VMD User's Guide

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12.3 Startup Files12.3.1 Core Script FilesIn the following, the value of $VMDDIR is the vmd installation directory. During the original installationthis is the value of INSTALLLIBDIR. It can also be found by looking at the first few linesof the vmd startup script (head ‘which vmd‘) or by starting VMD and using the command setenv(VMDDIR).As mentioned elsewhere, VMD uses the Tcl interpreter. VMD read Tcl scripts at initialization,which are contained in VMD distribution. The locations of the scripts is determined by theTCL LIBRARY environment variable, which is set in the vmd startup script to $VMDDIR/scripts/tcl.In addition, VMD has its own directory of core Tcl routines.The most important of these is $VMDDIR/scripts/vmd/vmdinit.tcl. This file sets up the basicTcl initialization commands, defines some environment variables, and adds the vmd script directoryto the Tcl autoindex path. Most of the other files are referenced through the auto path.There are a few non-Tcl scripts in this directory. Currently these are perl scripts used for theurlload command and web client startup (see section 8.3.19 and section 12.4).12.3.2 User Script FilesA user-written run-time command file, .vmdrc on Unix, vmd.rc on Windows, can be used with alist of initial VMD text commands to process. This file may be changed to customize individualuser’s initial screen appearance and to set the proper display characteristics for displaying in stereo.If it does not exist, default values are used.12.3.3 .vmdrc and vmd.rc FilesAfter everything is initialized, VMD reads the startup file using the equivalent of the command play.vmdrc. This file contains text commands for VMD to execute just as if they had been entered atthe VMD text console command prompt. The file can contain any number of commands, includingblank lines and comment lines (which begin with the # character). If an error is encountered whilereading this file, the command in error is skipped and processing of the file continues.VMD searches for this file in three locations on Unix; ./.vmdrc, $HOME/.vmdrc and $VMDDIR/.vmdrc.On Windows, VMD searches in ./vmd.rc, $HOME/vmd.rc and $VMDDIR/vmd.rc. Only the first filefound will be read in and processed.See chapter 8 for a description of the VMD text commands which may be put in this file. Also,section 4.1.3 discusses how to put commands into the .vmdrc file to customize the behavior of thehot keys.Here is an example of a startup file:# add personalized keyboard shortcutsuser add key E echo onuser add key e echo offuser add key g display resetuser add key A stage location bottomuser add key m mol list# position the stage and axes176
axes location lowerleftstage location off# position and turn on menusmenu main move 5 196menu display move 386 90menu graphics move 5 455menu files move 5 496menu main on# start the scene a-rockin’rock y by 112.4 Using VMD as a WWW Client (for chemical/* documents)Mosaic, Netscape, and possibly other browsers can be configured to use VMD as a helper applicationfor viewing some chemical/* documents.12.4.1 MIME typesWhen a web browser receives a document from a server it actually gets two pieces of information:the header and the body. The header contains information about the message and body. One ofthe most important pieces of data, called the MIME type specifies what the body of text describes.For instance, a GIF image is given the MIME type of image/gif, a JPEG image is image/jpg,and postscript is application/postscript. A class of types, chemical/*, has been created forchemical models so the MIME type for PDB files is chemical/pdb, for XYZ is chemical/xyz, etc.Helper ApplicationsThe web browser uses the MIME type to determine how to view the body of the message. Some ofthe documents are viewed by the browser itself, like text/html which describes HTML documents.In other cases, the browser has to start up another application. From here on, we’ll describe howMosaic and Netscape do this. First, it saves the incoming message body to a temporary file. Itthen scans the global and local mailcap files to determine which application is used to view thegiven MIME type. The application, which must take a file name on the command line, is thenexecuted. When the application exits, the temporary file is deleted.12.4.2 Setting up your .mailcapThe Unix versions of VMD have an extra -webhelper command line flag which causes VMD notto be spawned in the background, so that it has time to read temporary files downloaded by theweb browser. This command line flag is just slightly simpler to use than the chemical2vmd script,as it does not depend on having Perl installed, so may be more appropriate for some cases.In the VMD installation directory ($VMDDIR/scripts/vmd/) there is a perl script calledchemical2vmd which will create a VMD command file and execute VMD. Since VMD does notblock the calling process, Netscape and other web browsers cannot directly call VMD, as they do not177
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VMD User’s GuideVersion 1.8.6Apri
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4.4.4 Molecule File Browser Form .
