The new version of Modeller, 9.12, 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 9.12 - the same license key will work. (It won't do any harm to reregister if you want to, though!)
9.12 is primarily a bugfix release relative to the last public release (9.11). Major user-visible changes include:
# Modeller is now only supported on Mac OS X 10.6 or later. If you want to run Modeller on older OS X releases, use Modeller 9.11.
# alignment.align(), alignment.salign() and alignment.align2d() now attempt to keep chain breaks aligned when aligning multi-chain sequences. This behavior can be tuned with the break_break_bonus parameter.
# alignment.edit() has a new by_chain parameter; if set, overhangs are removed for each chain in multi-chain alignments.
# Align codes (identifiers of sequences in alignment objects) can now be of any length. (Codes in profile and sequence_db objects are still limited to 40 characters.)
# Modeller now matches residues in PDB files using both name and ATOM/HETATM indicator; previously just the name was used. This allows for correctly reading PDB files containing amino acid ligands, for example (they were previously forcibly mapped to ATOM on output).
# Added support for Python 3.3.
See the Modeller manual for a full change log: http://salilab.org/modeller/9.12/manual/node39.html
If you encounter bugs in Modeller 9.12, please see http://salilab.org/modeller/9.12/manual/node10.html for information on how to report them.
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Ben Webb, Modeller Caretaker