Changes since release 8v1

• 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().