This is a read-only mirror of pymolwiki.org

Difference between revisions of "Main Page"

From PyMOL Wiki
Jump to navigation Jump to search
m (2 revisions)
 
(78 intermediate revisions by 7 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:190%; font-weight: bold; color:#032d45; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Community 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: 135%; 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: 135%; font-style: italic; font-family: serif;"
+
|- style="text-align:center; font-weight:normal; color: #000000; font-size: 120%; font-family: sans-serif;"
−
| New accounts: email thomas (dot) holder (@) schrodinger dot com
+
| To request a new account, email SBGrid at:  accounts (@) sbgrid dot org
−
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 135%; font-style: italic; font-family: serif;"
+
|- 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]]'''  
+
| 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]]'')
−
 
+
||'''[[PyMOL_mailing_list|Getting Help]]'''
 
|}
 
|}
  
Line 26: Line 30:
 
|-
 
|-
 
! Official Release
 
! Official Release
−
| [http://pymol.org PyMOL, AxPyMOL, and JyMO v1.7 have all been released] today, January 14, 2014.
+
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
 
|-
 
|-
−
! New Plugin
+
! Python 3
−
| [[Bondpack]] is a collection of PyMOL plugins for easy visualization of atomic bonds.
+
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
 
|-
 
|-
−
! New Plugin
+
! POSF
−
| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.0]] is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.
+
| [https://pymol.org/fellowship New PyMOL fellows announced for 2018-2019]
 
|-
 
|-
−
! 3D using Geforce
+
! Tutorial
−
| PyMOL can now be [http://forums.geforce.com/default/topic/571604/3d-vision/3d-vision-working-with-qbs-in-opengl-software-using-geforce/2/ visualized in 3D using Nvidia GeForce video cards] (series 400+) with 120Hz monitors and Nvidia 3D Vision, this was previously only possible with Quadro video cards.
+
| [[Plugins Tutorial]] updated for PyQt5
 
|-
 
|-
 
! New Plugin
 
! New Plugin
−
| [[GROMACS_Plugin]] is a new plugin that ties together PyMOL and GROMACS.
+
| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
 +
|-
 +
! Selection keywords
 +
| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
 
|-
 
|-
−
! New Software
+
! Plugin Update
−
| [[CMPyMOL]] is a software that interactively visualizes 2D contact maps of proteins in PyMOL.
+
| [[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
−
| [[cgo_arrow]] draws an arrow between two picked atoms.
+
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
−
|-
 
−
! Tips & Tricks
 
−
| Instructions for [[Movie_pdf|generating movie PDFs]] using .mpg movies from PyMOL.
 
 
|-
 
|-
 
! Older News
 
! Older News
 
| See [[Older_News|Older News]].
 
| See [[Older_News|Older News]].
 
|}
 
|}
−
|style="vertical-align: top; width: 60%"|
+
|style="vertical-align: top; width: 40%"|
 
{| class="jtable" style="float: right; width: 90%"
 
{| 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...
 
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...
 
|-
 
|-
 
|<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=1050
 
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 74: Line 76:
 
|
 
|
 
|style="vertical-align: top; width: 18%"|
 
|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>
  
 
|}
 
|}
−
 
−
 
−
 
−
''The content of this site was substantially reproduced by Jarred Yacob in 2014 from pymolwiki.org, the content of which was authored significantly by Jason Vertrees."
 
−
"(c) 2014.  Schrödinger, Inc."'
 

Latest revision as of 03:21, 22 June 2021

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 v2.5 has been released on May 10, 2021.
Python 3 New Python 3 compatibility guide for scripts and plugins
POSF New PyMOL fellows announced for 2018-2019
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...

Cartoon gap cutoff

With cartoon_gap_cutoff > 0, if there are missing residues along the protein backbone (e.g. missing loops), PyMOL will create a dashed cartoon loop segment if the gap (in number of residues) is shorter than the cutoff.

New in PyMOL 1.8.2

Example

set cartoon_gap_cutoff, 10

fetch 2xwu, async=0
as cartoon
orient B//152-156/

Cartoon gap cutoff.png

Number of dashes

The number of dashes is directly affected by the cartoon_sampling setting: 

set cartoon_sampling, 20

See Also
A Random PyMOL-generated Cover. See Covers.


Retrieved from "http://wiki.pymol.org/index.php?title=Main_Page&oldid=14896"