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| Welcome to the PyMOL Wiki!
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|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
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{| align="center" style="padding-bottom: 3em;"
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|+ style="font-size:210%; font-weight: bold; color:#000000; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!
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|- style="text-align:center; font-weight: normal; color: #000000; font-size: 120%; font-family: sans-serif;"
 
| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.
 
| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.
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| This is a read-only mirror of [http://www.pymolwiki.org/index.php/Main_Page pymolwiki.org]
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| To request a new account, email SBGrid at:  accounts (@) sbgrid dot org
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{| align="center" width="45%" style="background: #FFFFFF; margin-bottom: 4em; border-bottom: 1px solid #AFB29E; border-left: 1px solid #AFB29E; border-right: 1px solid #AFB29E;"
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| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''
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| style="font-size: 1.1em; font-weight: normal; color #48A2B4; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''
 
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| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Script_Library|Script Library]]''' || '''[[:Category:Plugins|Plugins]]''' || '''[[:Category:FAQ|FAQ]]'''
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| style="font-size: 1.1em; font-weight: normal; color #48A2B4; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Script_Library|Script Library]]''' || '''[[:Category:Plugins|Plugins]]''' || '''[[:Category:FAQ|FAQ]]'''
 
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| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''
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||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
 
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
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|-
 
|-
 
! Official Release
 
! Official Release
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| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.4 have all been released] on December 3, 2014.
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| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
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! New Plugin
 
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| [[PyANM|PyANM]] is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
 
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! PyMOL Open-Source Fellowship
 
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| Schrödinger is now accepting applications for the PyMOL Open-Source Fellowship program! Details on http://pymol.org/fellowship
 
 
|-
 
|-
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! Official Release
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! Python 3
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| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.2 have all been released] on August 4, 2014.
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| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
 
|-
 
|-
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! Official Release
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! POSF
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| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7 have all been released] today, January 14, 2014.
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| [https://pymol.org/fellowship New PyMOL fellows announced for 2018-2019]
 
|-
 
|-
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! New Plugin
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! Tutorial
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| [[Bondpack]] is a collection of PyMOL plugins for easy visualization of atomic bonds.
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| [[Plugins Tutorial]] updated for PyQt5
 
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|-
 
! New Plugin
 
! New Plugin
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| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.0]] is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.
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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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|-
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! 3D using Geforce
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! Selection keywords
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| PyMOL can now be [http://forums.geforce.com/default/topic/571604/3d-vision/3d-vision-working-with-qbs-in-opengl-software-using-geforce/2/ 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.
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| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
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! New Plugin
 
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| [[GROMACS_Plugin]] is a new plugin that ties together PyMOL and GROMACS.
 
 
|-
 
|-
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! New Software
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! Plugin Update
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| [[CMPyMOL]] is a software that interactively visualizes 2D contact maps of proteins in PyMOL.
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| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.5]] is an updated version of channel analysis software in PyMOL
 
|-
 
|-
 
! New Script
 
! New Script
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| [[cgo_arrow]] draws an arrow between two picked atoms.
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| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
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|-
 
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! Tips & Tricks
 
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| Instructions for [[Movie_pdf|generating movie PDFs]] using .mpg movies from PyMOL.
 
 
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! Older News
 
! Older News
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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...

Cartoon Helix Settings

==Overview==

This setting sets the style in which cartoon helices are rendered. The default is a helix with an ellipsoid cross section. Fancy mode helices are ribbons with tubular edges à la MolScript. Cylindicial mode renders helices as solid cylinders.

Syntax

To turn on Fancy Helices: 

set cartoon_fancy_helices, 1

To turn on Cylindrical Helices: 

set cartoon_cylindrical_helices, 1

To return to default helices: 

set cartoon_fancy_helices, 0
set cartoon_cylindrical_helices, 0

Result

  • Fancy helix

  • Cylindrical helix

  • Default representation

Change size of default cartoon helix

To change the size of the cartoon helices when not in the fancy helix mode you change the dimensions of the oval that represents the cross section of the default cartoon representation.

Cartoon oval length.png 

set cartoon_oval_length , 0.8 # default is 1.20

and <source lang="python"> set cartoon_oval_width , ..→

A Random PyMOL-generated Cover. See Covers.


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