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Category:Script Library

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


  • 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 "" 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.
  • 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
  • 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.
  • WFMesh -- Imports wavefront object mesh files; Starwars as an example!
  • grepsel -- Make named selections using regular expressions (protein sequence).
  • 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).


This category has the following 7 subcategories, out of 7 total.







Pages in category "Script Library"

The following 195 pages are in this category, out of 195 total.