Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Tanner, John J.
Relevant to this discussion, the 2018 ACA meeting in Toronto will have a session on "Best practices for building, refining, and analyzing ligands in macromolecular structures” co-chaired by Anna Gardberg and Kurt Krause. I expect this session will include case studies of structures that went

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Tanner, John J.
Trevor, I can share our recent experience correcting the record about a misplaced ligand binding site. It represents one possible way to deal with erroneous structures. Our analysis of structures of the proline biosynthetic enzyme PYCR1 deposited by another group in 2006 suggested that the

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Tanner, John J.
Trevor, I can share our recent experience correcting the record about a misplaced ligand binding site. It represents one possible way to deal with erroneous structures. Our analysis of structures of the proline biosynthetic enzyme PYCR1 deposited by another group in 2006 suggested that the

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Constance Jeffery
Hi Trevor, I think you should also email the authors of the key paper in your field that you mention. They should be told that the structure they used to create the model of the mechanism was incorrectly interpreted and should have the opportunity to write a correction to their paper. Best

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Philippe BENAS
s5.fr/ , http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18 De : "Goldman, Adrian" <adrian.gold...@helsinki.fi> À : CCP4BB@JISCMAIL.AC.UK Envoyé le : Mardi 27 juin 2017 10h59 Objet : Re: [ccp4bb] Incorrect Structure in the PDB I agree: I don’t think this is fraud,

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Philippe BENAS
r/ , http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18 De : Bernhard Rupp <hofkristall...@gmail.com> À : Philippe BENAS <philippe_be...@yahoo.fr> Cc : "CCP4BB@JISCMAIL.AC.UK" <CCP4BB@jiscmail.ac.uk> Envoyé le : Mardi 27 juin 2017 10h55 Objet : Re: [

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Goldman, Adrian
___ De : "Goldman, Adrian" <adrian.gold...@helsinki.fi<mailto:adrian.gold...@helsinki.fi>> À : Philippe BENAS <philippe_be...@yahoo.fr<mailto:philippe_be...@yahoo.fr>> Envoyé le : Mardi 27 juin 2017 10h30 Objet

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Bernhard Rupp
*De :* "Goldman, Adrian" <adrian.gold...@helsinki.fi> *À :* Philippe BENAS <philippe_be...@yahoo.fr> *Envoyé le :* Mardi 27 juin 2017 10h30 *Objet :* Re: [ccp4bb] Incorrect Structure in the PDB Philippe All I did was take their deposited mtz and coordi

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Philippe BENAS
macie.univ-paris5.fr/ , http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18 De : "Goldman, Adrian" <adrian.gold...@helsinki.fi> À : Philippe BENAS <philippe_be...@yahoo.fr> Envoyé le : Mardi 27 juin 2017 10h30 Objet : Re: [ccp4bb] Incorrect Structure in the PDB

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Pietro Roversi
On the subject of withdrawal of entries from the PDB, I just flag up another interesting aspect. Four years ago I was Visiting Fellow in a colleague's lab, and in the course of the year I determined, refined and deposited 4 good structures, authored by me and my colleagues who were part of the

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Frank von Delft
What tiny fraction of the gazillions it would cost to store all the raw data, would be enough to arrange the training courses needed to get the ballooning population of practitioners up to speed, he mused idly. On 27/06/2017 09:21, Goldman, Adrian wrote: That’s quite something. To me, this

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Goldman, Adrian
That’s quite something. To me, this thread raises another issue: I see a lot of comments about extracting the last little bit from every byte of data collected - but that’s not our main problem. Our main problem appears to be shoddily-done refinement of data that are in fact perfectly decent

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread benjamin bax
letter to the editor of JBC. Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 From: Manfred S. Weiss <mailto:manfred.we...@helmholtz-berlin.de> Sent: Tuesday, June 27, 2017 8:46 AM To: Trevor Sewell <mailto:trevor.sew...@uct.ac.za> Subject: Re: [ccp

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Dale Tronrud
550986> for > Windows 10 > > > > *From: *Manfred S. Weiss <mailto:manfred.we...@helmholtz-berlin.de> > *Sent: *Tuesday, June 27, 2017 8:46 AM > *To: *Trevor Sewell <mailto:trevor.sew...@uct.ac.za> > *Subject: *Re: [ccp4bb] Incorrect Structure in the

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Tristan Croll
Note that in most cases a structure may only be obsoleted with the written agreement of a senior author. From experience it's by far the best approach to work together with the original authors on a correction, in any case. Goodwill is an important thing. If you wish, you can go it alone and

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Vellieux Frédéric
Hello, I think it makes sense to have a look at the policy of the PDB concerning obsoleting structures: The publication is retracted. The associated PDB entry will be obsoleted if requested by the journal. If a request has not been received, the wwPDB will do its best to contact the depositor