Difference between revisions of "Main Page"

From PyMOLWiki
Jump to navigation Jump to search
(2.3)
(12 intermediate revisions by 4 users not shown)
Line 1: Line 1:
 
__NOTOC__
 
__NOTOC__
 
{| 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;"
 
{| 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: 0.30em; border-top: 2px solid #B22222; border-bottom: 1px solid #fff;" |hosted by [[File:SBGridlogo2.jpg|140 px|link=https://sbgrid.org/]]
+
|+ 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;"
 
{| align="center" style="padding-bottom: 3em;"
Line 30: Line 30:
 
|-
 
|-
 
! Official Release
 
! Official Release
−
| [http://pymol.org PyMOL v1.8.4 has been released] on October 4, 2016.
+
| [https://pymol.org PyMOL v2.3 has been released] on February 11, 2019.
 
|-
 
|-
−
! New Script
+
! POSF
−
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
+
| [https://pymol.org/fellowship New PyMOL fellows announced for 2018-2019]
−
|-
 
−
! New Plugin
 
−
| [[Lisica|LiSiCA]] is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
 
−
|-
 
−
! Official Release
 
−
| [http://pymol.org 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
+
! Tutorial
−
| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.6 have all been released] on May 4, 2015.
+
| [[Plugins Tutorial]] updated for PyQt5
 
|-
 
|-
 
! New Plugin
 
! New Plugin
−
| [[PyANM|PyANM]] is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
+
| [[ProBiS_H2O|ProBiS H2O]] is a new plugin for identification of conserved waters in protein structures.
 
|-
 
|-
−
! New Plugin
+
! Selection keywords
−
| [[Bondpack]] is a collection of PyMOL plugins for easy visualization of atomic bonds.
+
| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
 
|-
 
|-
−
! New Plugin
+
! Plugin Update
−
| [[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.
+
| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.5]] is an updated version of channel analysis software in PyMOL
 
|-
 
|-
−
! 3D using Geforce
+
! New Script
−
| 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.
+
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
 
|-
 
|-
 
! Older News
 
! Older News

Revision as of 11:18, 11 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
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...

Cart to frac

= Overview =

This script will convert the real space orthonormal cartesian coordinates of a selection to the fractional coordinates given the loaded cell symmetry.

Example

# load the script

run cart_to_frac.py

# fetch a protein and test

fetch 1rx1, async=0

# get the coordinates for the organic small
# molecule as fractional coordinates

print cart_to_frac("org")

The Code

<source lang="python"> from pymol import cmd

def cart_to_frac(objSel,quiet=0,_self=cmd): 

   """
   Returns an array of fractional atomic coordinates
   for a given object or selection.

   PARAMS
     objSel -- any object or selection

     quiet -- suppress output (default, no)

     _self -- core CMD object; or none

   RETURNS
     Python list of fractional coordinates

   NOTES/EXAMPLES
     cart_to_frac org

     x = cart_to_frac("solvent", quiet=1)
   """
   import numpy
   from numpy import cos, sin, sqrt

   a2r =  ..→
A Random PyMOL-generated Cover. See Covers.


Retrieved from "http://pymolwiki.org/index.php?title=Main_Page&oldid=12879"