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! New Plugin
! New Plugin
| [[Contact_Map_Visualizer]] visualize residues corresponding to its contact map
| [[Contact_Map_Visualizer]] visualize residues corresponding to the contact map
|-
|-
! New Script
! New Script

Revision as of 04:43, 13 January 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 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...

Process All Files In Directory

=Explanation=

For a given directory with PDB files in it, the following code will output, for each PDB, the bound disulfide bond lengths like this:

1alk.pdb
  A CYS 168 SG
  A CYS 178 SG
    1.975
  A CYS 286 SG
  A CYS 336 SG
    1.995
  B CYS 168 SG
  B CYS 178 SG
    1.996
  B CYS 286 SG
  B CYS 336 SG
    2.032
1btu.pdb
   CYS 42 SG
   CYS 58 SG
    2.039
   CYS 136 SG
   CYS 201 SG
    2.031
   CYS 168 SG
   CYS 182 SG
    2.001
   
..→
A Random PyMOL-generated Cover. See Covers.