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8.3.20 molecule . . . . . . . . . .
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List of Figures2.1 Sample VMD sessi
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Chapter 1IntroductionVMD is a molec
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1.4 AcknowledgmentsThe authors woul
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• TachyonThe Tachyon multiprocess
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Figure 2.1: Sample VMD session disp
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2.5 An Introduction to Atom Selecti
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selection: protein and (name CA or
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no coordinate information. It must
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Chapter 4User Interface ComponentsV
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• Center (hot key ’c’)This mo
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Hot Key Command Purposer, R mouse m
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Hot Key Command Purpose+,f,F animat
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information. Atoms shows the number
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Animation SpeedThe rate of playback
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can change the view of the scene, e
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• Perspective - The view of the s
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4/3 SCRHEIGHTi.e. 8.0YViewer’sEye
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Hiding a rep. To hide a rep, double
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Periodic TabThe Periodic tab contro
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• Name - the name of the atom as
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Figure 4.10: The Material Formslide
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force-feedback (haptic) devices suc
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the simulated spring is connected t
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Figure 4.13: The Sequence formmolec
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• Selections by chain: When there
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Chapter 5Molecular Drawing MethodsE
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When three or more bonds join at on
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segment pieces are colored accordin
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• Representation Method - The sur
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5.1.19 BeadsA bounding sphere is dr
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those names to color the atoms. Mol
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Figure 5.1: RGB color scale: the th
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esname ALA to CYS TYRselects atoms
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esname ’A 1’More importantly, r
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the numeric sense) or greater than
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Keyword Arg Descriptionall bool eve
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FunctionDescriptionsqr(x) square of
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Chapter 6Viewing ModesThere are man
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sci-fi and horror movie showings. T
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Name Description Default Render Com
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• Dotted spheres are not drawn wi
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Chapter 8Tcl Text InterfaceThe Tcl
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• speed n: Set animation speed to
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last frame. If the frame is a speci
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- BWG - Blue to white to green.- Bl
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• antialias < on | off >: Turn an
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• cylinder {x1 y1 z1} {x2 y2 z2}
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• kill: Disconnect from the simul
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- ambient- specular- diffuse- shini
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the area contributions are coming f
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8.3.19 molLoad, modify, or delete a
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• modselect rep number molecule n
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• index n: Returns the id of the
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8.3.26 rockRotate the current scene
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8.3.33 vmdinfo(Tcl) Returns informa
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• -minmax {{ x min y min z min }
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In the VMD script library at http:/
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Sourceraster3dmsmsfaqbiocoretachyon
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Table 8.4: Description of Tcl callb
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Page 129 and 130: esid5.frame()50>>> resid5.frame(22)
Page 131 and 132: ef=AtomSel(’backbone’,frame=0)f
Page 133 and 134: functions (e.g., listall()) overlap
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Page 141 and 142: • set colorupdate(molid, rep, ono
Page 143 and 144: 9.6 High-level Python InterfaceVMD
Page 145 and 146: 9.6.2 MoleculeRepThe MoleculeRep cl
Page 147 and 148: Chapter 10Vectors and MatricesTcl d
Page 149 and 150: • veccross v1 v2 - Returns the ve
Page 151 and 152: • transaxis amount [deg|rad|pi]
Page 153 and 154: -axiszamount [rad|deg|pi] - Adds a
Page 155 and 156: Chapter 11Molecular Analysis11.1 Us
Page 157 and 158: vmd> set sel [atomselect top "water
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Page 161 and 162: # get the sidechain atoms (CB and o
Page 163 and 164: Applying this to the alanin.pdb coo
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Page 167 and 168: set transformation_matrix [measure
Page 169 and 170: }display update offfor {set i 0} {$
Page 171 and 172: Chapter 12Customizing VMD SessionsT
Page 173 and 174: • -nt : Do not display the VMD ti
Page 175: • VMDIMMERSADESKFLIP : Enable a s
Page 179 and 180: Index.mailcap, 177.vmdrc, 26, 89, 1
Page 181 and 182: VMDHTMLVIEWER, 174VMDIMAGEVIEWER, 1
Page 183 and 184: move, 35atom, 35fragment, 35highlig
Page 185 and 186: short circuit logic, 72, 75sleepcom
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