https://wiki.pymol.org/index.php?title=Category:Script_Library&feed=atom&action=history
Category:Script Library - Revision history
2024-03-28T17:18:47Z
Revision history for this page on the wiki
MediaWiki 1.35.1
https://wiki.pymol.org/index.php?title=Category:Script_Library&diff=3939&oldid=prev
Pyadmin: 78 revisions
2014-03-28T01:29:57Z
<p>78 revisions</p>
<p><b>New page</b></p><div>{| style="text-align: left; background: #D9CEB2; color: #7A6A53; border: 2px solid #D5DED9; padding: 3em;" align="center"<br />
|-<br />
! style="padding-top: 1em; padding-bottom: 2.5em; font-size: 1.25em; text-align: center;" |<br />
! style="padding-top: 1em; padding-bottom: 2.5em; font-size: 2.5em; text-align: center;" | PyMOL Script Library<br />
! style="padding-top: 1em; padding-bottom: 2.5em; font-size: 1.25em; text-align: center;" |<br />
|-<br />
! style="padding-bottom: 4em; font-size: 1.25em; text-align: center;" | [[Running_Scripts|Running Scripts]]<br />
! style="padding-bottom: 4em; font-size: 1.25em; text-align: center;"| [[Category_talk:Script_Library#Requests|Script Requests]] <br />
! style="padding-bottom: 4em; font-size: 1.25em; text-align: center;"| [[Category_talk:Script_Library#Policy|Policy]]<br />
|-<br />
! style="font-size: 1.25em; " | [[:Category:Structural_Biology_Scripts|Structural Biology]]<br />
! style="font-size: 1.25em; " | [[:Category:ObjSel_Scripts|Objects and Selections]] <br />
! style="font-size: 1.25em; " | [[:Category:Math_Scripts|Math/Geometry/CGO]]<br />
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! style="font-size: 1.25em; padding-top: 3.5em; width:33%;" | [[:Category:UI_Scripts|User Interface]]<br />
! style="font-size: 1.25em; padding-top: 3.5em; width:33%;" | [[:Category:Biochemical_Scripts|Biochemical Scripts]]<br />
! style="font-size: 1.25em; padding-top: 3.5em; width:33%;" | [[:Category:System_Scripts|System Scripts]]<br />
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|-<br />
! style="font-size: 1.25em; padding-top: 3.5em; width:33%" | [[:Category:ThirdParty_Scripts|Third Party]]<br />
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|}<br />
<br />
[[Category:Scripting|Script Library]]</div>
Pyadmin
https://wiki.pymol.org/index.php?title=Category:Script_Library&diff=3902&oldid=prev
Jcorn: /* Descriptions */
2009-04-27T16:24:27Z
<p><span dir="auto"><span class="autocomment">Descriptions</span></span></p>
<table class="diff diff-contentalign-left diff-editfont-monospace" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 16:24, 27 April 2009</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l5" >Line 5:</td>
<td colspan="2" class="diff-lineno">Line 5:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>= Descriptions =</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>= Descriptions =</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* [[<del class="diffchange diffchange-inline">ObjArrows</del>]] -- Navigate between objects by using the arrow keys</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* [[<ins class="diffchange diffchange-inline">ObjectByArrows</ins>]] -- Navigate between objects by using the arrow keys</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[ConnectedCloud]] -- Find connected clouds of objects in PyMOL</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[ConnectedCloud]] -- Find connected clouds of objects in PyMOL</div></td></tr>
</table>
Jcorn
https://wiki.pymol.org/index.php?title=Category:Script_Library&diff=3901&oldid=prev
Jcorn: /* Descriptions */
2009-04-27T16:21:01Z
<p><span dir="auto"><span class="autocomment">Descriptions</span></span></p>
<table class="diff diff-contentalign-left diff-editfont-monospace" data-mw="interface">
<col class="diff-marker" />
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 16:21, 27 April 2009</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l5" >Line 5:</td>
<td colspan="2" class="diff-lineno">Line 5:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>= Descriptions =</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>= Descriptions =</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* [[ObjArrows]] -- Navigate between objects by using the arrow keys</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[ConnectedCloud]] -- Find connected clouds of objects in PyMOL</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[ConnectedCloud]] -- Find connected clouds of objects in PyMOL</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
</table>
Jcorn
https://wiki.pymol.org/index.php?title=Category:Script_Library&diff=3900&oldid=prev
Slaw at 15:11, 2 April 2009
2009-04-02T15:11:44Z
<p></p>
<table class="diff diff-contentalign-left diff-editfont-monospace" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 15:11, 2 April 2009</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l114" >Line 114:</td>
<td colspan="2" class="diff-lineno">Line 114:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[pucker]] -- Calculates the sugar pucker information for a given selection</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[pucker]] -- Calculates the sugar pucker information for a given selection</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* [[modevectors]] -- A wonderful script that allows you to draw highly customizable vectors between two states (NMA, TMD, etc)</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Category:Scripting|Script Library]]</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Category:Scripting|Script Library]]</div></td></tr>
