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. Pavel 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 [email protected] mailto:[email protected]   +1 (734) 764-3353 mobile: (734) 276-6505

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On Mar 4, 2019, at 5:33 PM, Pavel Afonine mailto:[email protected]> wrote:

Hi Mark,

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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.

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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