VMD Cheat Sheet

VMD Cheat Sheet Command-Line Options Atom Selections Barry's .vmdrc functions Mouse mode View Representations Additional graphics Menus Animation Modifications Text Commands (for the console): Text Commands animate axes center rotation color debug display exit help or ? label light logfile menu mol or molecule mouse | Change the current state (mode) of the mouse. play quit render rock rot or rotate scale simulation stage trans translate user wait Povay tmp files mol defaul to change things DCD trajectory display matrix routines RMSD cavity/pocket representation Draw things Running in Text Mode Adding plugins

 

Command-Line Options

When started, the following command-line parameters may be given to VMD. Note that if a command-line parameter does not start with a dash (-), and is not part of another option, it is assumed to be a PDB filename. Thus, the command

 

vmd molecule.pdb

 

will start VMD and load a molecule from the file molecule.pdb.

 

Option	Function
-? or -h	Print a summary a command-line options to the console.
-m filename1 filename2	load multiple molecules
-e filename	execute the text commands in filename, and then resume normal operation.
-psf filename	Load the specified PSF (need a PDB or DCD file too)
-pdb filename	Load the specified molecule (in PDB format) at startup.
-dcd filename	Load the specified binary DCD (need a PDB or PSF file too)
-disp option	type of graphical display (win => standard, text or none => none)
-pos x y	position for the graphics display window.
-size x y	size for the graphics display window
-nt	Do not display the VMD title at startup.
-startup filename	Use filename as the VMD startup command script
-init filename	Use filename as the file containing VMD initialization data

 

To see the comand line help info screen type:

vmd -dispdev text -h

---

Atom Selections

To start off, here are some examples of valid selection commands in VMD. Following these will be a more in depth description of how selections work.

 

 

name CA

resid 35

name CA and resname ALA

backbone

not protein

protein (backbone or name H)

name 'A 1'

name 'A *'

name "C.*"

mass < 5

numbonds = 2

abs(charge) > 1

x < 6 and x > 3

sqr(x-5)+sqr(y+4)+sqr(z) > sqr(5)

within 5 of name FE

exwithin 3 of protein

protein within 5 of nucleic

same resname as (protein within 5 of nucleic)

protein sequence "C..C"

name eq $atomname

protein and @myselection

 

 

Barry's .vmdrc functions

Mouse mode

R enter rotate mode; stop rotation

T enter translate mode

S enter scaling mode

C assign rotation center

0 query item; show labels menu

1 pick atom

2 pick bond (2 atoms)

3 pick angle (3 atoms)

4 pick dihedral (4 atoms)

5 move atom

6 move residue

7 move fragment

8 move molecule

9 move highlighted rep

 

 

View

~` reset view

Q view from positive direction of x axis

W view from positive direction of y axis

E view from positive direction of z axis

F flip view 180º (view from the back of the current view)

X spin about x axis

Y spin about y axis

Z spin about z axis

J rotate 2º about x

K rotate -2º about x

L rotate 2º about y

H rotate -2º about y

 

 

Representations

N - apply preselected graphical representation

(new cartoon colored by index)

I - apply preselected graphical representation

(trace colored by index)

U - apply preselected graphical representation

(trace colored by molecule)

A - apply representations from the top molecule

to all other molecules

#U - make the selections of the top molecule

# to auto update each frame

 

___Background

V - set white background and 'exp2' depth cue

B - set black background without depthcue

P - switch depthcue on and off

 

 

Additional graphics

O (o) - draw coordinate cylinders in origin

(red x, green y, blue z)

G - draw coordinate grid

(red x, green y, blue z).

One tick 1Ã…, small square

5Ã… big square 10Ã….

