNTIL time]} The PAUSE is used to halt script processing for a specific time. Enter the number of seconds, n, as an integer or a value within a variable. If n equals zero, the pause is forever. The UNTIL time option allows you to specify a certain time of the day, using a 24-hour clock. For example, PAUSE 1 SECOND PAUSE UNTIL 14:45 \* pause for 1 second \* pause until 2:45 pm PRINT PRINT {ON OFF} Use the PRINT statement to turn slave printing on or off. Slave printing causes the transcript to be printed as the online session progresses. Slave printing is not recommended.

263 Script Language C 17 RAISE DTR RAISE DTR Use the RAISE DTR statement to set the DTR (Data Terminal Ready) circuit to an on state. See also DROP DTR. READ READ _varname The READ statement reads a single line from the OPEN file and stores the value, without a carriage return character, in _varname. For example, ECHO reading first line of INPUT FILE OPEN <INPUT FILE> READ _line CLOSE The cursor remains on the same line. The INPUT FILE is opened and the first line is read into the variable _line. If an error occurs, the _$filerror system variable will be non-zero. RETURN RETURN The RETURN statement is used to return the script processing to a saved point in your script. This is usually after a GOSUB statement. For example, ECHO processing will return to this point. ECHO After printing this line... RETURN displays the following: After printing this line... processing will return to this point. SEND SEND string [EDIT] [HIDDEN] [NOCR] The SEND statement is used to send a string to the online host. (Technically, the string is sent to the communication port specified in the logon setup. Therefore, for example, a string can be sent to a modem before STN Express is connected to the host.) The string and other parameters may occur in any order after the SEND statement. The => and : statements are specific forms of the SEND statement that are described earlier in this section.

264 C 18 Script Language EDIT is an option that allows the string to be edited before it is sent. EDIT works as \! does in the => and : statements. HIDDEN does not display the string as it is sent. This is useful when sending passwords. A carriage return is automatically included after the string. To suppress it, use the NOCR keyword. For example, SEND +++ NOCR SEND ATDT sends: +++ATDT to the modem. STNLOGON STNLOGON The STNLOGON statement is used to execute the STNLOGON script that logs you on to STN International. STNLOGON assumes that there is already a connection to STN. Specifically, STNLOGON sends a carriage return and expects the reply to be Welcome to STN International! Enter x: message is displayed.) SUBSTR SUBSTR (_var, begin, length) SUBSTR is more of a function than a statement. SUBSTR takes a string of characters and finds a substring. This statement takes on the value of a string. The value is a portion of the string _var. It begins with character number begin and continues for a length characters. begin and length must be numeric constants. For example the statements _var1 = xxx remove this portion xxx _var2 = SUBSTR(_var1,5,19) ECHO _var2 display the following contents of _var2: remove this portion SUBSTR may be used in conditions. For example, IF (SUBSTR(_var1,1,3) = xxx )

265 Script Language C 19 TRYAGAIN TRYAGAIN n [TIMES] [ [THEN] block] The TRYAGAIN statement is used to repeat the previous SEND statement a specified number of times. This statement works only in the context of the WAIT-SEND statement pair. It repeats the previous SEND up to n times. After the nth attempt, processing either performs the THEN block or EXITs. For example, SEND ATDT WAIT FOR CONNECT CONTINUE FOR NO CARRIER EXIT FOR 5 SECONDS TRYAGAIN 5 TIMES THEN This sends the phone number and waits 5 seconds for either CONNECT or NO CARRIER. If the response is not received, the phone number is sent up to four more times. If the response is still not received, the process jumps to label. UPLOAD UPLOAD [LNUM _var1,_var2,_var3...] <file name> The UPLOAD statement is used to upload a structure query to STN. The result of the UPLOAD on STN is one or more L-numbered queries. The LNUM keyword indicates the beginning of a list of variables. The variables are assigned the L-number or L-numbers of the uploaded structure. Usually, only one variable is needed. Multiple variables are needed when a reaction query with multiple participants is uploaded in an STN file that does not support reaction searching. In that situation, each of the participants is uploaded into its own L-numbered query. Commas must separate variables in the list. For example: UPLOAD LNUM _line1 <C:\PROGRAM FILES\STNEXP\Queries\STR1.STR> This statement uploads the structure query file STR1.STR to STN and store the resulting L-number value in the _line1 variable. The file name to upload should be preceded by a space. It is the name of a chemical structure file created Structure Drawing. If an error occurs, the _$filerror system variable is non-zero.

