[phenixbb] Clarification on ADPs in PDB files for TLS refinement ?
pjeffrey at princeton.edu
Thu Jan 7 10:19:19 PST 2010
Having a discussion with a colleague yesterday on differences in Phenix
and Refmac representations of TLS B-factors in the PDB file I came
across two different definitions for what the PDB ANISOU U's correspond
to as written by Phenix:
1. From necat.chem.cornell.edu/workshops/.../WK04_PavelAfonine.pdf on p.20
U(TOTAL)= U(ATOM) + U(TLS) + U(CRYST)
and only U(atom) + U(tls) is stored in the PDB ANISOU card.
2. From http://proteincrystallography.org/ccp4bb/message8948.html
"Utotal = Utls + Ulocal + Ucryst. So, the ANISOU records
always contain Utotal and ATOM records contain isotropic equivalent of
Which is not the same thing. I suspect it's #1. Am I right ?
I would think that U(cryst) is potentially a non-zero contribution to
atomic ANISOU values but is actually applied before the TLS/Anisotropic
B-factors are refined.
As a tie-breaker between #1 and #2 the program documentation suggest
that it is just U(tls)+U(atom) but the paragraph that nominally explains
it is not short of of inconsistencies, referring to the ANISOU record as
having the "the total B-factor (B_tls + B_individual)" whereas they're
not only not B's (they are U's) but it's also not the *total* U or B by
its own definitions. IMHO it would warrant a rewrite for clarity since
B and U are used interchangeably and "total" has variable usage.
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