Difference between revisions of "Category:Script Library"

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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).  
 
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).  
  
== Categorized Descriptions ==
+
= Categorized Descriptions =
=== User Interface ===
+
== User Interface ==
 
* [[ImmersiveViz]] -- A script used in conjunction with head tracking software to provide an immersive virtual experience.
 
* [[ImmersiveViz]] -- A script used in conjunction with head tracking software to provide an immersive virtual experience.
 
* [[ObjectByArrows]] -- Navigate between objects by using the arrow keys
 
* [[ObjectByArrows]] -- Navigate between objects by using the arrow keys
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* [[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.
 
* [[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.
  
=== Objects and Selections ===
+
== Objects and Selections ==
 
* [[ConnectedCloud]] -- Find connected clouds of objects in PyMOL
 
* [[ConnectedCloud]] -- Find connected clouds of objects in PyMOL
 
* [[Zero_residues]] -- Renumber residues such that the first residue is 0.  Useful for alignments.
 
* [[Zero_residues]] -- Renumber residues such that the first residue is 0.  Useful for alignments.
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* [[Split Movement]] -- Moves two parts of one object into different directions.
 
* [[Split Movement]] -- Moves two parts of one object into different directions.
  
=== System (OS/Filesystem/Web/etc) ===
+
== System (OS/Filesystem/Web/etc) ==
 
* [[FilterByMol]] -- Filter a directory of files, and save their ligands to disk (by molecule).
 
* [[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).
 
* [[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).
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* [[Read PDB-String]] -- Parses a string in PDB format to a PyMOL object.
 
* [[Read PDB-String]] -- Parses a string in PDB format to a PyMOL object.
  
=== Structural Biology ===
+
== Structural Biology ==
 
* [[Cealign]] -- Implementation of the CE Structure Alignment algorithm as a PyMOL plugin.
 
* [[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.)
 
* [[Kabsch]] -- Kabsch alignment of two sets of vectors.  (Part 2 of a protein alignment.)
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* [[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.  
 
* [[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 ===
+
== Third Party ==
 
* [[Rasmolify]] -- A work in progress - a script to map Rasmol commands onto the equivalent PyMOL commands.
 
* [[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!
 
* [[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.
 
* [[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 ===
+
== 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 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 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)
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* [[createAtom]] -- Make an atom at a distance along the line of a bond.
 
* [[createAtom]] -- Make an atom at a distance along the line of a bond.
  
=== Math/Geometry/CGO ===
+
== 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]])
 
* [[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.
 
* [[Axes]] -- Creates a 3D-CGO object that shows the three coordinate axes.

Revision as of 18:55, 29 April 2009

The PyMOLWiki script library houses many useful scripts. Here you will find premade scripts that will extend the power of PyMOL.

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.

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.

Depositing 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).

Categorized Descriptions

User Interface

  • ImmersiveViz -- A script used in conjunction with head tracking software to provide an immersive virtual experience.
  • ObjectByArrows -- Navigate between objects by using the arrow keys
  • PowerMate Dial OS X -- Script and instructions to use the PowerMate dial on Mac OS X.
  • mouse_modes -- customize the default mouse bindings for Viewing or Editing modes. - by EHP
  • Key Wait -- Process key events in a Python script.
  • 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
  • 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.

Objects and Selections

  • 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/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

Subcategories

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.