Main Page: Difference between revisions

From PyMOLWiki
Jump to navigation Jump to search
No edit summary
(PyMOL 3.0 release)
 
(233 intermediate revisions by 24 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="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]]'''
||'''[[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%" |
| [[TOPTOC|'''Table of Contents''']]
{| class="jtable" style="float: left; width: 90%;"
|| [[Special:Allpages|Index of all pages]]
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
|| '''PyMOL Cheat Sheet: [[Media:PymolRef.pdf|PDF]] | [[CheatSheet|Wiki Page]]
|-
|-
| [[:Category:Tutorials|Tutorials]]
! Official Release
|| [[:Category:Commands|Commands]]
| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
|| '''Settings''': [[Settings|All]]  | [[:Category:Settings|Documented]]
|-
|-
| [[:Category:Script_Library|'''Script Library''']]
! New Plugin
|| [[:Category:Plugins|'''Plugins''']]
| [[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
|| [[:Special:Categories| See All Categories]]
|-
|-
| [[:Category:FAQ|Frequently Asked Questions]]
! Official Release
|| [[Gallery|'''Gallery''']] | [[Covers|'''Covers''']]
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
|| [[About| '''About PyMOL''']]
|-
|-
|}
! Python 3
|
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
|}
 
{| 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"|
! 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;" | Wiki
! Tutorial
| [[Plugins Tutorial]] updated for PyQt5
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ Added a simple script for [[removeAlt|removing specific alternately located atoms]].
! 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;"| ♦ Added a starter gallery of PyMOL-created Journal [[Covers]].
! 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;"| ♦ Added some information on how PyMOL handles [[Nonstandard_Amino_Acids]].
! 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; 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!
! New Script
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
|-
|-
| 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!).
! Older News
|}
| See [[Older_News|Older News]].
|valign="bottom" width="150px" style="padding: 0 20px 20px 0; clear:right;" |[[Image:070920nature.pdf.jpg|155px]] 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...
|-
|-
|
|<div class="didyouknow" >
{|style="background-color: transparent;" width="100%"
<DynamicPageList>
|-
randomcount=1
|valign="top"|
category=Commands|Plugins|Script_Library|Settings
{|style="background-color: transparent;" width="100%"
includepage=*
|-
includemaxlength=1050
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | PyMOL
escapelinks=false
|-
allowcachedresults=false
| style="padding: 3px 5px 10px 15px;"| &diams; PyMOL now comes with some builtin examples: look in the '''examples''' directory of your source tree.
resultsheader=__NOTOC__ __NOEDITSECTION__
|-
listseparators=,<h3>[[%PAGE%]]</h3>,,\n
| style="padding: 3px 5px 10px 15px;"| &diams; [[group]] command has been added.
</DynamicPageList>
|-
</div>
| style="padding: 3px 5px 10px 15px;"| &diams; The truly awesome [[grid_mode]] setting has been added.
<div style="clear: both;"></div>
|-
| style="padding: 3px 5px 10px 15px;"| &diams; [[Ellipsoids]] representation added for drawing thermal ellipsoids.
|}
|valign="bottom" width="150px" style="padding: 0 20px 20px 0" |[[Image:Gm1.png|125px]] Screenshot of [[grid_mode|Grid Mode]] in action.
|}
|}
|-
|
|
{|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; Added a [[COM|simple script]] for finding the center or mass, or moving a selection to the origin.
listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover.  See [[Covers]].]],\n
|-
ordermethod=none
| style="padding: 3px 5px 10px 15px;"| &diams; [[ImmersiveViz]] -- Headtracking user interface for PyMOL  (watch the video)!
allowcachedresults=false
|-
</DynamicPageList>
| 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]].
|}
|}
|}

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...

FilterByMol

== Overview ==

This script filters through all the PDBs in the parent dir (you can easily the the directory it scans). For each molecule, it saves just the ligands/heteroatoms (excluding the waters). This gives you a simple way to filter through a database of proteins looking only at their ligands.

This script, as noted below, works on the objects at the level of a molecule. While we can iterate over atom number (ID), residue number (resi), etc we do not have any such "MOLID". So, we provide this simple workaround. You might need this file because if you have a residue (like #111 from 3BEP) that consists of a molecule and an atom then there's no other way to save the separate pieces (of molecule/atom) into two (or more files). As you can see in the following listing, if we iterate over the hetero atoms (and not waters) in 3BEP we get, <source lang="python"> PyMOL>iterate bymol het, print resi, resn, ID, chain, segi, alt 111 5CY 6473 C 111 5CY 6474 C 111 5CY 6476 C 111 5CY 6477 C 111 5CY 6478 C 111 5CY ..→

A Random PyMOL-generated Cover. See Covers.


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