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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
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! Official Release
| [[PyMOL, AxPyMOL, and JyMO v1.7 have all been released|http://pymol.org]] today, January 14, 2014.
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! New Plugin
! New Plugin

Revision as of 15:38, 14 January 2014

Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
New accounts: email jason (dot) vertrees (@) gmail dot com
Quick Links
Tutorials Table of Contents Commands
Script Library Plugins FAQ
Gallery | Covers PyMOL Cheat Sheet (PDF) GoogleSearch
News & Updates
Official Release http://pymol.org today, January 14, 2014.
New Plugin Bondpack is a 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.
New Plugin GROMACS_Plugin is a new plugin that ties together PyMOL and GROMACS.
New Software CMPyMOL is a software that interactively visualizes 2D contact maps of proteins in PyMOL.
New Script cgo_arrow draws an arrow between two picked atoms.
Tips & Tricks Instructions for generating movie PDFs using .mpg movies from PyMOL.
Older News See Older News.
Did you know...

Flatten obj

Type Python Script
Download scripts/flatten_obj.py
Author(s) Spencer Bliven
License Public Domain
This code has been put under version control in the project Pymol-script-repo

Description

The flatten_obj python script combines multiple objects or states into a single object, renaming chains where required.

This is particularly useful for dealing with biological assemblies, which are loaded as multi-state objects when fetched using fetch PDBID, type=pdb1. It can also be used as a quick way to combine multiple objects without causing collisions between chain identifiers.

The command re-letters chains to avoid collisions. Older versions of PyMOL restrict the chain id to a single character, so the script will fail for assemblies with >62 chains. With more recent versions, this problem is solved with multi-character chain IDs. Several options are available for how re-lettering should occur.

Usage

   flatten_obj name, selection[, state[, rename[, quiet[, chain_map]]]]

Arguments

  • name = a unique name for the ..→
A Random PyMOL-generated Cover. See Covers.