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News & Updates
Official Release PyMOL v2.4 has been released on May 20, 2020.
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...

AlphaToAll

alphatoall (all lower case) is a core command since PyMOL 1.7.2

Overview

AlphaToAll will expand the alpha-carbon property that you specify to all atoms in the residues. For example, if you set the b-factor column to some different value for all alpha carbons, this script will propagate those values into all the atoms as well.

In the example below, notice the color of the sticks.

Usage

<source lang="python">

  1. expand propertyName in objName on all the alpha carbons
  2. to every atom, for each residue

alphaToAll objName, propertyName

  1. Example #1
  2. For all objects, for each residue, set every atom's b-column value
  3. to match that residue's alpha carbon's b-column value.

alphaToAll *, b

  1. Example #2
  2. For selection 1qox and c. A ..→
A Random PyMOL-generated Cover. See Covers.