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)
 
(437 intermediate revisions by 44 users not shown)
Line 1: Line 1:
−
== PyMol Wiki Home ==
+
__NOTOC__
−
You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.
+
{| 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: 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/]]
 +
|}
 +
{| 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;"
 +
|}
  
−
We (will) strive to provide
+
{| 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;"
−
* updates on PyMol
+
|+ 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
−
* a stable user-oriented documentation base
+
|-  
−
* a thorough treatment of the PyMol program
+
| 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]]'''
−
* feature rich scripts for general PyMol use
+
|-
 +
| 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]]'''
 +
|}
  
−
== Links of Interest ==
+
{| width="100%"
−
* [[TOPTOC|Top Level Table of Contents]]
+
| style="vertical-align: top; width: 40%" |
−
* [[:Category:FAQ|Frequently Asked Questions]] -- new!
+
{| class="jtable" style="float: left; width: 90%;"
 +
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
 +
|-
 +
! Official Release
 +
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
 +
|-
 +
! Python 3
 +
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
 +
|-
 +
! POSF
 +
| [https://pymol.org/fellowship New PyMOL fellows announced for 2018-2019]
 +
|-
 +
! Tutorial
 +
| [[Plugins Tutorial]] updated for PyQt5
 +
|-
 +
! New Plugin
 +
| [[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]!
 +
|-
 +
! 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
 +
|-
 +
! New Script
 +
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
 +
|-
 +
! Older News
 +
| See [[Older_News|Older News]].
 +
|}
 +
|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" >
 +
<DynamicPageList>
 +
randomcount=1
 +
category=Commands|Plugins|Script_Library|Settings
 +
includepage=*
 +
includemaxlength=1050
 +
escapelinks=false
 +
allowcachedresults=false
 +
resultsheader=__NOTOC__ __NOEDITSECTION__
 +
listseparators=,<h3>[[%PAGE%]]</h3>,,\n
 +
</DynamicPageList>
 +
</div>
 +
<div style="clear: both;"></div>
 +
|}
 +
|
 +
|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>
  
−
* Updated! [[PyMolWiki:Community_Portal| How to get involved!]] -- read me if you want to add something
+
|}
−
* [[:Category:Scripting Script Library| Script Library]] -- add one! (rTools info!)
 
−
* [[:Category:Commands|PyMol Commands]] (>130 documented!)
 
−
* [[:Special:Allpages| All Pages]]
 
−
* [[:Category:Plugins|Plugins]]
 
−
* [[:Special:Categories| See All Categories]]
 

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 dumbbell width

== Overview ==

Only relavent when fancy helices is turned on, see Cartoon_Helix_Settings
set cartoon_dumbbell_width defines the width of the helix when the fancy helices setting has been engaged

Syntax

set cartoon_dumbbell_width, <number>        #default setting is 0.1

Adjust this value or that of cartoon_dumbbell_radius to remove the bulge at the edges of a fancy helix

Example

  • cartoon_dumbbell_width 0 (can cause problems, circled in red)

  • cartoon_dumbbell_width 0.1

  • cartoon_dumbbell_width 0.2

  • cartoon_dumbbell_width 1

A Random PyMOL-generated Cover. See Covers.


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