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Revision as of 12:54, 16 May 2005

  • 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)
  • 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)
  • Axes -- Creates a 3D-CGO object that shows the three coordinate axes.
  • 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.
  • 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)
  • pdbsurvey -- Surveys the pdb for recently added structures that are relevant to a user-specified keywords list (in a text file)
  • WFMesh -- Allow import of wavefront object mesh files; Starwars as an example!

Subcategories

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

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Pages in category "Script Library"

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

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