The new version of Modeller, 9.9, 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 9.9 - the same license key will work. (It won't do any harm to reregister if you want to, though!)
9.9 is primarily a bugfix release relative to the last public release (9v8). Major user-visible changes include:
# The Windows version of Modeller is now only supported on XP Service Pack 2 or later. If you want to run Modeller on Windows 98, ME, 2000, or NT, use Modeller 9v8.
# Added support for Python 2.7 to Windows and Linux Modeller; Python 2.5 is now supported on all platforms.
# Initial models generated by automodel now always contain valid PDB coordinates, i.e. each coordinate is in the range -999.999 to 9999.999.
# During loop modeling, if atoms are missing from the initial model, loopmodel.loop.write_defined_only can be set True to write out PDBs containing only non-loop atoms present in the initial model.
# When reading new-style PDB files (with element names in columns 77-78) Modeller will now use this information to determine whether an atom is a hydrogen. (With old-style or non-conformant PDB files, it will continue to guess based on the atom name, so will not read mercury ions for example unless env.io.hydrogen=True, since it cannot unambiguously determine whether HG is mercury or "hydrogen bonded to CG".)
See the Modeller manual for a full change log: http://salilab.org/modeller/9.9/manual/node38.html
If you encounter bugs in Modeller 9.9, please see http://salilab.org/modeller/9.9/manual/node10.html for information on how to report them.
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Ben Webb, Modeller Caretaker