Main Page: Difference between revisions

From PyMOLWiki
Jump to navigation Jump to search
No edit summary
(PyMOL 3.0 release)
 
(111 intermediate revisions by 17 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
|-
|-
! Search
! Official Release
| [[GoogleSearch]] widget fixed.
| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
|-
|-
! New Script
! New Plugin
| [[Spectrumany]] creates color gradients with arbitrary color sequences.
| [[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
| [[BbPlane]] will draw CGO planes across the backbone highlighting planarity of arrangement.
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
|-
|-
! New Script
! Python 3
| [[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). 
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
|-
|-
! New Script
! POSF
| [[Jump]] is a tool for jumping from one frame to another when you have a movie, MD simulation, or multiple models loaded into PyMOL.
| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
|-
|-
! New Scripts
! Tutorial
| [[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.
| [[Plugins Tutorial]] updated for PyQt5
|-
|-
! New Script
! New Plugin
| See [[BiologicalUnit]], for a workaround to the buggy [[Symexp]] command or if you just want to learn more about symmetry expansion in PyMOL.
| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
|-
|-
! New Script
! Selection keywords
| See [[Supercell]], the new script for making XxYxZ supercells.
| 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 [[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.
| [[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 [[Consistent_View/_Map_Inspect]], which is a toolkit for rapidly inspecting multiple maps and models.
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
|-
! 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.
! Older News
| Thanks to a eagle-eyed user, our search has been fixed.  Please let us know if you have any search-related problems.
| See [[Older_News|Older News]].
|-
! 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 90: 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 107: 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 114: 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...

AlphaToAll

alphatoall (all lower case) is a core command since PyMOL 1.7.2

Overview

AlphaToAll will expand the alpha-carbon property that you specify to all atoms in the residues. For example, if you set the b-factor column to some different value for all alpha carbons, this script will propagate those values into all the atoms as well.

In the example below, notice the color of the sticks.

  • The alpha carbon here has a color property that does not match the rest of the residue.

    The alpha carbon here has a color property that does not match the rest of the residue.

  • This script will fix that, expanding the color attribute to the rest of the atoms.

    This script will fix that, expanding the color attribute to the rest of the atoms.

Usage

<source lang="python">

  1. expand propertyName in objName on all the alpha carbons
  2. to every atom, for each residue

alphaToAll objName, propertyName

  1. Example #1
  2. For all objects, for each residue, set every atom's b-column value
  3. to match that residue's alpha carbon's b-column value.

alphaToAll *, b

  1. Example #2
  2. For selection 1qox and c. A ..→
A Random PyMOL-generated Cover. See Covers.


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