Thanks everybody for their valuable suggestions..
On 2/3/14, MARTYN SYMMONS <[log in to unmask]> 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 <[log in to unmask]>
> To: [log in to unmask]
> 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 Most pre-release 'withdrawn' entries are of course subsequently released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 although they maintain a list of withdrawn entries - which means ids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
>> *[log in to unmask]" target="_blank">https:[log in to unmask]
>>
>>
>>
>>
>>
>>
>>
>>
>> From: Robbie Joosten <[log in to unmask]>
>> To: [log in to unmask]
>> 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:[log in to unmask]] On Behalf Of
>> > Folmer Fredslund
>> > Sent: Saturday, February 01, 2014 10:33
>> > To: [log in to unmask]
>> > 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" <[log in to unmask]>
>> 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
|
