Main Page

From PyMOLWiki
Revision as of 12:50, 3 March 2013 by Tlinnet (Talk | contribs)
Jump to: navigation, search
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
Tips & Tricks Instructions for generating movie PDFs using .mpg movies from PyMOL.
New Script Cluster Count calculates statistics on the B-values for all atoms in the selected object.
New Script Make Figures aids you in making publication quality figures for the currently displayed scene.
New Script Distances RH
PyMOL on the iPad PyMOL is now available on the iPad as a free download from the AppStore. See for more info.
OS X Compatibility Mac OS X 10.8 doesn't ship with X11. But, you can get the libraries here X11 Libraries.
New Script select_sites can set author/paper selections according to SITE annotation in pdb file
New Script b2transparency can set surface transparency based on atom b-factor
New Extension psico is a python module which extends PyMOL with many commands
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...

Bounding Box

import math
from pymol import querying
from pymol.cgo import *
from pymol import cmd
#NOTE!! : These packages (numarray, Scientific) must be present in pymol's 
#'$PYMOLDIR/py23/lib/python2.3/site-packages/' directory!!
# OR..if you are using Mac PyMOL 0.99beta19 or later then the system installs will be used
from numarray import *
from import average
from numarray import linear_algebra as la
from  [[Bounding Box|..→]]
A Random PyMOL-generated Cover. See Covers.

Personal tools