Difference between revisions of "Main Page"

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__NOTOC__
 
__NOTOC__
{| align="center" style="padding-bottom: 4em;"
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{| 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;"
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|}
 +
{| 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;"
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|- 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;"
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|+ 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
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{| 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;"
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|+ 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]]'''
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| 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]]'''
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| 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]]'''
 
|}
 
|}
  
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|+ 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
 
|-
 
|-
Max OS X 10.8
+
! Official Release
! X11 Libraries
+
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
| Mac OS X 10.8 doesn't ship with X11. But, you can get the libraries here [http://xquartz.macosforge.org/landing/ X11 Libraries].
 
|-
 
Select_sites
 
! New Script
 
| [[select_sites]] can set author/paper selections according to SITE annotation in pdb file
 
|-
 
! New Script
 
| [[b2transparency]] can set surface transparency based on atom b-factor
 
|-
 
! New Extension
 
| [[psico]] is a python module which extends PyMOL with many commands
 
 
|-
 
|-
! New Script
+
! Python 3
| [[uniprot_features]] makes named selections for sequence annotations from uniprot
+
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
 
|-
 
|-
! New Plugin
+
! POSF
| [[Gyration_tensor]] Calculates chain-wise gyration tensor of a protein.
+
| [https://pymol.org/fellowship New PyMOL fellows announced for 2018-2019]
|-
 
! New Script
 
| [[set_phipsi]] can set phi/psi angles for all residues in a selection
 
|-
 
! New Script
 
| [[dehydron]] A plugin to calculate dehydrons and display them onto the protein structure. A dehydron is a main chain hydrogen bond incompletely shielded from water attack.
 
|-
 
! New Script
 
| [[pymol2glmol]] is script to export a scene in pymol to a webpage for GLmol. GLmol is a molecular viewer for Web browsers written in WebGL/Javascript. Like web Jmol, but MUCH faster. Try it out!
 
 
|-
 
|-
! New Script
+
! Tutorial
| [[cyspka]] is an experimental surface cysteine pKa predictor.
+
| [[Plugins Tutorial]] updated for PyQt5
 
|-
 
|-
 
! New Plugin
 
! New Plugin
| [[Contact_Map_Visualizer]] visualize residues corresponding to the contact map
+
| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
|-
 
! New Script
 
| [[spectrum_states]] colors states of multi-state object
 
 
|-
 
|-
! New Script
+
! Selection keywords
| [[TMalign]] is a wrapper for the TMalign program
+
| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
 
|-
 
|-
! Gallery Updates
+
! Plugin Update
| The [[Gallery|gallery]] has been updated to include a few new ideas and scripts for rendering
+
| [[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
| [[save_settings]] can dump all changed settings to a file
+
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
|-
 
! Tips & Tricks
 
| Instructions for [[3d_pdf|generating 3D PDFs]] using PyMOL.
 
|-
 
! Wiki Update
 
| Wiki has been updated. Please report any problems to the sysops.
 
|-
 
! New Scripts
 
| Create objects for each molecule or chain in selection with [[split_object]] and [[split_chains]]
 
|-
 
! New Script
 
| [[Rotkit]]: is a collection of usefull scripts to place your dye/molecule where you want. It includes a very handy, rotation around line, function. 
 
|-
 
! New Script
 
| [[Forster-distance-calculator]]: Can be used as a pymol-python shortcut to calculate the Förster distance between dyes from different companies. Useful, if the user have pymol installed, but not python. This script is meant as a tool to finding the right dyes, when labelling suitable positions for the site-directed cysteine mutants. See [[DisplacementMap]].
 
|-
 
! New Script
 
| [[propka]]: Fetches the pka values for your protein from the [http://propka.ki.ku.dk/ propka] server. [[propka]] generates a pymol command file that make pka atoms, color and label them according to your protein. Inspection is made easy by grouping the pka atoms in the pymol menu.
 
 
|-
 
|-
 
! Older News
 
! Older News
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|-
 
|-
 
|<div class="didyouknow" >
 
|<div class="didyouknow" >
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|
 
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|style="vertical-align: top; width: 18%"|
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imagecontainer=Covers
 
imagecontainer=Covers
 
randomcount=1
 
randomcount=1
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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
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Latest 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...

Key Wait

#use "spawn spawn_demo.py, local" to invoke this
#python script from within PyMOL

wait=""
i=0
while i < 12 and wait!="x":
  cmd.turn("y", 30)
  print "Press enter key to continue or x + enter to terminate"
  wait=raw_input()
  i=i+1
print "Done"

Note: this approach only works when you have a console window open.

A Random PyMOL-generated Cover. See Covers.