[phenixbb] TLS refinement
pafonine at lbl.gov
Tue May 2 08:07:46 PDT 2017
this may mean several things. Perhaps TLS group selection isn't optimal
or incorrect? phenix.find_tls_groups relies on B factors to annotate TLS
groups. Were B factors meaningful (refined before running
You can try weight optimization.
Values of TLS matrices cannot be interpreted directly, they can be
positive or negative. This is discussed in great details here:
You can check if TLS matrices are physically meaningful by running
If it runs all the way till completion - all is good. Otherwise, in
case of nonsensical TLS it will stop and tell what's wrong.
Perhaps you enabled TLS refinement too early (model isn't good yet)?
On 4/30/17 05:30, Reza Khayat wrote:
> I'm having difficulty with performing TLS refinement on a highly
> symmetric system. The difference between the R_work and R_free
> increases with TLS refinement (16.5/21.4 changes to 14.4/22.2). The
> TLS tensors for some of the group are not sensible (if I understand
> the literature correctly) -there are some negative numbers for the T
> and L tensors (see below). The TLS groups were identified with
> phenix.find_tls_groups. Any suggestions would be appreciated.
> REMARK 3 SELECTION: chain 'A'and (resid 38 through 68)
> REMARK 3 ORIGIN FOR THE GROUP (A): 56.6459-23.5648-59.0695
> REMARK 3 T TENSOR
> REMARK 3 T11: 0.2105T22: 0.2895
> REMARK 3 T33: 0.0962T12: 0.0829
> REMARK 3 T13: 0.0473T23: 0.0007
> REMARK 3 L TENSOR
> REMARK 3 L11: 0.0446L22: 0.0120
> REMARK 3 L33: 0.0096L12: 0.0246
> REMARK 3 L13: 0.0209L23: 0.0106
> REMARK 3 S TENSOR
> REMARK 3 S11: 0.0228S12: -0.0268S13: -0.0023
> REMARK 3 S21: -0.0507S22: 0.0526S23: -0.0287
> REMARK 3 S31: -0.0296S32: -0.0137S33: 0.0534
> The data set is complete at 2.3Å resolution and there are no strange
> crystal phenotypes.
> Best wishes,
> Reza Khayat, PhD
> Assistant Professor
> City College of New York
> Department of Chemistry
> New York, NY 10031
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> phenixbb at phenix-online.org
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