[phenixbb] Clarification on ADPs in PDB files for TLS refinement ?

Phil Jeffrey 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
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.

Phil Jeffrey

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