Hi Gerard, Very nice server indeed. I reviewed the 3D plots of some recent high res structures and am struck by the granularity which is not necessarily globally directional. For instance, I ran 4QRN and 5EHI and see "ripples" in the I/sigI plot between the various "layers" (higher res yellow to orange "transition" features are most easily visible but the purple to blue low res are very interesting as well). Can you comment on the significance of these intensity-weighted reciprocal lattice features as pertains to real space? It is tempting to see a manifestation of the solvent mask in the color coding :-)
best, Jeff Jeffrey B. Bonanno, Ph.D. Department of Biochemistry Albert Einstein College of Medicine 1300 Morris Park Avenue Bronx, NY 10461 off. 718-430-2452 fax. 718-430-8565 email jeffrey.bona...@einstein.yu.edu -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Gerard Bricogne Sent: Wednesday, March 28, 2018 2:35 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] A new capability on the STARANISO server: "PDBpeep" 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 > > +++++++++++++++++++++++++++++++++++++++++++++++++ > 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 > +++++++++++++++++++++++++++++++++++++++++++++++++ > > The content of this email is confidential and intended for the recipient > specified in message only. It is strictly forbidden to share any part of this > message with any third party, without a written consent of the sender. If you > received this message by mistake, please reply to this message and follow > with its deletion, so that we can ensure such a mistake does not occur in the > future. > > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Gerard > Bricogne > Sent: Wednesday, March 28, 2018 11:56 AM > To: CCP4BB@JISCMAIL.AC.UK > 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. -- =============================================================== * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===============================================================
