Hi,
I am currently refining some reasonably high (1.4-1.6 Å) resolution protein:RNA
complex structures and was trying the approach described in Schwartz et al.
Nat. Struct. Biol. 8 (2001) 761-765 where they divided each nucleotide into
three TLS groups – the ribose, the phosphorus atom plus both nonesterified
oxygens and the base.
When I define a tlsin file that does this with the ribose, P OP1 and OP2, and
base from 3 successive nucleotides everything seems to work fine so the groups
are defined correctly. However when I divide a single nucleotide into 3 TLS
groups only the first group has its origin calculated and actually has TLS
parameters refined:
TLS origin for group 1 -3.1622999 -6.9280601 -9.6330261
TLS origin for group 2 0.0000000 0.0000000 0.0000000
TLS origin for group 3 0.0000000 0.0000000 0.0000000
TLS group 1:
T tensor ( 1) = 0.046 0.115 0.103 -0.003 -0.008 0.087
L tensor ( 1) = 1.341 1.887 5.684 0.509 -2.040 -0.436
S tensor ( 1) = 0.015 0.015 -0.257 -0.220 -0.024 0.071 0.095
0.060
TLS group 2:
T tensor ( 2) = 0.031 0.031 0.031 0.000 0.000 0.000
L tensor ( 2) = 0.000 0.000 0.000 0.000 0.000 0.000
S tensor ( 2) = 0.000 0.000 0.000 0.000 0.000 0.000 0.000
0.000
TLS group 3:
T tensor ( 3) = 0.031 0.031 0.031 0.000 0.000 0.000
L tensor ( 3) = 0.000 0.000 0.000 0.000 0.000 0.000
S tensor ( 3) = 0.000 0.000 0.000 0.000 0.000 0.000 0.000
0.000
An excerpt from my tlsin is below:
TLS
RANGE 'B 3.' 'B 3.' P
RANGE 'B 3.' 'B 3.' O1P
RANGE 'B 3.' 'B 3.' O2P
TLS
RANGE 'B 3.' 'B 3.' C1*
RANGE 'B 3.' 'B 3.' C2*
RANGE 'B 3.' 'B 3.' C3*
RANGE 'B 3.' 'B 3.' C4*
RANGE 'B 3.' 'B 3.' C5*
RANGE 'B 3.' 'B 3.' O2*
RANGE 'B 3.' 'B 3.' O3*
RANGE 'B 3.' 'B 3.' O4*
TLS
RANGE 'B 3.' 'B 3.' N1
RANGE 'B 3.' 'B 3.' C2
RANGE 'B 3.' 'B 3.' O2
RANGE 'B 3.' 'B 3.' N3
RANGE 'B 3.' 'B 3.' C4
RANGE 'B 3.' 'B 3.' O4
RANGE 'B 3.' 'B 3.' C5
RANGE 'B 3.' 'B 3.' C6
I guess I've got the syntax of the tlsin file wrong? Any suggestions for what's
wrong would be much appreciated!
Thanks,
Huw
--
Dr Huw Jenkins
Astbury Centre for Structural Molecular Biology
University of Leeds
