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- Default gap_penalties_1d for alignment.align2d() have been
changed to match the optimized 2D penalties, as determined from a test
alignment set.
- automodel now constrains any protein-ligand close contacts
(less than 2.3Å) to attempt to preserve protein-ligand chemical bonds.
- New normalized DOPE assessment method, which returns a Z-score, and is
thus comparable between different proteins
(see model.assess_normalized_dope()).
- Bundled version of HDF5 updated to 1.8.1.
- PDB atom files are now also looked for in PDB-style subdirectories (the
first two characters after the digit); e.g. 1abc is searched for in the
'ab' subdirectory, pdb4xyz.ent in the 'xy' subdirectory.
- Libraries updated to correctly read and write remediated RNA and DNA,
some other HETATMs (e.g. ions) and to use the new hydrogen names, in PDB v3.
- Modeller now outputs new-style PDBs, with the element in columns 77 and
78, rather than older-style PDB which has a sequence number in this position.
- Enable Large File Support, to correctly read files bigger than 2GB on
32-bit Unix systems.
- Remove unused residue_grouping and distance_atoms arguments from
Restraints.make().
- Bugfix: no longer ignore excluded pairs between two BLK residues.
- Bugfix: selection.only_mainchain() now considers OXT atoms to be
mainchain.
- Bugfix: alignment.append_model() no longer crashes when trying
to add a structure containing only one atom.
- Bugfix: Topology.make() should now preserve complete IC/BILD
entries for patch residues.
Next: Comparative modeling class reference
Up: MODELLER updates
Previous: Changes since release 9v5
Contents
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Automatic builds
2009-01-30