D - remove all the graphics added

 

 

Menus

\[ - show main menu

\] - show files menu, and set the current folder

as of the top molecule file

' - show graphics (Graphical Representations) menu

\\ - show sequence menu

\; - show tkcon Tcl console (only works after

the first menu use)

 

 

Animation

+ move to next frame

- move to previous frame

. > play animation forward

, < play animation reverse

/ ? stop animation

 

 

Modifications

NOT IMPLIMENTED

#M - center molecule to the origin

#` ~ - orient top molecule (< 50,000 atoms)

by principal axes

(requires Orient script written

by Paul Grayson and linear algebra

from Hume Integration Software)

 

Text Commands (for the console):

h - Show this list of Hot keys and Text commands

 

n - Loads coordinates from the filelist and

adds them as new files.

Syntax:

n {file1.coor file2.pdb file3.dcd};

n {/net/home/bgrant/} {file1.dcd} 10

Filenames can be separated by new lines.

First argument can be path to files,

it can be omitted or empty.

The third argument can be step for

trajectory reading or can be omitted.

Filename can include full path.

 

a - Loads coordinates from the filelist and adds

them as new frames to the top molecule

Syntax:

a {file1.coor file2.pdb file3.dcd};

a {/net/home/bgrant/} {file1.dcd} 10

Filenames can be separated by new lines.

First argument can be path to files,

it can be omitted or empty.

The third argument can be step for

trajectory reading or can be omitted.

Filename can include full path.

 

 

pdb - Write current frame of the top file

to a pdb file _.pdb

 

cell - Sets the cell size for periodic images.

Usage:

cell {a, b, c, alpha, beta, gamma}

cell {line from xsc file}

cell {parameters from NAMD configuration}

cell {xsc filename}

E.g.

'cell {100 110 120 90 90 60}'

'cell {sim-mscs-007.xsc}'

 

lbl - Labels each atom in the 'selectionText' with

information 'labelInfo', with

arbitrary prefix 'labelPrefix',

color 'color' and font size 'size'.

Syntax:

'lbl <|selectionText>

<|labelInfo>

<labelPrefix> <color> <|size>'

E.g.

'lbl \{resid 1 to 10 and name CA\}'

'lbl \{name CA\} \{resname resid\} \{ \} blue 0.5'

 

#morph - !NOT IMPLEMENTED! Adds frames with linear

interpolation between the existing

frames of the top molecule.

Usage:

'morph

'

'morph

'

E.g.

'morph 10'

'morph 2 linear'

'morph 3 cycle'

'morph 100 sin2'

'morph 3:10:4 linear'

---

Text Commands

VMD understands commands which start with the following words. See below for a more complete synopsis.

 

• animate: Play/Pause/Rewind a molecular trajectory.
• axes: Position a set of XYZ axes on the screen.
• color: Change the color assigned to molecules, or edit the colormap.
• display: Change various aspects of the graphical display window.
• exit: Quit VMD.
• help or ?: Display this help file with an HTML viewer.
• label: Turn on/off labels for particular atoms, bonds, angles, or dihedral angles.
• light: Control the light sources used to illuminate graphical objects.
• logfile: Log commands to a text file or the VMD console.
• menu: Control or query the on-screen GUI menu forms.
• mol: Load, modify, or delete a molecule in VMD.
• molecule: Same as mol.
• mouse: Change the current state (mode) of the mouse.
• play: Start executing text commands from a specified file.
• quit: Same as exit.
• remote: Set up VMD to connect to or start a remote simulation program (optional).
• render: Output the currently displayed image (scene) to a file.
• rock: Rotate the current scene continually at a specified rate.
• rot: Rotate the current scene around a given axis by a certain angle.
• rotate: Same as rot.
• rotation: Same as rot.
• scale: Scale the current scene up or down.
• stage: Position a checkerboard stage on the screen.
• trans: Translate the objects in the current scene.
• translate: Same as trans.
• user: Add user-customized commands to the graphics display pop-up menu.
• wait: Specify a number of seconds to wait before reading another command.