266 C 20 Script Language USER USER The USER statement is used to temporarily halt script processing. Control is turned over to the user. This statement lets you place specific breaks in a script where you want to take control of the online session. Control is returned to the script when you press the END key. VT320 VT320 {ON OFF} The VT320 statement is used to turn ON or OFF VT320 terminal emulation and is useful when you connect to STN via a VAX with a menu system and when you connect to an online host that offers a menu system. WAIT WAIT [_var1] [LNUM _var2] for-list The WAIT statement is used to pause script processing until a specific response is received from the online host. This statement results in data being read from the incoming communication port one line at a time. A line includes everything up to a carriage return. _var1 contains the last line received from the host. LNUM _var2 puts an L-number into the variable _var2. for-list is one or more: FOR FORcond [THEN] block This is defined as: If the FORcond is met, then execute these statements. The block is optional, except for the last FORcondition. Often the block contains a CONTINUE statement. For example, FORcond is either: string (substring received from host) or: n [SECOND[S]] (passing of time, n, can be an integer or a variable) If n is zero, the WAIT is forever. WRITE WRITE string [NOCR] The WRITE statement is writes a line of text in the currently open file. WRITE places the string in the open file, followed by a carriage return. If NOCR is present, the carriage return is suppressed. Lines are always written to the end of the file. To erase the contents of the file before writing to it, use the DELETE statement. If an error occurs, the _$filerror system variable is non-zero.

267 Script Language C 21 Operators and Conditions Operators and conditions are components of statements. Arithmetic operators manipulate the values of numbers. String operators work on text strings. Conditional operators compare the values of strings and numbers in IF statements. Special operators are used in specific situations. Arithmetic Operators Use the arithmetic operators in assignment statements to perform arithmetic on numbers. The arithmetic operators do not function inside strings or conditions. + addition add two numbers together - subtraction subtract one number from another * multiplication multiply two numbers / division divide one number by another String Operators + concatenation join two strings (not inside double quotation marks). concatenation denote the end of a variable name inside double quotes Conditional Operators To control execution of a statement or a set of statements based on the value of a variable, use an IF statement with a condition. Numbers and strings = equality numbers or strings are equal <> inequality numbers or strings are not equal Numbers > greater than < less than >= greater than or equal to <= less than or equal to Strings INCL NOTINCL includes does not include

268 C 22 Script Language Examples _s = string IF _s = string IF _s = string IF _s = STRING IF _s INCL ring IF _s NOTINCL cow _var1 = 10 _var2 = IF _var2 = _var1 IF _var2 <> var1 IF _var1 > 0 IF _var2 < 4 IF _var1 >= 10 IF _var1 <= 10 \* True \* False \* False \* True \* True \* True \* False \* True \* False \* True \* True Use the OR, XOR (exclusive OR), and AND operators to combine conditions. Use parentheses to group and nest conditions up to eight levels deep. For example, IF ((_var2 = _var1) and (_var1 = string )) asks whether both _var1 and _var2 must equal string. If both operands are integers, comparison is based on their numerical values. Otherwise, an alphabetic comparison is made. Special Operators \! Edit Edit a command before sending it (=> statement). \> L-number Assign the result of a command to a variable (=> statement). # answer count Retrieve the number of answers from an L-number variable.

269 Script Language C 23 Other Script Examples Use these scripts as models for scripts that meet your needs. To see other scripts, look in the Scripts and PSSfiles folders in your STN Express installation. Registry Number Script Example Recall the script shown at the beginning of this appendix: \* Display CAS RNs in the Registry file on STN. => FILE REGISTRY => DIS => DIS => LOG Y It does its job but is not very flexible. For example, what if you have long list of CAS Registry numbers instead of just a few? Use the OPEN, READ, IF, and CLOSE statements to process a file of Registry Numbers. \* STN Express script to read list of RNs from a file \* and display information for each Registry Number. \* Open the data file for reading. There is one RN on \* each line. OPEN <rnlist.txt>/r => file registry \* Process all the RNs in the \* Read an RN from the data file. READ _rn \* If an RN was read, send a DISPLAY command to STN. IF (_$filerror = 0) BEGIN \* Display the requested substance => dis _rn END \* Close the input file CLOSE => EXIT

270 C 24 Script Language Author Search Script Example ECHO ECHO This is a script for running author searches. ECHO Press [Esc] at any time if you would like to\ stop. ECHO ECHO In the pop-up box, enter the last or family\ name of the author: GET _lastname ECHO In the pop-up box, enter first or given name\ or initial: GET _firstname \* Use the STN expand command to provide choices of \* names. => => expand _lastname _firstname/au ECHO Enter the e-numbers to search, e.g., e3-e5 or\ e3,e7) or end GET _enums IF (_enums = end ) BEGIN ECHO Ending author search at your request. => EXIT END => => search _enums \> _results \* If the search yielded zero answers, there is \* nothing to display. Inform the user and exit. IF (#_results = 0) BEGIN ECHO There are no answers for your query. => EXIT END

271 Script Language C 25 \* The search found hits, so ask how many should be \* displayed. ECHO How many answers would you like to display? (e.g., \#_results or 0): GET _display IF (_display > 0) BEGIN ECHO Please provide a transcript name to use to\ save your answers. CAPTURE ON <> \* Don t try to display more answers than are \* available. IF (_display > #_results) THEN _display = #_results => => dis 1-_display bib CAPTURE OFF <> END ECHO Your author search is now complete. => EXIT

