Subject: Re: How to check Mirror peaks in aromatic NOESY spectra?
From: evanspap
Date: May 11, 2007

Previous: 370

Thank you Tom,
I followed your advice and tried the trick of merging the spectra.
But instead of creating a huge file spanning from the aliphatic to the
aromatic carbon region I used the overlay function (ol) and overladed
the aromatic Noesy on the regular Noesy-hsqc.
One detail is that the proton axis directly attached to the carbon
dimension in aliphatic C-noesy-hsqc is usually extracted so as not to
contain the unnecessary amide proton region. But the aromatic protons
coincide with this region. Therefore for the overlay to work I had to
keep the amide region. Instead of extracting it I zeroed the spectrum
points above 6ppm on directly attached proton axis. This resulted on
an approximately double size spectrum but still manageable; a bit less
than 1GB.
Of course peak picking still has to be done in the aromatic-noesy
but at least visual inspection of mirror peaks assignments can be
semi-automaricaly performed.
Evangelos

--- In nmr_sparky@yahoogroups.com , Tom Goddard sparky@... wrote:

Hi Evangelos,

Heres a trick to use the mirror peaks tool with two C13-hsqc-noesy
spectra (aromatic and aliphatic). Copy all the peak markers in the
aromatic spectrum to the aliphatic one (select all peaks (pa), copy
peaks (oc), then paste peaks in aliphatic spectrum (op)). Now use the
mirror peak dialog (md) with just the aliphatic spectrum.

There are two problems with this. First the axes of the two spectra
must be in the same order (e.g. H1-C13-H1) and the proton attached to
the carbon must be the same axis in both spectra (e.g both the 3rd
axis, w3). The second problem is that reported signal/noise for the
aromatic peaks will be shown as zero because the mirror peak tool is
using the value from the aliphatic spectrum which is outside the
observed C ppm range. That might be ok if you just look at the
mirrors of the assigned aromatic peaks. You can instead copy the
aliphatic peak markers to the aromatic spectra to get the signal/noise
values for just the aromatic peaks.

Alternatives to the above trick look difficult. Could modify the
mirror peaks python code, but that looks rather complex. Could try to
merge the aliphatic and aromatic spectra into a single spectrum file
-- not sure if any software is available to do that, and the file
would be very large with lots of zeros in the missing C-ppm range.

Tom



--- In nmr_sparky@yahoogroups.com , evanspap evanspap@ wrote:

Hi all,
I have been using successfully the mirror peak assignments checking
tool. It is very useful for the NOESY spectra assignments to derive
constraints for the final structure calculation. However it supports
only one C-hsqc-Noesy and one N-hsqc-Noesy.

But I have acquired an aromatic C-hsqc-Noesy. By that I mean that the
Carbon dimension is centered in the aromatic region around 125ppm +-
10ppm. Therefore I can detect the aromatic ring protons in the direct
dimension labeled through hsqc by the aromatic Carbons attached to
them; and in the indirect dimension is see protons where the
magnetization has been transfered through NOE.

My question is how to automatically check between the mirror cross
peaks of the the aromatic proton to methyl proton labeled by aromatic
Carbon in the one NOESY spectra and then labeled by the methyl Carbon
in the other normal aliphatic C-Noesy-Hsqc? Does anyone know of any
trick or script available? Or I guess some modification to the
existing mirror peak assignments checking tool will do it.
Thank you in advance!
Evangelos