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- 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)
- 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.
- CGO Text -- Creates a 3D-CGO text object.
- List Selection -- Prints a list of all residues in a selection (both Python and .pml).
- List Colors -- Lists the color of all residues in a selection (both Python and .pml).
- List Secondary Structures -- Secondary structures (both predefined and those calculated with the 'dss' command) can be exported as a long string ('HHHHLLLLSSS').
- Split Movement -- Moves two parts of one object into different directions.
- Selection Exists -- Python method that returns true if a selection of a given name exists.
- Get Coordinates I -- Retrieves atom coordinates as Python objects.
- Get Coordinates II -- Retrieves atom coordinates as Python array (list object).
- grepset -- List all settings matching a given keyword.
- Measure Distance -- Measures the distance between two atoms (Python script).
- Read PDB-String -- Parses a string in PDB format to a PyMOL object.
- Color Objects -- Colors all objects differently (Python script).
- Key Wait -- Process key events in a Python script.
- Bounding Box -- Create a bounding box around a selection (Python script; requires numarray and Scientific; gilleain)
- pdbsurvey -- Surveys the pdb for recently added structures that are relevant to a user-specified keywords list (in a text file)
- TransformSelectionByCameraView -- Transforms the selection by the camera view.
- WFMesh -- Imports wavefront object mesh files; Starwars as an example!
This category has the following 7 subcategories, out of 7 total.
Pages in category "Script Library"
The following 196 pages are in this category, out of 196 total.
- Cart to frac
- Ccp4 contact
- Ccp4 ncont
- Ccp4 pisa
- Cealign plugin
- Center of mass
- Cgo arrow
- Cgo grid
- CGO Text
- Check Key
- Cluster Count
- Color by conservation
- Color By Mutations
- Color h
- Color Objects
- Consistent View/ Map Inspect
- Contact Surface
- Count molecules in selection
- Save Mopac
- Save pdb with anisou
- Save sep
- Save settings
- Select sites
- Selection Exists
- Set toggle
- Show aromatics
- Show bumps
- Show charged
- Show contacts
- Show hydrophilic
- Show hydrophobics
- Nmr cnstr
- Spectrum states
- Split chains
- Split Movement
- Split Object Along Axis
- Split object
- Split selection
- Stereo ray
- Stereo Figures
- Symmetry Axis