Joe,
I think this is neither a constructive or accurate statement. I
have collaborated with the PDB (both the RCSB and the EBI) for many
years and I believe that they are doing a very good job under very
difficult circumstances. They have been tasked with curating an ever
increasing volume of data from a community that, as you point out, is
constantly developing new methods. As a community we need to
communicate and collaborate with the PDB, not try to sideline them. I
know that they are willing to listen so we should take that opportunity.
Cheers,
Paul
On Aug 29, 2007, at 8:08 AM, Joe Krahn wrote:
> This is a reply to the below message posted under "[ccp4bb] The
> importance of USING our validation tool", which is a rather long
> thread now.
>
> This is part of why I claim that wwPDB and its members are doing a bad
> job. They have worked to systematically remove "general purpose"
> information that does not fit their pre-defined schemes, which are
> developed with out much interaction with the user community. the
> problem
> is that we are doing RESEARCH, which means that we will continue to
> develop new methods over time. The sensible thing to do is to allow
> unformatted user-defined information, and eventually work it in to a
> properly formatted, standard item if that information is seen as
> generally useful by the user community.
>
> I think that the lack of community involvement by the database
> administrations should be a clear indication of why we should NOT
> switch
> from PDB to mmCIF format for coordinate files. Instead, we should take
> this opportunity of wwPDB members abandoning the PDB format to take
> over
> management of the format ourselves. I was quite irate with them for
> going against our wishes on several features of the PDB format, like
> supporting the SegID. Instead, I think we should realize that "modern
> database" management goals are different from experimentalist
> goals, and
> that we should not rely on them to decide how our own data should be
> represented.
>
> I think that we should intentionally avoid mmCIF for coordinate files,
> and stick to the PDB format. The wwPDB has absolutely no policy for
> user
> involvement, and RCSB has clearly dropped the previously establish
> PDB-format change policy. Their task was never to manage a public file
> format standard. This is an opportunity to turn the PDB file format
> into
> a public standard.
>
> I have started a PDB Format Wiki, running on my home computer, at
> http://pdb.homeunix.org. If it gains interest, I will see about moving
> it to a proper Internet host.
>
> Joe Krahn
>
> Miller, Mitchell D. wrote:
>> Hi Boaz,
>> We were informed by an RCSB annotator in April 2006 that the
>> RCSB had suspended including REMARK 42 records in PDB files
>> pending the review of the process by the wwPDB.
>>
>> In looking at the new annotation guidelines, it looks
>> like the result of that review was to reject the REMARK 42
>> record and the listing of additional validation items.
>> See page 23 of the July 2007 "wwPDB Processing Procedures
>> and Policies Document"
>> http://www.wwpdb.org/documentation/wwPDB-A-20070712.pdf
>>
>> "REMARK 42 and use of other programs for validation Use of REMARK
>> 42 is
>> discontinued.
>>
>> If authors wish to indicate presubmission validation and other
>> programs used before
>> deposition, the programs may be listed in a new remark, REMARK 40.
>> This remark will
>> list the software name, authors and function of the program.
>> Results of the software will
>> not be listed. Use of this remark is voluntary."
>>
>> It seems that the wwPDB only allows the inclusion of validation
>> statistics output by the refinement program but not from additional
>> validation programs. So for additional statistics to be included
>> in the PDB header, they will either need to be implemented by the
>> refinement package or the wwPDB annotators.
>>
>> Regards,
>> Mitch
--
Paul Adams
Senior Scientist, Physical Biosciences Division, Lawrence Berkeley Lab
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Head, Berkeley Center for Structural Biology
Deputy Principal Investigator, Berkeley Structural Genomics Center
Building 64, Room 248
Tel: 510-486-4225, Fax: 510-486-5909
http://cci.lbl.gov/paul
Lawrence Berkeley Laboratory
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