Main Page: Difference between revisions

From PyMOLWiki
Jump to navigation Jump to search
No edit summary
(PyMOL 3.0 release)
 
(199 intermediate revisions by 22 users not shown)
Line 1: Line 1:
__NOTOC__
__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="width:90%; margin-bottom: 20px"
{| 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!
{| align="left" width="20%" style="border: 1px solid #333; text-align:center; height=100%;"
|- style="text-align:center; font-weight: normal; color: #000000; font-size: 120%; font-family: sans-serif;"
! style="font-weight: bold; font-size:120%; color: #333; background:#80AFFF;" | New Users
| 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;"
| 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]]!
| 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="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
{| 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: #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]]'''
|-
|-
| [[TOPTOC|'''Table of Contents''']] -- ''updated!''
| 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]]'''
|| [[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]
|-
|-
| 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]]'''
|}
|}


{| 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
|-
|-
{| align="center"
! Official Release
|
| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
==[http://www.surveymonkey.com/s.aspx?sm=NPHgdFVCWobsztKtjr5s5g_3d_3d Take the PyMOLWiki Survey! (click here)]==
|}
 
|
|}
{| 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="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
! 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;"| ♦ '''PyMOL now integrates seamlessly with MS Powerpoint. See [[Axpymol]].'''
! Official Release
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ PyMOL now comes with some builtin examples: look in the '''examples''' directory of your source tree.
! Python 3
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ [[group]] command has been added.
! POSF
| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ The truly awesome [[grid_mode]] setting has been added.
! Tutorial
| [[Plugins Tutorial]] updated for PyQt5
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ [[Ellipsoids]] representation added for drawing thermal ellipsoids.
! New Plugin
|}
| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
|valign="bottom" width="150px" style="padding: 0 20px 20px 0" |[[Image:Caver.png|125px]] Screenshot of [[Caver]] showing cavities.
|}
|-
|-
|
! Selection keywords
{|style="background-color: transparent;" width="100%"
| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
|-
|-
|valign="top"|
! Plugin Update
{|style="background-color: transparent;" width="100%"
| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.5]] is an updated version of channel analysis software in PyMOL
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Scripts & Plugins
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ [[Modevectors]] — creates arrow plots for normal mode analysis (NMA), NMR ensembles and other cases where you want to point out differences between similar objects.
! New Script
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ [[Pucker]] — finds the sugar pucker information (phase, amplitude, pucker) for a given selection.
! Older News
|-
| See [[Older_News|Older News]].
| style="padding: 3px 5px 10px 15px;"| ♦ [[GetNamesInSel]] — find the names of all objects in a selection.
|-
| style="padding: 3px 5px 10px 15px;"| ♦ [[CalcArea]] — find the area of any given object/selection;
|-
| style="padding: 3px 5px 10px 15px;"| ♦ [[ConnectedCloud]] — find connected clouds of objects in PyMOL.
|-
| style="padding: 3px 5px 10px 15px;"| ♦ [[MakeVinaCommand]] — Use PyMOL to create a valid command line for the new [http://vina.scripps.edu Vina] docking software.
|-
| style="padding: 3px 5px 10px 15px;"| ♦ [[DrawBoundingBox]] — Draw a bounding box around your selection.
|-
| style="padding: 3px 5px 10px 15px;"| ♦ Locate loaded PyMOL objects that are nearby some other object with [[FindObjectsNearby]].
|-
| style="padding: 3px 5px 10px 15px;"| ♦ Ever wanted to load all the PDBs in a directory within PyMOL?  Now you can load all files in a dir with [[LoadDir]].
|-
| style="padding: 3px 5px 10px 15px;"| ♦  [[PDB Web Services Script]] — Example using PyMOL and the PDB Web Services.
|-
| style="padding: 3px 5px 10px 15px;"| ♦  [[LigAlign]] — Ligand-based active site alignment and comparison.
|-
| style="padding: 3px 5px 10px 15px;"| ♦ Added a [[COM|simple script]] for finding the center or mass, or moving a selection to the origin.
|}
|}
|width="150px" style="padding: 0 20px 20px 0; text-align:left" |[[Image:DrawMinBB.png|165px]] Screenshot of [[DrawBoundingBox]] in action.
|style="vertical-align: top; width: 40%"|
|}
{| class="jtable" style="float: right; width: 90%"
{|style="background-color: transparent;" width="100%"
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...
|-
|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;"| &diams; The Wiki experienced a few moments of downtime due to system maintenance. The downtime was <10 minutes.
|-
| style="padding: 3px 5px 10px 15px;"| &diams; '''Please note the "Go" and "Search" buttons in the search bar.  They're not the same, and entering text and hitting ENTER is the same as using the "Go" button.'''  Please try using the "Search" button; we're using a new search engine and it has cool new features.
|-
| style="padding: 3px 5px 10px 15px;"| &diams; Documented a few more settings.  Also, check out the cool, [[Huge_surfaces]] page for handling very large objects and representing them as surfaces, in PyMOL.
|-
| style="padding: 3px 5px 10px 15px;"| &diams; We got our '''2,000,000th''' page view!
|-
| style="padding: 3px 5px 10px 15px;"| &diams; Added links in the table on the Main Page (above) for submitting & tracking bugs and feature reqeuests.
|-
|-
| 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).
|<div class="didyouknow" >
|-
<DynamicPageList>
| style="padding: 3px 5px 10px 15px;"| &diams; New category about PyMOL [[:Category:Performance|performance]]: making the impossible possible, and the difficult easier/faster.
randomcount=1
|}
category=Commands|Plugins|Script_Library|Settings
|valign="bottom" width="150px" style="padding: 0 20px 20px 0; clear:right;" |[[Image:080701_h.a.steinberg_biochemie.jpg|125px]] Sample Cover from the [[Covers]] gallery.
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>
|}
|}

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...

DynoPlot

Type PyMOL Plugin
Download plugins/dynoplot.py
Author(s) Dan Kulp
License -
This code has been put under version control in the project Pymol-script-repo

Introduction

This script was setup to do generic plotting, that is given a set of data and axis labels it would create a plot. Initially, I had it setup to draw the plot directly in the PyMol window (allowing for both 2D and 3D style plots), but because I couldn't figure out how to billboard CGO objects (Warren told me at the time that it couldn't be done) I took a different approach. The plot now exists in it's own window and can only do 2D plots. It is however interactive. I only have here a Rama.(phi,psi) plot, but the code can be easily extended to other types of data. For instance, I had this working for an energy vs distance data that I had generated by another script.

This script will create a Phi vs Psi(Ramachandran) plot of the selection given. The plot will display data points which can be dragged around Phi,Psi space with the corresponding residue's Phi,Psi angles changing in the ..→

A Random PyMOL-generated Cover. See Covers.


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