Dear Jonathan,
As you have correctly identified from the policy documentation at wwPDB,
if a structure factor file was never initially deposited for an entry
(i.e. before 2018 when this was not mandatory), this can be provided at
a later date. Please contact the wwPDB site where this was originally
deposited for information as to how to provide this data.
However, please be aware that this is not a new policy related to
versioning - any alteration of coordinates or structure factor files for
entries deposited in legacy systems is currently outside the scope.
Kind Regards,
David
On 02/08/2019 21:56, Jonathan Cooper wrote:
Thank you for that. Good idea to look at the policy. I think it would
be classed as a minor change after release:
https://www.wwpdb.org/documentation/policy#toc_changes
"Update or change on structure factor or constraint file due to format
corrections or addition of data set while coordinates remain unchanged."
On Friday, 2 August 2019, 21:28:50 BST, Robbie Joosten
<[email protected]> wrote:
Hi Jonathan,
It would be great if you deposit missing reflection data. It is very
commendable. I don't know what the policy is, but I have seen quite a
few legacy entries for which the data were deposited (or corrected)
much later than the model. Sometimes more than 20 years. These kept
the original PDBid.
Cheers,
Robbie
On 2 Aug 2019 21:18, Jonathan Cooper
<[email protected]> wrote:
Hello David
I note that no changes will be allowed to the experimental data,
but if there are no experimental data, will the depositor be
allowed to upload it/them, without starting a new deposition? I'm
finding a few reflection files that ought to be deposited so that
the corresponding structures can benefit from re_do's, etc, but I
would like to preserve the original PDB-IDs, as published, and I
don't want to spend too long on it!
Thank you, Jon.C.
On Thursday, 1 August 2019, 09:34:40 BST, David Armstrong
<[email protected]> wrote:
Dear CCP4BB,
The wwPDB are pleased to announce the availability of PDB
versioning, allowing depositors to update their entries while
retaining the same PDB accession code.
Depositors can now submit new coordinates for existing entries.
Initially, this is limited to PDB entries that were submitted via
the OneDep system, which was introduced in 2014. The wwPDB plans
to extend this functionality to entries deposited in the legacy
systems (ADIT and Autodep) in future, and will announce a timeline
for this in due course.
Requests should be initiated using the OneDep communication panel
within the deposition session for the entry in question. Once
submitted, the revised model will be processed by wwPDB
biocurators and a new version released. Versioning of PDB entries
will be limited to changes in the coordinate files, with no
changes permitted to the deposited experimental data. PDB
versioning will be limited to one replacement per PDB entry per
year, and three entries per Principal Investigator per year.
For more, please visit the wwPDB news pages
<https://www.wwpdb.org/news/news#5d3ef68aea7d0653b99c87fd>.
--
David Armstrong
Outreach and Training Coordinator
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492544
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--
David Armstrong
Outreach and Training Coordinator
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492544
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