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 Most pre-release 'withdrawn' entries are of course subsequently released 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 although they maintain a list of withdrawn entries - which means ids cannot 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/[email protected]/msg33403.html > > > > > > > > > From: Robbie Joosten <[email protected]> > To: [email protected] > 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:[email protected]] On Behalf Of > > Folmer Fredslund > > Sent: Saturday, February 01, 2014 10:33 > > To: [email protected] > > 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" <[email protected]> > 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 > > > > > >
