As a postscript it might be worth mentioning one problematic ligand that suggested to me a way to correct some of the errors mentioned in this thread R12 is indicated as 9-(4-HYDROXY-2,6-DIMETHYL-PHENYL)-3.... in the most recent Coot monomer library. But in the PDB ligand description it is 9-(4-hydroxy-2,3,6-trimethylphenyl)-3,7-dimethylnona-2,4,6,8-tetraenoic acid with an additional carbon C16. To make a long story short this ligand was originally deposited missing this extra methyl goup in 1999 (as part of 3CBS) and then apparently updated in 2011 by the PDB.
(the relevant lines in the cif are <<snip>> R12 C16 C16 C 0 1 N N N ? ? ? -6.631 1.502 0.990 C16 R12 44 R12 H1 H1 H 0 1 N N N ? ? ? -6.602 1.511 2.080 H1 R12 45 R12 H23 H23 H 0 1 N N N ? ? ? -6.422 2.503 0.613 H23 R12 46 R12 H24 H24 H 0 1 N N N ? ? ? -7.619 1.186 0.656 H24 R12 47 <<snip>> with the ? ? ? indicating that refined coordinates were not available at the time of the update. There was initially an explanation line at the end of the cif: <<snip>> R12 "Other modification" 2011-10-25 RCSB CS 'add missing methyl group, re-define bond order based on publication' <<snip>> But this has mutated for some reason (premature stop codon?) over the past year to the following. <<snip>> R12 "Other modification" 2011-10-25 RCSB <<snip>> Obviously the full correct ligand could not have been incorporated into the PDB entry coordinates without these undergoing a full obsolete - supersede process (somewhat embarrassing perhaps as one author is now a wwPDB PI ;) But it is frustrating for users of the PDB that in such cases easily correctable errors are not actually updated by the authors. Would it not be helpful if there were a mechanism to make and track useful improvements in deposited structures? - Perhaps suggested by members of the community to the authors. These changes could be considered as 'corrigenda' and could be documented and tracked - complete with an explanation of the reasoning behind the change and attributing the motivation and origin of the improvement. This would be a good way for the wider scientific community (who maybe do not read this bulletin board) to access the best current model without the authors suffering the full process of retracting and redepositing their PDB entry. The test for obsoleting would then be the same as for a paper - that the change invalidates a fundamental interpretation of the data. All the best Martyn ________________________________ From: Pavel Afonine <pafon...@gmail.com> To: CCP4BB@JISCMAIL.AC.UK Sent: Sunday, 20 October 2013, 19:49 Subject: Re: [ccp4bb] Problematic PDBs Hello, just for the sake of completeness: this paper lists a bunch of known pathologies (I would not be surprised if they've been remediated by now): http://www.phenix-online.org/papers/he5476_reprint.pdf Pavel On Thu, Oct 17, 2013 at 6:51 AM, Lucas <lucasbleic...@gmail.com> wrote: Dear all, > >I've been lecturing in a structural bioinformatics course where graduate >students (always consisting of people without crystallography background to >that point) are expected to understand the basics on how x-ray structures are >obtained, so that they know what they are using in their bioinformatics >projects. Practices include letting them manually build a segment from an >excellent map and also using Coot to check problems in not so good structures. > >I wonder if there's a list of problematic structures somewhere that I could >use for that practice? Apart from a few ones I'm aware of because of (bad) >publicity, what I usually do is an advanced search on PDB for entries with >poor resolution and bound ligands, then checking then manually, hopefully >finding some examples of creative map interpretation. But it would be nice to >have specific examples for each thing that can go wrong in a PDB construction. > >Best regards, >Lucas >
