Subject: Re: reading cyana peaklists in Sparky and overlapped peaks
From: betswanso
Date: Nov 7 4:30 AM

Previous: 287

Dear Eiso and Mandar,

Thanks for the suggestions. I used Gaussian fit method previously but
I tried peak heights yesterday. It worked wonderfully. The program
generated structures consiting of well defined secondary structural
regions.

Thanks a lot,

Betty Swanson





--- In nmr_sparky@yahoogroups.com , eiso e.ab@... wrote:

Betty Swanson wrote:


Dear Sparky Users,

I initially ran CYANA using peaks that were well defined (no
overlaps)
in the 15N-edited and 13C-edited spectra. After cycle7, the CYANA
run
generates cycle7-ref.peaks and cycle7.peaks. I input these files
in
SPARKY and tried using the command rp so that SPARKY reads the
peak
lists, but it doesnt work. Is there a way by which these files
can be
read by SPARKY so that I need not manually type and assign the
peaks in
the spectra?
you could try
http://www.nmr.chem.uu.nl/~eiso/bin/peaks2sparky.awk
to make a speaky peaklist. ambiguous assignments will be put in the
peak label.
(check if the nomenclature is what you want before you read in)

Also, my next CYANA run would include peaks that are
overlapped. When these peaks are integrated I feel SPARKY is
overestimating the peak volumes. How do you guys handle this
problem?
I usually take heights, that is more robust.
You could use the integral of a gaussian fit, or is that already
what youre doing?

Eiso


Thanks,

Betty Swanson