Difference between revisions of "Main Page"

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| [http://pymol.org PyMOL v1.8.4 has been released] on October 4, 2016.
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| [https://pymol.org PyMOL v2.2 has been released] on July 24, 2018.
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! POSF
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| [https://pymol.org/fellowship PyMOL Open-Source Fellowship program] accepting applications for 2018-2019
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! New Plugin
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| [[ProBiS_H2O|ProBiS H2O]] is a new plugin for identification of conserved waters in protein structures.
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! Selection keywords
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| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
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! Plugin Update
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| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.5]] is an updated version of channel analysis software in PyMOL
 
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| [[Lisica|LiSiCA]] is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
 
| [[Lisica|LiSiCA]] is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
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! Official Release
 
| [http://pymol.org PyMOL v1.8.0 has been released] on Nov 18, 2015.
 
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! PyMOL Open-Source Fellowship
 
| Schrödinger is now accepting applications for the PyMOL Open-Source Fellowship program! Details on http://pymol.org/fellowship
 
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! Official Release
 
| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.6 have all been released] on May 4, 2015.
 
 
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Latest revision as of 04:49, 24 July 2018

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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 v2.2 has been released on July 24, 2018.
POSF PyMOL Open-Source Fellowship program accepting applications for 2018-2019
New Plugin ProBiS H2O is a new plugin for identification of conserved waters in protein structures.
Selection keywords New polymer.protein and polymer.nucleic selection keywords. Thanks everyone who participated in the poll!
Plugin Update MOLE 2.5 is an updated version of channel analysis software in PyMOL
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.
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...

Map set

Map_set created this consensus volume representation of aligned ligands bound to kinases. See example below.

Map_set provides a number of common operations on and between maps. For example, with Map_set you can add two maps together or create a consensus map from a series of maps or even take a difference map.

Usage

map_set name, operator, operands, target_state, source_state

operator may be,

  • average
  • copy
  • difference
  • maximum
  • minimum
  • sum
  • unique

Examples

# add 3 maps
map_set my_sum, sum, map1 map2 map3

# calculate the average map
map_set my_avg, average, map1 map2 map3

Detailed Example

This example shows you how to create a consensus map of the bound ligand in a conserved pocket.

<source lang="python">

  1. fetch some similar proteins from the PDB

fetch 1oky 1h1w 1okz 1uu3 1uu7 1uu8 1uu9 1uvr, async=0

  1. align them all to 1oky; their ligands
  2. should all now be aligned

alignto ..→

A Random PyMOL-generated Cover. See Covers.