[buster-discuss] New Global Phasing BUSTER software release containing new features, improvements and fixes across several packages

[BUSTER Developers]

Dear BUSTER users,

     We are pleased to announce a new release of our software containing new
features, improvements and fixes across several packages, as well as some
new utility programs. More detailed descriptions can be found in the Release
Notes at

https://www.globalphasing.com/buster/ReleaseNotes/ReleaseNotes-BUSTER_snapshot_20240710.txt

of which a summary may be found below.

### Improvements and new features:

  * Initial support for partial charges (in steps of 0.1) on atoms via an
    extension of the PDB format, so that partial-charge form factors can be
    used in BUSTER.

    This feature needs to be explicitly switched on via a parameter setting.

  * New tool (cif2tls) to extract TLS information (selection and parameter
    values) from mmCIF files - similar to the existing pdb2tls tool.

  * The buster_maponly and buster_rvalues tools will now also report scale
    parameters (if run with increased verbosity, i.e. with the -v flag).

    It now also supports mmCIF reflection data files that only have
    intensities, I+/I- or F+/F- data.

  * We now analyse anisotropic restraint outliers in the Screen output.
    There are reports for each restraint type and also for the overall
    function value on a per-atom basis. The latter contains a breakdown into
    the different residual types as a relative percentage. This will be
    further consolidated and should provide a sensitive means of identifying
    any problematic atoms. We very much encourage user feedback: please
    remember to check 01-BUSTER/Cycle-5/shell.01/screen_final.txt from time
    to time.

  * For PDB entries that come only as mmCIF (and for which the PDB archive
    doesn't provide a PDB format version), the "fetch_PDB_gemmi" tool now
    supports changing the automatically renamed 5-character compound
    identifiers. Further improvements to the fetch_PDB_gemmi tool have been
    made: see the full Release Notes for much more detail on these.

  * GEMMI has been updated to version v0.6.6-18-gd726fa1 (June 28th 2024).

  * The BUSTER CSD-core configuration method, used by Grade2, Grade, and
    buster-report, has been revised following recent large-scale changes to
    the CSD directory structure and configuration processes. This alteration
    facilitates a procedure to speed up Grade2 by making a local copy of the
    databases used. This is useful when CSD-core is installed on a slow
    network disk. Again, much more detail can be found in the Release Notes.

  * If using the latest release of CSD-Core (2024.1 and later), Grade2 will
    now only use the main Mogul database based on the annually released CSD
    database, ignoring the update releases that are made 3 times a year and
    can cause bias.

  * Grade2 now supports using in-house Mogul databases produced from sets of
    internal small molecule structures.

  * In Grade2, added support for CXSMILES with enhanced stereochemistry and
    or group definitions.

  * Please note that in the next BUSTER release the old deprecated Grade
    restraint generator will be removed from the distribution.

    Furthermore, to simplify support, the next BUSTER release will not work
    with CSD-core versions older than 2024.1

    If you are using an old version of CSD-Core we recommend that you update
    to the latest version, as soon as possible.

### Fixes:

  * To support the CCP4-9 release, the wrapper that runs the modelcompare
    binary from the PDB_REDO suite (as part of the remediation features of
    Pipedream) has been updated.

  * Added a safety feature to ensure that when multiple files are given by
    multiple -Gelly arguments, they are certain to contain a final LF (line
    feed) character before concatenating them. Thanks to Eugene Krissinel,
    Rasmus Klintrot and Maria Fando for reporting that problem when running
    BUSTER through the CCP4 cloud (fixed there now too).

  * Improved handling of additional datablocks (that don't have actual
    amplitude/intensity data) for the "aB_deposition_combine" command (to
    combine mmCIF contents from model refinement with those from data
    processing).

  * Fixed MacOS versions of "buster_maponly" and "buster_rvalues" that
    inadvertently had the path wrongly set to the Linux binaries.
      
  * Fixed bug in fetch_PDB_gemmi when encountering reflection data
    containing only I+/I- (or F+/F-) data and not IMEAN (or F): the
    computation of IMEAN (or F) was incorrect for incomplete acentric
    reflections, i.e. where e.g. only I+ or only I- was given.

  * Small improvements and fixes to Grade2 are listed in the Changelog:
    https://gphl.gitlab.io/grade2_docs/changelog.html



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Please remember that these highlights are only a condensed summary of the
much more extensive information given in the Release Notes referred to at
the beginning of this announcement, that you are urged to consult in full.
--------------------------------------------------------------------------


     As always, we kindly ask that all support requests and feedback be sent
to our developers' mailing lists:
 
     buster-develop at globalphasing.com

rather than to individual developers.


     With best wishes,

The Global Phasing developers