Jump to content

Main Page: Difference between revisions

From PyMOL Wiki
← Older edit

Bene (talk | contribs)

1 user group
3 edits
Tlinnet (talk | contribs)
1,276 edits
New Script. DisplacementMap
No edit summary
 
(123 intermediate revisions by 19 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:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
|- style="text-align:center; font-weight:normal; color: #000000; font-size: 120%; font-family: sans-serif;"
|  
| If you want to contribute new content to this wiki, request an account by emailing  accounts (@) sbgrid dot org from your '''institutional''' email address.
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
|- style="text-align:center; font-weight:bold; color: #000000; font-size: 120%; font-family: sans-serif;"
| For Educational downloads go to http://pymol.org/educational
|}
|}
{| 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 26: 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
|-
|-
! New Script
! New Setup
| [[DisplacementMap]] Calculates CA-CA distances between Open and Closed form of protein. Output best suggestions for site-directed mutagenesis for EPR/FRET experiments. Make distance matrix file, and output a gnuplot plot file for easy visualisation of interesting residues. Parses best suggestions back to pymol, for visual inspections.
| [https://github.com/kullik01/pymol-open-source-windows-setup/releases/tag/v3.1.0 PyMOL-open-source-windows-setup v3.1] has been released on January 20, 2025. More information under [[Windows Install]].
|-
! New Script
| Two new scripts: [[AAindex]] and [[Sidechaincenters]]
|-
|-
! New Plugin
! New Plugin
| [[CAVER_2.0]] update to the CAVER plugin.
| [[PySSA]] aims to combine PyMOL and [https://github.com/sokrypton/ColabFold ColabFold] to enable the prediction and analysis of 3D protein structures for the scientific end-user. [https://github.com/urban233/PySSA/releases/tag/v1.0.1 v1.0 has been released] on July 10, 2024.
|-
|-
! New Script
! Official Release
| [[AngleBetweenHelices]] calculates the angle between two helices.
| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
|-
|-
! Search
! New Plugin
| [[GoogleSearch]] widget fixed.
| [[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
|-
|-
! New Script
! Official Release
| [[Spectrumany]] creates color gradients with arbitrary color sequences.
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
|-
|-
! New Script
! Python 3
| [[BbPlane]] will draw CGO planes across the backbone highlighting planarity of arrangement.
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
|-
|-
! New Script
! POSF
| [[Center Of Mass]] has been re-written to calculate either the center-of-geometry or (mass-weighted) center-of-mass for a given selection and represents that selection as a pseudoatom (rather than a CGO sphere). 
| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
|-
|-
! New Script
! Tutorial
| [[Jump]] is a tool for jumping from one frame to another when you have a movie, MD simulation, or multiple models loaded into PyMOL.
| [[Plugins Tutorial]] updated for PyQt5
|-
|-
! New Scripts
! New Plugin
| [[ResDe]] is a suite of programs designed to assist crystallographers in defining user defined hydrogen bond distance restraints, which can be helpful when refining low-resolution structures.
| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
|-
|-
! New Script
! Selection keywords
| See [[BiologicalUnit]], for a workaround to the buggy [[Symexp]] command or if you just want to learn more about symmetry expansion in PyMOL.
| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
|-
|-
! New Script
! Plugin Update
| See [[Supercell]], the new script for making XxYxZ supercells.
| [[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
| See [[Split_Object_Along_Axis]], for a script that allows one to select a bond, and then generate 2 selections: one for the selection of all atoms that are on one side of this bond, and the other selection for the atoms on the other side of the bond.
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
|-
|-
! New Script
! Older News
| See [[Consistent_View/_Map_Inspect]], which is a toolkit for rapidly inspecting multiple maps and models.
| See [[Older_News|Older News]].
|-
! Server updates
| The underlying servers upon which the PyMOLWiki runs were upgraded over the weekend.  We are now fully functional.  A '''deep''' thanks to [http://www.bitgnome.net BitGnome] for donating time and hardware for the PyMOL project.
|-
! fetch_host setting
| [[Fetch_Host]] has been added to allow users to download PDBs from their PDB server (pdb, pdb euro, or pdb japan) of choice.
|-
! Fetch
| [[Fetch]] has been updated to also load electron density maps.
|-
! Schrodinger Buys PyMOL
| Schrodinger has purchased PyMOL.  Development, support and open-source fun to continue!  Read about the [http://www.schrodinger.com/news/47/ sale].
|-
! User Movie
| One of our users has posted another [http://www.youtube.com/watch?v=eQWw6x3fLF0 interesting movie], images from which were created with PyMOL. 
|-
! New setting
| [[surface_cavity_mode]] to change how PyMOL displays cavities.
|-
! Search fixed.
| Thanks to a eagle-eyed user, our search has been fixed.  Please let us know if you have any search-related problems.
|-
! New Command
| [[Cache]]—stores information on structures, so we don't have to recompute them.
|-
! Warren
| News about Warren DeLano's passing may be read on [[Warren|Warren's memorial page]].
|-
! Setting
| [[Fetch_Path]]—Sets the default path for the [[fetch]] command.
|-
! New Script
| [[SelInside]]—Creates a custom selection of all atoms spatially inside some user-defined box.
|}
|}
|style="vertical-align: top; width: 40%"|
|style="vertical-align: top; width: 40%"|
Line 106: Line 73:
|-
|-
|<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 123: Line 88:
|
|
|style="vertical-align: top; width: 18%"|
|style="vertical-align: top; width: 18%"|
<DPL>
<DynamicPageList>
imagecontainer=Covers
imagecontainer=Covers
randomcount=1
randomcount=1
Line 130: Line 95:
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 15:10, 27 April 2026

hosted by
Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
If you want to contribute new content to this wiki, request an account by emailing accounts (@) sbgrid dot org from your institutional email address.
Quick Links
Tutorials Table of Contents Commands
Script Library Plugins FAQ
Gallery | Covers PyMOL Cheat Sheet (PDF) Getting Help
News & Updates
New Setup PyMOL-open-source-windows-setup v3.1 has been released on January 20, 2025. More information under Windows Install.
New Plugin PySSA aims to combine PyMOL and ColabFold to enable the prediction and analysis of 3D protein structures for the scientific end-user. v1.0 has been released on July 10, 2024.
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...

Wfmesh

Type Python Script
Download scripts/wfmesh.py
Author(s) Dan Kulp
License -
This code has been put under version control in the project Pymol-script-repo

DESCRIPTION

This script will create an object for any Wavefront(.OBJ) mesh file. This is a way to extend the number of objects you can use. Also, you have more control over the coloring, transformations, etc than the CGOs. Although there are a number of these obj files on the web, you can also easily created them with open source tools (OpenFX, Crossroads3D). It takes literally, 2 min to get an object created and then loaded into pymol. Simply open OpenFX Designer, click File->Insert->Model, then choose any of the models (or create your own of course!), then export it as .3ds file. Then open the .3ds file from Crossroads3D and export as Wavefront OBJ.

  • createWFMesh - create a mesh object from Wavefront (*.obj) formated file

IMAGES

Star Wars Anyone?
..→
A Random PyMOL-generated Cover. See Covers.


Retrieved from "https://pymolwiki.org/index.php?title=Main_Page&oldid=14090"