</table>
Slaw
https://wiki.pymol.org/index.php?title=Category:Script_Library&diff=3899&oldid=prev
Slaw at 21:22, 1 April 2009
2009-04-01T21:22:36Z
<p></p>
<p><b>New page</b></p><div>= Overview =<br />
Here we provide a trove of scripts. The descriptions immediately follow. For the entire category, please see the bottom of this page.<br />
<br />
'''Warning the following list is incomplete. For the complete list, see the category table beneath it.'''<br />
<br />
= Descriptions =<br />
* [[ConnectedCloud]] -- Find connected clouds of objects in PyMOL<br />
<br />
* [[FilterByMol]] -- Filter a directory of files, and save their ligands to disk (by molecule).<br />
<br />
* [[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).<br />
<br />
* [[LigAlign]] -- Ligand-based active site alignment and comparison.<br />
<br />
* [[ImmersiveViz]] -- A script used in conjunction with head tracking software to provide an immersive virtual experience.<br />
<br />
* [[Rasmolify]] -- A work in progress - a script to map Rasmol commands onto the equivalent PyMOL commands.<br />
<br />
* [[Zero_residues]] -- Renumber residues such that the first residue is 0. Useful for alignments.<br />
<br />
* [[Cealign]] -- Implementation of the CE Structure Alignment algorithm as a PyMOL plugin.<br />
<br />
* [[WriteSS]] -- Writes secondary structural elements, for each residues, to a file.<br />
<br />
* [[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).<br />
<br />
* [[Kabsch]] -- Kabsch alignment of two sets of vectors. (Part 2 of a protein alignment.)<br />
<br />
* [[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.<br />
<br />
* [[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.<br />
<br />
* [[Translate_And_Measure]] -- prints '''overlap''' if any of the atoms in molA or molB were within 4 Angstrom after translating by 1 along X<br />
<br />
* [[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)<br />
<br />
* [[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)<br />
<br />
* [[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)<br />
<br />
* [[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)<br />
<br />
* [[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. <br />
<br />
* [[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]])<br />
<br />
* [[PythonTerminal]] -- Allows execution of python commands from the PyMOL command line.<br />
<br />
* [[Axes]] -- Creates a 3D-CGO object that shows the three coordinate axes.<br />
<br />
* [[Symmetry Axis]] -- Draw a 3D-CGO line given a point and a direction. <br />
<br />
* [[CGO Text]] -- Creates a 3D-CGO text object.<br />
<br />
* [[List Selection]] -- Prints a list of all residues in a selection (both Python and .pml).<br />
<br />
* [[List Colors]] -- Lists the color of all residues in a selection (both Python and .pml).<br />
<br />
* [[List Secondary Structures]] -- Secondary structures (both predefined and those calculated with the 'dss' command) can be exported as a long string ('HHHHLLLLSSS').<br />
<br />
* [[Split Movement]] -- Moves two parts of one object into different directions.<br />
<br />
* [[Selection Exists]] -- Python method that returns true if a selection of a given name exists.<br />
<br />
* [[Get Coordinates I]] -- Retrieves atom coordinates as Python objects.<br />
<br />
* [[Get Coordinates II]] -- Retrieves atom coordinates as Python array (list object).<br />
<br />
* [[grepset]] -- List all settings matching a given keyword. - ''by EHP''<br />
<br />
* [[apropos]] -- List all commands matching a given keyword or whose docs contain the keyword. - ''by EHP''<br />
<br />
* [[mouse_modes]] -- customize the default mouse bindings for Viewing or Editing modes. - ''by EHP''<br />
<br />
* [[Measure Distance]] -- Measures the distance between two atoms (Python script).<br />
<br />
* [[Read PDB-String]] -- Parses a string in PDB format to a PyMOL object.<br />
<br />
* [[Color Objects]] -- Colors all objects differently (Python script).<br />
<br />
* [[Key Wait]] -- Process key events in a Python script.<br />
<br />
* [[Bounding Box]] -- Create a bounding box around a selection (Python script; requires numarray and Scientific; gilleain)<br />
<br />
* [[Ellipsoid]] -- Create callback object (opengl) ellipsoids. (Python script; gilleain)<br />
<br />
* [[pdbsurvey]] -- Surveys the pdb for recently added structures that are relevant to a user-specified keywords list (in a text file)<br />
<br />
* [[resicolor]] -- Colors proteins according to residue type.<br />
<br />
* [[TransformSelectionByCameraView]] -- Transforms the selection by the camera view.<br />
<br />
* [[WFMesh]] -- Imports wavefront object mesh files; Starwars as an example!<br />
<br />
* [[grepsel]] -- Make named selections using regular expressions (protein sequence).<br />
<br />
