Main Page: Difference between revisions

From PyMOLWiki
Jump to navigation Jump to search
No edit summary
No edit summary
 
(254 intermediate revisions by 26 users not shown)
Line 1: Line 1:
__NOTOC__
__NOTOC__
{| align="center"
{| 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="width: 90%; font-size:190%; font-weight: bold; color:#038; text-align:center; padding: 5px; margin-bottom: 15px" | Welcome to the PyMOL Wiki
|+ 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/]]
|- style="text-align:center; font-weight:bold; color: #333; font-size: 120%"
|}
| We are the community-based support site for the popular molecular visualization program, [http://pymol.sf.net PyMOL].
{| 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;"
|}
|}


 
{| 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;"
{| align="center" style="width:90%; margin-bottom: 20px"
|+ 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
|
|-
{| align="left" width="20%" style="border: 1px solid #333; text-align:center; height=100%;"
| 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-weight: bold; font-size:120%; color: #333; background:#80AFFF;" | New Users
|-
|-
| style="background:#E6EFFF; color:#333; font-size: 110%; padding: 4.5px"| New users are encouraged to join. Feel free to add any appropriate content; make an account and get started!
| 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]]'''
{| align="right" width="75%" style="border: 1px solid #333; text-align:left;"
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
! colspan="3" style="font-weight: bold; font-size:120%; color: #333; background:#80AFFF; text-align:center" | Quick Links
||'''[[PyMOL_mailing_list|Getting Help]]'''
|-
| [[TOPTOC|'''Table of Contents''']]
|| [[Special:Allpages|Index of all pages]]
|| '''PyMOL Cheat Sheet: [[Media:PymolRef.pdf|PDF]] [[CheatSheet|Wiki Page]]
|-
| [[:Category:Tutorials|Tutorials]]
|| [[:Category:Commands|Commands]]
|| '''Settings''': [[Settings|All]] [[:Category:Settings|Documented]]
|-
| [[:Category:Script_Library|'''Script Library''']]
|| [[:Category:Plugins|'''Plugins''']]
|| [[:Special:Categories| See All Categories]]
|-
| [[:Category:FAQ|Frequently Asked Questions]]
|| [[PyMolWiki:Community_Portal|'''How to get involved!''']]
|| [[About| '''About PyMOL''']]
|-
|}
|
|}
|}


