Main Page: Difference between revisions

From PyMOLWiki
Jump to navigation Jump to search
mNo edit summary
(PyMOL 3.0 release)
 
(123 intermediate revisions by 18 users not shown)
Line 1: Line 1:
__NOTOC__
__NOTOC__
{| align="center" style="padding-bottom: 4em;"
{| 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:210%; font-weight: bold; color:#032d45; text-align:center; padding: 5px; margin-bottom: 4px;" | 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: #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;"
 
|+ 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
{| 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; 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]]'''
|}
|}


Line 22: 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
|-
|-
! fetch_host setting
! Official Release
| [[Fetch_Host]] has been added to allow users to download PDBs from their PDB server (pdb, pdb euro, or pdb japan) of choice.
| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
|-
|-
! Fetch
! New Plugin
| [[Fetch]] has been updated to also load electron density maps.
| [[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
|-
|-
! Schrodinger Buys PyMOL
! Official Release
| Schrodinger has purchased PyMOL.  Development, support and open-source fun to continue!  Read about the [http://www.schrodinger.com/news/47/ sale].
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
|-
|-
! User Movie
! Python 3
| One of our users has posted another [http://www.youtube.com/watch?v=eQWw6x3fLF0 interesting movie], images from which were created with PyMOL. 
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
|-
|-
! New setting
! POSF
| [[surface_cavity_mode]] to change how PyMOL displays cavities.
| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
|-
|-
! Search fixed.
! Tutorial
| Thanks to a eagle-eyed user, our search has been fixed.  Please let us know if you have any search-related problems.
| [[Plugins Tutorial]] updated for PyQt5
|-
|-
! New Command
! New Plugin
| [[Cache]]—stores information on structures, so we don't have to recompute them.
| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
|-
|-
! Warren
! Selection keywords
| News about Warren DeLano's passing may be read on [[Warren|Warren's memorial page]].
| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
|-
|-
! Setting
! Plugin Update
| [[Fetch_Path]]—Sets the default path for the [[fetch]] command.
| [[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
! New Script
| [[SelInside]]—Creates a custom selection of all atoms spatially inside some user-defined box.
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
|-
! New Script
| [[ContactsNCONT]]—The script selects residues and atoms from the list of the contacts found by NCONT from CCP4 Program Suite
|-
! Fun
| [http://www.youtube.com/watch?v=oCRJ4r0RDC4 PCR Rap] video made with PyMOL (YouTube).
|-
! PyMOLWiki
| Reformatted Main Page. Some delays might occur from resizing images, but that should go away once the images are cached.
|-
|-
! PyMOLWiki
! Older News
| New — Search the PyMOLWiki via [[GoogleSearch]]
| See [[Older_News|Older News]].
|-
! PyMOL
| 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]].
|-
! PyMOL
| PyMOL now has a [[Set]] command for basic settings, and a [[Set_bond]] command for bond-only settings.
|}
|}
|style="vertical-align: top; width: 40%"|
|style="vertical-align: top; width: 40%"|
Line 75: Line 67:
|-
|-
|<div class="didyouknow" >
|<div class="didyouknow" >
<DPL>
<DynamicPageList>
namespace=
randomcount=1
category=Commands|Plugins|Script_Library|Settings
category=Commands|Plugins|Script_Library|Settings
includepage=*
includepage=*
includemaxlength=450
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 92: Line 82:
|
|
|style="vertical-align: top; width: 18%"|
|style="vertical-align: top; width: 18%"|
<DPL>
<DynamicPageList>
imagecontainer=Covers
imagecontainer=Covers
randomcount=1
randomcount=1
Line 99: Line 89:
listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover.  See [[Covers]].]],\n
listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover.  See [[Covers]].]],\n
ordermethod=none
ordermethod=none
</DPL>
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...

Color by conservation

Type Python Script
Download color_by_conservation.py
Author(s) Jason Vertrees
License Free
This code has been put under version control in the project Pymol-script-repo

Overview

This script reads an alignment object and colors the protein objects in the alignment by the sequence conservation found in the alignment.

Cbcon.png

Example Usage

reinitialize
import color_by_conservation
 
# get some kinases
fetch 1opk 3dtc 3p86 2eva 3efw, async=0
 
# turn on the sequence viewer
set seq_view

# align them into the "algn" object
for x in cmd.get_names(): cmd.align(x, "3efw and c. A", object="algn")
 
# color
color_by_conservation aln=algn, as_putty=1
A Random PyMOL-generated Cover. See Covers.


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