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| == PyMol Wiki Home == | | __NOTOC__ |
| You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.
| | {| 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: 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/]] |
| | |} |
| | {| 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;" |
| | |} |
|
| |
|
| == Go! == | | {| 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;" |
| You may now add content to the wiki. This is a semi-structured wiki in that the categories are pseudo-hierarchically linked.
| | |+ 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; 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; 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]]''' |
| | |} |
|
| |
|
| == New Categories/Content == | | {| width="100%" |
| If you feel we're missing a category, please find where it would most logically fit, add it to the main page via the [[Top Level Schema Policy]].
| | | style="vertical-align: top; width: 40%" | |
| | {| 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 |
| | |- |
| | ! 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]]. |
| | |} |
| | |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... |
| | |- |
| | |<div class="didyouknow" > |
| | <DynamicPageList> |
| | randomcount=1 |
| | category=Commands|Plugins|Script_Library|Settings |
| | includepage=* |
| | includemaxlength=1050 |
| | 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> |
|
| |
|
| == Helping ==
| | |} |
| * A wiki edit/user policy is needed.
| |
| * Graphic design and CSS layout: We need logos, BG images and CSS layout
| |
| * Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki
| |
| * If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].
| |
| | |
| We need your help. So join today & happy editing!
| |
| | |
| == New! GeShi: Syntax Highlighting for Python & More ==
| |
| We now have a syntax highlighter installed. It now supports something like 28 programming languages! When you paste your code simply wrap it in
| |
| <language_name> ... code here ... </language_name>.
| |
| | |
| Here's an example:
| |
| <pre>
| |
| <python>
| |
| # axes.py
| |
| from pymol.cgo import *
| |
| from pymol import cmd
| |
| from pymol.vfont import plain
| |
| | |
| # create the axes object, draw axes with cylinders coloured red, green,
| |
| #blue for X, Y and Z
| |
| | |
| obj = [
| |
| CYLINDER, 0., 0., 0., 50., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,
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| CYLINDER, 0., 0., 0., 0., 50., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.,
| |
| CYLINDER, 0., 0., 0., 0., 0., 50., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0,
| |
| ]
| |
| | |
| # add labels to axes object (requires pymol version 0.8 or greater, I
| |
| # believe
| |
| | |
| cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
| |
| cyl_text(obj,plain,[50.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
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| cyl_text(obj,plain,[0.,50.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
| |
| cyl_text(obj,plain,[0.,0.,50.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
| |
| | |
| # then we load it into PyMOL
| |
| cmd.load_cgo(obj,'axes')
| |
| | |
| <python>
| |
| </pre>
| |
| | |
| gives us the code
| |
| <source lang="python">
| |
| # axes.py
| |
| from pymol.cgo import *
| |
| from pymol import cmd
| |
| from pymol.vfont import plain
| |
| | |
| # create the axes object, draw axes with cylinders coloured red, green,
| |
| #blue for X, Y and Z
| |
| | |
| obj = [
| |
| CYLINDER, 0., 0., 0., 50., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,
| |
| CYLINDER, 0., 0., 0., 0., 50., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.,
| |
| CYLINDER, 0., 0., 0., 0., 0., 50., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0,
| |
| ]
| |
| | |
| # add labels to axes object (requires pymol version 0.8 or greater, I
| |
| # believe
| |
| | |
| cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
| |
| cyl_text(obj,plain,[50.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
| |
| cyl_text(obj,plain,[0.,50.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
| |
| cyl_text(obj,plain,[0.,0.,50.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
| |
| | |
| # then we load it into PyMOL
| |
| cmd.load_cgo(obj,'axes')
| |
| </source>
| |
| | |
| See [http://qbnz.com/highlighter/index.php The Geshi Home Page]
| |
| | |
| [[User:Tree|Tree]]
| |
| | |
| == Section Layout ==
| |
| Please do not ADD any content to the site yet. Just Organize the following list as logically as possible. Here's my first go at it.
| |
| | |
| Please see [[:Category:Discussion|Discussion]] for more thoughts on the site organizaiton.
| |
| | |
| === Layout Schema ===
| |
| # [[:Category:News|News]]
| |
| ## [[:Category:News Discussion|Discussion]]
| |
| ## [[:Category:News PyMol Beta|PyMol Beta]]
| |
| # [[:Category:Technical Issues|Technical Issues]]
| |
| ## [[:Category:Technical Issues Installation|Installation]]
| |
| ### [[:Category:Technical Issues Installation OS Dependent|OS Dependent]]
| |
| #### [[:Category:Technical Issues Installation OS Dependent Linux|Linux]]
| |
| #### [[:Category:Technical Issues Installation OS Dependent MAC|MAC]]
| |
| #### [[:Category:Technical Issues Installation OS Dependent Windows|Windows]]
| |
| # [[:Category:Launching PyMOL|Launching PyMOL]]
| |
| ## [[:Category:Launching PyMOL Command Line Options| Command Line Options]]
| |
| ## [[:Category:Launching PyMOL Launching From a Script|Launching From a Script]]
| |
| # [[:Category:Using Pymol|Using PyMol]]
| |
| ## [[:Category:Using Pymol Mouse Controls|Mouse Controls]]
| |
| ## [[:Category:Using Pymol Objects and Selections|Objects and Selections]]
| |
| ### [[:Category:Using Pymol Objects and Selections Working with Objects|Working with Objects]]
| |
| ### [[:Category:Using Pymol Objects and Selections Working with Selections|Working with Selections]]
| |
| ### [[:Category:Using Pymol Objects and Selections Selector Quick Reference|Selector Quick Reference]]
| |
| #### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Single-word Selectors|Single-word Selectors]]
| |
| #### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Property Selectors|Property Selectors]]
| |
| #### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Selection Algebra|Selection Algebra]]
| |
| #### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Selection Macros|Selection Macros]]
| |
| ### [[:Category:Using Pymol Objects and Selections Representations|Representations]]
| |
| #### [[:Category:Using Pymol Objects and Selections Representations Lines|Lines]]
| |
| #### [[:Category:Using Pymol Objects and Selections Representations Sticks|Sticks]]
| |
| #### [[:Category:Using Pymol Objects and Selections Representations Cartoon|Cartoon]]
| |
| #### [[:Category:Using Pymol Objects and Selections Representations Surface|Surface]]
| |
| #### [[:Category:Using Pymol Objects and Selections Representations Mesh|Mesh]]
| |
| #### [[:Category:Using Pymol Objects and Selections Representations Spheres|Spheres]]
| |
| #### [[:Category:Using Pymol Objects and Selections Representations Dots|Dots]]
| |
| ### [[:Category:Using Pymol Objects and Selections Color|Color]]
| |
| ### [[:Category:Using Pymol Objects and Selections Displaying Biochemical Properties|Displaying biochemical properties]]
| |
| ## [[:Category:Using Pymol Display Settings|Display Settings]]
| |
| ## [[:Category:Using Pymol Stereo 3D Display|Stereo 3D Display]] -- wrong place
| |
| ### [[:Category:Using Pymol Hardware Options|Hardware Options]] -- wrong place?
