It is worth doing sme rounds of non-NCS restrainded refinement then
sending it to the Ethan Merrit server to get TLS groups suggested..
Eleanor
Frank von Delft wrote:
Two points:
1. B-factors tend to differ lots between NCS copies, so you want to
set those restraints rather low (at least, I always do, by default)
2. NCS groups tend to need a far more fine-grained description than
just plonking in the whole domain. For structures in my lab, we often
see that tight NCS "does not work" -- until the group definitions are
selected more carefully.
Cheers
phx
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
