Hi all,

You can find our release policy in the chapter 2 of "Annotation 
Policies" document which is available from the following URL.
http://www.wwpdb.org/docs.html

We encourage all the PDB depositors to carefully check the journal 
policy for the availability of coordinates (and experimental data)
before depositing coordinate to wwPDB or submitting papers to the 
journal.

For example, Nature says:
   the author must authorize Protein DataBank (PDB) release on the
   Wednesday of (or before) online or print publication.
     From http://www.nature.com/authors/editorial_policies/availability.html
This means the PDB entry must be released BEFORE the journal 
publication.


We receive publication dates and citation information from some 
journals.  In this case, we send email that "your entry will be 
released by the journal request." to the contact person for the PDB 
entry.

For other journals, we search the publication information with using 
the deposited author names and deposited article title.  In this 
case, we send email notification to the contact person for the PDB 
entry.

In each case, depositors can request to postpone the release against 
the journal policy.  It is not the wwPDB responsibility to force to 
release data according to a journal policy.  It is the depositor's 
responsibility to follow the journal policies regarding release of 
the coordinates.  If depositors will be in any trouble with the 
journal office regarding their own decision, it's on their head.

The citation information that is sent to us from the depositors or 
community is also greatly appreciated.


Best regards,
Takanori
Annotators' leader, PDBj


From: Engin Ozkan <[log in to unmask]>
Subject: Re: [ccp4bb] friction or releasing pdb's
Date: Thu, 2 Apr 2009 09:56:20 -0700

> I do not mind PDB releasing only on Wednesdays at a certain time of
> the day. What should happen is the authors/publishers should let PDB
> know the publication date before it becomes available (supposedly 
> days
> or weeks before the actual publication, online or in print), and PDB
> can automatically release pdb/sf the week of the publication or the
> Wednesday before.
>
> With requesting pdb releases, I take two routes: ask the journal and
> ask RCSB.  Asking journals used to work, although my last attempt 
> was
> unsuccessful. If the journal agrees to do anything, they may let the
> authors or PDB know, so after a while, the release happens. Asking
> RCSB works if they can find the reference themselves, except in the
> bizarre case I cited.
>
> But still, the reader should not have to search for data supposed to
> publish simultaneously with the article, right?
>
> Engin
>
> On 4/2/09 8:53 AM, Phil Jeffrey wrote:
>> PDB seem to take about a week to release coordinates that are HPUB
>> (hold for publication) from when we ask them to.  Sometimes they 
>> drop
>> the ball, but mostly this is what we see.  If I ask them to release
>> the coordinates early to get around this lag, I can largely 
>> guarantee
>> that I'll forget to update the JRNL reference.
>>
>> I believe that the lead time is unnecessarily long.  Perhaps one 
>> day
>> might be more reasonable.
>>
>> Phil Jeffrey
>>
>> Engin Ozkan wrote:
>>> I agree that the pdb deposition process has gotten better, but I 
>>> still
>>> regularly have issues with releasing of newly published
>>> structures. There seem to be delays; just as you are reading this
>>> brand new, interesting structure, you realize that the pdb and
>>> structure factors are not released. Quite annoying. This is in 
>>> large
>>> part the fault of the authors, but maybe PDB could do better, too.


-- 
MATSUURA Takanori, Ph.D.
Visiting Associate Professor
Annotators' Leader, Group of Primary Annotation,
Protein Data Bank Japan (PDBj)
Research Center for Structural and Functional Proteomics,
Institute for Protein Research, Osaka University
3-2 Yamadaoka, Suita, Osaka 565-0871, JAPAN
Tel: +81-6-6879-8634
Fax: +81-6-6879-8636