Bichem 660 2008 145 VMD - cntinued: Making Mvies (This sectin can be used immediately after Desktp Mlecular Graphics) VMD (http://www.ks.uiuc.edu/research/vmd/) is a free prgram develped at the Theretical and Cmputatinal Biphysics Grup at the University f Illinis at Urbana- Champaign fr the visualizatin and animatin f bilgical (macr) mlecules. See als http://www.scripps.edu/rc/training/unixslides/vmd.pdf LABORATORY EXERCISES 1 -VMD-Exercise H: Starting VMD and pening a mlecule OPTIONAL This exercise summarizes the methds seen in the Desktp Mlecular Graphics sectin. Duble click n the VMD icn r select it within the task-bar. On the VMD Main windw menu select File > New Mlecule this will pen the Mlecule file brwser. Click the Brwse buttn t select a PDB file in yur flder within yet anther windw. Fr example use hrv2-3c-1cqq.pdb - Click Open Click Lad The selected PDB file is nw laded within VMD VMD Main: Graphics > Representatins Click n the Create Rep buttn a. Create Rep (buttn) b. Within the Selected Atms Edit ne representatin t prtein c. Edit the ther t nt prtein Resize the VMD OpenGL display t the size yu want yur mvie. Dnʼt make it t large and dnʼt make it t small either. Using the muse highlight the Rep selectin f the nt prtein Clring Methd: Name Drawing Methd: Licrice Using the muse highlight the Rep selectin f the prtein Clring Methd: Ps Drawing Methd: Surf Orient yur image, this will be the start psitin fr the mvie. Change the backgrund t white if yu wish: VMD Main: Clrs > Display > backgrund > white VMD Main: Display > Orthgraphic VMD Main: Display > Depth Cue VMD page 145
Bichem 660 2008 146 2 VMD-Exercise I: Making mvies with VMD INFO - Prerequisites: making mvies with VMD requires that ther sftware packages be installed. The DMC classrm is already set-up fr using the VMD mvie-making scripts. The Unix/MacOSX slutin is free while the windws versin requires the installatin f the VideMach shareware package. Sme installing infrmatin is given at the end f this tutrial. As f this writing the relevant infrmatin is lcated n the VMD web site at http://www.ks.uiuc.edu/research/vmd/plugins/vmdmvie/ Hwever: even if the required sftware fr making mvies is nt installed n yur cmputer, VMD will nevertheless make all the individual frames that can later be assembled int a mvie, fr example with Appleʼs QuickTime Pr (Macintsh and Windws) r a shareware such as Animagic (Windws) r freeware GIMP (Unix, Mac OS X) t make animated GIF. TASK within the VMD Main windw select the Extensins > Visualizatins> Mvie Maker menu. This will pen the VMD Mvie Generatr interactive windw. Verify the settings in the 3 pull-dwn menus within VMD Mvie Generatr Render: Shuld set n Snapsht Nte: if this ptin creates strange images (mst pssible under Windws) change t Internal Tachyn which is slwer but wuld wrk. Mvie Settings: T make a rtatin f the mlecule change the Rck and Rll setting t Rtatin abut Y axis. Nte: if yu want t keep the frames, then uncheck the 4: Delete image files as illustrated. Keep the preselected MPEG-1 selectin Nte: if yu want t place yur mvie n a web site select Animated GIF but nte the animated GIF files are larger than MPEG-1 files. VMD page 146
Bichem 660 2008 147 Set wrking directry: the default wrking directry is / (als called rt ) which wuld be the main hard drive n Mac OS X ften named Macintsh HD this is where mvies and frames are saved. If yu want t change the wrking directry smewhere n the Desktp click n the buttn Set wrking directry Click Users Click BNMC Click Desktp Click New Flder Name yur flder My Mvie Click Create Yur wrking flder is nw set n the desktp Nte: On Windws systems the desktp is available within the C:\Windws directry --- --- Name yur mvie mvie-1 r chse a name yu like. Set the number f frames t 36 if yu are making a Rck and Rll mvie, therwise set this number t 360 if yu selected earlier Rtatin abut Y axis (the default is 180). Make yur mvie: Press the Make mvie buttn. Yu can watch the prgress f the mvie making n the VMD Display as well as n the VMD Mvie Generatr windw by lking at the Status, Stage, and Prgress infrmatin prvided. Nte: The 360 Y-rtatin takes a few minutes since there are mre frames. If yu made a mistake yu can click Abrt and reset yur parameters. The temprary files will be discarded autmatically. VMD page 147
Bichem 660 2008 148 3 -VMD-Exercise J: Finding and viewing yur mvies a. Finding yur mvies: The mvies are created within the wrking directry which yu have set earlier. If yu have nt set the wrking directry yur mvie will be in the default wrking directry f / which is the main hard drive n a Mac OS X cmputer. If yu still dnʼt knw r cannt find yur mvie use the menu File > Find (Macintsh) r Start > Find Prgrams and Files (Windws) and search fr the mvie name yu have given, e.g. My Mvie. b. Playing yur mvies: The mvies will have either a.gif r.mpg attached t the name yu had given. Hwever depending n the settings f the cmputer yu are using these filename extensins may nt be visible. These filename extensins are a way fr yur cmputer t knw the frmat f these animatins and will warn yu if yu try t delete them. Playing MPEG-1 files: yur default multimedia