[phenixbb] TLS and ligand question

Pavel Afonine PAfonine at lbl.gov
Wed Nov 25 13:00:53 PST 2009

Hi Andy,

> 	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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