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Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
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News & Updates
Python 3 New Python 3 compatibility guide for scripts and plugins
Official Release PyMOL v2.3 has been released on February 11, 2019.
POSF New PyMOL fellows announced for 2018-2019
Tutorial Plugins Tutorial updated for PyQt5
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
Older News See Older News.
Did you know...

APBS Electrostatics Plugin

APBS-Electrostatics-Plugin-Options.png

The APBS Electrostatics Plugin integrates the APBS software package into PyMOL. Its primary purpose is electrostatic surface visualization. It superseedes the APBS Tool2.1 plugin.

New in Incentive PyMOL 2.0

Usage

A molecule must already be loaded into PyMOL.

For regular protein and DNA molecules, the plugin should be a one-click solution (just click "Run").

For RNA, the residue names might need adjustment, see troubleshooting RNA.

Non-protein/DNA/RNA molecules or modified residues need special preparation, see #Prepare Molecule.

Procedure

The default procedure involves three steps:

  1. preparing the molecule by assigning partial charges and adding hydrogens and other missing atoms
  2. calculating the electrostatic map
  3. visualization of the charged molecular surface

Each step can be run individually by unchecking the checkboxes on the other steps.

Prepare Molecule

APBS requires ..→

A Random PyMOL-generated Cover. See Covers.