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

Pavel Afonine pafonine at lbl.gov
Mon Mar 4 17:45:02 PST 2019

Hi Mark,

you can have TLS selections in parameter file, however unless you ask 
refinement to use TLS they won't be used.

This allows you to keep selections in your file and gives you freedom to 
use them when you decide to.


On 3/4/19 17:37, Mark Saper wrote:
> Pavel,
> Even when I turn off TLS refinement, the definition for TLS parameters 
> is still there in the .eff effective parameter file.  So I think it's 
> still being applied.  It’s confusing.
> -Mark
> _______________________________________________
> Mark A. Saper, Ph.D.
> Associate Professor of Biological Chemistry, U-M Medical School
> Room 3220B, MSRB IIIsaper at umich.edu <mailto:saper at umich.edu>   +1 
> (734) 764-3353 mobile: (734) 276-6505
>> On Mar 4, 2019, at 5:33 PM, Pavel Afonine <pafonine at lbl.gov 
>> <mailto:pafonine at lbl.gov>> wrote:
>> 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

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