Thanks everybody for their valuable suggestions.. On 2/3/14, MARTYN SYMMONS <[email protected]> wrote: > 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 <[email protected]> > To: [email protected] > 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 Most pre-release 'withdrawn' entries are of course subsequently released 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 although they maintain a list of withdrawn entries - which means ids 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/[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 >> > >> > >> >>
-- Regards Faisal School of Life Sciences JNU