 

 

Words which complete the above text command are shown below

 

animate

Play/Pause/Rewind a molecular trajectory.

forward	Play animation forward
for	Same as forward
reverse	Play animation backward
rev	Same as reverse
pause	Pause animation
prev	GO to previous frame
next	GO to next frame
skip n	Set stride to n+1 frames
delete all	Delete all frames from memory
speed n	Set animation speed to n
style once	Set to play animation once
style loop	Set to loop through animation continuously
style rock	Set to play animation foward and back continuously
goto start	GO to first frame
goto end	GO to last frame
goto n	GO to frame n
read filename nb ne ns molecule_number	read molecule data
write filename nb] ne ns molecule_number	Write data for molecule
delete nb ne ns molecule_number	Delete data for molecule
readdel filename nb ne ns molecule_number	Read data for molecule overwriting existing data

note. the last few comands operate on data from molecule_number from filename, beginning with frame nb, ending with frame ne, with a stride of ns+1

 

 

axes

Position a set of XYZ axes on the screen.

location (option)

Position axes (off , origin , lowerleft , lowerright , upperleft , upperright)

 

center rotation

Position the center of rotation to a point, in this case the origin (0,0,0).

molinfo 0 set center "{0.0 0.0 0.0}"

 

Center on an atom selection:

set sel [atomselect top "resid 770 to 778"]

set center [list [measure center $sel]]

molinfo 0 set center $center

 

color

Change the color assigned to molecules, or edit the colormap. All color values are in the range 0 ... 1.

category name color	Set color of object specified by category and name to color
scale method (option)	Set type of scale (RGB , RWB , BlkW)
scale midpoint x	Set midpoint of color scale to x, in the range 0 ... 1
scale min x	Set minimum of color scale to x, in the range 0 ... 1
scale max x	Set maximum of color scale to x, in the range 0 ... 1
change (options) color	Reset given property of color to default value ( alpha , shininess , rgb , ambient , diffuse , specular )
change (options) color othercolor	Set given property of color to match othercolor
change (options) color value	Set given (scalar) property of color to value ( alpha , shininess )
change (options) color r g b	Set given (3-valued) property of color to r g b (rgb , ambient , diffuse , specular )

 

 

debug

Turn on/off printing of debugging messages.

This will have no effect if VMD was compiled without the debugging option.

on , off	Turn debug on or off
level n	Set debug level to n

 

 

display

Change various aspects of the graphical display window.

reshape	Reshape the display
resetview	Reset the view
eyesep value	Set the eye separation to value
focallength value	Set the focal length to value
height value	Set the screen height to value
distance value	Set the screen distance to value
antialias < on , off >	Turn antialiasing on or off
depthcue < on , off >	Turn depth cueing on or off
stere (options)	Change the stereo mode (off , sidebyside , crystaleyes)
nearclip < set , add > value	Add to or set near clipping plane position
farclip < set , add > value	Add to or set far clipping plane position

 

 

exit

Quit VMD.

confirm	Ask user before quitting
now	Quit without asking

 

 

help or ?

Display this help file with an HTML viewer.

| help (command)

Jump to help for command |

 

 

label

Turn on/off labels for particular atoms, bonds, angles, or dihedral angles.

add category [atom1 ... atomN]	Add a label involving the N atoms to the given category
list category	list all labels in the given category
show category (all , label_number)	Turn on labels in the given category
hide category (all , label_number)	Turn off labels in the given category
delete category (all , label_number)	Delete labels in the given category
graph category label_number (command)	Show a graph of a label from the given category

The data will be written to a file, and the specified command will be run to graph the data. %s in the command string will be replaced by the temporary filename

 

 

light

Control the light sources used to illuminate graphical objects. There are four light sources, numbered 0 to 3

light_number on	Turn a light on
light_number off	Turn a light off
light_number highlight	Display a line indicating the position of a light source
light_number unhighlight	Hide the line indicating the position of a light source
light_number rot < x , y , z > angle	Rotate a light (at infinity) angle degrees about a given axis

 

 

logfile

Turn on/off logging a VMD session to a log file. This will create a log file with commands for all the actions taking during the session.

The log file may be played back later by using the play command.

console	Log commands to the VMD text console
filename	Turn on logging to filename
off	Turn off logging

 

 

menu

Control or query the on-screen GUI menu forms.

menu_name on	Turn a menu on
menu_name off	Turn a menu off
menu_name loc	Print the location of a menu
menu_name move x y	Turn a menu on

 

 

mol or molecule

Load, modify, or delete a molecule in VMD.

