Category:Script Library: Difference between revisions

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The PyMOLWiki script library houses many useful scripts.  Here you will find premade scripts that will extend the power of PyMOL.
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The scripts are now categorized based on their function.  Someone may have added a script but not listed it on this page, therefore please see the autogenerated list of scripts at the bottom of this page.
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! style="padding-top: 1em; padding-bottom: 2.5em; font-size: 2.5em; text-align: center;" | PyMOL Script Library
Please post any script requests to this page's discussion page.  Who knows, someone might have already written it or would be willing to write it.
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= Depositing Scripts =
! style="padding-bottom: 4em; font-size: 1.25em; text-align: center;" | [[Running_Scripts|Running Scripts]]
Please create a new page for your script. Once you've done that, please add it to the Script_Library Category and any subcategories appropriate for the script.  For example, if you have a script that performs some geometrical action upon various objects or selections you can then add the subcategories of ObjectsAndSelections_SL and also MathGeometry_SL.  The convention (which might change is CategoryName_SL (where indicates a subcategory of the ScriptLibrary).  
! style="padding-bottom: 4em; font-size: 1.25em; text-align: center;"| [[Category_talk:Script_Library#Requests|Script Requests]]
 
! style="padding-bottom: 4em; font-size: 1.25em; text-align: center;"| [[Category_talk:Script_Library#Policy|Policy]]
= Categorized Descriptions =
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== [[:Category:UI_Scripts|User Interface]] ==
! style="font-size: 1.25em; " | [[:Category:Structural_Biology_Scripts|Structural Biology]]
{{#menu:
! style="font-size: 1.25em; " | [[:Category:ObjSel_Scripts|Objects and Selections]]
! style="font-size: 1.25em; " | [[:Category:Math_Scripts|Math/Geometry/CGO]]
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category=Structural_Biology_Scripts
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category=ObjSel_Scripts
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category=Math_Scripts
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! style="font-size: 1.25em; padding-top: 3.5em; width:33%;" | [[:Category:UI_Scripts|User Interface]]
! style="font-size: 1.25em; padding-top: 3.5em; width:33%;" | [[:Category:Biochemical_Scripts|Biochemical Scripts]]
! style="font-size: 1.25em; padding-top: 3.5em; width:33%;" | [[:Category:System_Scripts|System Scripts]]
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== [[:Category:ObjSel_Scripts|Objects and Selections]] ==
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category=Biochemical_Scripts
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category=System_Scripts
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! style="font-size: 1.25em; padding-top: 3.5em; width:33%" | [[:Category:ThirdParty_Scripts|Third Party]]
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* [[ConnectedCloud]] -- Find connected clouds of objects in PyMOL
* [[Zero_residues]] -- Renumber residues such that the first residue is 0.  Useful for alignments.
* [[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').
* [[Selection Exists]] -- Python method that returns true if a selection of a given name exists.
* [[Color Objects]] -- Colors all objects differently (Python script).
* [[Get Coordinates I]] -- Retrieves atom coordinates as Python objects.
* [[Get Coordinates II]] -- Retrieves atom coordinates as Python array (list object).
* [[grepsel]] -- Make named selections using regular expressions (protein sequence).
* [[Split Movement]] -- Moves two parts of one object into different directions.
 
== System (OS/Filesystem/Web/etc) ==
* [[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).
* [[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).
* [[PythonTerminal]] -- Allows execution of python commands from the PyMOL command line.
* [[pdbsurvey]] -- Surveys the pdb for recently added structures that are relevant to a user-specified keywords list (in a text file)
* [[Read PDB-String]] -- Parses a string in PDB format to a PyMOL object.
 
== Structural Biology ==
* [[Cealign]] -- Implementation of the CE Structure Alignment algorithm as a PyMOL plugin.
* [[Kabsch]] -- Kabsch alignment of two sets of vectors.  (Part 2 of a protein alignment.)
* [[LigAlign]] -- Ligand-based active site alignment and comparison.
* [[WriteSS]] -- Writes secondary structural elements, for each residues, to a file.
* [[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.
* [[Helicity_check]] -- helicity_check show the evolution of O - N distances over an amino acid sequence
* [[Measure Distance]] -- Measures the distance between two atoms (Python script).
* [[Translate_And_Measure]] -- prints '''overlap''' if any of the atoms in molA or molB were within 4 Angstrom after translating by 1 along X
* [[motif]] -- Designed for easy display of backbone motifs (nests, catgrips, etc).
* [[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.
 
== Third Party ==
* [[Rasmolify]] -- A work in progress - a script to map Rasmol commands onto the equivalent PyMOL commands.
* [[WFMesh]] -- Imports wavefront object mesh files; Starwars as an example!
* [[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.
 
== Biochemical ==
* [[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)
* [[pucker]] -- Calculates the sugar pucker information for a given selection
* [[resicolor]] -- Colors proteins according to residue type.
* [[createAtom]] -- Make an atom at a distance along the line of a bond.
 
== Math/Geometry/CGO ==
* [[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/[[User:Tree|Tree]])
* [[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.
* [[Slerpy]] -- Pymol command extensions for key frame animation movie making.
* [[Plane Wizard]] -- Wizard to draw planes between three picked points.
* [[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)
* [[TransformSelectionByCameraView]] -- Transforms the selection by the camera view.
* [[modevectors]] -- A wonderful script that allows you to draw highly customizable vectors between two states (NMA, TMD, etc)
* [[Center Of Mass]] -- Given a selection of atoms (of equal weight) - Calculates the center of mass and represents it with a CGO sphere
 


[[Category:Scripting|Script Library]]
[[Category:Scripting|Script Library]]

Latest revision as of 11:07, 14 December 2011

PyMOL Script Library
Running Scripts Script Requests Policy
Structural Biology Objects and Selections Math/Geometry/CGO
User Interface Biochemical Scripts System Scripts
Third Party

Subcategories

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

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Pages in category "Script Library"

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