Wednesday, April 28, 2010

Modeller 9v8 release

I just received this e-mail about the modeller software for protein structure comparative modeling and alignment. It's not open source, but I remember that many people depended on it. How is the situation now?

The new version of Modeller, 9v8, is now available for download! Please see the download page at for more information.

If you have a license key for Modeller 8 or 9, there is no need to reregister for Modeller 9v8 - the same license key will work. (It won't do any harm to reregister if you want to, though!)

9v8 is primarily a bugfix release relative to the last public release (9v7). Major user-visible changes include:Silicon Graphics (IRIX) binaries are no longer provided. If you wish to use Modeller on an IRIX machine, please use the older 9v7 version.
  • Residues treated as BLK no longer have to be HETATM residues; they will be marked as ATOM if so defined in restyp.lib or in the template  PDB (for example, DNA or RNA residues). automodel.nonstd_restraints()  now builds restraints on both HETATM and BLK residues.
  • Bonds between BLK residues are now detected by a simple distance criterion and are restrained more strongly than other distances by automodel.nonstd_restraints().
  • A new method Chain.join() allows chain breaks between chains to be removed.
  • Files compressed with 'xz' can now be read, provided that the 'xz' binary is available on your system.
  • The allow_alternates option to alignment.append() will now allow G in the alignment sequence to match any non-standard residue type in the PDB file which maps to G. This is useful if the alignment sequence is 'cleaned' as by
See the Modeller manual for a full change log:

If you encounter bugs in Modeller 9v8, please see for information on how to report them.

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