* [[PowerMate Dial OS X]] -- Script and instructions to use the PowerMate dial on Mac OS X.<br />
<br />
* [[Plane Wizard]] -- Wizard to draw planes between three picked points.<br />
<br />
* [[Slerpy]] -- Pymol command extensions for key frame animation movie making.<br />
<br />
* [[Helicity_check]] -- helicity_check show the evolution of O - N distances over an amino acid sequence<br />
<br />
* [[Center Of Mass]] -- Given a selection of atoms (of equal weight) - Calculates the center of mass and represents it with a CGO sphere<br />
<br />
* [[ss]] -- Simple command to summarise the Secondary Structure as a list of "start-end type" like sses.<br />
<br />
* [[iterate_sses]] -- Slightly more complex version of "ss" that allows the user to pass in a function to act on the sse list.<br />
<br />
* [[motif]] -- Designed for easy display of backbone motifs (nests, catgrips, etc).<br />
<br />
* [[createAtom]] -- Make an atom at a distance along the line of a bond.<br />
<br />
* [[pucker]] -- Calculates the sugar pucker information for a given selection<br />
<br />
[[Category:Scripting|Script Library]]</div>
Slaw
https://wiki.pymol.org/index.php?title=Category:Script_Library&diff=3895&oldid=prev
Gilleain: /* Descriptions */
2008-10-20T12:23:33Z
<p><span dir="auto"><span class="autocomment">Descriptions</span></span></p>
<table class="diff diff-contentalign-left diff-editfont-monospace" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 12:23, 20 October 2008</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l103" >Line 103:</td>
<td colspan="2" class="diff-lineno">Line 103:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[motif]] -- Designed for easy display of backbone motifs (nests, catgrips, etc).</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[motif]] -- Designed for easy display of backbone motifs (nests, catgrips, etc).</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* [[createAtom]] -- Make an atom at a distance along the line of a bond.</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Category:Scripting|Script Library]]</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Category:Scripting|Script Library]]</div></td></tr>
</table>
Gilleain
https://wiki.pymol.org/index.php?title=Category:Script_Library&diff=3894&oldid=prev
Aheifets: /* Descriptions */
2008-10-03T22:41:31Z
<p><span dir="auto"><span class="autocomment">Descriptions</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 22:41, 3 October 2008</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l3" >Line 3:</td>
<td colspan="2" class="diff-lineno">Line 3:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>= Descriptions =</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>= Descriptions =</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* [[LigAlign]] -- Ligand-based active site alignment and comparison.</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[ImmersiveViz]] -- A script used in conjunction with head tracking software to provide an immersive virtual experience.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[ImmersiveViz]] -- A script used in conjunction with head tracking software to provide an immersive virtual experience.</div></td></tr>
</table>
Aheifets
https://wiki.pymol.org/index.php?title=Category:Script_Library&diff=3893&oldid=prev
Hazure at 22:03, 10 March 2008
2008-03-10T22:03:57Z
<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 22:03, 10 March 2008</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l3" >Line 3:</td>
<td colspan="2" class="diff-lineno">Line 3:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>= Descriptions =</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>= Descriptions =</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* [[ImmersiveViz]] -- A script used in conjunction with head tracking software to provide an immersive virtual experience.</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[Rasmolify]] -- A work in progress - a script to map Rasmol commands onto the equivalent PyMOL commands.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[Rasmolify]] -- A work in progress - a script to map Rasmol commands onto the equivalent PyMOL commands.</div></td></tr>
</table>
Hazure
https://wiki.pymol.org/index.php?title=Category:Script_Library&diff=3892&oldid=prev
Dan: /* Descriptions */
2008-02-18T16:55:57Z
<p><span dir="auto"><span class="autocomment">Descriptions</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 16:55, 18 February 2008</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l3" >Line 3:</td>
<td colspan="2" class="diff-lineno">Line 3:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>= Descriptions =</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>= Descriptions =</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* [[Rasmolify]] -- A work in progress - a script to map Rasmol commands onto the equivalent PyMOL commands.</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[Zero_residues]] -- Renumber residues such that the first residue is 0. Useful for alignments.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[Zero_residues]] -- Renumber residues such that the first residue is 0. Useful for alignments.</div></td></tr>
