I have read your paper. Now I have the following questions:

1) in the conclusions it is stated that quantitation of peak intensity should ideally be by the use of peak volumes unless there is resonance overlap present.

Does it mean that one should use peak volumes for some peaks (resolved) and peak heights for some other peaks (overlapped)? Wouldnt this procedure affect largely the possibility for comparison? Wouldnt the use of sum-over-a-fixed-small-box for all residues be more consistent?

2) you also conclude that in the case of peak height, one should exclude data at the end of the decay where the signal intensity is comparable to the noise: again, can this be done on a residue-by residue case?

Stefano

We argued over this question for quite a while and eventually put it together in this paper: http://www.ncbi.nlm.nih.gov/pubmed/11693564

The general conclusion is it depends on how long you have sampled your decay for. If you have sampled through two or three time constants (2 or three T1s or T2s) then at the longest delay the signal intensity will not have reached zero and you should fit with the two parameter equation. If you have sampled through five or more time constants then the signal intensity should be close to zero but you may have introduced an offset by the way in which you measured the intensity (by searching for a maximum in a grid about the peak center, for example) and you should then use a three parameter fit to eliminate the influence of the offset.

I hope this helps

brendan

--- In nmr_sparky@yahoogroups.com , Stefano Ciurli stefano.ciurli@... wrote:

Hi Tom,
thanks a lot. I would know how to use eq. b with another fitting
program but I will try to implement it in the python script within
Sparky. However, my question was also a bit more general: I wanted to
know how the community of NMR people deals with this problem, as it
is not clear from the literature and I am dealing with this problem
for the first time.
I hope someone in the list could also respond.
Stefano

On Jun 2, 2010, at 9:29 PM, Tom Goddard wrote:

Hi Stefano,

A modification to the Sparky relax.py file (sparky/python/sparky/
relax.py) could add the parameter C to the fitting. I think I did
this once upon a time but I cant find any code for it. Youd
modify the a_exp_bx_function class in the relax.py code. Maybe an
hours work to figure out change and test if you are familiar with
Python.

Tom


Hello,
when fitting T1 or T2 relaxation data one could use two equations:

a: A*exp(-t/B)

b: A*exp(-t/B) + C

In the first case one assumes that the maximum tau used in the set
of experiments is sufficient to bring to zero the intensity of the
signal, while in the second case one assumes that there may be a
residual intensity. Following my logic, I would prefer the second
case, because the spectrum with the largest tau still has non-zero
signals. However, Sparky uses the first equation. Of course, the
relaxation rates that are calculated in the two cases can be very
different. What is the commen/preferred protocol?
Stefano




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