VMD User's Guide

More documents

Recommendations

Info

– autobonds : Turn automatic bond calculation on/off. This can be useful forloading unusual non-molecular coordinates for which VMD’s bond-finding algorithm istoo slow (e.g., if the point density is very high). Default is on.– molid: For addfile only. The molecule id of the molecule into which the file should beloaded may be specified. It must be the last option specified. If omitted, the default isthe top molecule.• load structure file type structure file [coordinate file type coordinate file] : Load a new moleculefrom filename(s) using the given format. If an additional coordinate file is specified, load thisfile as well. New in VMD 1.8: All frames from the coordinate file will be loaded beforethe command returns. If this is not desirable, use the animate read command for more finegrainedcontrol over how coordinate files are loaded. Previous version of VMD loaded onlyone frame before returning. The function will return the id of the newly created molecule, orreturn an error if unsuccessful.• urlload : Load a molecule of file type from a given URL address. Returnthe id of the newly created molecule, or an error if unsuccessful.• pdbload : Retrieve the PDB file with the specified accessioncode from the RCSB web site. Returns the id of the newly created molecule, or an error ifunsuccessful.• list: Print a one-line status summary for each molecule.• list molecule number: Print a one-line status summary for each molecule matching themolecule number. If only one molecule matches the molecule number, also print the representationstatus for this molecule, i.e., number of representations as well as the representationnumber, coloring method , representation style and the selection string for each of therepresentations.• color coloring method: Change the default atom coloring method setting.• representation rep style: Change the default rendering method setting.• selection select method: Change the default atom selection setting.• clipplane center clipplane id rep number molecule number [ vector ]• clipplane color clipplane id rep number molecule number [ vector ]• clipplane normal clipplane id rep number molecule number [ vector ]• clipplane status clipplane id rep number molecule number [ boolean ]• modcolor rep number molecule number coloring method: Change the current coloring methodfor the given representation in the specified molecule.• modmaterial rep number molecule number material name: Change the current material forthe given representation in the specified molecule.• modstyle rep number molecule number rep style: Change the current rendering method(style) for the given representation in the specified molecule.108
• modselect rep number molecule number select method: Change the current selection for thegiven representation in the specified molecule.• addrep molecule number: Using the current default settings for the atom selection, coloring,and rendering methods, add a new representation to the specified molecule.• default category value: Set the default settings for color, style, selection, or material to thesupplied value.• delrep rep number molecule number: Deletes the given representation from the specifiedmolecule.• modrep rep number molecule number: Using the current default settings for the atom selection,coloring, and rendering methods, changes the given representation to the currentdefaults.• delete molecule number: Delete molecule(s).• active molecule number: Make molecule(s) active.• inactive molecule number: Make molecule(s) inactive.• on molecule number: Turn molecule(s) on (make drawn).• off molecule number : Turn molecule(s) off (hide).• fix molecule number: Fix molecule(s).• free molecule number: Unfix molecule(s).• top molecule number: Set the top molecule.• cancel molecule number: Cancel loading trajectories.• reanalyze molecule number: Re-analyze structure after bonding and atom name changes.• ssrecalc molecule number: Recalculate secondary structure.• rename molecule number newname: Rename the specified molecule.• repname molecule number rep number: Returns the name of the given rep. This name isguaranteed to be unique for all reps in the molecule, and will stay with the rep even if therep number changes.• repindex molecule number name: Return the rep number for the rep with the given name,or-1ifnorepwiththatnameexistsinthatmolecule.• selupdate rep number molecule number [onoff]: Update the selection for the specified repeach time the molecule’s timestep changes. If onoff is not specified, returns the current updatestate.• colupdate rep number molecule number [onoff]: Update the calculated color for the specifiedrep each time the molecule’s timestep changes. If onoff is not specified, returns the currentupdate state.109
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: 8.3.19 molLoad, modify, or delete a
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 and 174:
• -nt : Do not display the VMD ti
Page 175 and 176:
• VMDIMMERSADESKFLIP : Enable a s
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?