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Revision as of 10:57, 20 April 2016 by Speleo3 (talk | contribs) (PyMOL v1.8.2)
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The community-run support site for the PyMOL molecular viewer.
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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...

Fetch Host

The fetch_host setting controls from which PDB server you download files when using the fetch command. You options are:
  • pdb
  • pdbe
  • pdbj
  • mirror URL with "divided" layout (new in PyMOL 1.6)

for the standard RCSB (pdb), pdb mirror in europe, and the pdb mirror in Japan.

New in PyMOL 1.3

Details

The exact URL (or list of URLs to try) is stored in pymol.importing.hostPaths[type]. The fetch_host setting only applies to the incomplete (not starting with scheme://) URL entries there.

Usage

set fetch_host, pdb
set fetch_host, pdbe
set fetch_host, pdbj
set fetch_host, http://ftp.wwpdb.org/pub/pdb
set fetch_host, file:///local/mirror/pub/pdb
# Paths which are appended to fetch_host
import pymol
pymol.importing.hostPaths["cif"] = "/data/structures/divided/mmCIF/{mid}/{code}.cif.gz"
pymol.importing.hostPaths["pdb"] = "/data/structures/divided/pdb/{mid}/pdb{code}.ent.gz"

<syntaxhighlight lang="python">

  1. Don't use ..→
A Random PyMOL-generated Cover. See Covers.