player shuld autmatically play the MPEG-1 files. Yur default player is likely t be QuickTime n an Apple cmputer and Windws Media Player n a Windws system. Playing animated GIF files: animated GIF files may play within yur default media player just like the MPEG-1 files, but yu may have t use the File > Open menu sequence t pen it. Animated GIF files play well within web brwsers (Netscape, Internet Explrer, Safari, Mzzilla etc.). c. Using yur mvies: MPEG-1 files can be used fr presentatin r inserted within a PwerPint presentatin t illustrate yur mlecule. MPEG-1 images can als be made a part f a web page, hwever the viewer will need the apprpriate plug-in (t see the mvie within the brwser) r apprpriate media player (the mvie will be dwnladed and played). Animated GIF files can be used as an image n the web. Inserted as a regular GIF image file it will still be an animatin. The advantage is that this des nt require any plug-in fr the viewers t see yur animatin as it is the case fr QuickTime, MPEG r FLASH animatins. VMD page 148
Bichem 660 2008 149 4 -VMD-Exercise K: Mvies frm NMR multiple PDB files Usually NMR structures are published as bth a series f 10 t 20 pssible mdels, as well as an average mdel. The average structure cntains a single set f PDB crdinates, while the ther file cntains a series f PDB structures within the same file. Each structure starts with the PDB recrd MODEL # (where # is a number) and ends with ENDMDL recrd line. Sme sftware can smetimes nly see the first mdel in a multiple file, thers can be used t animate them. Here we will animate a file cntaining 20 mdels with VMD. TASK 1) pen VMD and lad PDB file 1NYZ.pdb a. VMD Main: File > New Mlecule b. Brwse (find 1NYZ.pdb in windw) c. Open d. Lad 2) VMD Main: Display > Orthgraphic 3) VMD Main: Graphics > Representatins a. Clring Methd: ClrID 5 b. Drawing Methd: Licrice c. Create Rep buttn d. Edit new rep t resid 19 e. Clring Methd: ClrID 3 f. Drawing Methd: Licrice Nte: as the mlecule pens yu can ntice it wiggle as the 20 mdels are laded. This cmmand selects residue 19 (a U) t be represented differently than the rest f the mlecule, here ClrID 3 is range. Yu can select an ther clr scheme, e.g. 6 (gray) fr the RNA and 1 (red) fr U19. Yu can als make the backgrund white if yu wish. Nte: resid keywrd is different than residue keywrd. First residue is internally renamed residue 0 (zer) by VMD. Therefre t select residue 19 we wuld have t select residue 18 r simply resid 19 VMD page 149
Bichem 660 2008 150 4) Scale the image within the windw and rient it s that residue 19 is n yur right, shwing its stacking psitin, in a side-way view. 5) VMD Main: Extensins > vmdmvie 6) Set parameters within VMD Mvie Generatr tp menus: a. Render: Snapsht (screen capture) b. Mvie Settings: i. Trajectry ii. Uncheck 4: Delete image files c. Frmat: MPEG-1 7) Set parameters within the rest f the windw: a. Set wrking directry: create a flder n the desktp and name it e.g. NMR b. Name f mvie: u19 (.mpg will be appended autmatically) c. Number f frames t render: 20 (default, because there are 20 mdels) 8) Click Make Mvie buttn 9) The mvie will be saved within the wrking directry (NMR), yu can duble click n it, it shuld autmatically pen within QuickTime Player in the BNMC classrm. 10) Yu can engage the menu Mvie > Lp t have it lp cntinuusly. Nte: the mvie speed is abut 30 frames per secnd. 11) If yu inspect the NMR directry, yu will see tw series f image frames: the riginal *.rgb r tga frames and thse cnverted t *.ppm by ImageMagick in the backgrund. Nte: PDB entry 1NYZ has nw been replaced by 1SY4 VMD page 150
Bichem 660 2008 151 INFO - Supplemental Infrmatin: Installing sftware pre-requisites fr mvie making with VMD 1.8.x n Mac OS X. Yu will need t have administratr privilege (passwrd) t accmplish this. 1) X11 is autmatically present n newer OS X versins (starting with 10.5) 2) Dwnlad Fink frm http://fink.surcefrge.net/dwnlad/ : Dwnlad Fink Binary Installer fr current versin fr later OS. Help is available at http://hmepage.mac.cm/sa1/fink/#tp8 Althugh there is a graphical interface ( Fink Cmmander ), fr sake f simplicity the fllwing will describes the line cmmand methd f installatin f binaries: 3) Launch a Terminal (lcated in Macintsh HD : Applicatins : Utilities : Terminal) 4) Within the terminal type the fllwing cmmands a the % r $ prmpt: a. % fink selfupdate-cvs b. % fink install system-xfree86 c. % fink list d. % sud apt-get install imagemagick-nx e. % sud apt-get install netpbm f. % rehash This shuld install all the necessary binary files fr making mvies frm VMD. Nte that yu will be asked a passwrd fr administrative privilege, and that mre binaries dependences may be installed at the same time. Nte fr Windws users frm the VMD script hme page http://www.ks.uiuc.edu/research/vmd/plugins/vmdmvie/ On Windws, the prgram VideMach is currently required fr all mvie generatin tasks. It is a shareware prgram and is available fr trial dwnlad frm the VideMach web site. Registratin csts $19 fr nncmmercial use, and $49 fr cmmercial use." Nte: the Vidematch web site is at http://www.grmada.cm/videmach.html - End f VMD Mvie - VMD page 151