The new version of Modeller, 8v2, is now available for download from http://salilab.org/modeller/.
If you have a license key for Modeller 8v1 or 7v7, there is no need to reregister for Modeller 8v2 - the same license key will work. (It won't do any harm to reregister if you want to, though!)
If you encounter bugs in Modeller 8v2, please see http://salilab.org/modeller/manual/node11.html for information on how to report them.
8v2 is largely a bug fix release for 8v1: no changes to your 8v1 Python scripts are necessary to use 8v2, and TOP scripts (from Modeller 7 or 8) will still work. Fixes include:
# Bug fix for model_segment: specifying 'FIRST:@', 'LAST:' will now read in all chains in a multi-chain PDB, even when the first has no ID. # Bug fix: chain breaks were sometimes being placed incorrectly in written-out alignments. # Bug fix: some Python circular references, which were preventing memory from being freed, have been removed, thus fixing some long-running scripts. # Bug fix: pseudo atom tables are now reset where necessary; fixes some 'atom index out of range' errors. # Bug fix: local alignments with alignment.salign() were incorrect in some cases. # Bug fix: alignment.compare_structures() was calculating incorrect RMS values in some cases. # New optimized 2D gap penalties are now used for alignment.salign() by default. # More explanatory error messages for the common 'mismatch between alignment and PDB' problem. # The number of segments for DRMS computation (nsegm) and the matrix offset for structural local alignment (matrix_offset_3d) can now be specified in alignment.salign().
Ben Webb, Modeller Caretaker