Difference between revisions of "Main Page"

From PyMOLWiki
Jump to navigation Jump to search
(PyMOL 3.0 release)
 
(147 intermediate revisions by 20 users not shown)
Line 1: Line 1:
 
__NOTOC__
 
__NOTOC__
−
 
+
{| 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;"
−
{| align="center" style="padding-bottom: 4em;"
+
|+ 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="font-size:210%; font-weight: bold; color:#032d45; text-align:center; padding: 5px; margin-bottom: 7px" | Welcome to the PyMOL Wiki!
+
|}
−
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
+
{| 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.
 
| 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: #EDEBD5; margin-bottom: 4em; border-bottom: 1px solid #AFB29E; border-left: 1px solid #AFB29E; border-right: 1px solid #AFB29E;"
+
{| 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;"
−
|+ style="font-size: 1.4em; font-weight: bold; color: #032d45; text-align:center; background: #5F7F96; padding-top:0.5em; padding-bottom: 0.25em; border-top: 2px solid #AFB29E; border-bottom: 1px solid #fff;" |Quick Links
+
|+ 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; color #61021F; 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:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''
 
|-
 
|-
−
| 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]]'''
+
| 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; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''
+
| 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]]'')
 
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
−
||'''[[GoogleSearch]]'''
+
||'''[[PyMOL_mailing_list|Getting Help]]'''
 
|}
 
|}
−
 
  
 
{| width="100%"
 
{| width="100%"
Line 25: Line 29:
 
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
 
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
 
|-
 
|-
−
! Warren
+
! Official Release
−
| News about Warren DeLano's passing may be read on [[Warren|Warren's memorial page]].
+
| [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
 
|-
 
|-
−
! PyMOLWiki
+
! POSF
−
| Reformatted Main Page. Some delays might occur from resizing images, but that should go away once the images are cached.
+
| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
 
|-
 
|-
−
! PyMOLWiki
+
! Tutorial
−
| New — Search the PyMOLWiki via [[GoogleSearch]]
+
| [[Plugins Tutorial]] updated for PyQt5
 
|-
 
|-
−
! PyMOL
+
! New Plugin
−
| PyMOL is known to work under Mac OS X 10+ (Snow Leopard) using the new Fink and incentive builds.  See [[MAC_Install#PyMOL_Install_from_Source.2C_Using_Fink|Installing PyMOL under Fink]].
+
| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
 
|-
 
|-
−
! PyMOL
+
! Selection keywords
−
| PyMOL now has a [[Set]] command for basic settings, and a [[Set_bond]] command for bond-only settings.
+
| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
 
|-
 
|-
−
! PyMOL
+
! Plugin Update
−
| [[Space]]— new command to control PyMOL's usage of color spaces.
+
| [[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%"|
 
|style="vertical-align: top; width: 40%"|
 
{| class="jtable" style="float: right; width: 90%"
 
{| class="jtable" style="float: right; width: 90%"
−
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Do you know this PyMOL command...
+
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...
 
|-
 
|-
 
|<div class="didyouknow" >
 
|<div class="didyouknow" >
−
<dpl>
+
<DynamicPageList>
−
namespace=
+
randomcount=1
−
category=Commands
+
category=Commands|Plugins|Script_Library|Settings
 
includepage=*
 
includepage=*
−
includemaxlength=300
+
includemaxlength=1050
 
escapelinks=false
 
escapelinks=false
 +
allowcachedresults=false
 
resultsheader=__NOTOC__ __NOEDITSECTION__
 
resultsheader=__NOTOC__ __NOEDITSECTION__
−
randomcount=1
 
−
mode=userformat
 
−
addpagecounter=true
 
 
listseparators=,<h3>[[%PAGE%]]</h3>,,\n
 
listseparators=,<h3>[[%PAGE%]]</h3>,,\n
−
</dpl>
+
</DynamicPageList>
 
</div>
 
</div>
 
<div style="clear: both;"></div>
 
<div style="clear: both;"></div>
Line 65: Line 82:
 
|
 
|
 
|style="vertical-align: top; width: 18%"|
 
|style="vertical-align: top; width: 18%"|
−
<dpl>
+
<DynamicPageList>
 
imagecontainer=Covers
 
imagecontainer=Covers
 
randomcount=1
 
randomcount=1
 
escapelinks=false
 
escapelinks=false
 
openreferences=true
 
openreferences=true
−
listseparators=[[,%PAGE%,|185px|A Random PyMOL-generated Cover.  See [[Covers]].]],Random PyMOL-generated Journal Cover\n
+
listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover.  See [[Covers]].]],\n
−
</dpl>
+
ordermethod=none
 +
allowcachedresults=false
 +
</DynamicPageList>
  
 
|}
 
|}

Latest revision as of 12:54, 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...

3Dstrut

{|class = infobox

|- !Type |Plugin |- !Download |https://github.com/raghuyennamalli/3Dstrut |- !Author |Tony Kamenick, Stuart Ballard |- !Other authors |George N Phillips Jr. |- !Other contributors |Shashank Ravichandran, Yatindrapravanan Narasimhan, Gautham Krishna, Ragothaman Yennamalli |}

3Dstrut is an external plugin for the molecular visualization program PyMOL. The plugin generates struts at optimal positions and thus enables 3D printing of any structure which can be visualized using PyMOL. This software is distributed freely for Windows and MacOS platforms.

Website

https://github.com/raghuyennamalli/3Dstrut

Version history

Version 2.0

Installation

The following steps are applicable to both windows and MacOS systems

I. Download the ‘.zip’ file and save it in your home directory. Once you unzip the file, you should see a directory named ‘3D_strut_plugin’ containing three files: 

   __init__.py, struts.py, build_struts.py


II. Open PyMOL and go to Plugin → Plugin ..→

A Random PyMOL-generated Cover. See Covers.


Retrieved from "http://pymolwiki.org/index.php?title=Main_Page&oldid=13571"