Subject: distance constraints using nOes
From: rruhayel
Date: Nov 20 6:47 PM

Next: 463


Hello users,

I have a NOESY spectrum of a 10 mer DNA strand with well separated
peaks . I am hoping to model the DNA based on these distance and other
dihedral angel constraints (COSY).

I am using Gaussian fitting for the peak fitting and when I compare
the fit (blue line) to the actual peak it looks pretty good.

I do however notice that for some peaks (no overlap, no smearing) I
have a very high rms value (50% - 100%). I am not sure why. I have
tried the integration at several thresholds and still have the same
problem. Is there something wrong with my integration method? I am
allowing peak motion (not sure that this is exactly) and fitting data
above the lowest contour level.

I have made an attempt to extract distance contraints from the volumes
that SPARKY creates after integration.

I have calibrated the C H5-H6 crosspeak intensity to 2.46 A and then
use the following equation get the supposed distance:

distance = 2.46 * (intensity of peak/intensity of C H5-H6 peak) ^ (1/6)


Most of my distances are coming out unrealistically short ( 1.3 A)
and distances that I know should be medium/long are coming out 2 A)

Is there any advice as to how one should go about this method of
extracting distance constraints from a NOESY spectrum.

Thanks

rasha