BUSTER provides mmCIF files ready for deposition to the wwPDB since the 20190214 release: these are automatically generated at the end of each refinement. In order to be aware of the latest developments for this feature, please:

  • ensure your BUSTER installation is up-to-date,
  • see if the issues page has release-specific information,
  • be careful about using conversion or harvesting tools (like PDB_EXTRACT or SF_CONVERT) as part of the deposition process. They are e.g. not always aware of autoPROC as a processing package - or of the type of analysis STARANISO would perform - and are not necessarily up-to-date with the correct source (log files etc) for a particular mmCIF item. All this can easily result in confusion and incorrect data making it into the archived file(s).

The two relevant files for deposition of BUSTER models are

  • BUSTER_model.cif: This file contains the atomic model as well as any non-standard restraint information (e.g. for a unique ligand or compound).
  • BUSTER_refln.cif: This file can contain several so-called data blocks. The first one contains all the standard reflection data (observed amplitudes and their sigmas, model structure factors, figure-of-merit, Hendrickson-Lattmann coefficients, test-set flags - see also here) as well as map coefficients (mFo-DFc difference map and 2mFo-DFc map) for all observed reflections.
    • To accomodate different types of map-coefficients (isotropically filled-in 2mFo-DFc and/or anisotropically filled-in 2mFo-DFc coefficients as defined by e.g. STARANISO), additional data loops could be present with relevant information stored in each "_diffrn.details" tag to describe these.

Additionally and if you used autoPROC for data processing:

  • autoPROC provides its own deposition-ready PDBx/mmCIF files for reflection data - including all the processing (scaling and merging) data quality metrics.
    • These need to be combined with the model and reflection data files coming from BUSTER.
    • In most cases the relevant file(s) from data processing will be called
      • Data_1_autoPROC_STARANISO_all.cif (for anisotropic/STARANISO analysis), or
      • Data_2_autoPROC_TRUNCATE_all.cif (for traditional/isotropic analysis)
    • A user needs to pick the relevant one, depending on what (MTZ) file from data processing was picked for further structure solution and refinement.
    • The aB_deposition_combine tool should be used to (1) detect/check for the correct processing result and (2) combine those with the two files from BUSTER - after taking potential re-indexing and SG differences into account. It will also ensure that the correct set of data quality metrics from data processing are transferred into the model mmCIF file (where they are kept for historical reasons within archived PDB entries).
    • See aB_deposition_combine -h for further information about the usage.
  • If the data quality metrics should be provided manually to the deposition system, the relevant scaling/merging statistics for STARANISO data (staraniso_alldata-unique.mtz) are in staraniso_alldata-unique.table1. Please do not use PDB_EXTRACT with a randomly picked log file from that processing directory: it will extract incorrect values!
  • For the traditional (isotropic) data (truncate-unique.mtz) these are in truncate-unique.table1. Again, do not use PDB_EXTRACT with a randomly picked log file from that processing directory: it will extract incorrect values!

Additional notes

  • Make sure to deposit the "all" versions of Rmerge, Rmeas (=Rrim) and Rpim and not the "within" ones! Do not deposit R-values from XDS/XSCALE if run with the FRIEDEL'S_LAW=FALSE flag set: these correspond to the "within" version and don't describe the merged intensity (IMEAN) values itself.
  • Remember that completeness is a measure of the number of actually observed reflections relative to the number of reflections that are expected to be observable in principle.
    • For anisotropic (STARANISO) data, only the reflections within the ellipsoid fitted to the cut-off surface (as determined by STARANISO) would ever be observable. So as a measure of the quality of the experiment (how well was it designed to record all observable reflections), the "Completeness (ellipsoidal)" is the correct value to look at.
    • The "Completeness (spherical)" assumes that all reflections within a sphere (or spherical shell) could be observed. This is true for isotropic data or for the (lower resolution) enclosed sphere of anisotropic data - but falls short for anisotropic data. However, taken together with the "Completeness (ellipsoidal)" it gives a good idea about the extent of anisotropy the data shows.
  • Be careful when using other automatic data extraction tools, since they might use a different file/source for those metrics: always check the deposited values with the values clearly presented by data processing software (e.g. autoPROC output like summary.html or the PDF reports, the STARANISO server results page etc).
  • See also this Gemmi tool for help in preparing reflection data mmCIF files containing both merged and unmerged data blocks.

This is ongoing work together with the wwPDB PDBx/mmCIF Working Group - for more details see: