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POSF PyMOL Open-Source Fellowship program accepting applications for 2018-2019
New Plugin ProBiS H2O is a new plugin for identification of conserved waters in protein structures.
Official Release PyMOL v2.1 has been released on March 13, 2018.
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
New Plugin LiSiCA is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
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...

PDB Web Services Script

== Overview ==

A short snippet of code utilizing the new PDB Web Services.

Notes:

  1. See PDB Web Services
  2. You need SOAP for Python installed
  3. The sequence of a chain fetched from the PDB does not always equal the sequence of a chain fetched from the PDB Web Services. I believe the PDB Web Services has the complete biological chain, not just what's in the structure.
  4. The offset is a hack; it uses a trick in PyMOL and may not be robust at all. Use at your own caution.

The Code

<source lang="python"> import pymol from pymol import stored, cmd import SOAPpy

  1. define a mapping from three letters to one
  2. Thanks to whomever posted this on the PyMOLWiki:
  3. http://www.pymolwiki.org/index.php/Label

one_letter ={'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q', \ 'ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y', \ 'ARG':'R', 'LYS':'K', 'SER':'S', 'THR':'T', 'MET':'M', 'ALA':'A', \ 'GLY':'G', 'PRO':'P', 'CYS':'C'}

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