[phenixbb] refine : peculiar TLS tensors

Bryan Lepore bryanlepore at gmail.com
Tue Oct 19 15:01:23 PDT 2010

[ phenix 1.6.4-486 ]
[ ALSO : tlsanl, refmac, etc. from ccp4 6.1.3 ]
[ molscript/povscript ]

the one-liner : i have some TLS tensors that sometimes do not compare
at all well with refmac/anisoanl tensors.

sometimes, the principal axes of a TLS tensor refines *very* far away
from the center of mass(=center of reaction), or the axes from tlsanl
are exceptionally small as if not scaled properly. the eigenvalues are
really small too. see [*] for troubleshooting and strategy used.

i suspect i am missing something. i also understand this might not be
a phenix question.


[*] i compared another .def that gave sensible TLS results with a
different dataset/model, and my {} are all good AFAIK.
anisoanl/refmac/parvati results are reasonable. the phenix refinement
appears well behaved. these are all using tlsextract to get the
eigenvalues/origins, and molscript to check the axes/centers of mass.
input B factors are Beq unless i made an error. the tls group
selections can vary - however, simple groups also can give these

in general, using strategy (excerpt) :

  refine {
    strategy = *individual_sites individual_sites_real_space rigid_body \
               *individual_adp group_adp *tls *occupancies *group_anomalous
    sites {
      individual = None
      torsion_angles = None
      rigid_body = None
    adp {
      individual {
        isotropic = None
        anisotropic = None
      group_adp_refinement_mode = *one_adp_group_per_residue \
                                  two_adp_groups_per_residue group_selection
      group = None
      tls = "chain A and (resid 1:41 or resid 42:159 or resid 195:237
or resid 263:420)"
      tls = "chain A and resid 160:194"
      tls = "chain A and resid 245:252"
[...cut off ... ]

example output of an ill-behaved S tensor from tlsanl :

                               X       Y       Z
   1                         70.667 154.197 308.627    -144.435
   2                        977.334 819.588********    6222.947
   3                        640.7191431.084 471.341     269.382

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