When last I checked a few months ago, of the 12 implicated structures only 4 had been moved to the PDB's repository of obsolete structures.
Eric On Fri, Dec 14, 2012 at 5:11 PM, Randy Read <rj...@cam.ac.uk> wrote: > Hi, > > It's hard to believe this has gone on so long, but the situation doesn't > seem to have changed since the wwPDB put up a statement about this case in > December 2009: http://www.wwpdb.org/UAB.html. This explains the wwPDB > policy that entries are only made obsolete when the corresponding papers > are retracted. As Zhijie noticed, the paper describing 2HR0 still hasn't > been retracted, along with a number of other relevant papers. > > Best wishes > > Randy Read > > ----- > Randy J. Read > Department of Haematology, University of Cambridge > Cambridge Institute for Medical Research Tel: +44 1223 336500 > Wellcome Trust/MRC Building Fax: +44 1223 336827 > Hills Road > E-mail: rj...@cam.ac.uk > Cambridge CB2 0XY, U.K. > www-structmed.cimr.cam.ac.uk > > On 14 Dec 2012, at 21:39, Folmer Fredslund wrote: > > > Hi, > > > > Sorry Eric I don't have an answer for your question. > > > > off topic: > > From the University's announcement ( > http://main.uab.edu/Sites/reporter/articles/71570/) you would have > thought that they had asked for this entry to be removed. > > > > But if I understand correctly, this is is completely at the discretion > of the depositors in question. > > > > mvh > > Folmer Fredslund > > > > > > > > > > 2012/12/14 Zhijie Li <zhijie...@utoronto.ca> > > Hi, > > > > Seems not officially retracted from Nature either. On the paper's web > page, there was only a line in small font read like this: > > > > > > There is a Brief Communications Arising (9 August 2007) associated with > this document. > > > > It took me more than half an hour to find this line. I normally won't > read any line above the title. Now it proves to be a bad habit. > > > > I am still trying to find this line in the PDF. > > > > Zhijie > > > > > > > > From: Michael Hadders > > Sent: Friday, December 14, 2012 2:57 AM > > To: CCP4BB@JISCMAIL.AC.UK > > Subject: Re: [ccp4bb] Boveral in SFCheck > > > > Hi, > > > > 2HR0???? I would stay far away from that one! It is a made up model, not > based on any real data. Unfortunately, for reasons unclear to me, this > structure has still not been retracted from the PDB. This B factor could > just be a figment of the senior authors imagination.... > > > > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0912&L=CCP4BB&D=0&P=88327 > > > > Regards, > > > > Michael > > > > On Fri, Dec 14, 2012 at 3:34 AM, Eric Williams <ericwilli...@pobox.com> > wrote: > > Please pardon me if this is a dumb question with an obvious answer... > > > > I'm parsing SFCheck's plain text output as part of my dissertation, and > I'm having trouble identifying one of the values. There are three overall > B-factor values reported, one based on the Patterson origin peak, one based > on the Wilson plot, and one that remains a mystery to me. Here's the > relevant line (from 2HR0) with some lines before and after for context: > > > > R_stand(I) = <sig(I)>/<I> : 0.397 > > Number of acceptable reflections: 194123 > > for resolution : 45.33 - 2.26 > > Optical Resolution: 1.80 > > Boveral,Effres,Padd: 40.751 2.032 777.887 > > Expected Optical Resolution for complete data set: 1.80 > > / Optical resolution - expected minimal distance between > > two resolved peaks in the electron density map./ > > Resmax_used(opt): 2.26 > > > > The mystery value is Boveral. I've found no explanation for it in either > the SFCheck manual or the original journal article. Perhaps I'm missing > something obvious, but someone would really make my day if they could point > me in the right direction. Thanks! :) > > > > Eric > > > > > > > > > > -- > > Folmer Fredslund > > >
