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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