Category:Script Library

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.

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.

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)

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

TransformSelectionByCameraView -- Transforms the selection by the camera view.

WFMesh -- Allow import of wavefront object mesh files; Starwars as an example!

Subcategories

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

B

► Biochemical Scripts‎ (24 P)

M

► Math Scripts‎ (29 P)

U

► UI Scripts‎ (29 P)

Pages in category "Script Library"

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Uniprot features

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VisLoad

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Zero residues

Category:Script Library

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