272 C 26 Script Language Helpful Hints As you begin writing scripts, you may want to keep the following hints in mind. Check Command File checks your script for some errors. Getting an error-free script from the command file checker does not guarantee that the script will do what it was intended to do. A clean bill of health from the command file checker also does not guarantee there are no errors in the script because some errors cannot be found until the script is run. You may create a script in any word processor or text editor that allows you to save a file as plain text. Add comments to a script by placing a \* anywhere on the line. To display a comment on the screen, use the ECHO statement. Comments help make your script more readable or understandable to others. The keywords in the STN Express with Discover! script language are not case sensitive. However, upper and lower case do matter in strings, and spaces count, too. For example, Yes is different from yes, and STN Express is different from STN Express. Use a standard spacing and indentation scheme to make your scripts more readable. Enclose strings in the SEND, WAIT, FOR, and ECHO statements in double quotes. Use the Escape or Clear key to stop a script from processing Place a \ at the end of a line to continue a statement or string on the next line All STN Express with Discover scripts must be in either the User Scripts folder or the Predefined Scripts folder. When looking for a script to execute, STN Express with Discover! first checks the User Scripts folder, then the Predefined Scripts folder. Εnter only the unique portion of the prompt when using the WAIT FOR statement. Use the SEND, WAIT FOR, and TRYAGAIN statements together because TRYAGAIN will resend the last item that was sent using a SEND statement. Many times, TRYAGAIN is an optional part of the statement trio because you would not want to resend some items, e.g., login ID or password.

273 Script Language C 27 Logon Scripts There are two separate steps to logging on to an online host: 1. connecting to the host through a telecommunications network 2. logging on to the host STN Express includes support for several telecommunications networks and online hosts. Before you take the time to write your own connection or logon script, find out whether STN Express already provides the scripts you need. Also, you may find it easier to use the Watchme feature than to write your own logon script. Refer to Chapter 3, Logon Setup for STN, for details about Watchme. Predefined Setup Variables If you intend to write your own scripts that connect through a network or log on to an online host, be sure you understand the details of a logon setup. Many of the values defined in a logon setup are available to STN Express with Discover! scripts as variables. Below is a list of these variables, organized by the area within Setup that sets the value. Setup Definition Dialog Box Host Information area _$logid Value of Login ID (for host) _$password Value of Password for host _$service Value of Host Name; set to STN for all STN hosts _$stncenter Name of STN Node (Columbus, Karlsruhe, or Tokyo) Path Information area _$connvia Value of Connect via Logon Method _$network Value selected from network list Network Logon area _$nua Value of NUA (Network User Address) _$nui Value of NUI (Network User Identifier) _$nup Value of NUP (Network User Password) Communication Settings area _$baud Value of Speed _$dialtype Value of Dial _$phoneno Value of Primary Phone # _$phoneno2 Value of Secondary Phone # Host Settings tab _$qservname Value of Choice of service (Questel) _$graphics Value of Graphics (STN) _$stnport Value of STN Port (STN) _$modinit Value of Modem Configuration - Initialization String

274 C 28 Script Language Advanced Dialog Box _$gwcomm1 through _$gwcomm5 Value of Execute at command prompt fields one through five _$gwloginp Value of Prompt Character strings - Login _$gwcommp Value of Prompt Character strings - Command _$gwpassp Value of Prompt Character strings - Password _$gwid Value of Gateway Login ID _$gwpw Value of Gateway Password

275 Appendix D Questel Features on STN Questel The following features are available while accessing Questel on STN Express with Discover!. Questel D 1 Offline Structure Building - build a structure query offline to search Questel s Generic DARC system. Use the STN Express with Discover! structure drawing tools and palettes described in Chapter 6, Structure Queries, to build your structure. Autologon - create a logon setup to automatically log on to Questel Upload Structure Query - upload structures drawn on STN Express with Discover! to search files on Questel s Generic DARC system Capture Online Displays - capture text and graphics results from an online session to a transcript. You may browse, print, edit, or export your transcript. Structure Query Building Select Prepare Structure Query from the Query menu or click the Prepare Query button if it is located on your Structure Drawing Toolbar. A new Untitled Standard structure drawing window is displayed. Select New/Questel from the File menu or click the button representing a new Questel structure query if it is located on your toolbar. See Chapter 6, Structure Queries, for details about adding buttons to the Structure Drawing Toolbar. Draw your Questel structure query using the STN Express with Discover! Structure Drawing menus, tools, and palettes. Refer to Chapter 6, Structure Queries, for details. Converting Existing STN Structures to Questel Structures Select Open from the File menu to display the Open Query dialog box. Select a query to open by highlighting its name in the scrollable File Name list. The structure is previewed to the right of this list. Then click the radio button next to Questel. The structure is converted to a Questel structure format in the preview box.

276 D 2 Questel Click OK. The structure is placed in an Untitled Questel structure drawing window. The original structure query is not changed. Because structure drawing features may differ for Questel, it is recommended that you check the structure attributes by selecting Query Verification from the QueryDef menu. This should be done before you save and upload the query. For example, during conversion from STN to Questel, ring isolation settings are ignored, bond settings are reinterpreted using the Questel bond algorithm, and other attributes are ignored. Differences also occur in the shortcuts and variables available on Questel. Unrecognized nodes are converted to A (Any Atom) settings. Query Verification STN Express with Discover! verifies structure building according to an algorithm that corresponds to Questel s use of aromatic, tautomeric, and exact settings. For example, bonds in even-numbered cyclic pathways with alternating single and double bonds are set as aromatic bonds. Bonds in tautomeric structures are marked as tautomeric.