</table>
Dan
https://wiki.pymol.org/index.php?title=Category:Script_Library&diff=3891&oldid=prev
Momeara: /* Descriptions */
2007-11-30T15:11:02Z
<p><span dir="auto"><span class="autocomment">Descriptions</span></span></p>
<p><b>New page</b></p><div>= Overview =<br />
Here we provide a trove of scripts. The descriptions immediately follow. For the entire category, please see the bottom of this page.<br />
<br />
= Descriptions =<br />
<br />
* [[Zero_residues]] -- Renumber residues such that the first residue is 0. Useful for alignments.<br />
<br />
* [[Cealign]] -- Implementation of the CE Structure Alignment algorithm as a PyMOL plugin.<br />
<br />
* [[WriteSS]] -- Writes secondary structural elements, for each residues, to a file.<br />
<br />
* [[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).<br />
<br />
* [[Kabsch]] -- Kabsch alignment of two sets of vectors. (Part 2 of a protein alignment.)<br />
<br />
* [[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.<br />
<br />
* [[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.<br />
<br />
* [[Translate_And_Measure]] -- prints '''overlap''' if any of the atoms in molA or molB were within 4 Angstrom after translating by 1 along X<br />
<br />
* [[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)<br />
<br />
* [[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)<br />
<br />
* [[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)<br />
<br />
* [[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)<br />
<br />
* [[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. <br />
<br />
* [[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]])<br />
<br />
* [[PythonTerminal]] -- Allows execution of python commands from the PyMOL command line.<br />
<br />
* [[Axes]] -- Creates a 3D-CGO object that shows the three coordinate axes.<br />
<br />
* [[Symmetry Axis]] -- Draw a 3D-CGO line given a point and a direction. <br />
<br />
* [[CGO Text]] -- Creates a 3D-CGO text object.<br />
<br />
* [[List Selection]] -- Prints a list of all residues in a selection (both Python and .pml).<br />
<br />
* [[List Colors]] -- Lists the color of all residues in a selection (both Python and .pml).<br />
<br />
* [[List Secondary Structures]] -- Secondary structures (both predefined and those calculated with the 'dss' command) can be exported as a long string ('HHHHLLLLSSS').<br />
<br />
* [[Split Movement]] -- Moves two parts of one object into different directions.<br />
<br />
* [[Selection Exists]] -- Python method that returns true if a selection of a given name exists.<br />
<br />
* [[Get Coordinates I]] -- Retrieves atom coordinates as Python objects.<br />
<br />
* [[Get Coordinates II]] -- Retrieves atom coordinates as Python array (list object).<br />
<br />
* [[grepset]] -- List all settings matching a given keyword. - ''by EHP''<br />
<br />
* [[apropos]] -- List all commands matching a given keyword or whose docs contain the keyword. - ''by EHP''<br />
<br />
* [[mouse_modes]] -- customize the default mouse bindings for Viewing or Editing modes. - ''by EHP''<br />
<br />
* [[Measure Distance]] -- Measures the distance between two atoms (Python script).<br />
<br />
* [[Read PDB-String]] -- Parses a string in PDB format to a PyMOL object.<br />
<br />
* [[Color Objects]] -- Colors all objects differently (Python script).<br />
<br />
* [[Key Wait]] -- Process key events in a Python script.<br />
<br />
* [[Bounding Box]] -- Create a bounding box around a selection (Python script; requires numarray and Scientific; gilleain)<br />
<br />
* [[Ellipsoid]] -- Create callback object (opengl) ellipsoids. (Python script; gilleain)<br />
<br />
* [[pdbsurvey]] -- Surveys the pdb for recently added structures that are relevant to a user-specified keywords list (in a text file)<br />
<br />
* [[resicolor]] -- Colors proteins according to residue type.<br />
<br />
* [[TransformSelectionByCameraView]] -- Transforms the selection by the camera view.<br />
<br />
* [[WFMesh]] -- Imports wavefront object mesh files; Starwars as an example!<br />
<br />
* [[grepsel]] -- Make named selections using regular expressions (protein sequence).<br />
<br />
* [[PowerMate Dial OS X]] -- Script and instructions to use the PowerMate dial on Mac OS X.<br />
<br />
* [[Plane Wizard]] -- Wizard to draw planes between three picked points.<br />
<br />
* [[Slerpy]] -- Pymol command extensions for key frame animation movie making.<br />
<br />
* [[Helicity_check]] -- helicity_check show the evolution of O - N distances over an amino acid sequence<br />
<br />
* [[Center Of Mass]] -- Given a selection of atoms (of equal weight) - Calculates the center of mass and represents it with a CGO sphere<br />
<br />
* [[ss]] -- Simple command to summarise the Secondary Structure as a list of "start-end type" like sses.<br />
<br />
* [[iterate_sses]] -- Slightly more complex version of "ss" that allows the user to pass in a function to act on the sse list.<br />
<br />
* [[motif]] -- Designed for easy display of backbone motifs (nests, catgrips, etc).<br />
<br />
[[Category:Scripting|Script Library]]</div>
Momeara