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== PyMol Wiki Home ==
__NOTOC__
You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.
{| align="center" width="100%" style="background: #B22222; margin-bottom: 4em; border-bottom: 1px solid #B22222; border-left: 1px solid #B22222; border-right: 1px solid #B22222;"
|+ style="font-size: 1.0em; font-weight: normal; color: #FFFFFF; text-align:right; background: #B22222; padding-top:0.5em; padding-bottom: 0.25em; padding-right: 0.60em; border-top: 2px solid #B22222; border-bottom: 1px solid #fff;" |hosted by [[File:SBGridlogo2.jpg|140 px|link=https://sbgrid.org/]]
|}
{| align="center" style="padding-bottom: 3em;"
|+ style="font-size:210%; font-weight: bold; color:#000000; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!
|- 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.
|- style="text-align:center; font-weight:normal; color: #000000; font-size: 120%; font-family: sans-serif;"
| To request a new account, email SBGrid at:  accounts (@) sbgrid dot org
|- style="text-align:center; font-weight:bold; color: #000000; font-size: 120%; font-family: sans-serif;"
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== Moving In ==
{| 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;"
Please excuse the mess as we create the PyMolWiki site. The wiki will be a valuable educational & reference tool for PyMol users.
|+ style="font-size: 1.4em; font-weight: bold; color: #FFFFFF; text-align:center; background: #000000; padding-top:0.5em; padding-bottom: 0.25em; border-top: 2px solid #000000; border-bottom: 1px solid #fff;" |Quick Links
|-
| 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]]'''
|-
| 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]]'''
|-
| style="font-size: 1.1em; font-weight: normal; color #48A2B4; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
||'''[[PyMOL_mailing_list|Getting Help]]'''
|}


== Helping ==
{| width="100%"
If you feel like helping out, please login and get to work. :-) For design/layout purposes you must be logged in to edit pages.  We now need people to assist with
| style="vertical-align: top; width: 40%" |
{| class="jtable" style="float: left; width: 90%;"
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
|-
! Official Release
| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
|-
! New Plugin
| [[CavitOmiX|CavitOmiX]] calculate [https://innophore.com Catalophore™ cavities], predict protein structures with [https://www.nvidia.com/en-us/gpu-cloud/bionemo OpenFold by NVIDIA-BioNeMo], [https://ai.facebook.com/blog/protein-folding-esmfold-metagenomics/ ESMFold] and retrieve [https://www.deepmind.com/research/highlighted-research/alphafold Alphafold] models
|-
! Official Release
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
|-
! Python 3
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
|-
! POSF
| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
|-
! Tutorial
| [[Plugins Tutorial]] updated for PyQt5
|-
! New Plugin
| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
|-
! Selection keywords
| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
|-
! Plugin Update
| [[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
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
|-
! Older News
| See [[Older_News|Older News]].
|}
|style="vertical-align: top; width: 40%"|
{| class="jtable" style="float: right; width: 90%"
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...
|-
|<div class="didyouknow" >
<DynamicPageList>
randomcount=1
category=Commands|Plugins|Script_Library|Settings
includepage=*
includemaxlength=1050
escapelinks=false
allowcachedresults=false
resultsheader=__NOTOC__ __NOEDITSECTION__
listseparators=,<h3>[[%PAGE%]]</h3>,,\n
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<div style="clear: both;"></div>
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|
|style="vertical-align: top; width: 18%"|
<DynamicPageList>
imagecontainer=Covers
randomcount=1
escapelinks=false
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listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover.  See [[Covers]].]],\n
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* Wiki schema/design/organization: Below you'll find the current layout design
|}
* Graphic design and CSS layout: We need logos, BG images and CSS layout
* Importing the email list content:  We have (lots) of email to sift through, extract data from and import into the Wiki
* Smoothing out the edges:  Editors are needed just to fix our typos!
* Etc...
 
=== Editors Needed ===
If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].
 
We need your help.  So join today & happy editing!
 
[[User:Tree|Tree]]
 
== [[Initial Wiki Layout Suggestion]] == (Warren Delano; [[User:Tree|Tree]]; Doug Kojetin; Michael George Werner; Kristian Rother; Nat Echols)
* [[Mouse Controls]]
* [[Command Language]]
* [[Atom Selections]]
* [[Ray-tracing]]
* [[Movies and Animations]]
* [[Cartoon Representations]]
* [[Settings Reference (all settings and what they do)]]
* [[Stereo 3D Display]]
** [[Hardware Options]]
** [[Linux XFree86 Configuration]]
* [[Crystallography Applications]]
** [[Symmetry]]
** [[Electron Density]]
* [[NMR Applications]]
** [[Working with a Family of Structures]]
** [[Superimposition and RMSD]]
** [[NMR Restraints Analysis]]
* [[Arbitrary Graphics Objects]]
* [[Python Integration]]
* [[Scenes]]
 
* [[Installation]]
** [[Hardware Requirements]]
** [[Software Requirements]]
** [[OS Dependent]]
*** [[Linux]]
*** [[MAC]]
*** [[Windows]]
*** [[Script Library]]
 
* [[Plugins/Modules]]
** [[APBS Plugin]]
** [[rtools Plugin]]
 
* [[Plugins]]
** [[List of Plugins]]
** [[Tutorial on writing plugins]]
** [[Others]]
 
* [[Structure Alignment]]
** [[Structure Alignment Editor]]
* [[3rd Party Applications]]
** [[Movies]]
** [[Codecs]]
 
* [[Rendering molecules]]
** [[Basics of displaying molecules]]
** [[Coloring molecules]]
** [[Displaying biochemical properties]]
 
* [[Modeling and editing structures. ]]
** [[Editing atoms]]
** [[Molecular sculpting]]
** [[Homology modeling]]
* [[How to do electrostatics and energy minimization.]]
* [[Launching PyMOL (has been asked often)]]
* [[Some kind of "script collection" would be very useful]]
* [[Creating publication-quality images HOWTO]]
 
== [[Proposal for structure]] ==
Most of these points fall into some higher category. Here is a proposal how they could be arranged:
* I. Technical issues (installation, hardware)
* II. Basic usage (controls, rendering, selections)
* III. Advanced issues (Ray tracing, settings, movies)
* IV. Scripting
* V. Plugins
* VI. High-level applications (Crystallography, NMR)
 
----
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
----

Latest revision as of 11:54, 12 March 2024

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 v3.0 has been released on March 12, 2024.
New Plugin CavitOmiX calculate Catalophore™ cavities, predict protein structures with OpenFold by NVIDIA-BioNeMo, ESMFold and retrieve Alphafold models
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 fellowship announced for 2022-2023
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...

Get area

get_area calculates the surface area in square Angstroms of the selection given. Note that the accessibility is assessed in the context of the object(s) that the selection is part of. So, to get the surface areas of e.g. a component of a complex, you should make a new object containing a copy of just that component and calculate its area.

The "get_area selection" command will return the effective surface area of the dots that you would see from "show dots, selection". This is a discrete approximation -- not an exact calculation.

Attention: Atoms with the "ignore" flag may lead to unexpected results. Clear the "ignore" flag first or exclude those atoms from the calculation. Fixed in PyMOL 2.5, ignored atoms are now excluded. Previously, their entire sphere surface was added to the surface area.

Usage

get_area [ selection [, state [, load_b ]]]

== Arguments ..→

A Random PyMOL-generated Cover. See Covers.


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