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Dear Martyn, Thank you for your additional comments. One of the future remediation projects will be to address carbohydrate-containing entries. Best wishes, Rachel Green ------------------------------------------------------------------------ Rachel Kramer Green, Ph.D. RCSB PDB [log in to unmask] Twitter: https://twitter.com/#!/buildmodels Facebook: http://www.facebook.com/RCSBPDB On 11/17/2013 3:39 PM, MARTYN SYMMONS wrote: > Hmm > So the backstory for the problematic ligand R12 in this thread is that > a sharp-eyed worker at the wwPDB recently spotted that there was an > error compared with the original 1999 paper. Correcting the R12 ligand > is a friendly gesture from the PDB as it appears that the error must > have been the authors' - the atom correcting the R12 ligand has been > inserted by the PDB staff rather than retreived from a deposited > structure. > It is a shame the same helpful approach is not always applied. One > current example I spotted is a separate 'problematic ligand' 5AX which > has been added by the wwPDB to at least four other authors' entries, > starting in 2006 with the latest in 2009. > 5AX is basically a fragment ligand which the PDB software produces if > a NAG has wandered too far from its Asn sidechain during refinement. > If 5AX is generated during the PDB processing of a deposition, then it > really should be highlighted for the authors as a geometric issue - > rather than, as in these cases, being simply added to the coordinates. > Reading the authors' papers for the 5AX-containing entries makes it > clear that they never expected anything other than NAG to appear in > their deposited coordinates. > And given its artifactual production during deposition, 5AX should > never have 'escaped into the wild'. > So if a retrospective fix can be applied to R12 (which similar > in lacking an atom) then it seems to me that, in fairness, a clean up > of the 5AX entries should be arranged. > Yours (not holding his breath), > Martyn > > *From:* Rachel Kramer Green <[log in to unmask]> > *To:* [log in to unmask] > *Sent:* Wednesday, 6 November 2013, 16:49 > *Subject:* Re: [ccp4bb] Problematic PDBs > > Dear Martyn, > > wwPDB staff regularly reviews and remediates PDB data and related > dictionaries such as the Chemical Component Dictionary (CCD). > > As part of our on-going remediation efforts, the chemical components > in the archive are regularly reviewed to ensure the correctness and > the completeness of the chemical representation. Such reviews show > that in some cases, the author has failed to provide a complete > description of the chemistry. To address any such errors, the > definitions are corrected. The chemical name and formula are changed > in the PDB file, but the coordinates are not changed. > > In the case of entry 3CBS, issues were found with the chemical > component definition for its ligand R12. The methyl group was not in > the deposited coordinates and it was missing from the original > definition. In addition, the bond order in one of the carbon-carbon > bonds was incorrectly defined. The CCD definition for R12 was updated > in 2011 to add the methyl group and to correct the bond order based on > information in the primary citation. The coordinates for this PDB > entry were not changed. Therefore, in accordance with wwPDB policy, > the file was not obsoleted. > > Sincerely, > Rachel Green > > Rachel Kramer Green, Ph.D. > RCSB PDB > [log in to unmask] <mailto:[log in to unmask]> > Twitter: https://twitter.com/#!/buildmodels > <https://twitter.com/#%21/buildmodels> > Facebook: http://www.facebook.com/RCSBPDB > On 10/21/2013 6:28 AM, MARTYN SYMMONS wrote: >> 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 mailto:[log in to unmask] >> *To:* [log in to unmask] <mailto:[log in to unmask]> >> *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 <[log in to unmask] >> <mailto:[log in to unmask]>> 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 >> >> >> >> > > >