In the following, molecule_number is a string describing which molecules are affected by the command.

It is of the form < m1,m2,....,mN >, where mN is either (all, top, active, inactive, displayed, on, off, fixed, free) or one of the unique integer ID codes assigned to the molecules when they are loaded.

< new , load > structure_file_type structure_file (coordinate_file_type coordinate_file)	Load a new molecule from given file(s)
list (all , top , active , displayed , none , molecule_number )	Print information about molecules
color color_method	Change the default atom coloring method setting
representation rep_method	Change the default rendering method setting
selection select_method	Change the default atom selection setting
modcolor rep_number molecule_number color_method	Change the current coloring method for the given representation in the given molecule
modstyle rep_number molecule_number rep_method	Change the current rendering method (style) for the given representation in the given molecule
modselect rep_number molecule_number select_method	Change the current atom selection for the given representation in the given molecule
addrep	Using the current default settings for the atom selection, coloring, and rendering methods, add a new representation to the top molecule
delrep rep_number molecule_number	Deletes the given representation from the specified molecule
delete (options)	Delete molecules (all , top , active , displayed , none , molecule_number)
active (options)	Make molecules active (all , top , active , displayed , none , molecule_number)
inactive (options)	Make molecules inactive (all , top , active , displayed , none , molecule_number)
on (options)	Turn molecules on (all , top , active , displayed , none , molecule_number)
off (options)	Turn molecules off (all , top , active , displayed , none , molecule_number)
fix (options)	Fix molecules (all , top , active , displayed , none , molecule_number)
free (options)	Unfix molecules (all , top , active , displayed , none , molecule_number)
top molecule_number	Set the top molecule

 

 

mouse | Change the current state (mode) of the mouse.

mode 0	Set mouse mode to rotation
mode 1	Set mouse mode to translation
mode 2	Set mouse mode to scaling
mode 3 N	Set mouse mode to rotate light N
mode 4 N	Set mouse mode to picking mode N

 

 

play

Start executing text commands from a specified file, instead of from the console. When the end of file is reached, VMD will resume reading commands from the previous source. This command may be nested, s|commands being read from one file can include commands to read other files.

filename

Execute commands from filename

 

 

quit

Same as exit

 

 

render

Output the currently displayed image (scene) to a file

list	List the available rendering methods
method filename	Render the global scene to filename using method
method filename command	Render the global scene to filename, then execute `command'

note. Any %s in `command' are replaced by the filename

 

 

rock

Rotate the current scene continually at a specified rate |

off	Stops rocking
< x , y , z > by step	Rock around the given axis at a rate of step degrees per redraw
< x , y , z > by step n	Rock around the given axis at a rate of step degrees per redraw for n steps, reverse, and repeat

 

 

rot or rotate

Rotate the current scene around a given axis by a certain angle |

stop	Stop all rotation, same as rock off
< x , y , z > by angle	Rotate around the given axis angle degrees
< x , y , z > to angle	Rotate the given axis to the absolute position angle
< x , y , z > < by , to > angle step	Rotate at a rate of step degrees per redraw

 

 

scale

Scale the current scene up or down.

by f	Multiply scene scaling factor by f
to f	Set scene scaling factor to f

 

 

simulation

Same as sim

 

 

stage

Position a checkerboard stage on the screen |

location < off , origin , bottom , top , left , right , behind >
panels n	Set number of panels in stage

 

 

trans

Translate the objects in the current scene.

by x y z	Translate by vector (x,y,z) in screen units
to x y z	Translate to the absolute position (x,y,z) in screen units

 

 

translate

Same as trans.

