[phenixbb] Are TLS parameters applied when TLS refinement is OFF?
saper at umich.edu
Mon Mar 4 17:38:01 PST 2019
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 A. Saper, Ph.D.
Associate Professor of Biological Chemistry, U-M Medical School
Room 3220B, MSRB III 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> 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.
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