277 Questel D 3 Free Sites Free sites are used to specify the degree of substitution allowed at a specified position. To insert a free site, select one or more nodes using the Selection tool. Then select Free Sites from the QueryDef menu. The Free Sites dialog box is displayed. Click the number of free sites for the nodes you selected from the scrollable list. Then click OK. The number you selected represents the maximum number of attachments at that node. Because free sites are a maximum, the retrieval includes all lower degrees of substitution as well. Bond types are not considered, e.g., an atom attached by a double bond is considered a single attachment. If no free sites are specified, the system completes the normal valency of the atoms with hydrogens when executing the search. Autologon For information on creating an automatic logon to Questel, refer to Chapter 5, Using non-stn Hosts and Appendix C, Script Language. As with STN, storing your logon ID and password are optional. If you do not enter them in your setup, you are prompted for them at logon. To logon to Generic DARC, set the choice of service in the Host Settings tab of your Setup to G. Always set the Host Name in your setup to Questel. After logging on to Generic DARC, you can run the Command file qst_op.sc to set the language and the terminal type. The terminal type is set to S for STN Express with Discover! support.

278 D 4 Questel Uploading Structure Queries Select Exit Structure Drawing from the File menu to search a structure query on Questel s Generic DARC system. You are prompted to save and name your structure query. Click the Logon menu from the STN Express Main Menu bar or click the Logon button if it is located on the Main Menu Toolbar. Choose to logon to your Questel setup. The Capture Session dialog box is displayed. If you are prompted to enter a transcript name to save your online session, i.e., text and graphics, type a name in the File Name text box and click Open. After you connect to Questel, select Upload Structure Query from the Query menu. Select a structure query to upload and click Open. Switching from Generic DARC to Questel You may switch from Generic DARC to the Questel system while online by using the BI option. If you experience problems, log off and then log back on to Questel.

279 Appendix E MDL Molfile Conversion Assumptions STN Express fi MDL Molfile exact exact/normalized normalized unspecified ring/chain chain ring manually set set by STN Express stereo G-groups shortcuts ring, ring/chain, chain variables X M,Q Id all others Nodes Nodes Attributes Reaction centers CC PC XC NC NON reactant, reactant/reagent, reagent product delocalized charge, match level, element count, variable points of attachment, stereo centers and bonds, and generic definitions connectivity ring bond counts of 2, 3, or 4 all other ring counts all other Non-H connections repeating units single node all others Bonds exact any any any ring/chain chain ring ring/chain single lists or R-groups superatoms ignored halogen list Q * A make/break change center not center none reactant product ignored translated ignored translated to substitution counts translated ignored H count H ct. (>4 fi 4) isotope, valency and charge translated ring isolation assigns ring bond count of *

280 E 2 MDL Molfile Conversion Assumptions MDL Molfile fi STN Express MDL Molfile fi STN Express Bonds single single exact double double exact aromatic single normalized S/D unspecified S/aromatic single exact/normalized D/aromatic double exact/normalized any unspecified ring ring ring/chain ring/chain chain chain stereo double double exact stereo single single exact reaction centers center make/break change make & change not center none XC CC PC CC NC NON Atoms Atoms list G-group R-group G-group * Id any unrecognized symbol A Attributes Attributes charge, valence, and isotope translated substitution count ring/chain connectivity ring bond count ring connectivity all bonds in a ring system are * repeating groups stereochemistry, unsaturated atom, exact change, and no implicit hydrogens ring isolated translated ignored

281 Appendix Connecting to a Host Through a Gateway Connecting to a Host F 1 FOverview STN Express can connect to STN or another host directly over the Internet using the telnet protocol. Depending on your organization s network or security requirements, there may be a telnet gateway, a firewall, or a proxy server (all referred to as a gateway) between your PC and the host computer. STN Express can connect through most gateways. If you can telnet to the host, STN Express will be able to connect to it. To connect through a telnet gateway, you must know the details of the gateway s prompts and interaction. For example, if the gateway prompts for a loginid, you must know the characters in that prompt. You must also know the gateway command for completing the connection to the host. Because a gateway is specific to your organization, you may wish to consult your network administrator or computer support group about connecting to and logging on to your gateway. Example Suppose you want to connect to STN Columbus and have a telnet gateway that requires that you log into it and then type the destination host name or IP address. After you connect to the gateway, a transcript of the steps required to navigate through the gateway might look like the following. The gateway s messages, which are not of interest to STN Express, are shown in a normal font, the gateway s prompts are shown in a bold font, and the information you type is shown in italics. (For security, the password is not shown.) Welcome to HQ telnet gateway. User: asmith Password: User asmith OK Ready> stnc.cas.org STN Express can automatically navigate through the gateway if it is aware of the gateway s login prompt (User:), password prompt (Password:), and command prompt (Ready>). You may use the STN Setup Wizard to provide this information to STN Express. If you want to connect to a host other than STN, or if you prefer not to use the Setup Wizard, create or modify your setup as described below.

