Category:Script Library: Difference between revisions

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* [[Kabsch]] -- Kabsch alignment of two sets of vectors.  (Part 2 of a protein alignment.)
{| style="text-align: left; background: #D9CEB2; color: #7A6A53; border: 2px solid #D5DED9; padding: 3em;" align="center"
 
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* [[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.
! 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
* [[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.
! style="padding-top: 1em; padding-bottom: 2.5em; font-size: 1.25em; text-align: center;" |
 
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* [[Translate_And_Measure]] -- prints '''overlap''' if any of the atoms in molA or molB were within 4 Angstrom after translating by 1 along X
! style="padding-bottom: 4em; font-size: 1.25em; text-align: center;" |  [[Running_Scripts|Running Scripts]]
 
! style="padding-bottom: 4em; font-size: 1.25em; text-align: center;"| [[Category_talk:Script_Library#Requests|Script Requests]]  
* [[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="padding-bottom: 4em; font-size: 1.25em; text-align: center;"| [[Category_talk:Script_Library#Policy|Policy]]
 
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* [[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; " | [[:Category:Structural_Biology_Scripts|Structural Biology]]
 
! style="font-size: 1.25em; " | [[:Category:ObjSel_Scripts|Objects and Selections]]  
* [[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; " | [[:Category:Math_Scripts|Math/Geometry/CGO]]
 
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* [[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)
|<DPL>
 
category=Structural_Biology_Scripts
* [[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.
redirects=include
 
mode=unordered
* [[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]])
format = <ul type="disc">,<li>[[%PAGE%]],</li>,</ul>
 
</DPL>
* [[Axes]] -- Creates a 3D-CGO object that shows the three coordinate axes.
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<DPL>
* [[CGO Text]] -- Creates a 3D-CGO text object.
category=ObjSel_Scripts
 
redirects=include
* [[List Selection]] -- Prints a list of all residues in a selection (both Python and .pml).
mode=unordered
 
format = <ul type="disc">,<li>[[%PAGE%]],</li>,</ul>
* [[List Colors]] -- Lists the color of all residues in a selection (both Python and .pml).
</DPL>
 
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* [[List Secondary Structures]] -- Secondary structures (both predefined and those calculated with the 'dss' command) can be exported as a long string ('HHHHLLLLSSS').
<DPL>
 
category=Math_Scripts
* [[Split Movement]] -- Moves two parts of one object into different directions.
redirects=include
 
mode=unordered
* [[Selection Exists]] -- Python method that returns true if a selection of a given name exists.
format = <ul type="disc">,<li>[[%PAGE%]],</li>,</ul>
 
</DPL>
* [[Get Coordinates I]] -- Retrieves atom coordinates as Python objects.
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! style="font-size: 1.25em; padding-top: 3.5em; width:33%;" | [[:Category:UI_Scripts|User Interface]]
* [[Get Coordinates II]] -- Retrieves atom coordinates as Python array (list object).
! 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]]
* [[grepset]] -- List all settings matching a given keyword. - ''by EHP''
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|<DPL>
* [[disconnect]] -- unbond a single atom from its neighbors. - ''by EHP''
category=UI_Scripts
 
redirects=include
* [[mouse_modes]] -- customize the default mouse bindings for Viewing or Editing modes. - ''by EHP''
mode=unordered
 
format = <ul type="disc">,<li>[[%PAGE%]],</li>,</ul>
* [[Measure Distance]] -- Measures the distance between two atoms (Python script).
</DPL>
 
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* [[Read PDB-String]] -- Parses a string in PDB format to a PyMOL object.
<DPL>
 
category=Biochemical_Scripts
* [[Color Objects]] -- Colors all objects differently (Python script).
redirects=include
 
mode=unordered
* [[Key Wait]] -- Process key events in a Python script.
format = <ul type="disc">,<li>[[%PAGE%]],</li>,</ul>
 
</DPL>
* [[Bounding Box]] -- Create a bounding box around a selection (Python script; requires numarray and Scientific; gilleain)
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<DPL>
* [[Ellipsoid]] -- Create callback object (opengl) ellipsoids. (Python script; gilleain)
category=System_Scripts
 
redirects=include
* [[pdbsurvey]] -- Surveys the pdb for recently added structures that are relevant to a user-specified keywords list (in a text file)
mode=unordered
 
format = <ul type="disc">,<li>[[%PAGE%]],</li>,</ul>
* [[TransformSelectionByCameraView]] -- Transforms the selection by the camera view.
</DPL>
 
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* [[WFMesh]] -- Imports wavefront object mesh files; Starwars as an example!
! style="font-size: 1.25em; padding-top: 3.5em; width:33%" | [[:Category:ThirdParty_Scripts|Third Party]]
 
! style="font-size: 1.25em; padding-top: 3.5em; width:33%;" |
* [[grepsel]] -- Make named selections using regular expressions (protein sequence).
! style="font-size: 1.25em; padding-top: 3.5em; width:33%;" |
|- valign=top
|<DPL>
category=ThirdParty_Scripts
redirects=include
mode=unordered
format = <ul type="disc">,<li>[[%PAGE%]],</li>,</ul>
</DPL>
|}


[[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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