12.4 Using VMD as a WWW Client (for chemical/* documents)
12.4.3 Example sites
Some web sites that sendchemical/pdbtypes are the Protein Data Bank athttp://www.rcsb.org/
and “Molecules R US” at http://www.nih.gov/htbin/pdb.
Index
.mailcap, 177 .vmdrc, 26, 89, 176 .vmdsensors, 49 vmd.rc, 89, 176 ACTC, 11 AMBER
files, 20, 34 analysis
scripting, 157 speed, 157 angles, 44 animate
command, 90, 120 form, 32
Python module, 133 animation, 16
frames , 34 appending, 34 delete, 32, 90, 91 duplicate frame, 90 goto end, 91 goto start, 91 hot keys, 29 jump, 33, 91 movie, 88 play, 90 read, 34, 91
smoothing, 42, 110, 141 speed, 33, 91
step, 33 style, 91
loop, 33 once, 33 rock, 33 write, 31, 91 antialiasing, 37, 96 atom
changing properties, 159
color
auto-update, 109 coordinates, 113, 114
changing, 18, 159 min and max, 162 info, 91, 156
name lists, 41 picking, 17
selection, 15, 17, 57, 70, 91, 156 auto-update, 109
changing properties, 127 comparison, 74
default, 108 examples, 17, 70
keywords, 41, 70, 77, 78 logic, 72
macros, 42, 92, 125 math functions, 79 modes, 70
Python, 125 quoting, 72
regular expression, 73 same, 75
sequence, 75 text, 156 update, 161
volumetric data, 79 within, 75
atoms
distance between, 18 plotting, 45 atomselect
command, 91, 120, 155, 156 axes, 37
command, 94, 120 Python module, 134 Babel, 21
backface culling, 37
batch mode, 173 beta values, 164 BioCoRE, 13 bonds
add or remove, 24 determining, 21 label, 44
resolution, 58 unusual, 21 cachemode, 38 callbacks
Python, 132 Tcl, 118, 123 center of mass, 159 CHARMM
files, 20, 34 chemical2vmd, 177 clipping planes, 38
user defined, 108 color
access definitions, 95 assignment, 18 background, 46
category, 46, 66, 67, 95, 170 command, 66, 94, 120 form, 18, 45, 66, 67 id, 39, 66
in user-defined graphics, 99 index, 95
map, 46
material properties, 99, 100 names, 66, 95
properties, 95 Python module, 134 redefinition, 46, 169 revert to default, 169 scale, 46, 68, 94, 168
changing, 46
set minmax, 110, 141 color map, 66
colorinfo
command, 95, 120 coloring
by category, 67 by color scale, 68 by property, 170
methods, 15, 39, 57, 65–67, 108, 170 Command line options, 171
contact residues, 76 copyright, 11 Coulomb potential
volumetric data, 116 culling, 97
debug
command, 120 density
volumetric data, 115 depth cue, 97
depth cueing, 37 display
command, 96, 120 device, 172
form, 36
Python module, 134 update, 96, 156, 169 distance
volumetric data, 115 distance between atoms, 18 draw
command, 97 drawing
method, 15, 39 drawn, 31
electrostatics
volumetric data, 116 environment variables, 173
DISPLAY, 173 MSMSSERVER, 63 SURF BIN, 63 TCL LIBRARY, 176
VMD EXCL GL EXTENSIONS, 175 VMDBABELBIN, 21, 173
VMDCAVEMEM, 174
VMDCUSTOMIZESTARTUP, 173 VMDDIR, 173
VMDFILECHOOSER, 173
VMDFORCECONSOLETTY, 174 VMDFORCECPUCOUNT, 174 VMDFREEVRMEM, 174 VMDGDISPLAY, 174 VMDGLSLVERBOSE, 174
VMDHTMLVIEWER, 174 VMDIMAGEVIEWER, 174 VMDIMMERSADESKFLIP, 175 VMDMSECDELAYHACK, 175 VMDMSMSUSEFILE, 175 VMDPREFERSTEREO, 175 VMDSCRDIST, 175
VMDSCRHEIGHT, 175 VMDSCRPOS, 175 VMDSCRSIZE, 175
VMDSHEARSTEREO, 175 VMDSIMPLEGRAPHICS, 175 VMDSPACEBALLPORT, 27 VMDTMPDIR, 173
VMDVMDMACENABLEEEXTENSIONS, 175
VMDWIREGL, 175 example scripts
Python
callbacks, 132 Tcl
customized startup file example, 176 exit