282 F 2 Connecting to a Host Modifying Your Setup Follow these steps to modify your setup in order to connect to an online host through a telnet gateway: 1. In the Setup Definition dialog box, type the name or address of the gateway in the Host Name or IP address box. This causes STN Express to connect to the gateway instead of directly to STN or another host. 2. In the Setup Definition dialog box, click the Advanced button to open the Advanced dialog box. Advanced Dialog Box Values Prompt Character Strings The values that you enter for Prompt Character strings define the prompts sent by the gateway. You may ignore other messages the gateway might display. Your gateway might issue all or only some of the three prompts that STN Express supports. In general, leave the Prompt Character strings box empty if your gateway does not display a particular prompt. Login The login prompt specifies the way the gateway asks for your loginid or user name. For the example gateway, the prompt is User:.

283 Connecting to a Host F 3 Password When a gateway asks for a password, it issues the password prompt. Password: is the example gateway s password prompt. Command A gateway displays the command prompt when it is ready to accept the command that causes it to connect to the online host. In the example gateway, Ready> is the command prompt. Optional Type the responses to the loginid and password prompts Optional area. If you choose not to save your loginid or password, or both, in the logon setup, STN Express will ask for them when needed. Type your gateway loginid in the box. If you do not know your gateway loginid, contact your network administrator. In the example, the loginid is asmith. If you enter your gateway password, it is encrypted and saved with the logon setup in express.ini. The password is not visible when typed. If you save your password in the logon setup, STN Express asks you to retype the password after you click OK. Execute at Command Prompt After you have logged in to the gateway, the gateway may display a prompt that indicates it is ready to accept commands. Enter up to five gateway commands in the boxes. Typically only one command is needed, and this might be a telnet command, a connect command, or something similar. In the example, all that s needed is the host name or IP address of the destination, stnc.cas.org. You can find the names and addresses of the supported hosts in the Setup Definition dialog by selecting the online host in the Host Name list and looking at the Host Name or IP address box. Interaction with a Gateway STN Express communicates with a gateway as follows: After matching the Login prompt, STN Express with Discover! sends the Gateway Login ID After matching the Password prompt, STN Express with Discover! sends the Password Each time the Command prompt is matched, STN Express with Discover! sends the value in the next Execute at command prompt field Matching of control characters within a prompt is not supported.

284 F 4 Connecting to a Host Custom Logon Setup for STN Express Versions prior to 5.0 Starting with STN Express 5.0, a custom logon procedure is not required to make use of the Advanced Gateway options. The Gateway.sc script will automatically run if any of the Prompt Character strings boxes are not empty. Older, custom logon setups for gateways can be used in STN Express 6.0, and the following information has been retained as documentation for them. Connecting to a host system through a gateway using a Custom Logon method requires several steps. Each step typically requires that an STN Express with Discover! script be included within the Custom Logon section. These steps include: 1. Connecting to the gateway: Identify a script to connect to the gateway. No script is needed for this step for a Winsock connection. Add this script as the first script in the Custom Logon section. Set the values of the Communication Settings section to allow connection to the gateway, not to the host system. 2. Logging on to the gateway and issuing the command to connect to the host system: Add Gateway.sc as the next (or first) script in the Custom Logon Fill in values in the Gateway Configuration section in the Advanced dialog box to allow logging on to the gateway. Enter the command used to connect from the gateway to the online host in the Execute at command prompt field, e.g., telnet stnc.cas.org. 3. Logging on to the host system: Add the script normally used to log on to the host system as the last script in the Custom Logon Script List. Always use STNLOGON to log on to STN. If you have difficulties using the Gateway.sc script to connect through a gateway, consider using the Watch Me function, described in Chapters 3 and 5, as an alternative.

285 Appendix G Overview Network Installation Network Installation G 1 The Setup program for STN Express with Discover! offers special features for shared, network installations. In general, creating a network installation of STN Express is a three-step process: 1. Install STN Express on the server. 2. Share the server installation (make it visibile on the network). 3. Install STN Express on one or more client PCs. The result is a shared network folder that contains the STN Express programs and one or more client installations that refer to the shared folder. Features and limitations STN Express with Discover! and its setup program support the Universal Naming Convention (UNC) standard, e.g., \\APPSRV\STNEXP and mapped network drive letters. If you use mapped drive letters, be aware that the EXPRESS.INI file, stored on the client PC, contains paths to the STN Express installation on the server. Therefore, the network share that contains the STN Express with Discover! applications must always be mapped to the same client drive letter (the drive letter may be different on each client). The server installation may be performed at the server or across the network. + Review the ReadMe file on the CD-ROM disc for details pertaining to network installations before proceeding. Any last minute changes are documented there.

