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

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

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