Hi Raphael,
I think everything should be just fine and you're just misunderstanding
how analysis is showing you stuff.
On Sun, 12 May 2013, Raphael Sayegh wrote:
> I'm having some troubles to get the proper dimensions (F1=H; F2=13C;
> F3=15N) in a HNCA experiment processed in Topspin.
>
> Before opening the spectrum, I have to create a window with 15N in F3
> and 13C in F2 dimensions to visualize it with 15N in the Z-axis.
> Otherwise I would get 13C in F3 (z-axis) and 15N in F2 (y-axis).
Analysis can show you an N-D spectrum in any of its possible views, so you
could even make an 15N 13C window with a 1H z dim and it would appear in
that. You can create new windows after a spectrum is loaded, as well as
before, to view it differently if you don't have the right combination set
up in advance.
> However, the 15N dimension keeps labeled as F2 in my peak lists. The
> peaks were picked using the "pick and assign from roots" tool.
That is as it should be - the order of the peak dimansions stays the same
as the order of dimensions in experiment type of the experiment associated
with the spectrum, not necessarily the order of dimensions of the
particular window you are displaying it in.
> I suspect that this creates troubles for the sequence assignment with
> the Assignment:Protein Sequence Assignment tool, because this tool
> doesn't list spectral windows for 13C, only for 1H...!
The order of dimensions of the peaks will not cause problems here. Most
often the problem arises either because analysis has not recognised or not
been told enough about the experiment to know that it can be used for
backbone assignment.
> Does anyone know how to change the 15N dimension label in the peak list?
So you should not need to do this, but the fix to the problem will most
likely be something to do with the experiment prototype assigned to your
HNCA. For Bruker processed data, this typically gets set automatically,
but it may be that there's some mismatch between how it's set in topspin
and in analysis. Take a peek in the wiki at:
https://sites.google.com/site/ccpnwiki/Home/documentation/ccpnmr-analysis/core-concepts/experiments-and-spectra
as a starting point.
Dr. Brian O. Smith --------------------------- Brian Smith at glasgow ac uk
Institute of Molecular, Cell and Systems Biology & School of Life Sciences,
College of Medical, Veterinary & Life Sciences,
Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
Tel: 0141 330 5167/6459/3089 Fax: 0141 330 4600
----------------------------------------------------------------------
The University of Glasgow, charity number SC004401
|