Dear all,
It is probably an all-too-frequent observation that
(1) the *transfer* of X-ray data quality metrics (DQMs for short) from
Table 1 in an MX structure paper to the PDB archive can be a lossy
process, and
(2) the *presentation* of those DQMs that are actually archived can be
surprisingly different across the various wwPDB front-ends to the
PDB provided by the RCSB, PDBe and PDBj .
We are pleased to offer a Web tool at
https://staraniso.globalphasing.org/table1/
that retrieves all available DQMs from the archived mmCIF file associated
with a PDB entry and presents them in a standardised tabular form. The
corresponding documents have been pre-generated for all relevant PDB entries
and are updated automatically on a weekly basis - either if the PDB entry
itself (model mmCIF) or the published PDBx/mmCIF dictionary [1] has changed.
The simplest mode of use is to enter the PDB identifier of interest
into the box at the top of the landing page, then click on the Go button. A
facility to access the PDB according to any of 14 other attributes is also
provided. The top of the form for each given PDB entry contains hyperlinks
to the RCSB, PDBe and PDBj presentations of its DQMs, so as to facilitate
comparisons.
Strict and explicit consistency with the PDBx/mmCIF dictionary [1,2]
has been a major goal in this work: throughout each Table, hovering over an
item in the left-hand side column will show its exact name in the PDBx/mmCIF
dictionary, while hovering over an item value in the right-hand side column
will show the associated item definition in that same dictionary.
We hope that this tool will prove useful, and will welcome enquiries
and any feedback on it that would enable us to improve it.
With best wishes,
Clemens and the GPhL developers
[1] https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic
[2] https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
