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## Changes since release 9v6

- A new method alignment.get_suboptimals() allows the suboptimal alignment file generated by alignment.salign() to be easily parsed.

- A new method iterative_structural_align() provides a straightforward way to obtain the best SALIGN structure-structure alignment.

- Problems with statistics (e.g. profile.build() on a small database) now raise a StatisticsError rather than the more generic ModellerError.

- Sequence mismatches between PDB files and alignments now raise a SequenceMismatchError rather than the more generic ModellerError.

- alignment.append() and alignment.read_one() now take a new argument, allow_alternates, which allow for alternate matches of one-letter codes when reading PIR sequence ranges from PDB files (B to N, Z to Q).

- An error message is now reported when using an alignment containing an empty sequence, and reading of the full sequence from a PDB file fails.

- Tab characters in alignment files are now treated the same as any other whitespace, and do not result in cryptic failures.

- Parallel jobs have a new method, job.yield_tasks_unordered(), which is like job.run_all_tasks() but which returns results as they are generated rather than when all the tasks have finished.

- Parallel jobs now default to trying to duplicate the current Python environment (using modslave.py and modpy.sh if necessary) when setting modeller_path, rather than running the mod9v7 script, since the latter may conflict with the Python version of the master.

- Bugfix: TER records are now emitted even for single chain proteins, and contain a unique serial number, the correctly formatted residue name, and the chain ID, as per PDB specifications.

- Bugfix: correct slave Python search path when a parallel job master script is run from a directory other than the current working directory.

- Bugfix: profile.build() no longer crashes when searching empty or very small (less than 10 sequences) sequence databases.

- Bugfix: density.grid_search() no longer exhausts the stack when using large density maps.

- Bugfix: PROFILE or BLOCK alignment with alignment.salign() should now work correctly even when align_block=1.

- Bugfix: alignment.malign() and alignment.salign() now work correctly with alignments containing zero-length sequences.

- Bugfix: when reading multiple copies of the same align code from an alignment file, all sequence metadata is now duplicated correctly.

- Bugfix: scores from the multiple binormal restraint were slightly incorrect in some cases.

- Bugfix: initial loop models containing hydrogens are now read back in correctly (fixes an 'Index x out of range' error).

- Bugfix: residues marked in PDB file REMARKs as BLK are preserved as BLK (rigid bodies) when the PDB is read back in, even when their name appears in the topology library.

- Bugfix: PDB RESOLUTION lines should now be parsed correctly in both old-style (v3.1 or older) PDB files and new-style (v3.2) PDBs.

Next: Comparative modeling class reference Up: MODELLER updates Previous: Changes since release 9v7 Contents Index