[phenixbb] A new capability on the STARANISO server: "PDBpeep"

Gerard Bricogne gb10 at globalphasing.com
Thu Mar 29 06:57:17 PDT 2018

Dear all,

     Ever since the WebGL viewer became available on the STARANISO
server, we have found ourselves using it with increasing frequency to
take a quick look (a "peep") at the diffraction data deposited with
various PDB entries - for example, to try and identify a root cause
for some sub-optimal refinement results, or, quite often, just out of
sheer curiosity!

     This involved a totally straightforward procedure whereby the
diffraction data file associated with a given PDB entry was downloaded
from the PDB and subsequently uploaded to the STARANISO server.

     Gradually, however, this operation became so popular among some
of us that we thought it would be useful to implement this simple
procedure as an autonomous capability - and thus was born "PDBpeep" !

     You can access this new feature by connecting to 


and enter a PDB code into the box. As indicated on that page, this
provides only a cursory look at the overall quality of each dataset,
and any further analysis or output can only be obtained by submitting
the datafile to the STARANISO server. Better results would clearly be
obtainable if the raw images for these datasets had been deposited and
could be reprocessed, with the untruncated output of that processing
then being submitted to the STARANISO server (reprocessing the images
with autoPROC would combine those two steps into a single one).

     Most of the deposited datasets have been isotropically truncated,
and their 3D view in WebGL often suggests that this truncation was too
drastic. A number of entries will show infelicities - such as cusps
and/or missing angular ranges, or even stripes caused by gaps between
the modules of pixel detectors if the beam centre is at a position
symmetric relative to those gaps - all marked up in blue.

     Our purpose in sharing this capability with the community is to
bring a further contribution to the process of making everyone more
"data quality aware" and keen to scrutinise more closely the protocols
by which they collect diffraction data, or have such data collected on
their behalf.

     We will be grateful to receive feedback about PDBpeep, just as we
have been about the STARANISO server itself.

     With best wishes,

 The STARANISO developers.

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