[buster-discuss] New snapshot release of the Global Phasing software with major improvements in Pipedream and mmCIF deposition

[Buster Developers]

Dear BUSTER users,

We are pleased to announce a new release of our software containing many new
developments, improvements and fixes relative to the previous (11 Dec 2020)
release. Several of them have benefited from close interactions with users
and from requests and guidance formulated by our Consortium members. As
always, all feedback is very much appreciated and gratefully acknowledged.

The pre-Rhofit (i.e. pre ligand fitting) stage of the Pipedream automation
pipeline has seen significant developments to provide a better distinction
between the refinement of the "best" (APO) model and the actual ligand
detection stage. Extensive internal testing has shown this to result on
average in better models (including solvent) and better ligand placement,
with only a relatively small impact on execution time due to improvements in
convergence and in the subsequent decision making.

Several improvements have been made in BUSTER regarding the handling of
hydrogens, of alternate conformations and of occupancy refinement. Please be
aware that CSD 2021 is currently unsupported on MacOS 11 (Big Sur) and that
therefore neither Grade (grade and grade_PDB_Ligand) nor buster-report are
supported on that platform.


Last but not least: as part of our sustained activities within the wwPDB's
PDBx/mmCIF Deposition SubGroup on Data Collection/Processing, we have
defined new dictionary items (over 50 in total), complete with detailed
descriptions, that have now been incorporated into the official PDB Exchange
(PDBx/mmCIF) Dictionary that supports deposition to the PDB - see :

     https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/   .

Their purpose is to facilitate the deposition and archiving of various types
of diffraction data, as well as accommodate new quality metrics pertaining
to these data. This includes, in particular, reflection data that have been
processed by STARANISO to take account of diffraction anisotropy, with
descriptors for that anisotropy, for the cut-off criterion applied to the
data, and for the ellipsoid fitted to the cut-off surface.

We have made sure that deposition-ready mmCIF files produced by our software
(autoPROC and BUSTER) take advantage of these new definitions and validate
against the updated mmCIF dictionary. As a consequence, users are very much
encouraged to upload these files directly to the PDB for deposition, and
thus avoid the MTZ + PDBEXTRACT route altogether. We have updated our
deposition instructions accordingly, see:

     https://www.globalphasing.com/buster/wiki/index.cgi?DepositionMmCif


Please consult the relevant Release Notes for more detailed descriptions of
these highlights and of all additional changes at

  https://www.globalphasing.com/buster/ReleaseNotes/ReleaseNotes-BUSTER_snapshot_20210224.txt

  https://www.globalphasing.com/autoproc/ReleaseNotes/ReleaseNotes-autoPROC_snapshot_20210224.txt


With best wishes,

The Global Phasing developers