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 As Zhijie noticed, the paper describing 2HR0 still hasn't been retracted, along with a number of other relevant papers.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: [log in to unmask]
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 <[log in to unmask]>
> 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: [log in to unmask]
> 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 Unfortunately, for reasons unclear to me, this structure has still not been retracted from the PDB.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 <[log in to unmask]> 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
>
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