[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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