Difference between revisions of "Main Page"

From PyMOLWiki
Jump to navigation Jump to search
(B2transparency)
(dssr_block)
(35 intermediate revisions by 9 users not shown)
Line 17: Line 17:
 
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''
 
| style="font-size: 1.1em; color #61021F; 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 26: Line 26:
 
|-
 
|-
 
! New Script
 
! New Script
−
| [[b2transparency]] can set surface transparency based on atom b-factor
+
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
−
|-
 
−
! 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
 
 
|-
 
|-
 
! New Plugin
 
! 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
+
! Official Release
−
| [[set_phipsi]] can set phi/psi angles for all residues in a selection
+
| [http://pymol.org PyMOL v1.8.0 has been released] on Nov 18, 2015.
 
|-
 
|-
−
! New Script
+
! PyMOL Open-Source Fellowship
−
| [[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.  
+
| Schrödinger is now accepting applications for the PyMOL Open-Source Fellowship program! Details on http://pymol.org/fellowship
 
|-
 
|-
−
! New Script
+
! Official Release
−
| [[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!
+
| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.6 have all been released] on May 4, 2015.
 
|-
 
|-
−
! New Script
+
! New Plugin
−
| [[cyspka]] is an experimental surface cysteine pKa predictor.
+
| [[PyANM|PyANM]] is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
 
|-
 
|-
 
! New Plugin
 
! New Plugin
−
| [[Contact_Map_Visualizer]] visualize residues corresponding to the contact map
+
| [[Bondpack]] is a collection of PyMOL plugins for easy visualization of atomic bonds.
 
|-
 
|-
−
! New Script
+
! New Plugin
−
| [[spectrum_states]] colors states of multi-state object
+
| [[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.
−
|-
 
−
! New Script
 
−
| [[TMalign]] is a wrapper for the TMalign program
 
 
|-
 
|-
−
! 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
 
! Older News
Line 90: Line 60:
 
|-
 
|-
 
|<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=450
+
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 107: Line 75:
 
|
 
|
 
|style="vertical-align: top; width: 18%"|
 
|style="vertical-align: top; width: 18%"|
−
<DPL>
+
<DynamicPageList>
 
imagecontainer=Covers
 
imagecontainer=Covers
 
randomcount=1
 
randomcount=1
Line 114: Line 82:
 
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 11:52, 26 January 2016

Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
New accounts: email jason (dot) vertrees (@) gmail dot com
Quick Links
Tutorials Table of Contents Commands
Script Library Plugins FAQ
Gallery | Covers PyMOL Cheat Sheet (PDF) Getting Help
News & Updates
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...

Supercell

Included in psico
This command or function is available from psico, which is a PyMOL extension.

Module psico.xtal
Example with 2 unit cells in c-direction, created with: supercell 1,1,2,2x19

supercell can display multiple copies of the unit cell. Can also fill the unit cell (and its copies) with symmetry mates.

See thread on pymol-users mailing list.

Requires numpy.

Example

# import psico.xtal, or run the standalone script:
run https://raw.githubusercontent.com/speleo3/pymol-psico/master/psico/xtal.py

fetch 2x19, async=0
supercell 2,1,1, 2x19, green
supercell 1,1,2, 2x19, orange, name=super2

See Also
A Random PyMOL-generated Cover. See Covers.


Retrieved from "http://pymolwiki.org/index.php?title=Main_Page&oldid=12276"