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Modeller Changelog

What's new in Modeller 9.14

Oct 13, 2014
  • The new PDB format (PDBx/mmCIF) is now handled.
  • Templates can be mmCIF files, and model.read() and model.write() also support mmCIF. See also automodel.set_output_model_format() to write out models in mmCIF format.
  • automodel-generated PDB or mmCIF files now contain extra header information, including the names of the sequence and template(s) and the values of any assessment scores.
  • Add Python 3.4 support.
  • Add support for 64-bit Windows.
  • density.read() now uses the origin in the MRC/CCP4 file if it is not specified.
  • Bundled version of HDF5 updated to 1.8.11.
  • Bugfix:
  • Doesn't generate invalid format PDB files when biso

New in Modeller 9v3 (Feb 7, 2008)

  • Mac OS X 10.5 (Leopard) is now supported (with Python 2.5).
  • Added structure.write() method, to write out current template structures as PDB files.
  • Added chain.write(), chain.filter(), and chain.atom_file_and_code() methods, to write out sequences of individual chains. These obsolete the model.make_chains() method.
  • Added selection.only_defined() method, which selects only atoms with defined coordinates.
  • The GB/SA scorer is now implemented as a user-defined energy term; energy_data.dynamic_gbsa has thus been removed.
  • User-defined energy terms in C now get passed additional libraries and energy_data parameters.
  • Invalid headers in PIR alignment files now result in an error, to avoid potential problems with these headers going unnoticed.
  • File format errors now have their own Python exception - FileFormatError - which is a subclass of the generic ModellerError.
  • alignment.align() and alignment.consensus() no longer take a max_gap_length parameter, as it is not used in any case.
  • Profile objects now have a positions member, which is a list of all aligned positions, similar to the same member for alignment objects.
  • selection.debug_function() now returns the number of derivatives which exceeded the cutoffs.
  • Bundled version of HDF5 updated to 1.6.6.
  • Bugfix: always read the first PDB alternate location encountered for each residue, not only A or 1, which resulted in skipping of residues which used neither of these codes.
  • Bugfix: no longer limit atom file names in PIR comment lines to 80 characters.
  • Bugfix: user-defined mathematical forms no longer cause an error in restraints.pick() when restraints_filter is not -999.
  • Bugfix: the scoring function will return an error if a coordinate has become infinite or not-a-number (e.g. due to a bad optimization).
  • Bugfix: the INITIAL_MALIGN3D option works again with TOP scripts.
  • Bugfix: selection.superpose() now returns correct values for num_equiv_pos and num_equiv_dist (previously these were erroneously the same as the cutoff values).
  • Bugfix: calling selection.energy() from within an optimizer periodic action no longer causes the optimization to cycle endlessly.
  • Bugfix: alignment.append_model() now puts the current model coordinates into the alignment, not the PDB in its original orientation.