Brian Smith wrote:
> 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.
well in principle you're free to use whatever level of
sophistication you want, when you calculate NOE intensities or
corresponding'corrected' distances from your protein model.
spin diffusion, anisotropic rotational diffusion etc.
Instead of the simple 1/r^6 sum you can choose a more complicated
formula to calculate the distances.
so in principle it's still possible to use ambiguous restraints,
it's just not implemented usually.
another effect that might be considerable is caused by the
slower T1 relaxation of methyl groups, which causes them to
have a lower initial magnetisation, because they are not fully
relaxed at the start of the next scan.
this leads to an asymmetry in the crosspeak intensity above
and below the diagonal.
Tom James (CORMA, MARDIGRAS, etc) published quite a few papers
on the proper treatment of a lot of effects.
Eiso
>
>> 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
>
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