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
