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.
{| style="text-align: left; background: #D9CEB2; color: #7A6A53; border: 2px solid #D5DED9; padding: 3em;" align="center"
 
|-
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.
! style="padding-top: 1em; padding-bottom: 2.5em; font-size: 1.25em; text-align: center;" |
 
! 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.
! style="padding-top: 1em; padding-bottom: 2.5em; font-size: 1.25em; text-align: center;" |
 
|-
= 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 =
|-
== User Interface ==
! style="font-size: 1.25em; " | [[:Category:Structural_Biology_Scripts|Structural Biology]]
* [[ImmersiveViz]] -- A script used in conjunction with head tracking software to provide an immersive virtual experience.
! style="font-size: 1.25em; " | [[:Category:ObjSel_Scripts|Objects and Selections]]  
* [[ObjectByArrows]] -- Navigate between objects by using the arrow keys
! style="font-size: 1.25em; " | [[:Category:Math_Scripts|Math/Geometry/CGO]]
* [[PowerMate Dial OS X]] -- Script and instructions to use the PowerMate dial on Mac OS X.
|- valign=top
* [[mouse_modes]] -- customize the default mouse bindings for Viewing or Editing modes. - ''by EHP''
|<DPL>
* [[Key Wait]] -- Process key events in a Python script.
category=Structural_Biology_Scripts
* [[grepset]] -- List all settings matching a given keyword. - ''by EHP''
redirects=include
* [[apropos]] -- List all commands matching a given keyword or whose docs contain the keyword. - ''by EHP''
mode=unordered
* [[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.
format = <ul type="disc">,<li>[[%PAGE%]],</li>,</ul>
 
</DPL>
== Objects and Selections ==
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* [[ConnectedCloud]] -- Find connected clouds of objects in PyMOL
<DPL>
* [[Zero_residues]] -- Renumber residues such that the first residue is 0. Useful for alignments.
category=ObjSel_Scripts
* [[List Selection]] -- Prints a list of all residues in a selection (both Python and .pml).
redirects=include
* [[List Colors]] -- Lists the color of all residues in a selection (both Python and .pml).
mode=unordered
* [[List Secondary Structures]] -- Secondary structures (both predefined and those calculated with the 'dss' command) can be exported as a long string ('HHHHLLLLSSS').
format = <ul type="disc">,<li>[[%PAGE%]],</li>,</ul>
* [[Selection Exists]] -- Python method that returns true if a selection of a given name exists.
</DPL>
* [[Color Objects]] -- Colors all objects differently (Python script).
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* [[Get Coordinates I]] -- Retrieves atom coordinates as Python objects.
<DPL>
* [[Get Coordinates II]] -- Retrieves atom coordinates as Python array (list object).
category=Math_Scripts
* [[grepsel]] -- Make named selections using regular expressions (protein sequence).
redirects=include
* [[Split Movement]] -- Moves two parts of one object into different directions.
mode=unordered
 
format = <ul type="disc">,<li>[[%PAGE%]],</li>,</ul>
== System (OS/Filesystem/Web/etc) ==
</DPL>
* [[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).
! style="font-size: 1.25em; padding-top: 3.5em; width:33%;" | [[:Category:UI_Scripts|User Interface]]
* [[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).
! style="font-size: 1.25em; padding-top: 3.5em; width:33%;" | [[:Category:Biochemical_Scripts|Biochemical Scripts]]
* [[PythonTerminal]] -- Allows execution of python commands from the PyMOL command line.
! style="font-size: 1.25em; padding-top: 3.5em; width:33%;" | [[:Category:System_Scripts|System Scripts]]
* [[pdbsurvey]] -- Surveys the pdb for recently added structures that are relevant to a user-specified keywords list (in a text file)
|- valign=top
* [[Read PDB-String]] -- Parses a string in PDB format to a PyMOL object.
|<DPL>
 
category=UI_Scripts
== Structural Biology ==
redirects=include
* [[Cealign]] -- Implementation of the CE Structure Alignment algorithm as a PyMOL plugin.
mode=unordered
* [[Kabsch]] -- Kabsch alignment of two sets of vectors.  (Part 2 of a protein alignment.)
format = <ul type="disc">,<li>[[%PAGE%]],</li>,</ul>
* [[LigAlign]] -- Ligand-based active site alignment and comparison.
</DPL>
* [[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.
<DPL>
* [[iterate_sses]] -- Slightly more complex version of "ss" that allows the user to pass in a function to act on the sse list.
category=Biochemical_Scripts
* [[Helicity_check]] -- helicity_check show the evolution of O - N distances over an amino acid sequence
redirects=include
* [[Measure Distance]] -- Measures the distance between two atoms (Python script).
mode=unordered
* [[Translate_And_Measure]] -- prints '''overlap''' if any of the atoms in molA or molB were within 4 Angstrom after translating by 1 along X
format = <ul type="disc">,<li>[[%PAGE%]],</li>,</ul>
* [[motif]] -- Designed for easy display of backbone motifs (nests, catgrips, etc).
</DPL>
* [[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.
||
 
<DPL>
== Third Party ==
category=System_Scripts
* [[Rasmolify]] -- A work in progress - a script to map Rasmol commands onto the equivalent PyMOL commands.
redirects=include
* [[WFMesh]] -- Imports wavefront object mesh files; Starwars as an example!
mode=unordered
* [[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.
format = <ul type="disc">,<li>[[%PAGE%]],</li>,</ul>
 
</DPL>
== 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)
! style="font-size: 1.25em; padding-top: 3.5em; width:33%" | [[:Category:ThirdParty_Scripts|Third Party]]
* [[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)
! style="font-size: 1.25em; padding-top: 3.5em; width:33%;" |
* [[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)
! style="font-size: 1.25em; padding-top: 3.5em; width:33%;" |
* [[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)
|- valign=top
* [[pucker]] -- Calculates the sugar pucker information for a given selection
|<DPL>
* [[resicolor]] -- Colors proteins according to residue type.
category=ThirdParty_Scripts
* [[createAtom]] -- Make an atom at a distance along the line of a bond.
redirects=include
 
mode=unordered
== Math/Geometry/CGO ==
format = <ul type="disc">,<li>[[%PAGE%]],</li>,</ul>
* [[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]])
</DPL>
* [[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

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