| |
| ### [[Linux XFree86 Configuration]] -- wrong place
| |
| ## [[:Category:Using Pymol Scenes|Scenes]]
| |
| ## [[:Category:Using Pymol Mouse Settings|Mouse Settings]]
| |
| ## [[:Category:Using Pymol Wizards|Wizards]]
| |
| ## [[:Category:Using Pymol Plugins |Plugins]] -- wrong place?
| |
| ## [[:Category:Using Pymol Ray-tracing|Ray-tracing]]
| |
| ## [[:Category:Using Pymol Settings Reference|Settings Reference]]
| |
| ## [[:Category:Using Pymol Movies and Animations|Movies and Animations]]
| |
| ## [[:Category:Using Pymol Structure Alignment|Structure Alignment]]
| |
| ## [[:Category:Using Pymol Structure Alignment Editor|Structure Alignment Editor]]
| |
| # [[:Category:Commands|Command Language]]
| |
| ## [[:Category:Commands PyMOL Command Script|PyMOL Command Script]]
| |
| ## [[:Category:Commands PyMOL Python API|PyMOL Python API]]
| |
| # [[:Category:Advanced Issues|Advanced Issues]]
| |
| ## [[:Category:Advanced Issues Modeling and Editing Structures|Modeling and editing structures]]
| |
| ### [[:Category:Advanced Issues Modeling and Editing Structures Editing atoms|Editing Atoms]]
| |
| ### [[:Category:Advanced Issues Modeling and Editing Structures Molecular Sculpting|Molecular sculpting]]
| |
| ### [[:Category:Advanced Issues Modeling and Editing Structures Homology Modeling|Homology modeling]]
| |
| ## [[:Category:Advanced Issues Image Manipulation|Image Manipulation]]
| |
| ### [[:Category:Advanced Issues Image Manipulation labels|labels]]
| |
| ### [[:Category:Advanced Issues Image Manipulation Photoshop and GIMP|Photoshop/GIMP]]
| |
| ### [[:Category:Advanced Issues Image Manipulation Stereo Figures|Stereo Figures]]
| |
| ### [[:Category:Advanced Issues Image Manipulation Publication Quatlity Images|Publication-quality images]]
| |
| # [[:Category:Scripting|Scripting]]
| |
| ## [[:Category:Scripting Example Scripts|Example Scripts]]
| |
| ## [[:Category:Scripting Script Library|Script Library]]
| |
| # [[:Category:Plugins|Plugins]]
| |
| ## [[:Category:Plugins Electrostatics and Energy Minimization| How to do electrostatics and energy minimization.]]
| |
| ### [[:Category:Plugins Electrostatics and Energy Minimization APBS| APBS Plugin]]
| |
| ## [[:Category:Plugins rtools | rtools]]
| |
| ## [[:Category:Plugins Tutorial|Tutorial on writing plugins]]
| |
| ## [[:Category:Plugins Others| Others]]
| |
| # [[:Category:High-Level Applications|High-Level Applications]]
| |
| ## [[:Category:High-Level Applications Crystallography Applications|Crystallography Applications]]
| |
| ### [[:Category:High-Level Applications Symmetry|Symmetry]]
| |
| ### [[:Category:High-Level Applications Electron Density|Electron Density]]
| |
| ## [[:Category:High-Level Applications NMR Applications|NMR Applications]]
| |
| ### [[:Category:High-Level Applications NMR Applications Working with a Family of Structures|Working with Structure Families]]
| |
| ### [[:Category:High-Level Applications NMR Applications Superimposition and RMSD|Superimposition and RMSD]]
| |
| ### [[:Category:High-Level Applications NMR Applications NMR Restraints Analysis|NMR Restraints and Analysis]]
| |
| # [[:Category:Third Party Software|Third Party Software]]
| |
| ## [[:Category:Third Party Software Movies|Movies]]
| |
| ## [[:Category:Third Party Software Codecs|Codecs]]
| |
| # [[:Category:Python Integration|Python Integration]]
| |
| # [[:Category:Using PyMol For Unintended Uses|Unintended Uses]] (OpenGL Object Renderer)
| |
| ## [[:Category:Using PyMol For Unintended Uses Arbitrary Graphics Objects| Arbitrary Graphics Objects]]
| |
| # [[:Category:Uncategorized|Uncategorized]] For new pages, misplaced pages, etc.
| |
| ----
| |
| [[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
| |
| ----
| |