286 G 2 Network Installation Installing STN Express on a Server To install or upgrade the software on your server, run SETUP.EXE and choose the Network Server option from the Setup Type section of the Install STN Express with Discover! window. One Setup Option is available for Network Server installs: Softcopy documentation copy the PDF User Guide to the server. Type the path to the server installation folder, or click the > button to browse. Click Install STN Express with Discover! to continue. The Setup program will then build the STN Express with Discover! folder. It will not create a Windows Start Menu item, nor will it create the EXPRESS.INI control file. These will be created during the Network Client setup (see below). The Setup program creates a special version of itself and stores it in the STN Express root folder (typically STNEXP) on the server. This program, SETUP.EXE, can be run by users to install STN Express with Discover! on their local machines. It will build the local STN Express folder structure and create a Windows Start Menu item for STN Express. It also builds the EXPRESS.INI control file and stores it in the local Windows folder. See the Changing SETUP.INF section below for important information about the network patch to the server isntallation. Sharing the server installation on the network Share the STN Express installation on the network. Client may refer to the network share by its UNC name or by mapping a drive letter to it. It is recommended that all files residing on the server be write protected from the network.

287 Network Installation G 3 Changing SETUP.INF After the Network Server installation is complete, you may need to modify the contents of the setup control file for user installations. To do this, edit the file SETUP.INF located in the STN Express folder on the server. The following section should be verified. [server] - verify that this section contains the proper network path to the server installation. This value is used as the default path for the Network User setup. If this value will not be consistent across all network user machines, e.g., on one client PC it is N:\STNEXP and another it is I:\STNEXP, leave this field blank ( Express= ). Installing STN Express on a client PC Each user of STN Express with Discover! should run SETUP.EXE from the server drive. Simply select the Network User option from the Setup Type section of the opening dialog box. The Path to Network STN Express is activated. Verify that it contains the appropriate path specification to the network folder for STN Express. Contact your network administrator if it does not specify the network folder for STN Express. Enter the appropriate storage location on the local PC in the following dialog box. The Setup program will then build the local STN Express with Discover! environment. The Setup program located on the CD may also be used; however, it contains a generic specification for network installations and further changes may be needed after it is complete. Upgrading to 6.0 from a Network Server If you are currently running STN Express 5.0 from a network server on your client PC, first make sure the server installation has been updated to 6.0. Then run setup.exe from the server. This gives you everything needed to use the new features.

288 G 4 Network Installation Information for Network Administrators If you wish to set up a standard set of logon procedures and preferences for all of your users, follow the steps below: 1. Install STN Express with Discover! on the server as described above. Then perform a Network Client install on one user s PC. 2. Start STN Express with Discover! on the user s PC and define options that you want all users to have, i.e., logon procedures and user preferences. 3. Exit STN Express with Discover! and save changes when prompted. 4. Copy the EXPRESS.INI file and any additional.ini files beginning with the letters STN from this PC s WINDOWS folder to the server. Also, any files that are created in the USCRIPTS folder (as the result of Custom Logon or Logoff scripts) should also be copied to all client machines. They can then be copied to any user s PC after a Network User setup has been done. Please note the following limitations: Store any.ini files on the server, using a different name, e.g., name.net. This will prevent any confusion when running the program. Users must copy these files to their WINDOWS folder and rename them to the original name. This is a requirement! All users of STN Express must have STN Express with Discover! loaded in the same path on their local machines. For example, all users must have c:\stnexp as the root folder for STN Express with Discover!. The reason for this is that the EXPRESS.INI file contains path names for storing and accessing files. If this is not done, path specifications will be incorrect and STN Express with Discover! will not work properly. If you have any questions or problems, please contact your Help Desk.

289 Network Installation G 5 Converting a Single-User Installation to a Network Share Follow the steps in the Installing STN Express on a Server section of this Appendix to install the Network Server copy. Follow the steps in the Installing STN Express on a Client PC section of this Appendix to convert each copy of STN Express with Discover! to a Network User copy. Select the location where STN Express currently resides. The installation program upgrades the files and the program group to access STN Express with Discover! on the server. + Only files provided by your previous STN Express installation programs are overwritten. Any structures, scripts, guided search strategies, or transcripts that you have created are unaffected by this installation. However, STN Express scripts that you have modified should be moved out of the STN Express directory. Changes to those files should be added to the new versions supplied with version 6.0.

290 Appendix H Overview Removing STN Express and Its Applications H 1 Removing STN Express and Its Applications STN Express 6.0 includes an uninstaller program. See the ReadMe.txt file for details. If the uninstaller program is not available, STN Express may be removed manually. Removing STN Express From Your Hard Disk To remove STN Express from your hard disk, follow these steps: 1. Copy or move all queries and transcripts that you want to keep to a safe location. 2. Remove the STNEXP folder and all folders contained within. Consult the file Desetup.inf for a list of files installed by STN Express with Discover!. 3. Remove Express.ini and all other Stnxxxxx.ini files from the WINDOWS folder. To remove the STN Express Start menu item: 1. Right click on the Windows Task Bar. 2. Click Properties. 3. Select the Start Menu Programs tab. 4. Click the Remove button. 5. Scroll down the list to find the STN Express Group. Select this group. 6. Click the Remove button.

