Overview

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

Descriptions

• 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).