Main Page: Difference between revisions

From PyMOLWiki
Jump to navigation Jump to search
No edit summary
(PyMOL 3.0 release)
 
(264 intermediate revisions by 25 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]]'''
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
||'''[[PyMOL_mailing_list|Getting Help]]'''
|}
|}
{| align="right" width="75%" style="border: 1px solid #333; text-align:left;"
 
! colspan="3" style="font-weight: bold; font-size:120%; color: #333; background:#80AFFF; text-align:center" | Quick Links
{| width="100%"
| 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
|-
|-
| [[TOPTOC|'''Table of Contents''']]
! Official Release
|| [[Special:Allpages|Index of all pages]]
| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
|| [http://pymol.sf.net PyMOL] Homepage
|-
|-
| [[Practical_Pymol_for_Beginners|Beginner's Tutorial]]
! New Plugin
|| [[:Category:Commands|PyMol Commands]]
| [[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
|| '''Settings''': [[Settings|All]] [[:Category:Settings|Documented]]
|-
|-
| [[:Category:Script_Library|'''Script Library''']]
! Official Release
|| [[:Category:Plugins|'''Plugins''']]
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
|| [[:Special:Categories| See All Categories]]
|-
|-
| [[:Category:FAQ|Frequently Asked Questions]]
! Python 3
|| [[PyMolWiki:Community_Portal|'''How to get involved!''']]
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
|| [[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"
|+ 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="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Wiki
|-
| style="padding: 3px 5px 10px 15px;"| ♦ Adding a special category/section for active PyMOL [[:Category:Development|Development]].
|-
| style="padding: 3px 5px 10px 15px;"| ♦ Rather large changes to the style of the main page.  Hopefully this will transition into something more pleasing.
|-
| style="padding: 3px 5px 10px 15px;"| ♦ We need experienced PyMOL users to link pages to their respective categories and make new categories.  Some new categories that need to be filled: [[:Category:Settings]], [[:Category:Publication_Quality]], [[:Category:Image_Manipulation]], [[:Category:Nucleic_Acids]].  We also need a category -- or categories -- on biochemical analysis and other useful things we do in PyMOL.  This will help people expand their knowledge (by being able to see related issues), and make it easier for the power users to find what they need.  The editing is '''very simple''' -- all you do is add a category tag(s) at the end of the pages.
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦  We also need folks to link to the pages in the [[Special:Lonelypages|Orphaned Pages]].  These pages are only found by direct searching, so we should change that to help make this more usable.
! POSF
| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
|-
|-
|
! Tutorial
{|style="background-color: transparent;" width="100%"
| [[Plugins Tutorial]] updated for PyQt5
|-
|-
|valign="top"|
! New Plugin
{|style="background-color: transparent;" width="100%"
| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
|-
|-
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | PyMOL
! 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="top" width="150px" style="padding: 0 20px 20px 0" |[[Image:Ell2.png|125px]] Screenshot of thermal [[Ellipsoids]].
|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; [[Colorama]] --a PyMOL plugin which allows to color objects using adjustable scale bars
listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated CoverSee [[Covers]].]],\n
|-
ordermethod=none
| style="padding: 3px 5px 10px 15px;"| &diams; [http://ase-web.rit.edu/~ez-viz/ProMOL_dl.html ProMOL] plugin addedCatalytic site prediction, other tools.  Redirects to website.
allowcachedresults=false
|-
</DynamicPageList>
| 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 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...

Ramp New

ramp_new creates a color ramp based on a map potential value or based on proximity to a molecular object.

Usage

ramp_new name, map_name [, range [, color [, state [, selection [,
       beyond [, within [, sigma [, zero ]]]]]]]]
  • name = string: name of the ramp object to create
  • map_name = string: name of the map (for potential) or molecular object (for proximity)
  • range = list: values corresponding to slots in the ramp {default: [-1, 0, 1]}
  • color = list or str: colors corresponding to slots in the ramp or a given palette name: afmhot, grayscale, object, rainbow, traditional, grayable, hot, ocean, and sludge {default: [red, white, blue]}
  • state = integer: state identifier {default: 1}
  • selection = selection: for automatic ranging (maps only) {default: }
  • with automatic ranging only:
    • beyond = number: are we excluding values beyond a certain distance from the selection? {default: 2.0}
    • within = number: are we only including valuess within a certain distance from the ..→
A Random PyMOL-generated Cover. See Covers.