VMD Script Library

Most VMD functions can be accessed through text commands implemented in Tcl and Python. This allows scripts to be written which can load molecules, make movies, or run entire demos automatically. These scripts can include control loops, variable substitution, if-then-else constructs, function and procedure definitions, and many other features.

The scripts provided here are relatively simple examples of what can be done using the scripting interfaces in VMD. As such, most of these scripts perform a very specific task, and would need to be modified for more general-purpose use, though some of them may serve your needs as-is.

If you would like to learn more about these scripts, you can read the Tcl and Python scripting sections in the VMD User's Guide and consult Tcl and Python references.

Python VMD scripts

fit_angle — finds the angle between the best-fit line through two selections or a given vector
reswin — sequence selection and coloring script
selpath — draws a trace through the average position of an atom selection over a trajectory

Tcl VMD scripts

Structure building scripts

mergemultiframepdb — Merge large multi-frame virus capsid structures into a single structure using the psfgen plugin
mutate_res — Mutate a residue
splitmultiframepdb — Split multi-frame NMR structures into separate molecules and load them into VMD.
mergepdbs — Merge several PDB files together into a single structure using the psfgen plugin
mono2poly — Build complete biological unit from PDB BIOMT records

Analysis scripts

bigdcd — Analyze large Charmm/X-PLOR/NAMD "DCD" trajectories
ca-dist — Given a selection, plot the CA-CA distance
ColorCoord — set residue user field according to number of hbonds formed with neighbors
HOLE — a script for running the HOLE program written by Oliver Smart
metal_environment — Finds the propensity of residues near given ions
stride_workaround — Works around a limitation in STRIDE, allowing determination of secondary structure of proteins in very large structures
trajectory_path — Draws the path of the center of mass of a selection through an animation
frame_rmsd — computes rmsd between two frames of a trajectory
geometry — measure various molecular geometry
difference_matrix — makes a matrix of center of mass distances between residues of two proteins
total_mass — returns the total mass of a selected molecule
get_total_charge — returns the total charge of a selected molecule
residmap — converts resids between different numbering schemes
orient — align molecules to their principal axes

Trajectory processing scripts

animatepdbs — Load a consecutively numbered sequence of PDB files as a trajectory animation
bridging_waters — Example of how to display a selection that changes over an animation
fitframes — fits a selection to all frames in a trajectory
morph — generates an interpolated animation between two given frames
parallel-analysis — examples of parallel Timeline analysis scripts, using the MPI features of VMD
PBCTools — Set up and display periodic boundary conditions.
PBCWrap — Wrap atoms of selection $sel around PBC unit cell boundaries, requires pbctools script.
pdbbfactor — Load a multi-frame PDB file's B-Factor values into the User data attribute as a trajectory
rmsd_matrix — calculates a matrix of rmsds between the frames in a trajectory
sscache — Automatically stores secondary structure information for animations
sscachebunch — FAST storage of secondary structure information for animations
trajectory_analyze — An example of an efficient way to analyze large trajectories within VMD while they load.
trajectory_path — Draws the path of the center of mass of a selection through an animation
trajectory_smooth — Computes average position for the atoms in a sliding window of N frames, so one can see net movements of residues and eliminate thermal noise.

File conversion scripts

top2psf — Convert Gromacs topology files to CHARMM PSF format
write_charmm_crd — Write a CHARMM CRD file from a loaded molecule in VMD

Collaboration and BioCoRE related scripts

vmdcollab — Connect two or more VMD sessions together in an interactive collaborative session.

User-customization scripts

vmd_use_pdb_ss — Build secondary structure from information in a PDB record, rather than from STRIDE
save_restore_viewpoint — Allows you to save or load particularly good viewing points

Demo and presentation scripts

dnademos — VMD DNA demos, lac repressor, sophisticated Tk controls over VMD processes
vmd_kiosk — VMD kiosk demo script

User-defined graphics scripts

blink — blink a selected representation
box_molecule — Frames a molecule with a box
colordisplacement — Color structures by displacement
Swing — Animation using the "draw" commands
2dgraph — A good example of how to graph a quantity in VMD, in this case a one variable function
3dgraph — Uses VMD graphics features to plot the surface of a two variable function
3dparplot — An example of how to plot parametric surfaces of two variables in VMD
color_scale_bar — draws a color bar on the screen to show all of the current colors
eye_line — Draws a cylinder from the picked atom through the eye
delaunay_triangulate — calculate various types of molecular surfaces using delaunay triangulation
graphicspick — Example use of user-defined graphics picking callback
pbcbox — Draws the periodic simulation box
spring — Draws a spring from a picked atom outward toward the eye
dials — Draws dials which indicate the amount of time which has passed when playing back a simulation or the amount of force being applied to a certain part of the system
highlight_bases — Draws small slabs at the locations of DNA bases for emphasis
mk3drama — Creates a nice color coded 3d-ramachandran histogram graph
rotate_display — Rotates the display around the molecule, rather than altering the coordinates as is usually done.

Interactive scripts based on picking, mouse clicks, etc

eye_line — Draws a cylinder from the picked atom through the eye
pickbond — Allows the user to interactively add or delete bonds using the mouse

Movie making scripts

animated_gif — A good example of how to directly make animated gifs for WWW pages. Uses rotation of a molecule as an example
roll - Rolls the display in a lemniscape pattern on two axes, a very nice alternative to rotations and single-axis rocking.
rotation_movie — Writes out a series of screen shots corresponding to stages in a rotation
trajectory_movie_short — Writes out screen shots corresponding to frames of an animation
trajectory_movie — Again writes out screen shots corresponding to frames of an animation, but provides more options than trajectory_movie_short
take_picture — A flexible procedure to capture, render, and manage multiple screen shots.
userani — user-defined movie generation scripts.
view_change_render — Five procedures to save, restore, and smoothly animate VMD's camera/eye position by interpolating between them, optionally rendering to image files to create movies.

Sequence display scripts

reswin — Browse sequence, highlight and color structure by sequence selections

Scripts for displaying volumetric data, Electron density maps, etc

potsel — gets electrostatic grid via Delphi for VMD
potsurf — uses Delphi to show electrostatic potential on a molecular surface
readedm — read X-PLOR ASCII Electron Density Map files
readcube — read Gaussian ASCII "cube" files

Web-based VMD scripts

webvmd — Example scripts for controlling VMD from within a web browser
sandbox — A safe VMD "sandbox" for execution of untrusted VMD scripts

Submitting a script

If you have a useful or interesting script to contribute, please contact <vmd@ks.uiuc.edu>, which will be answered by one of the VMD maintainers. When you submit a script, fill in all the information given above (if appropritate). If you want, you may add more headers. We will go over the script and make sure it works properly. We have final say on adding a script. Unless otherwise agreed, any submitted script must follow the standard VMD script library redistribution policy.