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(poll protein/nucleic)
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|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
! Poll
! Selection keywords
| [https://goo.gl/forms/r0Ck03VTytZQxN4A2 New protein/nucleic selection keywords for PyMOL] - Tell us what you think!
| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
! Official Release
! Official Release

Revision as of 12:30, 7 February 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
Selection keywords New polymer.protein and polymer.nucleic selection keywords. Thanks everyone who participated in the poll!
Official Release PyMOL v2.0 has been released on September 20, 2017.
Plugin Update MOLE 2.5 is an updated version of channel analysis software in PyMOL
Official Release PyMOL v1.8.6 has been released on March 9, 2017.
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...


orient aligns the principal components of the atoms in the selection with the XYZ axes. The function is similar to the orient command in X-PLOR.


orient object-or-selection [, state]
orient (selection)


cmd.orient( string object-or-selection [, state = 0] )


  state = 0 (default) use all coordinate states
  state = -1 use only coordinates for the current state
  state > 0  use coordinates for a specific state


For models with NCS symmetry, orient will align the model with the symmetry axis centered along the viewport's z axis. For example,

  fetch 1hiw, async=0
  as cartoon
  remove (!chain A,B,C)

will produce the first image below. However, if there is a larger symmetry, e.g. two trimers, this will not work. In the above example, leaving out remove (!chain A,B,C) from the script results in the second image below. <gallery> Image:1hiw orient.png|One trimer from 1hiw after "orient" ..→

A Random PyMOL-generated Cover. See Covers.