Main Page

From PyMOLWiki
Revision as of 22:39, 6 November 2016 by MichelleOttaviano (Talk | contribs)

Jump to: navigation, search
hosted by SBGridlogo2.jpg
Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
To request a new account, email SBGrid at: accounts (@) sbgrid dot org
Quick Links
Tutorials Table of Contents Commands
Script Library Plugins FAQ
Gallery | Covers PyMOL Cheat Sheet (PDF) Getting Help
News & Updates
Official Release PyMOL v1.8.4 has been released on October 4, 2016.
New Script dssr_block is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
New Plugin LiSiCA is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
Official Release PyMOL v1.8.0 has been released on Nov 18, 2015.
PyMOL Open-Source Fellowship Schrödinger is now accepting applications for the PyMOL Open-Source Fellowship program! Details on http://pymol.org/fellowship
Official Release PyMOL, AxPyMOL, and JyMOL v1.7.6 have all been released on May 4, 2015.
New Plugin PyANM is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
New Plugin Bondpack is a collection of PyMOL plugins for easy visualization of atomic bonds.
New Plugin MOLE 2.0 is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.
3D using Geforce PyMOL can now be visualized in 3D using Nvidia GeForce video cards (series 400+) with 120Hz monitors and Nvidia 3D Vision, this was previously only possible with Quadro video cards.
Older News See Older News.
Did you know...

Protect

protect protects a set of atoms from tranformations performed using the editing features. This is most useful when you are modifying an internal portion of a chain or cycle and do not wish to affect the rest of the molecule.

USAGE

protect (selection)

PYMOL API

cmd.protect(string selection)

Example

This example makes a very cool little, and fake, molecular movie. Copy/paste this into PyMOL:

load $PYMOL_PATH/test/dat/pept.pdb, obj

# create the fake trajectory (of states)
for a in range(2,31): cmd.create("obj","obj",1,a)
# remove the bond
unbond 5/C, 6/N
# This protects everything but all atoms witing 4
# Ang. of residue 5's carbon and residue 6's nitrogen.
protect not ((5/C or 6/N) extend 4)

# do some quick sculpting
sculpt_activate obj, 30
sculpt_iterate obj, 30, 100
smooth obj, 30, 3

# then program a bond-break/re-form movie
mset 1 x30 1 -30 30 x30 30 -1 
mdo 45: unbond 5/C, 6/N, quiet=1
mdo 100: bond 5/C, 6/N, quiet=1

frame 100

as sticks
orient  [[Protect|..]]
A Random PyMOL-generated Cover. See Covers.