 

 

user

Add user-customized hotkey commands to the graphics window and input devices

add key key (command)

Assign the given text command to the hotkey key

When key is then pressed while the mouse is in the display window, the specified command will be executed.

print keys

Print out the current definition of the hotkeys

 

 

wait

Specify a number of seconds to wait before reading another command.

time	Wait time seconds

 

Povay tmp files

temporary povray file is written to the working directory. However, you

may want to use the attached script instead. This will write your scene in

two parts, a .pov file containing all meta data, such as the lights, camera

and #defaults, and an include file (.inc) which contains the structure. In

this way you have maximum control over your scene without having to edit a

huge povray file. You may even want to consider splitting your scene up in

separate parts (taken from the same perspective), which you combine in a

global .pov file using #include statements. This will give even more control

with regards to modifications to the scene.

 

The magic word in pymol (after run make_pov.py) is make_pov

 

NB. the .pov file contains a commented statement with regards to a povray

script, which allows transforming scenes and objects from model space to

camera space and vice versa.

 

f1, f2 = file, file:-4 + '.inc'

if meta: povfile.write(header)

povview = cmd.get_view()

povfile.write("""\n

%10.5f, %10.5f, %10.5f,

%10.5f, %10.5f, %10.5f,

%10.5f, %10.5f, %10.5f,

%10.5f, %10.5f, %10.5f )

povfile.write('#include "%s"\n\n' % f2)

povfile.close()

povfile = open(f2,'w')

 

mol defaul to change things

There is a new "mol default" command that you can use to alter default graphical representations

in the test versions of VMD 1.8.4. Here's an example of how you'd use it in your .vmdrc file:

 

DCD trajectory display

You can use the CatDCD program to strip

away atoms you're not interested in seeing. Typically, you'd use atom

selections in VMD to generate an 'index' file that CatDCD can use to

select the atoms you want to keep. You'd also produce matching psf/pdb files

using the '$sel writeXXX' atom selection file writing feature in VMD.

Once you have matching PSF/PDB/DCD files, you could then load it all up

into VMD.

 

matrix routines

To rotate a molecule so the long axis will be aligned to Z you can do this by using the VMD matrix routines, documented at:

http://www.ks.uiuc.edu/Research/vmd/current/ug/node172.html

 

For example, if the long axis of your molecule is along

the vector {a b c}, you can rotate it to align it with the z axis as

follows:

 

 

This performs your task in two steps: transvec inv rotates your vector

to be along the x axis, and then transaxis rotates about the y axis to

align your vector with z.

 

RMSD

You can calculate RMSD for any collection of atoms you like using the 'measure rmsd' command:

http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.4/ug/node124.html

You may need to use 'measure fit' and '$sel move' if you need to align

structures first.

 

cavity/pocket representation

For cavities and pores, you could try using the new volumetric map

generation plugin, found in the Extensions->Analysis->VolMap Tool menu

in the main VMD window. (requires VMD 1.8.4, not available in older versions)

To display cavities or pores you'd generate a density or occupancy map,

and then display the map with an isosurface with a isovalue of zero,

or a near-zero value to show the regions not containing atoms. Much would

depend on the details of your structure of course, but it should be possible

to do this with the built-in VolMap tool, or by using the 'volmap'

text command if the graphical tool doesn't afford enough control for

your purposes.

http://www.ks.uiuc.edu/Research/vmd/plugins/volmapgui/

The previously most common way of displaying pores in VMD was via

the HOLE program by Oliver Smart, and load the resulting sphere set into

VMD with an example script for this purpose in the VMD script library.

The HOLE program and scripts work with older versions of VMD as well as

the latest version.

 

Dr. Smart's home page (contact him to get HOLE):

http://www.globalphasing.com/people/osmart/

 

VMD hole script:

http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/hole/

 

Another approach is to use VOLBL to calculate the volume of cavities and represented the

cavity-bordering atoms by their VDW radii, after changing the VDW radii

values to those used in VOLBL. You can have a look at BJ: 85 p. 886-896

(2003).

 

 

Draw things

See the HowTos page DrawVMD

 

Running in Text Mode

vmd -dispdev text

(still interactive), or in a pure batch mode with

vmd -dispdev text -eofexit < input.tcl > output.log

 

Adding plugins

You can either copy them over an existing one,

or load it on-the-fly with commands like these (your filesystem paths):

plugin dlopen /home/user/myplugins/dlpolyplugin.so

plugin update