[phenixbb] refine : peculiar TLS tensors

Alexandre OURJOUMTSEV sacha at igbmc.fr
Wed Oct 20 00:32:14 PDT 2010

Hi, Bryan,

Do not going into details of TLS, the very first remark is that the center of reaction that characterizes the MOVEMENT of the group is NOT AT ALL the center of mass that characterizes the GROUP as it is independently of any its movement. They should not be confused.


-----Message d'origine-----
De : phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] De la part de Bryan Lepore
Envoyé : mercredi 20 octobre 2010 00:01
À : phenixbb at phenix-online.org
Objet : [phenixbb] refine : peculiar TLS tensors

[ 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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