Wow, this is really cool--just tried a quick look at a recent membrane protein (5eqi) and you can see right away that there is anisotropy.
I would guess this can be found in the literature, but how prevalent is anisotropy in the PDB?
Jacob Keller
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Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
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-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Gerard Bricogne
Sent: Wednesday, March 28, 2018 11:56 AM
To: [log in to unmask]
Subject: [ccp4bb] A new capability on the STARANISO server: "PDBpeep"
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
http://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi
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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