Category:Script Library: Difference between revisions

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
Rotamer Toggle CreateSecondaryStructure WriteSS Iterate sses Helicity check Measure Distance Translate And Measure Motif Nmr cnstr FindSurfaceResidues InterfaceResidues ColorByRMSD Centroid Average b Ss Ccp4 ncont AutoMultiFit Consistent View/ Map Inspect BiologicalUnit BbPlane AngleBetweenHelices AAindex Sidechaincenters Displacementmap HighlightAlignedSS BiologicalUnit/Quat Color By Mutations Ccp4 contact Ccp4 pisa Propka DynoPlot Cart to frac Colorbydisplacement Resicolor plugin Color by conservation Cyspka Elbow angle Transformations DistancesRH Contact Surface Pairwise distances ShowLigandWaters Bondpack Colorblindfriendly Load new B-factors RotationAxis Draw Protein Dimensions Dssr block PDB plugin RmsdByResidue Angle between domains Mcsalign Msms surface Dssp LigAlign Xfit Intra xfit Sst Load aln Show contacts FindSurfaceCharge	ConnectedCloud Zero residues List Selection List Colors List Secondary Structures Selection Exists Color Objects Get Coordinates I Get Coordinates II Grepsel Findseq ToGroup Save sep FindSurfaceResidues AlphaToAll Expand To Surface Removealt GetNamesInSel FindObjectsNearby CollapseSel SelInside Split selection Split Object Along Axis Split Movement SaveGroup SelectClipped Rotkit Get raw distances Find buried waters Count molecules in selection DistancesRH Cluster Count ListSelection2 Pairwise distances ShowLigandWaters Flatten obj Annotate v Color cbcobj FindSurfaceCharge	Perp maker Symmetry Axis CGO Text Plane Wizard Bounding Box Ellipsoid TransformSelectionByCameraView Modevectors Center of mass DrawBoundingBox Slerpy CgoCircle SuperSym Supercell BiologicalUnit BbPlane BiologicalUnit/Quat Radius of gyration Cart to frac Mark center Dump2CGO Axes Contact Surface Cgo arrow Cubes Distancetoatom Cgo grid RotationAxis Draw Protein Dimensions
User Interface	Biochemical Scripts	System Scripts
ObjectByArrows PowerMate Dial OS X Mouse modes Key Wait Grepset Apropos Stereo ray PDB Web Services Script Stereo Figures Movit Spectrumbar Save2traj VisLoad Aa codes Set toggle Movie fade Save settings Dynamic mesh ObjectFocus Make Figures Inertia tensor ImmersiveViz RUCAP UM-5 Format bonds Get colors Movie color fade Quickdisplays Distancetoatom Pytms Frame slider	Show aromatics Show hydrophobics Show charged Show hydrophilic Pucker Resicolor CreateAtom Color h FindSurfaceResidues Average b AAindex Polarpairs Propka Forster distance calculator Cyspka DistancesRH ListSelection2 Pairwise distances ShowLigandWaters Quickdisplays Distancetoatom Load new B-factors Pytms Show contacts Color cbcobj FindSurfaceCharge	FilterByMol LoadDir Process All Files In Directory PythonTerminal Pdbsurvey Read PDB-String Pml2py Tiff2ccp4 Monitor file continuously XML-RPC server FetchLocal Find symbol
Third Party
Rasmolify Wfmesh Transform odb PovRay Ccp4 ncont Ccp4 contact Ccp4 pisa Tiff2ccp4 Pymol2glmol Save Mopac PoseView RUCAP UM-5

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

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ThirdParty Scripts

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UI Scripts

Pages in category "Script Library"

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Zero residues

@@ Line 1: / Line 1: @@
-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 =
+|-
-== [[: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]]
-<DPL>
+! style="font-size: 1.25em; " | [[:Category:Math_Scripts|Math/Geometry/CGO]]
-category=UI_Scripts
+|- valign=top
+|<DPL>
+category=Structural_Biology_Scripts
 redirects=include
 mode=unordered
+format = <ul type="disc">,<li>[[%PAGE%]],</li>,</ul>
 </DPL>
-}}
+||
-== [[:Category:ObjSel_Scripts|Objects and Selections]] ==
-{{#menu:
 <DPL>
 category=ObjSel_Scripts
 redirects=include
 mode=unordered
+format = <ul type="disc">,<li>[[%PAGE%]],</li>,</ul>
 </DPL>
-}}
+||
-== [[:Category:System_Scripts|System (OS/Filesystem/Web/etc)]] ==
-{{#menu:
 <DPL>
-category=System_Scripts
+category=Math_Scripts
 redirects=include
 mode=unordered
+format = <ul type="disc">,<li>[[%PAGE%]],</li>,</ul>
 </DPL>
-}}
+|-
+! style="font-size: 1.25em; padding-top: 3.5em; width:33%;" | [[:Category:UI_Scripts|User Interface]]
-== [[:Category:Structural_Biology_Scripts|Structural Biology]] ==
+! style="font-size: 1.25em; padding-top: 3.5em; width:33%;" | [[:Category:Biochemical_Scripts|Biochemical Scripts]]
-{{#menu:
+! style="font-size: 1.25em; padding-top: 3.5em; width:33%;" | [[:Category:System_Scripts|System Scripts]]
-<DPL>
+|- valign=top
-category=System_Scripts
+|<DPL>
+category=UI_Scripts
 redirects=include
 mode=unordered
+format = <ul type="disc">,<li>[[%PAGE%]],</li>,</ul>
 </DPL>
-}}
+||
-== [[:Category:ThirdParty_Scripts|Third Party]] ==
-{{#menu:
 <DPL>
-category=ThirdParty_Scripts
+category=Biochemical_Scripts
 redirects=include
 mode=unordered
+format = <ul type="disc">,<li>[[%PAGE%]],</li>,</ul>
 </DPL>
-}}
+||
-== [[:Category:Biochemical_Scripts|Biochemical Scripts]] ==
-{{#menu:
 <DPL>
-category=Biochemical_Scripts
+category=System_Scripts
 redirects=include
 mode=unordered
+format = <ul type="disc">,<li>[[%PAGE%]],</li>,</ul>
 </DPL>
-}}
+|-
+! style="font-size: 1.25em; padding-top: 3.5em; width:33%" | [[:Category:ThirdParty_Scripts|Third Party]]
-== [[:Category:Math_Scripts|Math/Geometry/CGO]] ==
+! style="font-size: 1.25em; padding-top: 3.5em; width:33%;" |
-{{#menu:
+! style="font-size: 1.25em; padding-top: 3.5em; width:33%;" |
-<DPL>
+|- valign=top
-category=Math_Scripts
+|<DPL>
+category=ThirdParty_Scripts
 redirects=include
 mode=unordered
+format = <ul type="disc">,<li>[[%PAGE%]],</li>,</ul>
 </DPL>
-}}
+|}
-* [[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:Script Library: Difference between revisions

Latest revision as of 11:07, 14 December 2011

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