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