[phenixbb] TLS and ligand question
PAfonine at lbl.gov
Wed Nov 25 13:00:53 PST 2009
> Thanks for the suggestions. I will try group occupancy refinement as
> you suggest. Consequently, I "know" that at intermediate resolution the
> B-factor and occupancy are coupled and my understanding was that it
> isn't appropriate to refine both. However, I haven't read anything that
> rigorously describes when it is appropriate to do so (i.e. at what
> resolutions or other characteristics of the data). How can one tell
> whether the result of refining both B-factor and occupancy
> simultaneously (one occupancy per group in the case of ligands) achieves
> a reasonable result? Obviously you'd expect potentially to see lower
> R/Rfree, more uniform B-factors and better electron density (i.e. no or
> reduced difference electron density). Conversely, what would indicate
> to you that it is inappropriate to refine both together?
Dale comprehensively replied to this part, so I have nothing to add.
> Also, I didn't mention that I also tried to set all the isotropic
> B-factors to a uniform value before running TLS (recommended in Martyn
> Winn's manual), but that didn't help.
In case of phenix.refine this shouldn't matter indeed, because all such
things are highly optimized internally, so normally you do not need to
re-set B-factors before TLS run.
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