My obvious dislike of the PDB v3 format is not entirely from the bad
design choices. Most of the changes were actually good. My anger comes
from the history of the format's development. AMBER developers use their
own variant PDB format, so they are probably not as aware. Here is a
brief summary.
Several years ago, RCSB tried to implement the v3 hydrogen naming
scheme. During the standard established 90-day comment period, many
people complained that it was a bad idea, and they withdrew that part of
the format change. They also declared that they didn't like the PDB
format and wanted to make it obsolete. The experimentalists insisted on
continuing to use the PDB format.
A few years later, they continued work on implementing that same PDB
hydrogen name format change, but this time they proceeded in secret. No
kidding. A short time in advance of the release, they wrote to selected
software developers, not to ask for advice, but only to ask if there
were any serious "show stoppers". Most of them responded that there were
significant design flaws, but Helen Berman's report to the scientific
board only included a few sentences about the format change, stating
that there were just minor issues, and that no changes were needed.
Then, they announced the change publicly at the American Crystallography
Association meeting, basically stating that the format had already
changed, and that it is not open for discussion. (Like the Borg "You
will be assimilated".) Part of this involved establishment of the wwPDB,
which has no public policy for discussing format changes, and
essentially answers to nobody.
It makes no sense for them to be so stubborn about format changes for a
file format they they no longer even want, and to intentionally exclude
the PDB format's actual user community from managing the format.
Joe
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Received on Fri Apr 03 2009 - 01:09:26 PDT
