VMD User's Guide

More documents

Recommendations

Info

native Windows interface on Windows platforms. The Fltk file chooser looks the same on allplatforms, supports tab completion but not drive letters, and is probably most appropriatefor Unix environments. The file chooser can be overridden at any time by changing theenvironment variable (e.g., in Tcl, set env(VMDFILECHOOSER) FLTK).• VMDFORCECPUCOUNT : Specifies the maximum number of CPUs or CPU cores that VMD shoulduse when running on a multiprocessor or multicore computer system. By default, VMDwill use all of the processors on the host machine. This option can be used to preventVMD from “hogging” CPUs or to make it abide by job submission policies required on largesupercomputer systems, when running batch mode.• VMDCAVEMEM : (Unix-only) This overrides the default size of the shared memory arena whichis allocated by VMD when the CAVE starts up. The variable must be an integer number ofmegabytes. Since this is the only shared memory pool allocated, and it is done only once, youmust choose a value sufficient to account for the largest scene you intend to render in VMDin that CAVE session. The default value unless otherwise specified is 80 Megabytes. Valuesof 200MB to 512MB are commonly needed for large molecular systems containing severalhundred thousand atoms.• VMDFREEVRMEM : (Unix-only) This overrides the default size of the shared memory arenawhich is allocated by VMD when the FreeVR starts up. The variable must be an integernumber of megabytes. Since this is the only shared memory pool allocated, and it is doneonly once, you must choose a value sufficient to account for the largest scene you intend torender in VMD in that FreeVR session. The default value unless otherwise specified is 80Megabytes. Values of 200MB to 512MB are commonly needed for large molecular systemscontaining several hundred thousand atoms.• VMDFORCECONSOLETTY : (Unix-only, intended only for clusters This environment variableforces VMD to treat the text console as an interactive terminal, despite what the operatingsystem says. This is only useful for running an interactive VMD session on a Clustermaticor Scyld Linux cluster node.• VMDGDISPLAY : (Unix-only) The name of an X-Windows display that VMD will use to displaythe graphics window. This environment variable is only used on Unix systems. Through theuse of the the DISPLAY and VMDGDISPLAY envrironment variables, the VMD graphicswindow can be placed on a separate screen from the forms and menus. This is particularlyuseful when giving 3-D demonstrations using a projector. The forms and menus can be kepton a different screen from the graphics so that they do not distract the audience.• VMDGLSLVERBOSE : OpenGL Shading language compiler diagnostic errors only printed onlywhen this environment variable is set.• VMDHTMLVIEWER : The name of a command that will run a web browser in the background(Netscape, Mozilla, Firefox or whatever you prefer) that VMD should use to display HTMLdocuments (such as this help file). By default, on UNIX, this is mozilla. (usage examples inTcl: set env(VMDHTMLVIEWER) ‘‘mozilla -remote openURL(%s)", set env(VMDHTMLVIEWER)‘‘mozilla %s &")• VMDIMAGEVIEWER : The name of the external program to use for displaying VMD snapshots(or other images), in various formats.174
• VMDIMMERSADESKFLIP : Enable a special reversed/reflected stereo projection mode for usewith experimental displays based on LCD panels, phase plates, and beam splitters.• VMDVMDMACENABLEEEXTENSIONS : Enable performance-oriented OpenGL rendering extensionswhich are disabled by default. These extensions have been observed to trigger instability onsome MacOS X systems.• VMDMSECDELAYHACK : Add in a user-specified delay which causes VMD to sleep for specifiednumber of milliseconds each time it renders the molecular scene on the display. This feature ismeant as a workaround to poor performing display drivers which make the windowing systemunresponsive if VMD is allowed to run unrestricted at maximum drawing rate.• VMDMSMSUSEFILE : Force VMD to communicate with MSMS through the filesystem ratherthan with the socket-based network interface. This option can be used when the socketinterface isn’t working properly for some reason. This is the default behavior when usingVMD on Windows.