[buster-discuss] New Global Phasing software release with numerous fixes and improvements in Grade2

[BUSTER Developers]

Dear BUSTER users,

We are pleased to announce a new release of our software that includes
numerous fixes and improvements in the Grade2 restraint dictionary
generator and in related matters.

The highlights below are only a subset of the Release Notes, that should be
consulted for full details at

  https://www.globalphasing.com/buster/ReleaseNotes/ReleaseNotes-BUSTER_snapshot_20220203.txt

Highlights of Grade2 Improvements and fixes:

* A bug in the Grade2 --big_planes option has been fixed. The --big_planes
  option merges smaller planes into as large a single plane as possible. In
  the last release, this was done ignoring the sigmas (standard deviation
  of the out-of-plane distance) for individual restraints when merging
  them. The problem is that Grade2 produces weak planar restraints for
  torsion angles that, according to the CSD, have a moderate preference for
  planarity and these were then incorporated into a big plane. Weak planes
  (those with a sigma above 0.020 Angstrom) are now no longer incorporated
  into big planes. Thanks to Dirk Reinert for reporting this bug.
  
* Grade2 has also been altered to produce a single-plane restraint for each
  separate ring that is judged to be flat. Previously, planar rings were
  held flat by a number of four-atom planes. The --4_atom_planes option can
  be used to restore the previous behaviour.

  For further details on both of the above changes, please see the
  "Treatment of Planar Groups" chapter of the Grade2 documentation:

           https://gphl.gitlab.io/grade2_docs/planes.html

* The ligand analysis performed within buster-report against the CSD (via
  Mogul) will now use a MOL2 file whose chemistry is based on the bond
  orders and atom charges given in the ligand's CIF restraint dictionary
  used in the refinement (after CSD standardisation). A tool based on
  Grade2 routines is used to write the MOL2 file, replacing the OpenBabel
  conversion that has proved unreliable. The chemical markup used in the
  CSD Mogul analysis should now correspond exactly to that used in
  restraint dictionary analysis. Thanks to Michael Blaesse and Dirk Reinert
  for reporting the problem.

* Grade2 now produces CIF restraint dictionaries containing both
  electron-cloud and nucleus X-H bond distance restraints, avoiding the
  need for separate restraint dictionaries for the two use cases. The
  --ecloud option is retained to specify that the ideal coordinates for the
  ligand should use the electron cloud rather than nuclear distances. The
  BUSTER refine option "-M Ecloud" can be be used to select the e-cloud
  model, or the option "-M HydrogenHybridModel" to select the hybrid model.

* Grade2 can now read eLBOW and Grade CIF restraint dictionaries as input
  files. As Grade CIF restraint dictionaries lack atom formal charge
  (_chem_comp_atom.charge) records, charges are set to zero when the
  restraint dictionary is read, and care must be taken as this may cause
  the output molecule to be incorrectly specified.

* Grade2 now uses LIG as the default residue name (aka PDB chemical
  component id or 3-letter code). This follows the recent wwPDB
  announcement that LIG is now reserved for new ligands. Please see:

       https://gphl.gitlab.io/grade2_docs/faqs.html#output-residue-name

* Most of the restraint dictionaries distributed in the common-compounds
  directory have been regenerated with the new Grade2 version.


Support has been added to BUSTER for restraint dictionaries containing both
e-cloud and nucleus X-H bond distances, as produced not only by Grade2, but
also by AceDRG and eLBOW. Another fix-up function has been added to
aB_hydrogenate to address the problem that the default Reduce binary (as
e.g. distributed by CCP4) has hardwired hydrogen atom names for HEM that
are no longer correct: these will now be adjusted automatically.


Pipedream will now by default use the number of unique molecules within the
asymmetric unit to let Rhofit search for the appropriate number of
compounds.


As always, we kindly ask that support requests and feedback be sent to our
developer mailing list for BUSTER, Pipedream, Rhofit, Grade and Grade2:

     buster-develop at globalphasing.com   

rather than to individual developers.


With best wishes,

The Global Phasing developers