Jump to content

Main Page

From PyMOL Wiki
Revision as of 20:36, 13 March 2018 by Speleo3 (talk | contribs) (v2.1)
hosted by
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 v2.1 has been released on March 13, 2018.
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...
Type Python Module
Download scripts/get_raw_distances.py
Author(s) Takanori Nakane and Thomas Holder
License BSD-2-Clause
This code has been put under version control in the project Pymol-script-repo

Included in psico
This command or function is available from psico, which is a PyMOL extension.

Module psico.querying

get_raw_distances can dump distance objects, created with distance.

This script also provides the command select_distances, which selects atoms from distance objects.

Warning: the atoms are hashed by coordinates; this could cause issues if coordinates are altered after distance objects have been created (see also dynamic_measures setting).

Usage

get_raw_distances [ names [, state [, selection ]]]
select_distances [ names [, name [, state [, selection [, cutoff ]]]]]

Arguments

  • names = string: names of distance objects (no wildcards!) {default: all measurement objects}
  • state = integer: object state {default: 1}
  • selection = string: atom selection {default: all}

Example

<syntaxhighlight lang="python"> fetch 2xwu, ..→

A Random PyMOL-generated Cover. See Covers.