Difference between revisions of "Category:Script Library"
Line 53: | Line 53: | ||
</DPL> | </DPL> | ||
}} | }} | ||
− | |||
− | |||
− | |||
== [[:Category:Biochemical_Scripts|Biochemical Scripts]] == | == [[:Category:Biochemical_Scripts|Biochemical Scripts]] == |
Revision as of 08:47, 30 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
- Aa codes
- Apropos
- Distancetoatom
- Dynamic mesh
- Format bonds
- Frame slider
- Get colors
- Grepset
- ImmersiveViz
- Inertia tensor
- Key Wait
- Make Figures
- Mouse modes
- Movie color fade
- Movie fade
- Movit
- ObjectByArrows
- ObjectFocus
- PDB Web Services Script
- PowerMate Dial OS X
- Pytms
- Quickdisplays
- RUCAP UM-5
- Save2traj
- Save settings
- Set toggle
- Spectrumbar
- Stereo Figures
- Stereo ray
- VisLoad
Objects and Selections
- AlphaToAll
- Annotate v
- Cluster Count
- CollapseSel
- Color Objects
- Color cbcobj
- ConnectedCloud
- Count molecules in selection
- DistancesRH
- Expand To Surface
- FindObjectsNearby
- FindSurfaceCharge
- FindSurfaceResidues
- Find buried waters
- Findseq
- Flatten obj
- GetNamesInSel
- Get Coordinates I
- Get Coordinates II
- Get raw distances
- Grepsel
- ListSelection2
- List Colors
- List Secondary Structures
- List Selection
- Pairwise distances
- Removealt
- Rotkit
- SaveGroup
- Save sep
- SelInside
- SelectClipped
- Selection Exists
- ShowLigandWaters
- Split Movement
- Split Object Along Axis
- Split selection
- ToGroup
- Zero residues
System (OS/Filesystem/Web/etc)
- FetchLocal
- FilterByMol
- Find symbol
- LoadDir
- Monitor file continuously
- Pdbsurvey
- Pml2py
- Process All Files In Directory
- PythonTerminal
- Read PDB-String
- Tiff2ccp4
- XML-RPC server
Structural Biology
- FetchLocal
- FilterByMol
- Find symbol
- LoadDir
- Monitor file continuously
- Pdbsurvey
- Pml2py
- Process All Files In Directory
- PythonTerminal
- Read PDB-String
- Tiff2ccp4
- XML-RPC server
Third Party
- Ccp4 contact
- Ccp4 ncont
- Ccp4 pisa
- PoseView
- PovRay
- Pymol2glmol
- RUCAP UM-5
- Rasmolify
- Save Mopac
- Tiff2ccp4
- Transform odb
- Wfmesh
Biochemical Scripts
- AAindex
- Average b
- Color cbcobj
- Color h
- CreateAtom
- Cyspka
- DistancesRH
- Distancetoatom
- FindSurfaceCharge
- FindSurfaceResidues
- Forster distance calculator
- ListSelection2
- Load new B-factors
- Pairwise distances
- Polarpairs
- Propka
- Pucker
- Pytms
- Quickdisplays
- Resicolor
- ShowLigandWaters
- Show aromatics
- Show charged
- Show contacts
- Show hydrophilic
- Show hydrophobics
- 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
- Axes
- BbPlane
- BiologicalUnit
- BiologicalUnit/Quat
- Bounding Box
- CGO Text
- Cart to frac
- Center of mass
- CgoCircle
- Cgo arrow
- Cgo grid
- Contact Surface
- Cubes
- Distancetoatom
- DrawBoundingBox
- Draw Protein Dimensions
- Dump2CGO
- Ellipsoid
- Mark center
- Modevectors
- Perp maker
- Plane Wizard
- Radius of gyration
- RotationAxis
- Slerpy
- SuperSym
- Supercell
- Symmetry Axis
- TransformSelectionByCameraView
- 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 197 pages are in this category, out of 197 total.
C
- CalcArea
- Cart to frac
- Ccp4 contact
- Ccp4 ncont
- Ccp4 pisa
- Cealign plugin
- Center of mass
- Centroid
- Cgo arrow
- Cgo grid
- CGO Text
- CgoCircle
- Check Key
- Cluster Count
- CMPyMOL
- CollapseSel
- Color by conservation
- Color By Mutations
- Color cbcobj
- Color h
- Color Objects
- Colorblindfriendly
- Colorbydisplacement
- ColorByRMSD
- ConnectedCloud
- Consistent View/ Map Inspect
- Contact Surface
- Count molecules in selection
- CreateAtom
- CreateSecondaryStructure
- Cubes
- Cyspka
D
F
J
L
M
P
R
S
- Save Mopac
- Save pdb with anisou
- Save sep
- Save settings
- Save2traj
- SaveGroup
- Ss
- Select sites
- SelectClipped
- Selection Exists
- SelInside
- Set toggle
- Show aromatics
- Show bumps
- Show charged
- Show contacts
- Show hydrophilic
- Show hydrophobics
- Nmr cnstr
- ShowLigandWaters
- Sidechaincenters
- Slerpy
- Spectrum states
- Spectrumany
- Spectrumbar
- Split chains
- Split Movement
- Split Object Along Axis
- Split object
- Split selection
- Sst
- Stereo ray
- Stereo Figures
- Supercell
- SuperSym
- Symmetry Axis