My frustration comes from what I deem to be an obvious action to disregard the opinion of the user community. From Bernhard's comments below, it sounds like a better plan of action is in the works.
Bernhard Rupp wrote: ... > > Anyhow, if I understand correctly, your suggestion of polling the user > community, > is on an grander scale already on the mind of the PDB folks. I am sure your > voice will be heard. > > Best regards, BR Several years ago, a plan was put into action by RCSB to implement the same IUPAC names in the current 3.0 standard. At that time, discussions of standards changes were encouraged on the pdb-l list. There were several complaints about messing up atom name alignment along without good justification. So, the planned change of hydrogen names was canceled. In the current PDB revision, they intentionally had no "public comment period" which any decent standards organization has when a new standard is released. I see it as a blatant disregard for the user communities opinion, because it actually includes the IUPAC hydrogen name change that was specifically shot down several years ago. I think that they see the structural biologist community as having too many people with strong opinions that make it difficult to form any real consensus, and that may in fact be true. The problem is that it is impossible to make the best choices if you don't at least listen to the user community. The way Standards organizations normally work is that a public comment period allows people to bring up issues that the limited group of standards developers did not think of. The standards committees then go over those comments, but still get the final say. This way, a lack of consensus does not impede progress. It also results in a set of official answers to those public comments so we can see why those choices were made. One problem is that the PDB/RCSB was never designed as a standards organization. Their job is to manage the public macromolecular structure database. However, the PDB format is a community standard as well, and so is mmCIF (and it's schema) which will one day replace the PDB format completely. Therefore, this part of the RCSB needs to be managed more like a standards organization. I felt that things were continuing to move towards less community involvement, and that we needed to make some noise. My hope is that wwPDB will be able to function more like a standards organization and deal with public file format issues, while RCSB can focus more on database management. I don't mean to imply that RCSB sucks. Most of what they have done is quite good, and I realize that trying to manage all sorts of new structural data is far from trivial. All I ask is that the file formats and data schemas which we all have to use be considered public standards, and not just for their own internal database design. Joe Krahn
