On Tue, 7 Jan 2014, Jan Zalesak wrote:
> I did not find a reliable way to follow the distance calculations from
> intensities/volumes of the peaks.
>
> I have tried 3 steps (lets say I have overlap of 3Adenine H6-H2' peak with 2Ura H6-H2'
> peak)
> 1) I have put 3Adenine H6-H2' peak
> 2) I have manually added the second (2Ura H6-H2' peak) - "crosses" - on one peak
> (manually).
> 3) I have deleted (2Ura H6-H2' peak) and filled the assignment of it to the assignment
> of the first peak (so i have ambiguous restraint)
>
> After every step I check the peak intensities, peak volumes) and I calculate the
> distances.
> But surprisingly the values (all of them - intensities, peak volumes, calculated
> distances) do not change for any of the two resonances.
If your peak created in step 2 is close to the first peak then it will
pick up the same intensity value & volume because it's looking at the same
bit of the spectrum.
When you create a distance restraint from a peak in analysis, you simply
map the intensity or volume to a distance by the algorithm you choose
(1/r6, bins, etc.), so that won't change from situation to situation you
describe. What that then means to the structure calculation program
depends on the structure calculation program - for ambiguous restraints
you want to use one that treats the distance to intensity mapping as "sum"
in ARIA/CNS terminology.
You should use the third case you have (ambiguous) - you might want to
reduce the weighting of the contribution of the NOE spectrum in the
chemical shift list if you're going to manually assign multiple
possibilities to an ambiguous peak that might be a little off the exact
shift of each possible contributor. You could leave ambiguous peaks
(partially) unassigned and use "make shift match restraints" to avoid this
issue.
> Is there a way to handle this?
> Or is there a way to do it properly, but in a way program will understand that there are
> two peaks and the distance I want him to calculate should be smaller than if there was a
> single peak?
I think you misunderstood the intensity->distance mapping process.
> Can I for example change the peak boxes manually (or at least visualize them?)
It would be nice to have peak "footprints" that would allow the use of
overlapped NOE peaks more completely in the creation of ambiguous distance
restraints - currently, really overlapped peaks just have to be discarded.
--
Dr. Brian O. Smith --------------------------- Brian Smith at glasgow ac uk
Institute of Molecular, Cell and Systems Biology & School of Life Sciences,
College of Medical, Veterinary & Life Sciences,
Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
Tel: 0141 330 5167/6459/3089 Fax: 0141 330 4600
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