[phenixbb] Default anisotropic B-factor refinement in phenix.refine?

Pavel Afonine pafonine at lbl.gov
Mon Jul 2 10:37:54 PDT 2012

Hi Filip,

> But in this case after the second run of phenix.refine i will lose the 
> TLS contribution and the anisoU lines (?).

yes, you will loose them! This is why if you started using TLS you 
should use it from that point on, or you should realize that if you 
stopped using TLS the information about it will be lost.

> How am I supposed to continue with TLS then 

Just make sure that "tls" is included in "strategy" (if you are using 
the command line; note your original choice will be preserved in the 
.def file) or you have tls box checked in the GUI.

>  Or you mean that i can do the 2 consecutive runs (with and without 
> TLS) in the end of the refinement?

The example with two consecutive refinements in my previous email was 
obviously meant to illustrate phenix.refine default behavior in that 
specific case; and this is not how you should run refinement.


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