291 H 2 Removing STN Express and Its Applications STN Express Applications STN Express with Discover! consists of the following distinct programs: Program icon Program name Function Express.exe Stnpsi.exe Stnsetup.exe Stnterm.exe Stnacct.exe Stnedit.exe Stnwpi.exe Stnocc.exe The main program and toolbar provide access to STN Express programs. Logon setups and General Preferences are stored in the file: express.ini. Structure Drawing. Preferences are stored in stnpsi.ini. Logon setup program. Use it to create and change logon setups. Its configuration file is stnsetup.ini, but the logon setups themselves are stored in express.ini. STN Online and Results. Preferences are stored in stnterm.ini. STN Accounting. Preferences are stored in stnacct.ini. STN Edit (text editor). Its configuration file is stnedit.ini. Fragmentation Code Generator for Derwent WPI queries. Other Code Concepts program for Derwent WPI queries. Applications may be removed from the STN Express directory if you do not intend to use them.

292 Removing STN Express and Its Applications H 3 STN Express Folders and Files Additional folders and files that are added to your hard disk include: Folder or File Content.dll files.dta files.hlp files Networks file Pssfiles Queries Scripts Template Trnscript Umanual Uscripts Library files essential to the function of the applications Data files used in Derwent WPI Fragmentation Code Strategy generation STN Express Help files for the Windows help system. Data file for supported communication networks Scripts that implement specific (Predefined Search Strategies) Default location for storing your structure queries STN Express scripts for connecting through supported networks and logging on to supported online hosts Pre-drawn chemical structure templates used for building structure queries. Standard (.std), stereo (.str), and SpecInfo (.spe) templates are included. Default location for storing your STN Express session transcripts, reports, and tables Electronic User Guide in PDF format Scripts and command files written by you; the STN accounting file; and other user-specific files

293 Appendix I Overview Troubleshooting Troubleshooting I 1 This section provides answers to common problems that you may encounter while using STN Express with Discover!. You may also visit CAS Software Support on the Web at software.html. Problems with Transcripts This information pertains to traditional,.trn transcripts, not to transcripts that are captured as RTF. STN Express transcripts that contain structure diagrams are stored in two main files. You provide the name for the files when the transcript is created. One file, with a.trn extension, contains the text of the transcript. The other file, with a.gra extension, contains the graphic (structure diagrams) part of the transcript. For example, if you name the transcript STN search.trn, then that file contains the text part of the transcript, and the file STN search.gra contains the structure diagrams for the transcript. If you downloaded images, there will be one.tif,.jpg, or gif file for each image. 1. Graphics (structure diagrams and downloaded images) are missing from a transcript on your screen STN Express Browse Transcript knows how to combine the text and graphics files into one display. If graphics are missing, check to see that both the.trn and.gra files exist and are stored in the same folder. STN Express Edit Transcript reads only the text portion (.trn file) of a transcript and cannot display graphics. If you open a transcript in Microsoft Word or another program, be sure to Export the transcript first. The export process combines the.trn,.gra, and.tif files into one RTF file. 2. Graphics (structure diagrams and TIFF images) are missing from a printed transcript If graphics are missing from a printed transcript, check for the existence of the files as noted above. Print the transcript from Browse Transcript or from the main menu bar (Results -> Print Transcript). Because STNEdit does not display graphics, it cannot print them. Go to Terminal Emulation Preferences, the Online tab, and check the Print Chemical Structures box.

294 I 2 Troubleshooting 3. Line wrap in printed transcripts If you see the ends of lines wrapping to the start of the next line, check the margins and font size. By default, STN Express uses a 10 pt. Courier New font and 0.75-inch left and right margins. To solve the line-wrap problem, switch to a smaller font or use smaller left and right margins. To change the font, select Preferences, then STN Online and Results, and then the Colors/Fonts/Scaling tab. To change the margins while browsing a transcript, select Page Layout from the File menu. Downloaded Images TIFF, JPEG, and GIF images, such as patent drawings or complete page images, are available in several STN files. See the appropriate section in Chapter 4 for more information. 1. Problems downloading images For faster TIFF, JPEG, and GIF image downloads in STN files such as CAOLD, DEMAS, and WPINDEX, use the default setting of Long Packets and a packet size of 4000 that is found on the Online tab of the STN Online and Results Preferences. If you see Kermit error messages, try reducing the packet size. A packet size of 4000 is not recommended for low-speed connections. Recommendations are: Connection Speed Packet Size Internet/Winsock and higher and up and up Locating downloaded images When you download images while you capture a transcript, the images are named the same as your transcript plus a three-digit number. The image files have appropriate extensions (.tif,.jpg,.gif) in their names. When you download images when no transcript is captured, the image files are named starting with Image001 and continuing with Image002, etc. Appropriate extensions (.tif,.jpg,.gif) are used.

