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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;"
|}


== 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
</DynamicPageList>
</div>
<div style="clear: both;"></div>
|}
|
|style="vertical-align: top; width: 18%"|
<DynamicPageList>
imagecontainer=Covers
randomcount=1
escapelinks=false
openreferences=true
listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover.  See [[Covers]].]],\n
ordermethod=none
allowcachedresults=false
</DynamicPageList>


* 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...
 
We need your help.  So join today & happy editing!
 
[[User:Tree|Tree]]
 
== [[Initial Wiki Layout Suggestion]] == (Warren Delano)
* [[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]]
* [[Arbitrary Graphics Objects]]
* [[Python Integration]]
* [[Scenes]]
 
== [[User Additions]] ==
* [[Installation]] ([[User:Tree|Tree]])
** [[Hardware Requirements]]
** [[Software Requirements]]
** [[OS Dependent]]
*** [[Linux]]
*** [[MAC]]
*** [[Windows]]
*** [[Script Library]]
 
* [[NMR Applications]] (Doug Kojetin)
* [[Plugins/Modules]] (Doug Kojetin)
** [[APBS Plugin]]
 
* [[Plugins]] (Michael George Werner)
** [[List of Plugins]]
** [[Tutorial on writing plugins]]
** [[Others]]
 
* [[Structure Alignment]] (Nat Echols)
** [[Structure Alignment Editor]]
* [[3rd Party Applications]]
** [[Movies]]
** [[Codecs]]
 
* [[Displaying biochemical properties]] (Kristian Rother)
* [[Coloring molecules]]
* [[Rendering molecules]]
** [["basics of displaying molecules".]]
** [["displaying basic chemical properties", like double bonds, h-bonds, bond angles and b-factors.]]
* [[Modeling and editing structures. ]]
* [[How to do electrostatics and energy minimization.]]
* [[Launching PyMOL (has been asked often)]]
* [[Some kind of "script collection" would be very useful.]]
 
----
[[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...

Depth cue

== Overview ==

One can adjust the fog that PyMol overlays on objects in the viewer window. This fog helps to assist in emphasizing what is in the foreground and backgound of the image with respect to the camera.

In mouse mode, 3-Button Viewing:

Rear clipping plane- hold down the shift key and the right mouse button and drag the mouse to the right, more fog will be added to the background. Drag to the left and more fog will be removed from the background.

Front clipping plane- hold down the shift key and the right mouse button and drag the mouse toward you. You should see the clipping plane come into view. Adjust the front and rear clipping plane to focus on the area of the molecule you wish to display.

Syntax

set depth_cue, 1  # turn on depth cueing
set depth_cue, 0  # turn off depth cueing
set fog_start, 0.45 #use a number between 0.01 and 0.99 to adjust where the fog will start in the plane of view. Default is 0.45

Example

..→
A Random PyMOL-generated Cover. See Covers.


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