Dear Jacob and Gerard,
we performed a statistical analysis of anisotropy of the entire PDB,
with a special focus on membrane proteins (Jacb, your other post).
You can find more details on this article:
https://www.nature.com/articles/s41598-017-17216-1
We also performed an analysis by space group, not reported in the
article, but not seeing anything coming out. The data used in the
article is being reviewed at the moment to be available for you to play
with. Hopefully, the reviewer is going to read your posts and is going
to agree on the importance of analyzing this phenomenon.
all the best
Vincent
On 28/03/2018 20:35, Gerard Bricogne wrote:
Dear Jacob,
Thank you for the appreciative comment.
I am not sure that there is any such thing as an up-to-date
estimate of the prevalence of anisotropy in the PDB - but now you can
get a feel for it yourself by looking at any entries you want. However
please do not submit the whole PDB to the server - yet ;-) .
From looking at anisotropy as visible through the overall scaling
Debye-Waller factor, I would say that whenever anisotropy is allowed
by the Laue group, it will be present, even if mild. Symmetry lower
than cubic means that intermolecular contacts along directions that
are not symmetry-equivalent will be different, and there is no reason
why different contacts should create identical degrees of long-range
order.
Have fun!
Gerard.
--
On Wed, Mar 28, 2018 at 06:13:29PM +0000, Keller, Jacob wrote:
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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-----Original Message-----
From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Gerard
Bricogne
Sent: Wednesday, March 28, 2018 11:56 AM
To: [email protected]
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.
--
Vincent Chaptal, PhD
Institut de Biologie et Chimie des Protéines
Drug Resistance and Membrane Proteins Laboratory
7 passage du Vercors
69007 LYON
FRANCE
+33 4 37 65 29 01
http://www.ibcp.fr
