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