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- Modeller is now only supported on Windows XP Service Pack 2 or later.
If you want to run Modeller on Windows ME, 2000, or NT, use Modeller 9v8.
- Added support for Python 2.7; Python 2.5 is now supported on all
platforms.
- Bundled version of HDF5 updated to 1.8.5-patch1.
- Initial models generated by automodel now always contain valid PDB
coordinates, i.e. each coordinate is in the range -999.999 to 9999.999.
- During loop modeling, if atoms are missing from the initial model,
loopmodel.loop.write_defined_only can be set True to write out PDBs
containing only non-loop atoms present in the initial model.
- Restraints using user-defined one-dimensional mathematical forms can now
be converted to splines using Restraints.spline().
- Bonds between protein atoms and BLK residues are now restrained more
strongly than regular BLK-Calpha distances.
- alignment.salign() now generates the requested number of suboptimal
alignments, not one less.
- When reading new-style PDB files (with element names in columns 77-78)
Modeller will now use this information to determine whether an atom is a
hydrogen. (With old-style or non-conformant PDB files, it will continue to
guess based on the atom name, so will not read mercury ions for example
unless env.io.hydrogen=True, since it cannot unambiguously determine
whether HG is mercury or "hydrogen bonded to CG".)
- The Windows installer now supports silent installation with the /S flag.
Use the /D flag to specify install location and /KEY to specify the Modeller
license key, e.g. setup.exe /S /KEY=xxx /D=C:\Program Files\modeller
- Bugfix: complete_pdb() now preserves chain IDs.
- Bugfix: environ.dendrogram() no longer crashes if given a distance
matrix of size zero.
- Bugfix: Random seed is no longer ignored by model.make_region().
- Bugfix: MET residues marked as HETATM (e.g. ligands) are now correctly
skipped when env.io.hetatm=False (previously they were read in).
- Bugfix: lookup of atoms by name in models containing duplicated
residue and/or chain names now works correctly.
- Bugfix: fix PSA crash on models containing no amino acids.
- Bugfix: alignment.get_suboptimals() no longer fails to parse
alignments where neither sequence starts at the N terminus, and now
correctly handles alignments where the C termini are misaligned.
- Bugfix: sequences in PAP files can now start in any column (as long as
all the sequences start in the same column), not just column 11.
- Bugfix: allow atom names in the group_restraints atom class file to
contain single-quote characters (e.g. nucleic acid atoms such as O3').
- Bugfix: fix range of spline math forms when resplined by
Restraints.spline().
Next: Changes since release 9v7
Up: MODELLER updates
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Automatic builds
2011-03-29