Hi, 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: 0.2105 T22: 0.2895 REMARK 3 T33: 0.0962 T12: 0.0829 REMARK 3 T13: 0.0473 T23: 0.0007 REMARK 3 L TENSOR REMARK 3 L11: 0.0446 L22: 0.0120 REMARK 3 L33: 0.0096 L12: 0.0246 REMARK 3 L13: 0.0209 L23: 0.0106 REMARK 3 S TENSOR REMARK 3 S11: 0.0228 S12: -0.0268 S13: -0.0023 REMARK 3 S21: -0.0507 S22: 0.0526 S23: -0.0287 REMARK 3 S31: -0.0296 S32: -0.0137 S33: 0.0534? The data set is complete at 2.3Å resolution and there are no strange crystal phenotypes. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031
Hi Reza, 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 phenix.find_tls_groups)? 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: http://journals.iucr.org/d/issues/2015/08/00/rr5096/rr5096.pdf You can check if TLS matrices are physically meaningful by running phenix.tls_analysis model.pdb 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)? Pavel On 4/30/17 05:30, Reza Khayat wrote:
Hi,
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
Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031
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Pavel Afonine -
Reza Khayat