The new version of Modeller, 9v5, 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 9v5 - the same license key will work. (It won't do any harm to reregister if you want to, though!)
9v5 is primarily a bugfix release relative to the last public release (9v4). Major user-visible changes include:
# New normalized DOPE assessment method, which returns a Z-score, and is thus comparable between different proteins. # PDB atom files are now also looked for in PDB-style subdirectories (the first two characters after the digit); e.g. 1abc is searched for in the 'ab' subdirectory, pdb4xyz.ent in the 'xy' subdirectory. # Libraries updated to correctly read and write remediated RNA and DNA, some other HETATMs (e.g. ions) and to use the new hydrogen names, in PDB v3. # Modeller now outputs new-style PDBs, with the element in columns 77 and 78, rather than older-style PDB which has a sequence number in this position.
See the Modeller manual for a full change log: http://salilab.org/modeller/9v5/manual/node38.html
If you encounter bugs in Modeller 9v5, please see http://salilab.org/modeller/9v5/manual/node10.html for information on how to report them.
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Ben Webb, Modeller Caretaker