Well, like Folmer says, you don't have to withdraw the entry, you could just let it be released before the paper is accepted. While in some projects there may be a legitimate fear that other scientists use your unpublished entry for things you don't want them to, in many projects this doesn't matter too much. Also, for the PDB staff it is rather annoying to have to re-check the entry later, so these withdrawals should only be done when there is a real justification.
On 1 Feb 2014, at 23:29, MARTYN SYMMONS wrote: > 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 Most pre-release 'withdrawn' entries are of course subsequently released 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 although they maintain a list of withdrawn entries - which means ids cannot 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/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 > > > > > >
