Difference between revisions of "Main Page"

From PyMOLWiki
Jump to navigation Jump to search
(fellowship)
(PyMOL 2.5 release announcement)
(39 intermediate revisions by 9 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:bold; color: #6d6003; font-size: 140%; 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 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: #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 25: 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
 
|-
 
|-
−
! PyMOL Open-Source Fellowship
+
! Official Release
−
| Schrödinger is now accepting applications for the PyMOL Open-Source Fellowship program! Details on http://pymol.org/fellowship
+
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
 
|-
 
|-
−
! Official Release
+
! Python 3
−
| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.2 have all been released] on August 4, 2014.
+
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
 
|-
 
|-
−
! Official Release
+
! POSF
−
| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7 have all been released] today, January 14, 2014.
+
| [https://pymol.org/fellowship New PyMOL fellows announced for 2018-2019]
 
|-
 
|-
−
! New Plugin
+
! Tutorial
−
| [[Bondpack]] is a collection of PyMOL plugins for easy visualization of atomic bonds.
+
| [[Plugins Tutorial]] updated for PyQt5
 
|-
 
|-
 
! New Plugin
 
! New Plugin
−
| [[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.
+
| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
 
|-
 
|-
−
! 3D using Geforce
+
! Selection keywords
−
| 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.
+
| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
 
|-
 
|-
−
! New Plugin
+
! Plugin Update
−
| [[GROMACS_Plugin]] is a new plugin that ties together PyMOL and GROMACS.
+
| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.5]] is an updated version of channel analysis software in PyMOL
−
|-
 
−
! New Software
 
−
| [[CMPyMOL]] is a software that interactively visualizes 2D contact maps of proteins 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
Line 63: Line 61:
 
|-
 
|-
 
|<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 80: Line 76:
 
|
 
|
 
|style="vertical-align: top; width: 18%"|
 
|style="vertical-align: top; width: 18%"|
−
<DPL>
+
<DynamicPageList>
 
imagecontainer=Covers
 
imagecontainer=Covers
 
randomcount=1
 
randomcount=1
Line 87: Line 83:
 
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 12:11, 10 May 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...

Optimize

Type PyMOL Plugin
Download plugins/optimize.py
Author(s) Osvaldo Martin
License MIT
This code has been put under version control in the project Pymol-script-repo

Introduction

Optimize provides a PyMOL graphical interface to some of the molecular mechanics features available in openbabel, allowing the user to optimize (minimize) the energy of any molecule uploaded on PyMOL.

Installation

The plugin can be downloaded through the project Pymol-script-repo.

Optimize needs OpenBabel (and OpenBabel Python bindings) to be installed on your computer (see instructions here).

Note to Windows users: If you are using a 64-bit Windows, please install OpenBabel 64-bit from here

Usage

The plugin can be accessed using a graphic user interface (see figure 0) or from the PyMOL`s terminal. There are 5 types of optimization routines available now, 2 local and 3 global optimization routines.

== Local ..→

A Random PyMOL-generated Cover. See Covers.


Retrieved from "http://pymolwiki.org/index.php?title=Main_Page&oldid=13429"