Hi Ian,
All - I was just in a discussion about TLS and one thing that came out
that I hadn't been aware of is that for the Biso restraints Refmac
restrains the difference between the 'residual' Bs, i.e. with the TLS
contributions subtracted, not the 'total' Bs. Now it seems to me that
this isn't quite correct, because it's the total motion of the atoms
that matters, i.e. the total mean square along-bond displacements for
bonded atoms should be equal. However, I can see that in practical
terms it won't make any significant difference provided appropriate
precautions are taken with the choice of TLS groups.
given the formula for total atomic B-factor:
Btotal = Bcryst + Btls + Blocal + ...
my naive understanding is that the B-factors describing local atomic
vibrations Blocal (or residual B-factors as named in Refmac) should obey
Hirshfeld's "rigid-bond test" (Acta Cryst. (1976). A32, 239-244), which
is (to some approximation) enforced by the restraints applied to
"residual" B-factors (as it is Refmac or in phenix.refine).
I think given the arbitrariness (or accuracy if you like) in defining
TLS groups, applying similarity restraints to the total B would not be a
good idea. I faced this dilemma a few years ago when implementing TLS
refinement in phenix.refine. And to prove my feelings and make a
decision, I systematically tried both possibilities, and the best result
was to apply the restraints to residual B-factors. The NCS restraints
are applied to residual B-factors too (although I didn't test it
systematically).
Cheers,
Pavel.
