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.
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.) Most pre-release 'withdrawn' entries are of course subsequently released after re-submission. But the PDB does not seem to track these connections - although they maintain a list of withdrawn entries - which means ids cannot really be recycled. 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. 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 > >
