Yes, thanks Robbie That is just my point - a structure submitted and then validated for paper reviewers by the PDB can be changed almost completely after the paper is accepted. The data can be changed too and only stipulation seems to be that it cannot be new data i.e. it has to have a date of collection _before_ submission.
Changes are of course not bad in principle - they may be motivated by peer review. But they need to be tracked. ln a way that is understandable for users of the data. Perhaps they are available in the new mmCif-based deposition and annotation system. I have not used it yet. The PDB provides a comparison between obsoleted and superseding entries (coordinates at least). So a similar approach could be used. all the best Martyn ________________________________ From: Robbie Joosten <robbie_joos...@hotmail.com> To: CCP4BB@JISCMAIL.AC.UK Sent: Sunday, 2 February 2014, 20:13 Subject: Re: [ccp4bb] resubmission of pdb Hi Martyn, > I have recently had the same problem. But generally, the PDB will usually > allow a further 6 months hold for review or modifications to an already > submitted paper. That is good to hear. I guess the 1 year limit is mostly to avoid structures to stay in limbo too long. > But what I wanted to say was that the correct term is 'withdrawal' if the entry > is removed pre-release - 'retraction' carries a pejorative connotation. Even > after release, pulling an entry would be called obsoleting (status OBS) > without superseding. So some structures have been 'obsoleted' owing to > retraction of a published paper. (Superseding is when a better structure > replaces the original - this process is tracked by the PDB.) Indeed, bad choice of words on my side. Just to complete the list, the possible statuses are here: http://www.ebi.ac.uk/pdbe-srv/status/search/doc > Most pre-release 'withdrawn' entries are of course subsequently released > after re-submission. But the PDB does not seem to track these connections - > although they maintain a list of withdrawn entries - which means ids cannot > really be recycled. That's too bad, there are not that many possible PDBids. > Interestingly, before release entries can be 'replaced' which means a new > structure can take the place (and 4 letter code) of the old one - this would > have to have the same meta-data - so source and expression - but could > have different resolution, space group, coordinates, and small molecules. > Changes in these could for example be motivated by referees' comments on > the submitted paper or maybe the authors got lucky with a better crystal. But > this pre-release replacement could also be potentially used to 'sex up' a > structure - for example by adding a 'novel' small molecule 'overlooked' in the > original deposition. Such changes are tracked privately by the PDB but are not > publically available... even after release. I didn't know this was an option. It seems sensible for peer review, but does present a potential loop-hole. I saw a fairly recent PDB entry that was deposited as a C-alpha trace (in 2013), but presented as a full model in Table 2 of the linked publication. The model was deposited a month before the paper was accepted, so referees could have noticed this (in theory). But now I wonder I the model was not 'downgraded' before the release. Perhaps I'm just paranoid. Cheers, Robbie > Even more interestingly, the ligand definitions such as bond orders can be > modified _after_ release (as in the recent R12 case I noticed*)... I think this is > owing to the lack of clear rules on small molecule changes - which means the > PDB should be considered of limited value as a definitive record of small > molecule chemistry. > > Cheers - M > *https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg33403.html > > > > > > > > > From: Robbie Joosten <robbie_joos...@hotmail.com> > To: CCP4BB@JISCMAIL.AC.UK > Sent: Saturday, 1 February 2014, 12:48 > Subject: Re: [ccp4bb] resubmission of pdb > > > Hi Folmer, > > Perhaps because of the one year limit of keeping PDB entries in the 'HPUB' > status. > > So when a PDB entry is retracted before release, is the PDBid recycled after > a while? > > Cheers, > Robbie > > > -----Original Message----- > > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > > Folmer Fredslund > > Sent: Saturday, February 01, 2014 10:33 > > To: CCP4BB@JISCMAIL.AC.UK > > Subject: Re: [ccp4bb] resubmission of pdb > > > > Hi Faisal, > > > > There is one thing I don't understand: > > > > "Some time back i had submitted a coordinate in PDB but because of > > unacceptance of the manuscript we had to retract the submission" > > > > Why would you need to retract your deposited structure just because the > > paper describing the structure didn't get accepted? > > > > > > Venlig hilsen > > Folmer Fredslund > > > > On Jan 31, 2014 10:04 PM, "Faisal Tarique" <faisaltari...@gmail.com> > wrote: > > > > > > Dear all > > > > Dear Dr. PDB, > > > > Some time back i had submitted a coordinate in PDB but because of > > unacceptance of the manuscript we had to retract the submission. During > > this procedure i got few zipped file from the annotator such as 1>. > > rcsb0xxxx.cif-public.gz, 2>. rcsb0xxxx.pdb.gz and 3>. rcsb0xxxx- > > sf.cif.gz..Now i want to submit the same ..My question is what is the best > > way to do it again..?? > > Should we start from the beginning through ADIT Deposition tool > > and resubmit it with a new PDB id or there is some way to submit again > those > > zip files which the annotator sent us after retraction..May you please > suggest > > what could be the easiest way to submit our structure to PDB without > much > > efforts. > > > > > > -- > > Regards > > > > Faisal > > School of Life Sciences > > JNU > > > > > >
