Dear Nick
Using TLS sometimes improves behaviour of NCS restraints (it makes
sense since remaining B values should be similar). However in other
cases it does not improve. Perhaps removal of B value restraints for
these domains may improve NCS restrained refinement. I have not done
tests without B value restraints so I cannot say what would be
behaviour.
I would do several tests before making decision:
1) TLS (as Martyn suggests - domain level) with NCS restraints
2) TLS with NCS restraints without B value NCS
3) NCS without B value restraints
regards
Garib
On 8 Jan 2009, at 10:54, Nicholas Keep wrote:
I am refining a low (3A) resolution structure of a 3 domain protein.
There are 4 copies in the ASU. I have been applying tight NCS
restraints by domain in refmac and have pulled the weak MR solution
down to Rfree below 30 (just).
However my question is that in 2 of the 4 copies one of the domains
is very poorly resolved. I can lower Rfree by around 0.5% by
omitting the domains from the PDB entirely or not applying the NCS
restraints to these copies of the domain. Clearly they are there
and should resemble the moderately well resolved copies by
coordinates but the way Bfactor restraints are applied between NCS
copies seems to be the issue. If tight restraints are included the
B factors are much lower (30-40) rather than 60-80 for the poor
domains.
I was wondering if there is a theoretically correct way to treat this?
Would applying TLS scaling to each domain lead to the residual B
factors being more balanced?
Can a B factor offset be applied to the NCS restraints or could I
only apply a coordinate restraint not a B factor restraint between
certain copies?
Comments welcomed especially from Garib.
Happy New Year
Nick
--
Dr Nicholas H. Keep
Dean of Faculty of Science
Reader in Structural Biology
School of Crystallography,
Birkbeck, University of London,
Malet Street,
Bloomsbury
LONDON
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email n.k...@mail.cryst.bbk.ac.uk
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