- Modeller now includes a variety of SOAP (statistically optimized atomic
potential) scores for assessing proteins, loops, and interfaces.
- Bundled version of HDF5 updated to 1.8.10.
- The Lennard-Jones interaction energy is now artificially truncated at
very short distance; this makes simulations with poor starting conditions
much less likely to 'blow up'.
- Residue, Atom and Chain objects can now be
meaningfully compared in Python (previously == would always return False).
- model.get_insertions(), model.get_deletions() and
model.loops() now have an include_termini option; if False,
residue ranges that include chain termini are excluded from the output.
- Most Modeller objects can now be written to or read from file handles
(e.g. modfile.File(), or any Python filelike object) as well as named
files.
- automodel now accepts file handles or alignment objects for
the alnfile parameter.
- Structure.read() allows reading an alternative conformation
of a template.
- User-defined energy terms can now report violations and energy profiles.
- The sigma factor for EM fitting can now be modified
(density.sigma_factor).
- Bugfix: have Restraints.make_distance() restrain distances where the
template is a non-standard residue with a standard backbone (e.g. UNK,
ASX, GLX).
- Bugfix: don't falsely warn about topology being available for every
BLK residue when automodel reads the initial model PDB file back in.
- Bugfix: model.get_insertions() previously ommitted the first residue
of insertions in some cases, while model.get_deletions() incorrectly
handled overhangs and a single residue between two deletions.
- Bugfix: model.build() no longer crashes when trying to interpolate and
exactly one atom in the segment has defined coordinates.
- Bugfix: model.build() no longer uses atoms in a different chain
as anchors for interpolation.
- Bugfix: derivatives of the angle feature are now more stable when the
angle is close to 180 degrees.
Automatic builds
2014-07-26
