[phenixbb] TLS group definition
Pavel Afonine
pafonine at lbl.gov
Thu Apr 28 10:41:23 PDT 2011
Hi Andres,
> I am trying to refine using TLS parameter as in the attached file
> generated in ccp4.
which program you use to refine your model? If it is phenix.refine then
the attached file is not suitable to define TLS groups for
phenix.refine. For example, translation of these lines:
TLS
RANGE 'A 1.' 'A 230.' ALL
RANGE 'A 416.' 'A 568.' ALL
RANGE 'A 629.' 'A 794.' ALL
RANGE 'A 899.' 'A 899.' ALL
RANGE 'A 900.' 'A 900.' ALL
RANGE 'B 84.' 'B 87.' ALL
ORIGIN -26.886 1.710 -76.557
T 0.1151 0.0090 0.0533 0.0096 0.0154 0.0014
L 2.1545 1.4001 0.7879 1.1375 -0.4178 -0.5303
S -0.0027 -0.0004 -0.0810 0.0603 -0.0219 0.1132 -0.0538 0.0233
TLS
RANGE 'B 1.' 'B 83.' ALL
ORIGIN -58.568 8.877 -85.204
T 0.0929 0.0996 0.2885 -0.0113 -0.0037 0.0229
L 2.4389 2.2023 1.2365 0.2174 0.7759 -0.0156
S 0.2584 -0.1495 -0.0520 0.1045 0.5167 0.0232 0.0277 -0.3204
(...)
into phenix.refine format would look like this (I guess):
refinement {
refine {
adp {
tls = (chain A and (resseq 1:230 or resseq 416:568)) or (chain B
and resseq 84:87)
tls = chain B and resseq 1:83
#... and so on for all other groups
}
}
}
Note, you don't need to provide initial values for TLS matrices and
origin - they are determined as part of refinement.
Also, you can use (or equivalent in the GUI)
phenix.find_tls_groups model.pdb
that will find TLS groups for you and output in ready-to-use in
phenix.refine format.
Pavel.
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