User Tools

Site Tools


PyMOL v1.3r2 (Dec. 2010)

  • Fully dynamic measures (see demo [32MB MP4])
  • A > Generate > Selection > Surface Residues
  • Fixed dihedral bug

PyMOL v1.3r1

Released Aug 6, 2010

  • Updated the fetch command to work with new server paths, internationally
  • Updated the fetch command to handle all forms of biological units “pdb1,” “pdb2,” “pdb3,” etc.
  • Corrected mis-matched map naming in fetch
  • Added filtering step in File>Save Molecule…
  • Added mouse-mode tracking, improved neighbor finding, mixed-mode measurements to the Measurement Wizard
  • Fixed

PyMOL v1.3

Released May, 2010

New and Modified Commands


  • cealign – cealign is a new command that performs protein structure alignment using the CE algorithm.


  • fetch – This command has the new capability of downloading omit maps from the EDS server. To download a map, supply the type=mapType flag to PyMOL, where mapType={“fofc”, “2fofc”} is the type of map you want. Here's an example:

# fetch the protein 1CLL
fetch 1cll;

# now fetch its map
fetch 1cll, type=2fofc


  • obscure 1: introduction to the 'obscure' command (1280x720 HD).
  • obscure 2: command options for the 'obscure' command (1280x720 HD).

New Settings

  • fetch_host: set to “pdb” to download from; “pdbe” to download from European PDB server, or “pdbj” for Japanese PDB server.
  • movie_quality: set to any value between 1 and 100. The higher the better the final movie quality; 60 is default.
  • neighbor_cutoff: cutoff for finding neighbors in measurements wizard; defaults to 3.5 Angstroms.
  • polar_neighbor_cutoff: cutoff for finding polar neighbors in measurements wizard; defaults to 3.5 Angstroms.
  • heavy_neighbor_cutoff: cutoff for finding heavy neighbors in measurements wizard; defaults to 3.5 Angstroms.
  • label_anchor: set to “CA” for alpha carbon, “CB” for beta carbon; determines where residues are labeled by default.
  • dynamic distances: introduction to dynamic_measures setting (1280x720 HD).

APBS Plugin v2.0

media/new13.txt · Last modified: 2013/11/06 23:34 by holder