VMD - continued: Making Movies

Transcription

1 Bichem VMD - cntinued: Making Mvies (This sectin can be used immediately after Desktp Mlecular Graphics) 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 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

2 Bichem 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 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

3 Bichem 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

4 Bichem 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

5 Bichem 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

6 Bichem ) 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

7 Bichem 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 : Dwnlad Fink Binary Installer fr current versin fr later OS. Help is available at 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 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 - End f VMD Mvie - VMD page 151