know when to delete the temporary file containing the molecule or other data. The chemical2vmdscript starts <strong>VMD</strong> with the -e command line option which runs the saved <strong>VMD</strong> script or moleculefile.It is also possible to install the previous script in the global .mailcap file to make it accessibleto everyone. You will have to consult the documentation for your web browser(s) to find out how.12.4.3 Example sitesSome web sites that send chemical/pdb types are the Protein Data Bank at http://www.rcsb.org/and “Molecules R US” at http://www.nih.gov/htbin/pdb.178
Index.mailcap, 177.vmdrc, 26, 89, 176.vmdsensors, 49vmd.rc, 89, 176ACTC, 11AMBERfiles, 20, 34analysisscripting, 157speed, 157angles, 44animatecommand, 90, 120form, 32Python module, 133animation, 16frames , 34appending, 34delete, 32, 90, 91duplicate frame, 90goto end, 91goto start, 91hot keys, 29jump, 33, 91movie, 88play, 90read, 34, 91smoothing, 42, 110, 141speed, 33, 91step, 33style, 91loop, 33once, 33rock, 33write, 31, 91antialiasing, 37, 96atomchanging properties, 159colorauto-update, 109coordinates, 113, 114changing, 18, 159min and max, 162info, 91, 156name lists, 41picking, 17selection, 15, 17, 57, 70, 91, 156auto-update, 109changing properties, 127comparison, 74default, 108examples, 17, 70keywords, 41, 70, 77, 78logic, 72macros, 42, 92, 125math functions, 79modes, 70Python, 125quoting, 72regular expression, 73same, 75sequence, 75text, 156update, 161volumetric data, 79within, 75atomsdistance between, 18plotting, 45atomselectcommand, 91, 120, 155, 156axes, 37command, 94, 120Python module, 134Babel, 21backface culling, 37179
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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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version (2.2). Thus if you have Pyt
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