Difference between revisions of "Main Page"

Revision as of 07:41, 13 July 2017

hosted by

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
Plugin Update	MOLE 2.5 is an updated version of channel analysis software in PyMOL
Official Release	PyMOL v1.8.6 has been released on March 9, 2017.
Official Release	PyMOL v1.8.4 has been released on October 4, 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...
Dump The dump command writes the geometry of an isosurface, isomesh, or isodot object to a simple text file. Each line contains one vertex. For surface objects, XYZ coordinates and the normal are exported. Three lines make one triangle (like `GL_TRIANGLES`). For mesh objects, XYZ coordinates are exported (no normals). The vertices form line strips (like `GL_LINE_STRIP`), a blank line starts a new strip. For dot objects, XYZ coordinates are exported. Usage dump filename, object Arguments filename = str: file that will be written object = str: object name Example fetch 1ubq, mymap, type=2fofc, async=0 isosurface mysurface, mymap dump surfacegeometry.txt, mysurface isomesh mymesh, mymap dump meshgeometry.txt, mymesh isodot mydot, mymap dump dotgeometry.txt, mydot See Also COLLADA export

A Random PyMOL-generated Cover. See Covers.

@@ Line 1: / Line 1: @@
 __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.
-|- 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]]'')
-||'''[[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 &amp; Updates
 |-
-Max OS X 10.8
+! Plugin Update
-! X11 Libraries
+| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.5]] is an updated version of channel analysis software in PyMOL
-| 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
+! Official Release
-! New Script
+| [http://pymol.org PyMOL v1.8.6 has been released] on March 9, 2017.
-| [[select_sites]] can set author/paper selections according to SITE annotation in pdb file
 |-
-! New Script
+! Official Release
-| [[b2transparency]] can set surface transparency based on atom b-factor
+| [http://pymol.org PyMOL v1.8.4 has been released] on October 4, 2016.
-|-
-! New Extension
-| [[psico]] is a python module which extends PyMOL with many commands
 |-
 ! New Script
-| [[uniprot_features]] makes named selections for sequence annotations from uniprot
+| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
 |-
 ! New Plugin
-| [[Gyration_tensor]] Calculates chain-wise gyration tensor of a protein.
+| [[Lisica|LiSiCA]] is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
-|-
-! New Script
-| [[set_phipsi]] can set phi/psi angles for all residues in a selection
 |-
-! New Script
+! Official Release
-| [[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.
+| [http://pymol.org PyMOL v1.8.0 has been released] on Nov 18, 2015.
 |-
-! New Script
+! PyMOL Open-Source Fellowship
-| [[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!
+| Schrödinger is now accepting applications for the PyMOL Open-Source Fellowship program! Details on http://pymol.org/fellowship
 |-
-! New Script
+! Official Release
-| [[cyspka]] is an experimental surface cysteine pKa predictor.
+| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.6 have all been released] on May 4, 2015.
 |-
 ! New Plugin
-| [[Contact_Map_Visualizer]] visualize residues corresponding to the contact map
+| [[PyANM|PyANM]] is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
 |-
-! New Script
+! New Plugin
-| [[spectrum_states]] colors states of multi-state object
+| [[Bondpack]] is a collection of PyMOL plugins for easy visualization of atomic bonds.
 |-
-! New Script
+! New Plugin
-| [[TMalign]] is a wrapper for the TMalign program
+| [[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.
 |-
-! Gallery Updates
+! 3D using Geforce
-| The [[Gallery|gallery]] has been updated to include a few new ideas and scripts for rendering
+| 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 Script
-| [[save_settings]] can dump all changed settings to a file
-|-
-! 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
@@ Line 98: / Line 73: @@
 |-
 |<div class="didyouknow" >
-<DPL>
+<DynamicPageList>
-namespace=
+randomcount=1
 category=Commands|Plugins|Script_Library|Settings
 includepage=*
-includemaxlength=450
+includemaxlength=1050
 escapelinks=false
+allowcachedresults=false
 resultsheader=__NOTOC__ __NOEDITSECTION__
-randomcount=1
-mode=userformat
-addpagecounter=true
 listseparators=,<h3>[[%PAGE%]]</h3>,,\n
-</DPL>
+</DynamicPageList>
 </div>
 <div style="clear: both;"></div>
@@ Line 115: / Line 88: @@
 |
 |style="vertical-align: top; width: 18%"|
-<DPL>
+<DynamicPageList>
 imagecontainer=Covers
 randomcount=1
@@ Line 122: / Line 95: @@
 listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover.  See [[Covers]].]],\n
 ordermethod=none
-</DPL>
+allowcachedresults=false
+</DynamicPageList>
 |}

Difference between revisions of "Main Page"

Revision as of 07:41, 13 July 2017

Dump

Usage

Arguments

Example

See Also

Navigation menu

Search