TLS is VERY fussy about format -
Here is an example which works.
I always prepare it from the GUI - that means it is more or less correct..
Eleanor
bmbsb
TLS Chain Z
RANGE 'Z 4.' 'Z 261.' ALL
TLS Chain A
RANGE 'A 4.' 'A 253.' ALL
TLS Chain B
RANGE 'B 4.' 'B 253.' ALL
TLS Chain D
RANGE 'D 4.' 'D 261.' ALL
TLS Chain E
RANGE 'E 4.' 'E 253.' ALL
TLS Chain F
RANGE 'F 4.' 'F 253.' ALL
[EMAIL PROTECTED] wrote:
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Date: Thu, 26 Jan 2006 09:39:35 +0000
From: Stephen Brian Carr <[EMAIL PROTECTED]>
To: [email protected]
Subject: TLS refinement problems
Message-ID: <Pine.VMS.3.91-2 (vms)[EMAIL PROTECTED]>
MIME-Version: 1.0
Content-Type: TEXT/PLAIN; charset=US-ASCII
Dear CCp4ers,
I am currently refining a model for a dimeric protein at a resolution of
2.8 A. The protein is dimeric with each monomer consisting of
approximately 450 amino-acids. The problem is that the R and R-free have
stalled at 30 and 35% respectively. All refinement has been carried out
using tight NCS restraints in refmac5 - loosening the restraints doesn't
help matters. I have also tried simulated annealing in CNS and this also
doesn't help.
Consequently I would like to try TLS refinement. I have created
a TLS input file using the CCP4i gui (we are running version 5.0.2) and
denoted each monomer as an independent TLS group. I have also fixed the
B-factors at 20 before refinement.
However, when I run refmac the TLS refinement doesn't appear to be
working as no T,L or S parameters are calculated/refined (the TLSout file
is full of zeros). The manual suggests that refmac should calculate
these from starting values of zero along with the centroid of each group,
but this has again been calculated as 0 0 0. I have also tried
inputing different random origins and initial TLS tensors, but it seems
whatever values I put in are not refined and simply output. I am
currently struggling to make any sense of these observations and so any
help would be greatly appreciated.
Thanks for any replies in advance
Steve
~~~~~~~~~~~~~~~~~
Dr Stephen Carr
Astbury Centre for Structural Molecular Biology
Instutute for Cellular and Molecular Biology
University of Leeds
Leeds
LS2 9JT
TLS Chain Z
RANGE 'Z 4.' 'Z 261.' ALL
TLS Chain A
RANGE 'A 4.' 'A 253.' ALL
TLS Chain B
RANGE 'B 4.' 'B 253.' ALL
TLS Chain D
RANGE 'D 4.' 'D 261.' ALL
TLS Chain E
RANGE 'E 4.' 'E 253.' ALL
TLS Chain F
RANGE 'F 4.' 'F 253.' ALL
begin:vcard
fn:Eleanor Dodson
n:Dodson;Eleanor
email;internet:[EMAIL PROTECTED]
tel;work:+44 (0) 1904 328259
tel;fax:+44 (0) 1904 328266
tel;home:+44 (0) 1904 424449
version:2.1
end:vcard
