Difference between revisions of "Main Page"

From PyMOLWiki
Jump to navigation Jump to search
(PyMOL v1.8.2)
(28 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 25: Line 25:
 
|+ 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
 
|-
 
|-
−
! Tips & Tricks
+
! Official Release
−
| Instructions for [[Movie_pdf|generating movie PDFs]] using .mpg movies from PyMOL.
+
| [http://pymol.org PyMOL v1.8.2 has been released] on April 20, 2016.
−
|-
 
 
|-
 
|-
 
! New Script
 
! New Script
−
| [[Cluster_Count|Cluster Count]] calculates statistics on the B-values for all atoms in the selected object.
+
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
 
|-
 
|-
−
! New Script
+
! New Plugin
−
| [[Make_Figures|Make Figures]] aids you in making publication quality figures for the currently displayed scene.
+
| [[Lisica|LiSiCA]] is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
 
|-
 
|-
−
! New Script
+
! Official Release
−
| [[DistancesRH|Distances RH]]
+
| [http://pymol.org PyMOL v1.8.0 has been released] on Nov 18, 2015.
 
|-
 
|-
−
! PyMOL on the iPad
+
! PyMOL Open-Source Fellowship
−
| PyMOL is now available on the iPad as a free download from the AppStore. See [http://pymol.org/mobile pymol.org/mobile] for more info.
+
| Schrödinger is now accepting applications for the PyMOL Open-Source Fellowship program! Details on http://pymol.org/fellowship
 
|-
 
|-
−
! OS X Compatibility
+
! Official Release
−
| Mac OS X 10.8 doesn't ship with X11. But, you can get the libraries here [http://xquartz.macosforge.org/landing/ X11 Libraries].
+
| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.6 have all been released] on May 4, 2015.
 
|-
 
|-
−
! New Script
+
! New Plugin
−
| [[select_sites]] can set author/paper selections according to SITE annotation in pdb file
+
| [[PyANM|PyANM]] is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
−
|-
 
−
! 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
 
−
| [[uniprot_features]] makes named selections for sequence annotations from uniprot
 
 
|-
 
|-
 
! New Plugin
 
! New Plugin
−
| [[Gyration_tensor]] Calculates chain-wise gyration tensor of a protein.
+
| [[Bondpack]] is a collection of PyMOL plugins for easy visualization of atomic bonds.
−
|-
 
−
! 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
 
−
| [[cyspka]] is an experimental surface cysteine pKa predictor.
 
 
|-
 
|-
 
! New Plugin
 
! New Plugin
−
| [[Contact_Map_Visualizer]] visualize residues corresponding to the contact map
+
| [[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
 
−
| [[spectrum_states]] colors states of multi-state object
 
−
|-
 
−
! New Script
 
−
| [[TMalign]] is a wrapper for the TMalign program
 
−
|-
 
−
! Gallery Updates
 
−
| The [[Gallery|gallery]] has been updated to include a few new ideas and scripts for rendering
 
−
|-
 
−
! 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
+
! 3D using Geforce
−
| Create objects for each molecule or chain in selection with [[split_object]] and [[split_chains]]
+
| 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
 
−
| [[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 112: Line 63:
 
|-
 
|-
 
|<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 129: Line 78:
 
|
 
|
 
|style="vertical-align: top; width: 18%"|
 
|style="vertical-align: top; width: 18%"|
−
<DPL>
+
<DynamicPageList>
 
imagecontainer=Covers
 
imagecontainer=Covers
 
randomcount=1
 
randomcount=1
Line 136: Line 85:
 
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 10:57, 20 April 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
Official Release PyMOL v1.8.2 has been released on April 20, 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...

Pml2py

This script converts a pml script to a python script.

See pymol-users mailing list (Subject: Convert pml script to Pymol Python script, Fri, 8 Apr 2011).

<source lang="python"> from __future__ import print_function

import sys from pymol import cmd, parsing

def pml2py(filename, out=sys.stdout):

DESCRIPTION 

   Convert a pml script to python syntax.

USAGE 

   pml2py infile [, outfile]
   
   def quote(args):
       args = iter(args)
       for arg in args:
           if '=' not in arg:
               prefix = 
           else:
               prefix, arg = arg.split('=', 1)
               prefix += '='
               arg = arg.lstrip()
           yield prefix + repr(arg)

   class stackiter:
       def __init__(self, collection):
           self.iterator = iter(collection)
           self.stack = []
       def __iter__(self):
           return self
       def next(self):
           if len(self.stack):
               return  ..→
A Random PyMOL-generated Cover. See Covers.


Retrieved from "http://pymolwiki.org/index.php?title=Main_Page&oldid=12352"