command, 120 eye separation, 83, 96 file
load, 14 file types
input, 20, 34 output, 31 files
output, 16 read, 91
reading, 14, 16, 20, 33, 34, 108 startup, 26, 173, 176
writing, 31, 91 fit
RMSD, 166 focal length, 83, 96 form
animate, 16, 32 color, 18, 45, 66, 67 display, 36
files, 14
graphics, 15, 17, 39 hot keys, 28
label, 43 main, 30, 32 material, 46
molecule file browser, 33 mouse, 34
RamaPlot, 55 render, 16, 47 sequence, 52 sim, 51 tool, 48 forms, 106 frame
delete, 32, 91 duplicate, 90 write, 91 frames, 31
frames per second indicator, 37 geometric center, 158
gettimestep
command, 100, 120 gopython
command, 124 graphics
command, 98 delete, 100 form, 39 loading, 98 primitives, 98 Python module, 135 replace, 100
user-defined, 97 Gromacs
files, 20, 34
gyration, radius of, 162 help, 30
command, 100, 120 topics, 121
highlight, 53 hot keys, 26, 114
animation control, 29 customizing, 26 menu control, 28 mouse control, 27 rotation and scaling, 28 hydrogen bonds, 59, 104
image
lighting controls, 24, 37
shading and material properties, 46 IMD, 51
imd
command, 100, 120 Python module, 136 requirements, 51 implicit ligand sampling
volumetric data, 116
Interactive Molecular Dynamics, 51 joystick
using, 29 label
command, 101, 120 Python module, 137 labels, 17
categories, 44, 101 delete, 44
form, 43 hide, 44
picking with mouse, 24 plotting, 45, 123 show, 44
text, 98 light
command, 101, 120
controlling with mouse, 24 toggle, 37
logfile
command, 102, 120 logging tcl commands, 102 mask
volumetric data, 116 mass
center of, 159
of residue atoms, 119 total, 161
material
changing, 108 command, 102, 120 methods, 39
Python module, 137 material properties, 99, 100 matrix routines
alignment, 151 identity, 150
inverse alignment, 151 list of, 150
multiplication, 150 rotation, 151
trans command, 152 translation, 151 transpose, 150 MDTools, 13 measure
command, 103, 120, 161, 162 menu
command, 106, 120 molecular surface, 62, 63 molecule
active, 31, 32 analysis, 161
best-fit alignment, 166 command, 106, 110, 120 data, 122
deleting, 32 drawn, 31 fixed, 18, 31 graphics, 98 id, 107 index, 107 info, 155 list, 30
loading, 14, 16, 98, 164 Python module, 138 status, 31, 108
changing, 31, 110, 155 top, 31, 33, 110
translation, 18 molinfo
command, 110, 155 keywords, 122 molrep
Python module, 140 mouse
add or remove bonds, 24 callback, 111
command, 111, 120 modes, 14, 18, 23, 27, 111 mouse mode, 35
move, 35 atom, 35 fragment, 35 highlighted rep, 35 molecule, 35 residue, 35 object menus, 35 pick information, 44 rocking, 112
stop rotation, 112 using, 23
movies, 88 NAMD, 13
files, 20, 34 occupancy
volumetric data, 116 orthographic view, 37, 81 output
format, 16 PCRE, 12
periodic boundary conditions, 43 periodic image display, 43
perspective view, 37, 81 picking
angles, 24, 25 atoms, 17, 24, 25 bonds, 17, 24, 25 center, 25
dihedrals, 24, 25 distances, 17 hot keys, 27 modes, 18, 24 move atom, 25 move fragment, 25 move highlighted rep, 26 move molecule, 26 move residue, 25 query, 25
text command, 112 play
command, 89, 112, 120, 172 plot
geometry monitors, 45 postscript, 87
potential of mean force
volumetric data, 116 Python, 12
interface, 124 RMSD, 126, 127 Tkinter, 132 version, 124 python
atomsel, 125
environment variables, 124 libraries, 124
