Overview

Here we provide a trove of scripts. The descriptions immediately follow. For the entire category, please see the bottom of this page.

Warning the following list is incomplete. For the complete list, see the category table beneath it.

Descriptions

• ObjectByArrows -- Navigate between objects by using the arrow keys

• ConnectedCloud -- Find connected clouds of objects in PyMOL

• FilterByMol -- Filter a directory of files, and save their ligands to disk (by molecule).

• LoadDir -- loads all the files of a type you specify from the path you specify and puts them into the group you specify (or none).

• LigAlign -- Ligand-based active site alignment and comparison.

• ImmersiveViz -- A script used in conjunction with head tracking software to provide an immersive virtual experience.

• Rasmolify -- A work in progress - a script to map Rasmol commands onto the equivalent PyMOL commands.

• Zero_residues -- Renumber residues such that the first residue is 0. Useful for alignments.

• Cealign -- Implementation of the CE Structure Alignment algorithm as a PyMOL plugin.

• WriteSS -- Writes secondary structural elements, for each residues, to a file.

• Process_All_Files_In_Directory -- Do something to all files in a directory. The examples show how to print the disulfide bond lengths, then in general all sulfur distances (not necessarily bound).

• Kabsch -- Kabsch alignment of two sets of vectors. (Part 2 of a protein alignment.)

• Transform_odb -- Transform a selection of an existing object and output as a new object. The transformation matrix is read from an "O"-style tranformation matrix file (.odb) written by "O" or by any of the Uppsala Software Factory programs (from Gerard Klegweit) such as LSQMAN.

• Stereo_Ray -- This script will create two resolution specific ray traced images rotated appropriately for inclusion into a single file to represent a stereo view of the desired macromolecule.

• Translate_And_Measure -- prints overlap if any of the atoms in molA or molB were within 4 Angstrom after translating by 1 along X

• Show aromatics -- This script will display a backbone "worm" for your protein, with all of the sidechains for aromatic residues displayed as green "sticks". Usage: Save this as "show_aromatics.pml", load your protein in PyMOL, and run the script (select "Run" from the "File" menu). (PyMOL script; TStout)

• Show hydrophobics -- This script will display a backbone "worm" for your protein, with all of the sidechains for hydrophobic residues displayed as orange "sticks". Usage: Same as "show aromatics". (PyMOL script; TStout)

• Show charged -- This script will display a backbone "worm" for your protein, with all of the sidechains for charged residues displayed as red (negative) or blue (posititve) "sticks". Usage: Same as "show aromatics". (PyMOL script; TStout)

• Show hydrophilic -- This script will display a backbone "worm" for your protein, with all of the sidechains for hydrophilic residues displayed as green "sticks". Usage: Same as "show aromatics". (PyMOL script; TStout)

• Show NMR constrains -- This script will display the NMR constrains used for a structure calculation atop a structure. Usage: Save this as "NMRcnstr.py" load your protein in PyMOL, and run the script. type upl('fname') or cns('fname') where fname is the filename with the NMR constrains you want to display.

• Perp Maker -- Creates a perpendicular plane through the center of your protein with respect to the camera's current position. (If you translate the protein towards the camera a bit, you get a nice surface, sometimes.) A stupid little script I wrote in response to a request a few months ago (and it doesn't even conform to the request!) Load a protein, run the script (read the documentation in the script). (Jason Vertrees/Tree)

• PythonTerminal -- Allows execution of python commands from the PyMOL command line.

• Axes -- Creates a 3D-CGO object that shows the three coordinate axes.

• Symmetry Axis -- Draw a 3D-CGO line given a point and a direction.

• CGO Text -- Creates a 3D-CGO text object.

• List Selection -- Prints a list of all residues in a selection (both Python and .pml).

• List Colors -- Lists the color of all residues in a selection (both Python and .pml).

• List Secondary Structures -- Secondary structures (both predefined and those calculated with the 'dss' command) can be exported as a long string ('HHHHLLLLSSS').

• Split Movement -- Moves two parts of one object into different directions.

• Selection Exists -- Python method that returns true if a selection of a given name exists.

• Get Coordinates I -- Retrieves atom coordinates as Python objects.

• Get Coordinates II -- Retrieves atom coordinates as Python array (list object).

• grepset -- List all settings matching a given keyword. - by EHP

• apropos -- List all commands matching a given keyword or whose docs contain the keyword. - by EHP

• mouse_modes -- customize the default mouse bindings for Viewing or Editing modes. - by EHP

• Measure Distance -- Measures the distance between two atoms (Python script).

• Read PDB-String -- Parses a string in PDB format to a PyMOL object.

• Color Objects -- Colors all objects differently (Python script).

• Key Wait -- Process key events in a Python script.

• Bounding Box -- Create a bounding box around a selection (Python script; requires numarray and Scientific; gilleain)

• Ellipsoid -- Create callback object (opengl) ellipsoids. (Python script; gilleain)

• pdbsurvey -- Surveys the pdb for recently added structures that are relevant to a user-specified keywords list (in a text file)

• resicolor -- Colors proteins according to residue type.

• TransformSelectionByCameraView -- Transforms the selection by the camera view.

• WFMesh -- Imports wavefront object mesh files; Starwars as an example!

• grepsel -- Make named selections using regular expressions (protein sequence).

• PowerMate Dial OS X -- Script and instructions to use the PowerMate dial on Mac OS X.

• Plane Wizard -- Wizard to draw planes between three picked points.

• Slerpy -- Pymol command extensions for key frame animation movie making.

• Helicity_check -- helicity_check show the evolution of O - N distances over an amino acid sequence

• Center Of Mass -- Given a selection of atoms (of equal weight) - Calculates the center of mass and represents it with a CGO sphere

• ss -- Simple command to summarise the Secondary Structure as a list of "start-end type" like sses.

• iterate_sses -- Slightly more complex version of "ss" that allows the user to pass in a function to act on the sse list.

• motif -- Designed for easy display of backbone motifs (nests, catgrips, etc).

• createAtom -- Make an atom at a distance along the line of a bond.

• pucker -- Calculates the sugar pucker information for a given selection

• modevectors -- A wonderful script that allows you to draw highly customizable vectors between two states (NMA, TMD, etc)