VMD User's Guide

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3. All advertising materials mentioning features or use of this software must display the followingacknowledgment: This product includes software developed by Brad Grantham andApplied Conjecture.4. Neither the name Brad Grantham nor Applied Conjecture may be used to endorse orpromote products derived from this software without specific prior written permission.5. Notification must be made to Brad Grantham about inclusion of this software in a productincluding the author of the product and the name and purpose of the product. Notificationcan be made using email to Brad Grantham’s current address (grantham@plunk.org as ofSeptember 20th, 2000) or current U.S. mail address.• PythonPython is made available subject to the terms and conditions in CNRI’s License Agreement.This Agreement together with Python may be obtained from a proxy server on the Internetusing the following URL: http://hdl.handle.net/1895.22/1012• PCREThe Perl Compatible Regular Expressions (PCRE) library used in VMD was written byPhilip Hazel and is Copyright (c) 1997-1999 University of Cambridge.Permission is granted to anyone to use this software for any purpose on any computer system,and to redistribute it freely, subject to the following restrictions:1. This software is distributed in the hope that it will be useful, but WITHOUT ANYWARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESSFOR A PARTICULAR PURPOSE.2. The origin of this software must not be misrepresented, either by explicit claim or byomission.3. Altered versions must be plainly marked as such, and must not be misrepresented as beingthe original software.4. If PCRE is embedded in any software that is released under the GNU General PurposeLicense (GPL), then the terms of that license shall supersede any condition above with whichit is incompatible.• STRIDESTRIDE, the program used for secondary structure calculation, is free to both academic andcommercial sites provided that STRIDE will not be a part of a package sold for money. The useof STRIDE in commercial packages is not allowed without a prior written commercial licenseagreement. See http://www.embl-heidelberg.de/argos/stride/stride info.html• SURFThe source code for SURF is copyrighted by the original author, Amitabh Varshney, and theUniversity of North Carolina at Chapel Hill. Permission to use, copy, modify, and distributethis software and its documentation for educational, research, and non-profit purposes ishereby granted, provided this notice, all the source files, and the name(s) of the originalauthor(s) appear in all such copies.BECAUSE THE CODE IS PROVIDED FREE OF CHARGE, IT IS PROVIDED ”AS IS”AND WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED.This software was developed and is made available for public use with the support of theNational Institutes of Health, National Center for Research Resources under grant RR02170.12
• TachyonThe Tachyon multiprocessor ray tracing system and derivative code built into VMD is Copyright(c) 1994-2007 by John E. Stone. See the Tachyon distribution for redistribution andlicensing information.1.6 For information on our other softwareVMD is part of a suite of tools developed by the Theoretical and Computational Biophysics groupat the University of Illinois.• BioCoREBioCoRE is a web-based collaborative environment for structural biology which providestools to allow collaboration between researchers down the hall or around the world. Anyonewith access to the internet and a standard web browser can join BioCoRE and create or beadded to research projects, and information about a particular project is shared among allmembers of that project. More information is available at the BioCoRE home page 1• NAMDA parallel, object-oriented molecular dynamics code designed for high-performance simulationof large biomolecular systems. NAMD uses the CHARMM force field and file formatscompatible with both CHARMM and X-PLOR. NAMD supports both periodic and nonperiodicboundaries with efficient full electrostatics, multiple timestepping, constant pressureand temperature ensemble simulation methods. More information is available at the NAMDhome page 2• MDToolsMDTools is a collection of programs, scripts, and utilities provided for researchers to makevarious modeling and simulation tasks easier. More information is available at the MDToolshome page 3For more information on our software efforts, see the Theoretical and Computational BiophysicsGroup home page 4 .1 http://www.ks.uiuc.edu/Research/biocore2 http://www.ks.uiuc.edu/Researach/namd3 http://www.ks.uiuc.edu/Development/MDTools4 http://www.ks.uiuc.edu/13
Page 1 and 2: VMD User’s GuideVersion 1.8.6Apri
Page 3 and 4: 4.4.4 Molecule File Browser Form .
Page 5 and 6: 8.3.20 molecule . . . . . . . . . .
Page 7 and 8: List of Figures2.1 Sample VMD sessi
Page 9 and 10: Chapter 1IntroductionVMD is a molec
Page 11: 1.4 AcknowledgmentsThe authors woul
Page 15 and 16: Figure 2.1: Sample VMD session disp
Page 17 and 18: 2.5 An Introduction to Atom Selecti
Page 19 and 20: selection: protein and (name CA or
Page 21 and 22: no coordinate information. It must
Page 23 and 24: Chapter 4User Interface ComponentsV
Page 25 and 26: • Center (hot key ’c’)This mo
Page 27 and 28: Hot Key Command Purposer, R mouse m
Page 29 and 30: Hot Key Command Purpose+,f,F animat
Page 31 and 32: information. Atoms shows the number
Page 33 and 34: Animation SpeedThe rate of playback
Page 35 and 36: can change the view of the scene, e
Page 37 and 38: • Perspective - The view of the s
Page 39 and 40: 4/3 SCRHEIGHTi.e. 8.0YViewer’sEye
Page 41 and 42: Hiding a rep. To hide a rep, double
Page 43 and 44: Periodic TabThe Periodic tab contro
Page 45 and 46: • Name - the name of the atom as
Page 47 and 48: Figure 4.10: The Material Formslide
Page 49 and 50: force-feedback (haptic) devices suc
Page 51 and 52: the simulated spring is connected t
Page 53 and 54: Figure 4.13: The Sequence formmolec
Page 55 and 56: • Selections by chain: When there
Page 57 and 58: Chapter 5Molecular Drawing MethodsE
Page 59 and 60: When three or more bonds join at on
Page 61 and 62: 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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version (2.2). Thus if you have Pyt
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• align(ref=None, move=None, fram
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esid5.frame()50>>> resid5.frame(22)
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ef=AtomSel(’backbone’,frame=0)f
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functions (e.g., listall()) overlap
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• update ui():• update on():Upd
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9.5.7 labelPython operations availa
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• add volumetric(molid, name, ori
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• set colorupdate(molid, rep, ono
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9.6 High-level Python InterfaceVMD
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9.6.2 MoleculeRepThe MoleculeRep cl
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Chapter 10Vectors and MatricesTcl d
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• veccross v1 v2 - Returns the ve
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• transaxis amount [deg|rad|pi]
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-axiszamount [rad|deg|pi] - Adds a
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Chapter 11Molecular Analysis11.1 Us
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vmd> set sel [atomselect top "water
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The decimal in ”1.0” is importa
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# get the sidechain atoms (CB and o
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Applying this to the alanin.pdb coo
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have the same number of atoms, then
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set transformation_matrix [measure
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}display update offfor {set i 0} {$
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Chapter 12Customizing VMD SessionsT
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• -nt : Do not display the VMD ti
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• VMDIMMERSADESKFLIP : Enable a s
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axes location lowerleftstage locati
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Index.mailcap, 177.vmdrc, 26, 89, 1
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VMDHTMLVIEWER, 174VMDIMAGEVIEWER, 1
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move, 35atom, 35fragment, 35highlig
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short circuit logic, 72, 75sleepcom
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