• VMDPREFERSTEREO : (Unix, MacOS X) On Unix systems using X11, this environment variableallows NVidia Quadro users to override the normal X11 visual search order, skippingmultisample capable visuals in favor of stereo visuals. VMD still attempts to get the morecomplex visuals first, but if it comes down to a choice between stereo and multisample asmutually exclusive options, this variable provides the ability to force the use of stereo if available.On MacOS X, this environment variable tells VMD to create a a stereo-capable displaywindow, even at the risk of terminating the program if the request is denied.• VMDSCRDIST : Distance to the VMD image plane.• VMDSCRHEIGHT : Height of the VMD image plane.• VMDSCRPOS : Position of the VMD graphics window (x,y).• VMDSCRSIZE : Size of the VMD graphics window (x,y).• VMD EXCL GL EXTENSIONS : Disable the use of named OpenGL extensions according to theirofficial OpenGL extension names. This is intended to be used only when one encounterssevere stability problems caused by buggy display drivers.• VMDSHEARSTEREO : Enable the use of an alternative perspective projection mode which mayresult in improved stereoscopic display. Uses the shear-matrix stereo formulation rather thaneye rotation.• VMDSIMPLEGRAPHICS : Forces VMD to use absolutely minimalistic graphics features withno use of OpenGL extensions. Essentially, nothing but bread-and-butter vertex arrays andimmediate mode rendering will be used. This mode is intended to be used only when oneencounters severe stability problems caused by buggy display drivers.• VMDWIREGL : This environment variable disables several graphics features which are unsupported(or poorly supported) by WireGL and Chromium. This variable will be supercededwith a more general implementation in a future release.175
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 and 12:
1.4 AcknowledgmentsThe authors woul
Page 13 and 14:
• TachyonThe Tachyon multiprocess
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
Page 63 and 64:
• Representation Method - The sur
Page 65 and 66:
5.1.19 BeadsA bounding sphere is dr
Page 67 and 68:
those names to color the atoms. Mol
Page 69 and 70:
Figure 5.1: RGB color scale: the th
Page 71 and 72:
esname ALA to CYS TYRselects atoms
Page 73 and 74:
esname ’A 1’More importantly, r
Page 75 and 76:
the numeric sense) or greater than
Page 77 and 78:
Keyword Arg Descriptionall bool eve
Page 79 and 80:
FunctionDescriptionsqr(x) square of
Page 81 and 82:
Chapter 6Viewing ModesThere are man
Page 83 and 84:
sci-fi and horror movie showings. T
Page 85 and 86:
Name Description Default Render Com
Page 87 and 88:
• Dotted spheres are not drawn wi
Page 89 and 90:
Chapter 8Tcl Text InterfaceThe Tcl
Page 91 and 92:
• speed n: Set animation speed to
Page 93 and 94:
last frame. If the frame is a speci
Page 95 and 96:
- BWG - Blue to white to green.- Bl
Page 97 and 98:
• antialias < on | off >: Turn an
Page 99 and 100:
• cylinder {x1 y1 z1} {x2 y2 z2}
Page 101 and 102:
• kill: Disconnect from the simul
Page 103 and 104:
- ambient- specular- diffuse- shini
Page 105 and 106:
the area contributions are coming f
Page 107 and 108:
8.3.19 molLoad, modify, or delete a
Page 109 and 110:
• modselect rep number molecule n
Page 111 and 112:
• index n: Returns the id of the
Page 113 and 114:
8.3.26 rockRotate the current scene
Page 115 and 116:
8.3.33 vmdinfo(Tcl) Returns informa
Page 117 and 118:
• -minmax {{ x min y min z min }
Page 119 and 120:
In the VMD script library at http:/
Page 121 and 122:
Sourceraster3dmsmsfaqbiocoretachyon
Page 123 and 124: Table 8.4: Description of Tcl callb
Page 125 and 126: version (2.2). Thus if you have Pyt
Page 127 and 128: • align(ref=None, move=None, fram
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
Page 135 and 136: • update ui():• update on():Upd
Page 137 and 138: 9.5.7 labelPython operations availa
Page 139 and 140: • add volumetric(molid, name, ori
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
Page 159 and 160: The decimal in ”1.0” is importa
Page 161 and 162: # get the sidechain atoms (CB and o
Page 163 and 164: Applying this to the alanin.pdb coo
Page 165 and 166: have the same number of atoms, then
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: • -nt : Do not display the VMD ti
Page 177 and 178: axes location lowerleftstage locati
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
show all

VMD User's Guide

Create successful ePaper yourself

Delete template?

Save as template?