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| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
 
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! Python 3
 
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| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
 
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
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| [https://pymol.org PyMOL v2.3 has been released] on February 11, 2019.
 
 
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| [[ProBiS_H2O|ProBiS H2O]] is a new plugin for identification of conserved waters in protein structures.
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| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
 
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! Selection keywords
 
! Selection keywords

Latest revision as of 03:21, 22 June 2021

hosted by SBGridlogo2.jpg
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 v2.5 has been released on May 10, 2021.
Python 3 New Python 3 compatibility guide for scripts and plugins
POSF New PyMOL fellows announced for 2018-2019
Tutorial Plugins Tutorial updated for PyQt5
New Plugin PICv is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
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...

Optimize

Type PyMOL Plugin
Download plugins/optimize.py
Author(s) Osvaldo Martin
License MIT
This code has been put under version control in the project Pymol-script-repo

Introduction

Optimize provides a PyMOL graphical interface to some of the molecular mechanics features available in openbabel, allowing the user to optimize (minimize) the energy of any molecule uploaded on PyMOL.

Installation

The plugin can be downloaded through the project Pymol-script-repo.

Optimize needs OpenBabel (and OpenBabel Python bindings) to be installed on your computer (see instructions here).

Note to Windows users: If you are using a 64-bit Windows, please install OpenBabel 64-bit from here

Usage

The plugin can be accessed using a graphic user interface (see figure 0) or from the PyMOL`s terminal. There are 5 types of optimization routines available now, 2 local and 3 global optimization routines.

== Local ..→

A Random PyMOL-generated Cover. See Covers.


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