{| align="center" width="90%" style="background: #fafafa; border-right: 1px solid #333; border-left: 1px solid #333; border-bottom: 1px solid #333"
{| width="100%"
|+ style="text-align: left; font-weight:bold; font-size:150%; color:#333; background: #EFE6FF; padding:10px; border: 1px solid #333" | News and Updates ([[Older_News|archive]])
| style="vertical-align: top; width: 40%" |
|
{| class="jtable" style="float: left; width: 90%;"
{|style="background-color: transparent;" width="100%"
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
|-
|valign="top"|
{|style="background-color: transparent;" width="100%"
|-
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Wiki
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ [[CheatSheet|PyMOL Cheat Sheet]] (reference card) has been donated. It's also posted in the table above for quick access.
! New Setup
| [https://github.com/kullik01/pymol-open-source-windows-setup/releases/tag/v3.1.0 PyMOL-open-source-windows-setup v3.1] has been released on January 20, 2025. More information under [[Windows Install]].
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ [[Gsoc2008|Google Summer of Code 2008 for PyMOL]] has been created.
! New Plugin
| [[PySSA]] aims to combine PyMOL and [https://github.com/sokrypton/ColabFold ColabFold] to enable the prediction and analysis of 3D protein structures for the scientific end-user. [https://github.com/urban233/PySSA/releases/tag/v1.0.1 v1.0 has been released] on July 10, 2024.
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ Added a special category/section for active PyMOL [[:Category:Tutorials|Tutorials]].  These are pages not just with information, but easy to understand, step-by-step pages from which to learn.
! Official Release
| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ Updated the wiki. Also installed the newer GeSHI extension. Please keep an eye out for source code that is improperly tagged and so improperly formatted.  See [http://www.mediawiki.org/wiki/Extension:SyntaxHighlight_GeSHi#Parameters GeSHI Parameters].
! 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
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ Adding a special category/section for active PyMOL [[:Category:Development|Development]].
! Official Release
|}
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
|valign="bottom" width="150px" style="padding: 0 20px 20px 0" |[[Image:refcard.png|155px]] Screenshot of the donated PyMOL reference card.
|}
|-
|-
|
! Python 3
{|style="background-color: transparent;" width="100%"
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
|-
|-
|valign="top"|
! POSF
{|style="background-color: transparent;" width="100%"
| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
|-
|-
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | PyMOL
! Tutorial
| [[Plugins Tutorial]] updated for PyQt5
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ [[group]] command has been added.
! New Plugin
| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ The truly awesome [[grid_mode]] setting has been added.
! Selection keywords
| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ [[Ellipsoids]] representation added for drawing thermal ellipsoids.
! 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
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ PyMOL 1.0 has been released!
! New Script
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ [http://delsci.info/dsc/ PyMOL Official Documentation] is also available for subscribers.
! Older News
| See [[Older_News|Older News]].
|}
|}
|valign="bottom" width="150px" style="padding: 0 20px 20px 0" |[[Image:Gm1.png|155px]] Screenshot of [[grid_mode|Grid Mode]] in action.
|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="background-color: transparent;" width="100%"
|style="vertical-align: top; width: 18%"|
|-
<DynamicPageList>
|valign="top"|
imagecontainer=Covers
{|style="background-color: transparent;" width="100%"
randomcount=1
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Scripts &amp; Plugins
escapelinks=false
|-
openreferences=true
| style="padding: 3px 5px 10px 15px;"| &diams; [[ImmersiveViz]] -- Headtracking user interface for PyMOL  (watch the video)!
listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover.  See [[Covers]].]],\n
|-
ordermethod=none
| style="padding: 3px 5px 10px 15px;"| &diams; [[Colorama]] --a PyMOL plugin which allows to color objects using adjustable scale bars
allowcachedresults=false
|-
</DynamicPageList>
| style="padding: 3px 5px 10px 15px;"| &diams; [http://ase-web.rit.edu/~ez-viz/ProMOL_dl.html ProMOL] plugin added.  Catalytic site prediction, other tools.  Redirects to website.
 
|-
| style="padding: 3px 5px 10px 15px;"| &diams; [[EMovie]] plugin added.  Easy movies in PyMol using a GUI.
|-
| style="padding: 3px 5px 10px 15px;"| &diams; [[DYNMAP]] plugin page created.  Check it out!
|-
| style="padding: 3px 5px 10px 15px;"| &diams; [[EZ-Viz]]
|}
|width="150px" style="padding: 0 20px 20px 0; text-align:left" |[[Image:COLORAMA-screenshot.jpg|125px]] Screenshot of [[Colorama]].
|}
|}
|}

Latest revision as of 13:01, 21 January 2025

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
New Setup PyMOL-open-source-windows-setup v3.1 has been released on January 20, 2025. More information under Windows Install.
New Plugin PySSA aims to combine PyMOL and ColabFold to enable the prediction and analysis of 3D protein structures for the scientific end-user. v1.0 has been released on July 10, 2024.
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...

Light

= Overview =

Lighting is important for high-quality shots. PyMOL supports of up to 10 virtual lights. You can turn the lights on/off and also position them where you want (behind the camera).

Light2..Light9 control where the other lights go.

  • Normal lighting

    Normal lighting

  • Light1 moved a bit. Notice how the shadows have changed.

    Light1 moved a bit. Notice how the shadows have changed.

Syntax

# set the light to some position.  The 'position'
# must be a vector specifying the XYZ location
# to put the light.
set light, position

# for example
set light, [ -0.55, -0.70, 0.15 ]

User Hint

  • Moving lights make for a cool effect; you can make this look better by smoothing out the distances and ranges.

    Moving lights make for a cool effect; you can make this look better by smoothing out the distances and ranges.

:

One neat trick, for rendering a "sunset" on your protein is to turn off all the lights, then render the scene as you move the light across the scene. The shadows move across the protein based on the light position and it looks like the sun is setting.


The Code

Here's the code for ..→

A Random PyMOL-generated Cover. See Covers.


Retrieved from "https://pymolwiki.org/index.php?title=Main_Page&oldid=13837"