[phenixbb] Are TLS parameters applied when TLS refinement is OFF?

[Pavel Afonine]

Hi Mark,

> I have a structure where at one stage TLS parameters were determined 
> and then refined.  It caused the R-free to increase so I stopped 
> refining the TLS parameters.  Are the TLS parameters still applied to 
> the structure on subsequent refinement runs even when the TLS 
> refinement is off?

phenix.refine does not use TLS parameters from PDB file header. So if 
you disable TLS atoms are likely to loose TLS component in total ADP. 
Optionally, it can use ANISOU (which includes TLS contribution). At 
1.35A is probably what it just does by default. At lower resolution it 
would convert anisotropic ADPs to isotropic.

> Is it appropriate to refine anisotropic B’s for a high resolution 
> (1.35 Å) structure AND apply TLS parameters?

At this resolution you are best to use individual anisotropic ADPs for 
non-H atoms of macro-molecule, and isotropic ADPs for other atoms.

Pavel