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__NOTOC__
* [[TOPTOC|'''Table of Contents''']]
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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.
|- 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;"
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* [[Special:Allpages|Alphabetized Index of all pages]]
{| 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: 1.1em; font-weight: normal; color #48A2B4; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''
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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; 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]]'''
|}


* [[Improvements|Discussion of PyMolWiki Improvements]]
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{| class="jtable" style="float: left; width: 90%;"
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News &amp; Updates
|-
! Official Release
| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
|-
! New Plugin
| [[CavitOmiX|CavitOmiX]] calculate [https://innophore.com Catalophore™ cavities], predict protein structures with [https://www.nvidia.com/en-us/gpu-cloud/bionemo OpenFold by NVIDIA-BioNeMo], [https://ai.facebook.com/blog/protein-folding-esmfold-metagenomics/ ESMFold] and retrieve [https://www.deepmind.com/research/highlighted-research/alphafold Alphafold] models
|-
! 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 fellowship announced for 2022-2023]
|-
! 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]].
|}
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{| 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...
|-
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== PyMol Wiki Home ==
|}
You have reached the home of the PyMolWiki, a user-driven web-oriented CMS.
 
We provide
* updates on [http://pymol.sf.net PyMol]
* a stable user-oriented documentation base
* a thorough treatment of the PyMol program
* feature-rich scripts for general PyMol use
 
== New Users ==
Welcome!  New users who wish to contribute appropriate content are welcome to join.  Feel free to add any appropriate content; make an account and get started!
 
==News==
===PyMol===
* [[DYNMAP]] plugin page created.  Check it out!
* [[Cealign|CE Align v0.8-RBS]] released.  Better than before.  See test case comparisons.
* [[Slerpy]], a set of pymol command extensions to simplify complex movie making is now available.
* Updated the [[Kabsch#The_New_Code|Kabsch]] code with a more elegant solution; fixed a small rotation bug.
* Pymol 0.99 is out! Get it [http://delsci.com/rel/099/ here].
* A new version of APBS plugin is available on [http://www-personal.umich.edu/~mlerner/PyMOL/ Michael Lerner's Page].
* New [http://www.delsci.com/beta Beta Releases] available.
* New cool [[ray]] tracing features added!
 
===Wiki===
* Added useful mini-script for re-assigning the B Factor column to something new and coloring it.
* captcha system installed.
* If you notice something out of the ordinary, please contact the admin.  I updated some software.
* [[Settings]] now contains documentation on:
              - helix roundness
              - ribbon sampling
              - cartoon sampling
              - cartoon highlight coloring
              - cartoon color blending vs discrete colors
              - and more!  now 48 documented (with examples); just 470 to go....
 
* [[SURFNET]] information on reading surfaces from other programs added.
* Two new [[:Category:Plugins|Plugins]] have been added, [[NsSNP Loader]] and [[Proxy Config]].
* Added a page that lists all [[Settings|PyMol settings]].  We need to start documenting these.
* [[MAC_Install]] page has been developed. It describes pymol and apbs issues specific to Mac OS X.
* [[APBS]] page has been established. 
* [[APBS]] How to set this up on OS X and on Linux has been started but needs contributions.
** Added info on installing APBS from source
 
===News Archive===
*See our [[Older_News]].
 
== Links of Interest ==
* [[TOPTOC|Top Level Table of Contents]]
* [[:Category:FAQ|Frequently Asked Questions]] -- new!
* [[PyMolWiki:Community_Portal| How to get involved!]] -- read me if you want to add something
* [[:Category:Script Library| Script Library]] -- add one! (rTools info!)
* [[:Category:Commands|PyMol Commands]] (>130 documented!)
* [[Settings|PyMol Settings]]  (6 newly documented; only 470 to go...)
* [[:Special:Allpages| All Pages]]
* [[:Category:Plugins|Plugins]]
* [[:Special:Categories| See All Categories]]

Latest revision as of 11:54, 12 March 2024

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 v3.0 has been released on March 12, 2024.
New Plugin CavitOmiX calculate Catalophore™ cavities, predict protein structures with OpenFold by NVIDIA-BioNeMo, ESMFold and retrieve Alphafold models
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 fellowship announced for 2022-2023
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...

CreateSecondaryStructure

===DESCRIPTION===

To build a peptide sequence.

SETUP

run CreateSecondaryStructure.py

NOTES / STATUS

  • Tested on Pymolv1.0, Windows platform
  • Many bugs to be found

USAGE

  • seqInfo = getTableFromCsvFile("seqInfo.csv")
with in the file something like:
MET,-54,-47
PRO,-54,-47
  • seqInfo = [['MET',-57,-47],['PRO',-57,-47]]
  • createPeptide(seqInfo)

EXAMPLES

seqInfo = [['MET',-57,-47],['PRO',-57,-47]]
createPeptide(seqInfo)

SCRIPTS (CreateSecondaryStructures.py)

CreateSecondaryStructures.py 

<source lang="python">
  2. Original Author: Dan Kulp
  3. Date  : 9/8/2005
  4. MOdified by Jurgen F. Doreleijers
  5. For Hamid Eghbalnia
  7. Call in window like :
  8. @C:\Documents and Settings\jurgen.WHELK.000\workspace\Wattos\python\Wattos\Utils\CreateSecondaryStructures.py
  9. Next line is a pymol directive

python import urllib


  1. Well I guess one can build a protein with it but the vdw contacts would be ..→
A Random PyMOL-generated Cover. See Covers.


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