Difference between revisions of "Main Page"

From PyMOLWiki
Jump to navigation Jump to search
(Replace link to "Google search" page with link to "PyMOL mailing list" page)
(13 intermediate revisions by 4 users not shown)
Line 1: Line 1:
 
__NOTOC__
 
__NOTOC__
−
{| align="center" style="padding-bottom: 4em;"
+
{| align="center" style="padding-bottom: 3em;"
 
|+ 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:210%; font-weight: bold; color:#032d45; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!
−
|- 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: #6d6003; font-size: 140%; font-family: 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:bold; color: #6d6003; font-size: 140%; font-family: serif;"
−
| New accounts: email jason (dot) vertrees (@) gmail 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: 140%; font-style: italic; font-family: serif;"
+
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-family: 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;"
 
{| 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
 
|+ 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
Line 24: Line 25:
 
{| class="jtable" style="float: left; width: 90%;"
 
{| 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="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
 +
|-
 +
! Official Release
 +
| [http://pymol.org PyMOL v1.8.2 has been released] on April 20, 2016.
 +
|-
 +
! New Script
 +
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
 +
|-
 +
! New Plugin
 +
| [[Lisica|LiSiCA]] is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
 +
|-
 +
! Official Release
 +
| [http://pymol.org PyMOL v1.8.0 has been released] on Nov 18, 2015.
 
|-
 
|-
 
! PyMOL Open-Source Fellowship
 
! PyMOL Open-Source Fellowship
Line 51: Line 64:
 
|-
 
|-
 
|<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 68: Line 79:
 
|
 
|
 
|style="vertical-align: top; width: 18%"|
 
|style="vertical-align: top; width: 18%"|
−
<DPL>
+
<DynamicPageList>
 
imagecontainer=Covers
 
imagecontainer=Covers
 
randomcount=1
 
randomcount=1
Line 75: Line 86:
 
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>
  
 
|}
 
|}

Revision as of 12:08, 15 September 2016

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 v1.8.2 has been released on April 20, 2016.
New Script dssr_block is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
New Plugin LiSiCA is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
Official Release PyMOL v1.8.0 has been released on Nov 18, 2015.
PyMOL Open-Source Fellowship Schrödinger is now accepting applications for the PyMOL Open-Source Fellowship program! Details on http://pymol.org/fellowship
Official Release PyMOL, AxPyMOL, and JyMOL v1.7.6 have all been released on May 4, 2015.
New Plugin PyANM is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
New Plugin Bondpack is a collection of PyMOL plugins for easy visualization of atomic bonds.
New Plugin MOLE 2.0 is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.
3D using Geforce PyMOL can now be 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.
Older News See Older News.
Did you know...

Color by conservation

Type Python Script
Download color_by_conservation.py
Author(s) Jason Vertrees
License Free
This code has been put under version control in the project Pymol-script-repo

Overview

This script reads an alignment object and colors the protein objects in the alignment by the sequence conservation found in the alignment.

Cbcon.png

Example Usage

reinitialize
import color_by_conservation
 
# get some kinases
fetch 1opk 3dtc 3p86 2eva 3efw, async=0
 
# turn on the sequence viewer
set seq_view

# align them into the "algn" object
for x in cmd.get_names(): cmd.align(x, "3efw and c. A", object="algn")
 
# color
color_by_conservation aln=algn, as_putty=1
A Random PyMOL-generated Cover. See Covers.


Retrieved from "http://pymolwiki.org/index.php?title=Main_Page&oldid=12443"