Numeric, 125, 142 startup, 172 Tkinter, 125 quit, 30
command, 98, 112 quoting, 72
radius of gyration, 162 Ramachandran plot, 55 Raster3D, 22, 87
regular expression, 73, 79 X-PLOR conversion, 80 remote
connection, 100 detaching, 52 killing, 52
modifiable parameters, 52 options, 100
simulation control, 100 render
command, 112, 120 form, 16, 47
Python module, 141 rendering, 16, 47, 84
ART, 86
caveats and considerations, 85 exec command, 112
Gelato, 85
in background process, 48 list of supported renderers, 85 methods, 86, 112
PostScript, 85 POV-Ray, 86 Radiance, 86 Raster3D, 85 Rayshade, 86
RenderMan, 85 stereo, 87 STL, 85
Tachyon, 11, 13, 16, 86, 112 TachyonInternal, 112 VRML, 85
rendering modes, 97 rendermode, 38
representation, 57, 107 add new, 40 adding, 40 auto-update, 42 Beads, 65 Bonds, 58 Cartoon, 62
changing, 17, 39, 108 clipping planes
user defined, 108 CPK, 60
deleting, 40
dotted van der Waals, 65 draw multiple frames, 110 DynamicBonds, 59
examples, 18 HBonds, 59 hiding, 40 Isosurface, 64 Licorice, 60 Lines, 58
list of available, 58 MSMS, 63
NewCartoon, 62 NewRibbons, 61 Points, 59 Ribbons, 61
show/hide, 110, 141 solvent representation, 65 style, 15, 39, 57, 108 Surf, 62
Trace, 60 Tube, 60
van der Waals, 59 VolumeSlice, 63 represention
auto-update, 109 reset view, 36, 96
restore
viewpoint, 155 vmd state, 19 RMS
Fit, 164
RMS:Alignment, 164
RMSD, 126, 127, 129, 163, 166, 167 rock, 33
command, 112, 120 rotate
command, 113, 120 side chain, 160 rotation
continuous, 24 hot keys, 28 stop, 24
using mouse, 24 save
configuration, 19 viewpoint, 155 vmd state, 19, 146 scale
command, 113, 120 scaling
using mouse, 24 screen parameters, 38 scripts
play, 89 source, 89
secondary structure codes, 53
selection, 15, 17, 39, 57, 91, 108, 156 comparison, 74
keywords, 41, 70, 77 boolean, 72 logic, 72
math functions, 79 modes, 70
text, 156
volumetric data, 79 sensor configuration file, 49 sensors, 49
sequence, 52 caveats, 54 dna, 52 form, 52 zooming, 54
short circuit logic, 72, 75 sleep
command, 118, 120 source
command, 89 spaceball
driver, 11, 27 MacOS X, 27 Unix, 27 Windows, 27 modes, 27 using, 27 stage, 37
command, 113, 120 startup files, 26, 173, 176 stereo
mode, 82 cross-eyed, 82 CrystalEyes, 83 DTI side-by-side, 82 scanline interleaved, 82 side-by-side, 82
off, 81
parameters, 37, 83, 96, 97 stop rotation, 36
stride, 12 surf, 12 surface
molecular, 65
solvent accessible, 65 Tachyon, 13
Tcl, 90
tcl commands, 90 text
displayed, 99 Tk, 90
tool
CAVE, 49
command, 113, 120 form, 48
FreeVR, 49 Spaceball, 49 VRPN, 49 tools, 50
topology files, 20 trajectory
draw multiple frames, 42, 110 files, 20
read, 34
smoothing, 42, 110, 141 write, 31
trans
Python module, 141 translate
command, 114, 120 translation
change atom coordinates, 160 using mouse, 24
transparency, 39
unit cell information, 43 universal sensor locator, 49 user
command, 114, 120 user interfaces
python, 124 text, 89 USL, 49 variables
env, 173, 176 M PI, 153 trace, 118 vector command
coordtrans, 153 vecadd, 147 veccross, 149 vecdist, 149 vecdot, 148 vecinvert, 150 veclength, 149 veclength2, 149 vecmean, 148 vecnorm, 149 vecscale, 148 vecstddev, 148 vecsub, 147 vecsum, 148 vectrans, 153 veczero, 147 vector routines, 147 view, 107
viewing modes