The new version of Modeller, 9v7, 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 9v7 - the same license key will work. (It won't do any harm to reregister if you want to, though!)
9v7 is primarily a bugfix release relative to the last public release (9v6). Major user-visible changes include:
# A new method alignment.get_suboptimals() allows the suboptimal alignment file generated by alignment.salign() to be easily parsed.
# A new method iterative_structural_align() provides a straightforward way to obtain the best SALIGN structure-structure alignment.
# alignment.append() and alignment.read_one() now take a new argument, allow_alternates, which allow for alternate matches of one-letter codes when reading PIR sequence ranges from PDB files (B to N, Z to Q).
# Parallel jobs have a new method, job.yield_tasks_unordered(), which is like job.run_all_tasks() but which returns results as they are generated rather than when all the tasks have finished.
# Parallel jobs now default to trying to duplicate the current Python environment (using modslave.py and modpy.sh if necessary) when setting modeller_path, rather than running the mod9v7 script, since the latter may conflict with the Python version of the master.
See the Modeller manual for a full change log: http://salilab.org/modeller/9v7/manual/node38.html
If you encounter bugs in Modeller 9v7, please see http://salilab.org/modeller/9v7/manual/node10.html for information on how to report them.
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Ben Webb, Modeller Caretaker