I've remained silent as this thread evolved into a discussion of how the PDB deals with
water names and numbers. But Nat's comment about the PDB "not advertising itself as
anything other than an archival service" finally prodded me into saying something.
Something I've slowly come to realize is that the PDB, while it started as an archive,
has developed into a working database. That's why they (the PDB
workers/organizers/managers) have gotten into this mode where they change things from the
original deposited files. I learned several years ago that the PDB is willing to change
the atom names in a ligand from those previously used in the published literature. This
was done in the name of "consistency" and essentially made the PDB files into
database entries, rather than archival files since the atom names no longer matched the
atom names used in the papers.
Given the difficulties I had in discussing this with the annotaters, I've come
to realize that as soon as I hit the submit button on a PDB submission, I've
lost control over what will appear in the distributed file. In a way, it's
been liberating to reach that point. It reduces my sense of responsibility for
the contents of the file.
Ron
On Wed, 6 Nov 2013, Nat Echols wrote:
On Wed, Nov 6, 2013 at 12:39 AM, Bernhard Rupp <hofkristall...@gmail.com> wrote:
Hmmm….does that mean that the journals are now the ultimate authority of
what stays in
the PDB?
I find this slightly irritating and worthy of change.
http://www.wwpdb.org/UAB.html
"It is the current wwPDB (Worldwide PDB) policy that entries can be made
obsolete following a request
from the people responsible for publishing it (be it the principal author or journal
editors)."
I'm not sure I understand why things should be any different; the PDB is not
advertising itself as
anything other than an archival service, unlike the journals which are supposed
to be our primary
mechanism of quality control.
-Nat
