[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.
-bryan
[*] 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
results.
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 :
SCREW ROTATION AXIS ABSOLUTE POSITION (A) PITCH (A)
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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