Difference between revisions of "Main Page"

Latest revision as of 12:54, 12 March 2024

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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...
Color color sets the color of an object or an atom selection to a predefined, named color, an RGB hex color, or a color ramp. For an overview of predefined colors, see Color Values. For a script that enumerates all the colors see, List_Colors. If you want to define your own colors, see Set_Color. Usage color color-name color color-name, object-name color color-name, (selection) Arguments color-name = str or int: named color, index of a named color, `0xRRGGBB` string, `0x40RRGGBB` integer, name of a ramp object, or special value `atomic` object-name = str: Name of an object or name pattern (with Asterisk (`*`)) which matches multiple objects. Changes the object color, and if it is a molecular object, also the color of all atoms. {default: all} selection = str: atom selection, this is any expression which is not a valid object pattern. E.g. an ..→

A Random PyMOL-generated Cover. See Covers.

@@ Line 1: / Line 1: @@
 __NOTOC__
-{| align="center" width="90%"
+{| 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: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 [[Special:Userlogin|join]]. Feel free to add any appropriate content; make an account and [[PyMolWiki:Community_Portal|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''']] -- ''updated!''
-|| [[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]]
-|| [[Gallery|'''Gallery''']] | [[Covers|'''Covers''']]
-|| [[About| '''About PyMOL''']]
-|-
-| ''Track:'' [http://sourceforge.net/tracker/?atid=104546&group_id=4546&func=browse Bugs] [http://sourceforge.net/tracker/?group_id=4546&atid=354546 Feature Req] [http://sourceforge.net/tracker/?group_id=4546&atid=204546 Support Req]
-|-
-|}
-|
 |}
-{| 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 &amp; Updates
 |-
-|valign="top"|
+! Official Release
-{|style="background-color: transparent;" width="100%"
+| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
 |-
-! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Wiki
+! 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;"| &diams; Added links in the table on the Main Page (above) for submitting & tracking bugs and feature reqeuests.
+! Official Release
+| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
 |-
-| style="padding: 3px 5px 10px 15px;"| &diams; New logo for the wiki.  It's DNA.  You can easily see the major/minor grooves.  If you don't see it, force a reload of the page (CTRL-F5, usually).
+! Python 3
+| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
 |-
-| style="padding: 3px 5px 10px 15px;"| &diams; New category about PyMOL [[:Category:Performance|performance]]: making the impossible possible, and the difficult easier/faster.
+! POSF
+| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
 |-
-| style="padding: 3px 5px 10px 15px;"| &diams; Information about PyMOL and [[Stereo_3D_Display_Options|Stereo 3D Displays]].
+! Tutorial
+| [[Plugins Tutorial]] updated for PyQt5
 |-
-| style="padding: 3px 5px 10px 15px;"| &diams; Massively restructured the [[TOPTOC]] and make the [[OLD_TOPTOC]] for the older version.  Still need to add more content to the [[TOPTOC]].
+! 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;"| &diams; Added a simple script for [[removeAlt|removing specific alternately located atoms]].
+! 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;"| &diams; Added a starter gallery of PyMOL-created Journal [[Covers]].
+! 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;"| &diams; Added some information on how PyMOL handles [[Nonstandard_Amino_Acids]].
+! New Script
+| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
 |-
-| style="padding: 3px 5px 10px 15px;"| &diams; Downtime: The PyMOLWiki underwent some downtime due to FS problems.  There are also upgrades planned for this week, so we may expect a little downtime for that.  We've been <b>very</b> fortunate to have hosting from [http://www.bitgnome.net/ BitGnome.Net]; they've done an incredible job!
+! Older News
-|-
+| See [[Older_News|Older News]].
-| style="padding: 3px 5px 10px 15px;"| &diams; [[Gallery]] -- Did you make a [[:Image:Ccp4_map.png|cool image]]?  Pop it into the PyMOLWiki Gallery with the PyMOL command you used.  Looking for a particular representation--start here (new!).
 |}
-|valign="bottom" width="150px" style="padding: 0 20px 20px 0; clear:right;" |[[Image:070920nature.pdf.jpg|125px]] Sample Cover from the [[Covers]] gallery.
+|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...
-|
-{|style="background-color: transparent;" width="100%"
-|-
-|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;" | PyMOL
 |-
-| style="padding: 3px 5px 10px 15px;"| &diams; PyMOL now comes with some builtin examples: look in the '''examples''' directory of your source tree.
+|<div class="didyouknow" >
-|-
+<DynamicPageList>
-| style="padding: 3px 5px 10px 15px;"| &diams; [[group]] command has been added.
+randomcount=1
-|-
+category=Commands|Plugins|Script_Library|Settings
-| style="padding: 3px 5px 10px 15px;"| &diams; The truly awesome [[grid_mode]] setting has been added.
+includepage=*
-|-
+includemaxlength=1050
-| style="padding: 3px 5px 10px 15px;"| &diams; [[Ellipsoids]] representation added for drawing thermal ellipsoids.
+escapelinks=false
-|}
+allowcachedresults=false
-|valign="bottom" width="150px" style="padding: 0 20px 20px 0" |[[Image:Gm1.png|125px]] Screenshot of [[grid_mode|Grid Mode]] in action.
+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; Ever wanted to load all the PDBs in a directory within PyMOL?  Now you can load all files in a dir with [[LoadDir]].
+listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover.  See [[Covers]].]],\n
-|-
+ordermethod=none
-| style="padding: 3px 5px 10px 15px;"| &diams;  [[LigAlign]] -- Ligand-based active site alignment and comparison.
+allowcachedresults=false
-|-
+</DynamicPageList>
-| style="padding: 3px 5px 10px 15px;"| &diams; Added a [[COM|simple script]] for finding the center or mass, or moving a selection to the origin.
-|-
-| style="padding: 3px 5px 10px 15px;"| &diams; [[ImmersiveViz]] -- Headtracking user interface for PyMOL  (watch the video)!
-|-
-| style="padding: 3px 5px 10px 15px;"| &diams; [[Colorama]] --a PyMOL plugin which allows to color objects using adjustable scale bars
-|-
-| 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]].
-|}
 |}

Difference between revisions of "Main Page"

Latest revision as of 12:54, 12 March 2024

Color

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