295 Troubleshooting I 3 3. TIFF images print smaller than expected When TIFF images are printed in the context of a transcript, they appear smaller than you might desire. Check the 1 TIFF Image/page box on the Page Layout dialog box that opens during the transcript printing process. When TIFF images are printed from the TIFF image viewer, they are printed at a size that is proportional to the viewer s zoom factor. For the largest possible printed image, zoom in (View -> Zoom In) as far as possible and then select File -> Print. Modem Problems Communications problems include characters lost from answer displays, corrupt structure diagrams, and difficulty downloading images. These problems occur much more frequently under modem connections than with Internet/Winsock connections. Missing characters and corrupt structure diagrams: For modem speeds of 4800 baud and higher, use hardware (RTS/CTS flow) control. For modem speeds under 4800 baud, use software (XON/XOFF) flow control. The flow control setting is found in your modem Control Panel or in your STN Express logon setup. For modem speeds of 9600 baud and higher, the correct communications parameters are data bits: 8; parity: none; stop bits: 1. Make sure you have a current version of the driver for your modem brand and model. Not Able to Connect - General Script SYSCNCT - Unable to open command file pop-up message Terminal Emulation is not able to locate a script that is needed to log on to the host. The most likely cause is that the path to the Predefined Scripts folder is incorrect in General Preferences. To check the path, go to the main STN Express menu bar, select Setup -> Preferences -> General. The Predefined Scripts box must contain the location of a folder that holds the scripts that are packaged with STN Express. By default, the path is C:\Program Files\Stnexp\Scripts, but your installation location might be different. The paths in General Preferences can be rendered incorrect by moving the STN Express installation folder from one place to another.

296 I 4 Troubleshooting Not able to connect - modem In general, look for messages in the Terminal Emulation window that point to the problem. Check to see that the modem has power and is connected to the computer and a working telephone line. 1. The modem is not responding to modem commands message Check to make sure an external modem is turned on. Check to make sure the modem is connected to a serial port on the computer. Check that COM port setting in the STN Express logon setup is the one to which the modem is attached. 2. The telephone line is not providing a tone for dialing message Check that the modem is connected to a live, working phone line. Check that the phone line is not being used by a telephone or another modem (is the line busy?). If you selected a modem from the Connect via list in your logon setup, try selecting the modem s COM port instead. Not able to connect Internet In general, look for pop-up messages and messages in the Terminal Emulation window that point to the problem. 1. Unable to Establish Connection pop-up message Check the Host Name or IP address in the logon setup. Be sure there are no typing mistakes or leading or trailing spaces. If you re not able to connect to the specified host name, try the equivalent IP address. Try to connect to the Host Name or IP address using the Windows telnet.exe program. This tests the ability to connect without STN Express. Your connection attempt might be hitting a firewall or gateway. Contact your network administrator for instructions on how to use telnet outside your organization s network. 2. Terminal Emulation hangs, or the connection times out See #1 immediately above. 3. Dial-Up Networking does not launch The DUN connection might already be established. Try establishing the dial-up connection first, outside of STN Express. If the connection cannot be made, the problem is probably in the DUN configuration or modem Control Panel.

297 Troubleshooting I 5 Unexpected behavior after reconnecting Always begin and complete your STN session using the same telecommunications software. If you initially logged on through STN Express, end your session through STN Express. For example, if you initially connect to STN using Windows telnet, then disconnect, and then reconnect to the same session using STN Express, you will observe abnormal behavior in STN Express. Problems switching from Generic DARC to Questel If you have trouble switching from the Generic DARC system to Questel using the BI command, log off from Generic DARC and then connect to Questel directly and log on. Creating a Setup 1. Error opening Network Control file pop-up message after clicking New or Modify The file Express.ini is stored in the Windows (Windows 95/98/Me) folder or the WinNT folder (Windows NT 4.0/2000). In Express.ini, in the [Paths] section, the value of the express= parameter must be the STN Express installation folder. By default this folder is C:\Program Files\Stnexp. The parameter can be incorrect if the STN Express installation folder is moved from one place to another. To correct the problem, edit Express.ini and change the value of the express= line to the location of your STN Express installation. 2. The OK button is grey Some piece of required information is missing. A Setup Name is required for every logon setup. A Logon Method other than None and a Primary Phone # are required for each setup that uses a modem.

298 I 6 Troubleshooting Structure Upload 1. General problems Try uploading the structure again. Line noise or a poor connection can cause the upload to fail. Communications settings might be incorrect. If you are experiencing data loss in general, see the Communications problems - modem section above. Be sure that STN recognizes your terminal as STN Express. Always use the STNLOGON script to complete your log on to STN. The problem could be due to the particular structure. If you can successfully upload other structure queries, report the problem structure to the Help Desk. 2. Fatal Kermit Error pop-up message See the information in #1 immediately above. The maximum size of a structure query for uploading might have been exceeded. Modify your query to make it smaller, or use the STRUCTURE command on STN. Additional Help If you need further assistance, contact the Help Desk for your STN Service Center: Go to the STN Express Help menu, select Request Help, and then select your STN Service Center to send . Telephone your Help Desk as listed in Chapter 1, Introduction. Please have the following information available when you call or write. STN Express with Discover! version number, e.g., 6.0a. To find the exact version, go to the Help menu on the main menu bar and select About STN Express. Operating System, e.g., Windows NT 4.0 System information, including amount of memory (RAM) Specific information about your problem.