Re: [ccp4bb] resubmission of pdb
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 robbie_joos...@hotmail.com To: CCP4BB@JISCMAIL.AC.UK 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to complete the list, the possible statuses are here: http://www.ebi.ac.uk/pdbe-srv/status/search/doc Most pre-release 'withdrawn' entries are of course subsequently released after re-submission. But the PDB does not seem to track these connections - although they maintain a list of withdrawn entries - which means ids cannot really be recycled.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/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
Re: [ccp4bb] resubmission of pdb
Thanks everybody for their valuable suggestions.. On 2/3/14, MARTYN SYMMONS martainn_oshioma...@btinternet.com 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 robbie_joos...@hotmail.com To: CCP4BB@JISCMAIL.AC.UK 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/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
Re: [ccp4bb] resubmission of pdb
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. rcsb0.cif-public.gz, 2. rcsb0.pdb.gz and 3. rcsb0- 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
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/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. rcsb0.cif-public.gz, 2. rcsb0.pdb.gz and 3. rcsb0- 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
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. rcsb0.cif-public.gz, 2. rcsb0.pdb.gz and 3. rcsb0-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
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. rcsb0.cif-public.gz, 2. rcsb0.pdb.gz and 3. rcsb0- 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
Re: [ccp4bb] resubmission of pdb
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. rcsb0.cif-public.gz, 2. rcsb0.pdb.gz and 3. rcsb0- 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
[ccp4bb] resubmission of pdb
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. rcsb0.cif-public.gz, 2. rcsb0.pdb.gz and 3. rcsb0-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
Re: [ccp4bb] resubmission of pdb
I would write back to the annotator who send the processed files to you and ask if you can restart the deposition. The worst they can say is no and you're back to ADIT. On the other hand they will probably be as happy as you to save the work that has already been done. Dale Tronrud On 01/31/2014 01:04 PM, Faisal Tarique 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. rcsb0.cif-public.gz, 2. rcsb0.pdb.gz and 3. rcsb0-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
