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 http://salilab.org/modeller/ 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.
See the Modeller manual for a full change log: http://salilab.org/modeller/
- 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 sequence_db.read().
If you encounter bugs in Modeller 9v8, please see http://salilab.org/modeller/
9v8/manual/node10.html for information on how to report them.