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
m (2 revisions)
 
(314 intermediate revisions by 23 users not shown)
Line 1: Line 1:
 
__NOTOC__
 
__NOTOC__
−
{| align="center"
+
{| 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="width: 90%; font-size:190%; font-weight: bold; color:#038; text-align:center; padding: 5px; margin-bottom: 15px" | 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: #333; font-size: 120%"
+
|}
−
| We are the community-based support site for the popular molecular visualization program, [http://pymol.sf.net PyMOL].
+
{| 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;"
 
|}
 
|}
  
−
 
+
{| 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;"
−
{| align="center" style="width:90%; margin-bottom: 20px"
+
|+ 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
−
|
+
|-
−
{| align="left" width="20%" style="border: 1px solid #333; text-align:center; height=100%;"
+
| 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-weight: bold; font-size:120%; color: #333; background:#80AFFF;" | New Users
 
−
|-
 
−
| style="background:#E6EFFF; color:#333; font-size: 110%; padding: 4.5px"| New users are encouraged to join. Feel free to add any appropriate content; make an account and get started!
 
−
|-
 
−
|}
 
−
{| align="right" width="75%" style="border: 1px solid #333; text-align:left;"
 
−
! colspan="3" style="font-weight: bold; font-size:120%; color: #333; background:#80AFFF; text-align:center" | Quick Links
 
−
|-
 
−
| [[TOPTOC|'''Table of Contents''']]
 
−
|| [[Special:Allpages|Index of all pages]]
 
−
|| [http://pymol.sf.net PyMOL] Homepage
 
−
|-
 
−
| [[Practical_Pymol_for_Beginners|Beginner's Tutorial]]
 
−
|| [[:Category:Commands|PyMol Commands]]
 
−
|| '''Settings''': [[Settings|All]] [[:Category:Settings|Documented]]
 
−
|-
 
−
| [[:Category:Script_Library|'''Script Library''']]
 
−
|| [[:Category:Plugins|'''Plugins''']]
 
−
|| [[:Special:Categories| See All Categories]]
 
 
|-
 
|-
−
| [[:Category:FAQ|Frequently Asked Questions]]
+
| 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]]'''
−
|| [[PyMolWiki:Community_Portal|'''How to get involved!''']]
 
−
||
 
 
|-
 
|-
−
|}
+
| 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]]'''
 
|}
 
|}
  
−
{| align="center" width="90%" style="background: #fafafa; border-right: 1px solid #333; border-left: 1px solid #333; border-bottom: 1px solid #333"
+
{| width="100%"
−
|+ style="text-align: left; font-weight:bold; font-size:150%; color:#333; background: #EFE6FF; padding:10px; border: 1px solid #333" | News and Updates ([[Older_News|archive]])
+
| style="vertical-align: top; width: 40%" |
−
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Wiki
+
{| 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
−
| style="padding: 3px 5px 10px 15px;"| ♦ Rather large changes to the style of the main page.  Hopefully this will transition into something more pleasing.
 
−
|-
 
−
| style="padding: 3px 5px 10px 15px;"| ♦ We need experienced PyMOL users to link pages to their respective categories and make new categories.  Some new categories that need to be filled: [[:Category:Settings]], [[:Category:Publication_Quality]], [[:Category:Image_Manipulation]], [[:Category:Nucleic_Acids]].  We also need a category -- or categories -- on biochemical analysis and other useful things we do in PyMOL.  This will help people expand their knowledge (by being able to see related issues), and make it easier for the power users to find what they need.  The editing is '''very simple''' -- all you do is add a category tag(s) at the end of the pages.
 
 
|-
 
|-
−
| style="padding: 3px 5px 10px 15px;"| ♦  We also need folks to link to the pages in the [[Special:Lonelypages|Orphaned Pages]].  These pages are only found by direct searching, so we should change that to help make this more usable.
+
! Official Release
 +
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
 
|-
 
|-
−
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | PyMOL
+
! Python 3
 +
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
 
|-
 
|-
−
| style="padding: 3px 5px 10px 15px;"| ♦ PyMOL 1.0 has been released!
+
! POSF
 +
| [https://pymol.org/fellowship New PyMOL fellows announced for 2018-2019]
 
|-
 
|-
−
| style="padding: 3px 5px 10px 15px;"| ♦ [http://delsci.info/dsc/ PyMOL Official Documentation] is also available for subscribers.
+
! Tutorial
 +
| [[Plugins Tutorial]] updated for PyQt5
 
|-
 
|-
−
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Scripts & Plugins
+
! New Plugin
 +
| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
 
|-
 
|-
−
|
+
! Selection keywords
−
{|style="background-color: transparent;" width="100%"
+
| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
 
|-
 
|-
−
|valign="top"|
+
! Plugin Update
−
{|style="background-color: transparent;" width="100%"
+
| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.5]] is an updated version of channel analysis software in PyMOL
 
|-
 
|-
−
| style="padding: 3px 5px 10px 15px;"| ♦ [[Colorama]] --a PyMOL plugin which allows to color objects using adjustable scale bars
+
! New Script
 +
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
 
|-
 
|-
−
| style="padding: 3px 5px 10px 15px;"| ♦ [http://ase-web.rit.edu/~ez-viz/ProMOL_dl.html ProMOL] plugin added. Catalytic site prediction, other tools. Redirects to website.
+
! 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...
 
|-
 
|-
−
| style="padding: 3px 5px 10px 15px;"| ♦ [[EMovie]] plugin added.  Easy movies in PyMol using a GUI.
+
|<div class="didyouknow" >
−
|-
+
<DynamicPageList>
−
| style="padding: 3px 5px 10px 15px;"| &diams; [[DYNMAP]] plugin page created.  Check it out!
+
randomcount=1
−
|-
+
category=Commands|Plugins|Script_Library|Settings
−
| style="padding: 3px 5px 10px 15px;"| &diams; [[EZ-Viz]]
+
includepage=*
−
|}
+
includemaxlength=1050
−
|valign="top" width="150px"|[[Image:COLORAMA-screenshot.jpg|150px]]
+
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>
 +
 
|}
 
|}

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...

Specular

= Overview =

This controls whether or not specular reflections are shown unrendered, in the GUI. Turning this off only makes a slight improvement in speed.

  • Specular set to 0

  • Specular set to 1

  • Specular set to 5

  • Specular set to 10

Notice in the images above that the setting is controlling the amount of directly reflected light and not the shininess of the reflection.

Syntax

# turn the setting on or off
set specular, boolean

# turn it off
set specular, off

# turn it on
set specular, on

See Also

Pages on Specular Reflections

A Random PyMOL-generated Cover. See Covers.


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