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| [[dehydron]] A plugin to calculate dehydrons and display them onto the protein structure.
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| [[uniprot_features]] makes named selections for sequence annotations from uniprot
A dehydron is a main chain hydrogen bond incompletely shielded from water attack.  
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! New Plugin
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| [[Gyration_tensor]] Calculates chain-wise gyration tensor of a protein.
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| [[set_phipsi]] can set phi/psi angles for all residues in a selection
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! New Script
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| [[dehydron]] A plugin to calculate dehydrons and display them onto the protein structure. A dehydron is a main chain hydrogen bond incompletely shielded from water attack.  
 
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| [[pymol2glmol]] is script to export a scene in pymol to a webpage for GLmol. GLmol is a molecular viewer for Web browsers written in WebGL/Javascript.
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| [[pymol2glmol]] is script to export a scene in pymol to a webpage for GLmol. GLmol is a molecular viewer for Web browsers written in WebGL/Javascript. Like web Jmol, but MUCH faster. Try it out!
Like web Jmol, but MUCH faster. Try it out!
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! New Script

Revision as of 10:35, 13 February 2012

Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
New accounts: email jason (dot) vertrees (@) gmail dot com
Quick Links
Tutorials Table of Contents Commands
Script Library Plugins FAQ
Gallery | Covers PyMOL Cheat Sheet (PDF) GoogleSearch
News & Updates
New Script uniprot_features makes named selections for sequence annotations from uniprot
New Plugin Gyration_tensor Calculates chain-wise gyration tensor of a protein.
New Script set_phipsi can set phi/psi angles for all residues in a selection
New Script dehydron A plugin to calculate dehydrons and display them onto the protein structure. A dehydron is a main chain hydrogen bond incompletely shielded from water attack.
New Script pymol2glmol is script to export a scene in pymol to a webpage for GLmol. GLmol is a molecular viewer for Web browsers written in WebGL/Javascript. Like web Jmol, but MUCH faster. Try it out!
New Script cyspka is an experimental surface cysteine pKa predictor.
New Plugin Contact_Map_Visualizer visualize residues corresponding to the contact map
New Script spectrum_states colors states of multi-state object
New Script TMalign is a wrapper for the TMalign program
Gallery Updates The gallery has been updated to include a few new ideas and scripts for rendering
New Script save_settings can dump all changed settings to a file
Tips & Tricks Instructions for generating 3D PDFs using PyMOL.
Wiki Update Wiki has been updated. Please report any problems to the sysops.
New Scripts Create objects for each molecule or chain in selection with split_object and split_chains
New Script Rotkit: is a collection of usefull scripts to place your dye/molecule where you want. It includes a very handy, rotation around line, function.
New Script Forster-distance-calculator: Can be used as a pymol-python shortcut to calculate the Förster distance between dyes from different companies. Useful, if the user have pymol installed, but not python. This script is meant as a tool to finding the right dyes, when labelling suitable positions for the site-directed cysteine mutants. See DisplacementMap.
New Script propka: Fetches the pka values for your protein from the propka server. propka generates a pymol command file that make pka atoms, color and label them according to your protein. Inspection is made easy by grouping the pka atoms in the pymol menu.
Older News See Older News.
Did you know...

Seq view

==Overview==

The seq_view command turns the sequence viewer on and off. The sequence viewer is a very handy tool, you can use it for example to select residues very easily. When the sequence viewer is turned on, you can select individual residues or multiple residues by selecting residues, using the mouse, on the sequence viewer.

Note: The sequence viewer, seems to decrease PyMOL's performance when very many ..→

A Random PyMOL-generated Cover. See Covers.


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