On Wed, 22 Feb 2006, igor barsukov wrote:
> Just a little remark on Me-protons. Even if they are treated as ambihuous,
> the NOE intensity somewhat depends on the orientation of the C-C axis due to
> the fast rotation of the Me-group. People used to take this into account by
> adding 0.3-0.5A to the upper limit.
But that was when we were using pseudo-atoms rather than r^-6 sum
averaging wasn't it? Due to the proximity of the three methyl protons,
all three will almost always contribute to an ambiguous restraint (unless
you filter too hard) so that should handle everything but the difference
in relaxation behaviour.......
> Is there a possibilty to do this in the analysis?
.....so this can only really apply to unambiguously assigned crosspeaks
where the methyl/non-methylness is known before you convert intensity to
distance. A more general solution that covers ambiguous assignments also
is a posterior recalibration of the restraints based on the structures
calculated as implemented in various ways in different XPLOR/CNS/ARIA
versions.
> Probably will not have any effect on the calculated structure.
Indeed, but appropriate calibration of restraints involving methyl groups
may assist in avoiding the situation that I have often seen where I have a
few persistent violations of restraints involving methyl groups when
everything else is fine. That said these are often things like
intra-residue methyl to HN crosspeaks, that might be better handled by
local relaxation matrix recalibration that would allow for spin diffusion
as well as methyl-ness.
Brian
--
Dr. Brian O. Smith ---------------------- B Smith at bio gla ac uk
Division of Biochemistry & Molecular Biology,
Institute Biomedical & Life Sciences,
Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
Tel: 0141 330 5167/6459/3089 Fax: 0141 330 8640
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