[phenixbb] can I turn off TLS for subsequent rounds of refinement?

Pavel Afonine PAfonine at lbl.gov
Mon Mar 30 11:55:17 PDT 2009

Hi Scott,

> As the TLS refinement can take a significant amount of time, I'm  
> wondering if I can turn it off after a few rounds with it on? 

technically, you can (=program will not crash). But in this case 
phenix.refine will automatically convert all anisotropic ADP into 
isotropic which will in turn invalidate previous TLS refinement. To stop 
this you will need to turn off the B-factor refinement completely, which 
is unlikely to be a good idea.

> or will  
> phenix.refine "see" the ANISOU records and assume I am doing  
> anisotropic ADP?

This was the behavior in earlier versions. We fixed it sometime ago. Now 
if phenix.refine "sees" ANISOU and these atoms do not participate in TLS 
group and the resolution is "low enough", then it automatically converts 
ADPs to isotropic. If resolution is "high enough" then these atoms will 
be refined with individual anisotropic B-factors.

The parameter used to decide about "low/high enough" resolution is:
switch_to_isotropic_high_res_limit = 1.7

So once you started using TLS then it is the best to keep using it.


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