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2) Some files list in the ATOM "B" column the residual B after TLS
has been accounted for while others list the total B (TLS and
residual). There is no clear indication in the PDB file which
interpretation is being used.
That is a fundamental deficiency in the existing PDB standard. It simply
doesn't specify how to present this critical information. A draft change
covering this was circulated at the PDB get-together of last summer's ACA
meeting, and I discussed with Garib and Eleanor that we should as a community
decide how we would like it handled. The consensus as I understand it is
that people would prefer that the B field of individual ATOM records contain
the *net* B rather than the residual B, so that old programs will continue
to work as expected. However, this puts even more importance on the TLS
description in the header being correct, since the information is otherwise
not recoverable. We were going to circulate a letter, but I plead guilty
to letting the matter slide.