Difference between revisions of "Main Page"

From PyMOLWiki
Jump to navigation Jump to search
(poll protein/nucleic)
(2to3)
(8 intermediate revisions by 2 users not shown)
Line 29: Line 29:
 
|+ 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
 
|-
 
|-
−
! Poll
+
! Python 3
−
| [https://goo.gl/forms/r0Ck03VTytZQxN4A2 New protein/nucleic selection keywords for PyMOL] - Tell us what you think!
+
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
 
|-
 
|-
 
! Official Release
 
! Official Release
−
| [https://pymol.org PyMOL v2.0 has been released] on September 20, 2017.
+
| [https://pymol.org PyMOL v2.3 has been released] on February 11, 2019.
 
|-
 
|-
−
! Plugin Update
+
! POSF
−
| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.5]] is an updated version of channel analysis software in PyMOL
+
| [https://pymol.org/fellowship New PyMOL fellows announced for 2018-2019]
−
|-
 
−
! Official Release
 
−
| [http://pymol.org PyMOL v1.8.6 has been released] on March 9, 2017.
 
 
|-
 
|-
−
! Official Release
+
! Tutorial
−
| [http://pymol.org PyMOL v1.8.4 has been released] on October 4, 2016.
+
| [[Plugins Tutorial]] updated for PyQt5
−
|-
 
−
! New Script
 
−
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
 
 
|-
 
|-
 
! New Plugin
 
! New Plugin
−
| [[Lisica|LiSiCA]] is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
+
| [[ProBiS_H2O|ProBiS H2O]] is a new plugin for identification of conserved waters in protein structures.
 
|-
 
|-
−
! Official Release
+
! Selection keywords
−
| [http://pymol.org PyMOL v1.8.0 has been released] on Nov 18, 2015.
+
| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
 
|-
 
|-
−
! PyMOL Open-Source Fellowship
+
! Plugin Update
−
| Schrödinger is now accepting applications for the PyMOL Open-Source Fellowship program! Details on http://pymol.org/fellowship
+
| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.5]] is an updated version of channel analysis software in PyMOL
 
|-
 
|-
−
! Official Release
+
! New Script
−
| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.6 have all been released] on May 4, 2015.
+
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
−
|-
 
−
! New Plugin
 
−
| [[PyANM|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: advanced approach for analysis of biomacromolecular channels|MOLE 2.0]] is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.
 
−
|-
 
−
! 3D using Geforce
 
−
| 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.
 
 
|-
 
|-
 
! Older News
 
! Older News

Revision as of 05:27, 19 February 2019

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
Python 3 New Python 3 compatibility guide for scripts and plugins
Official Release PyMOL v2.3 has been released on February 11, 2019.
POSF New PyMOL fellows announced for 2018-2019
Tutorial Plugins Tutorial updated for PyQt5
New Plugin ProBiS H2O is a new plugin for identification of conserved waters in protein structures.
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...

Super

super aligns two selections.

It does a sequence-independent (unlike align) structure-based dynamic programming alignment followed by a series of refinement cycles intended to improve the fit by eliminating pairing with high relative variability (just like align). super is more robust than align for proteins with low sequence similarity.

Usage

See align command.

Caveats

  • Alternative Conformations: If super ever tells you no matched atoms, then instead of 
    super p1, p2
    try 
    super p1 & alt A+'', p2 & alt B+''

User Scripts

Write rmsd to file

pymol_rmsd_test.pml 

reinitialize

fetch 1F9J, async=0
fetch 1YX5, async=0

extract 1F9J_A, 1F9J and chain A
extract 1YX5_B, 1YX5 and chain B

test=cmd.super("1F9J_A","1YX5_B")

python
writefile=open("rmsd_file.txt","a")
writefile.write(' '.join('%s' % x for x in test))
writefile.write('\n')
writefile.close()
python end

In ..→

A Random PyMOL-generated Cover. See Covers.


Retrieved from "http://pymolwiki.org/index.php?title=Main_Page&oldid=12882"