NUS setup on Topspin 3.0

[Yunfei Hu]

Dear all,

I have tried out setting up NUS on Topspin 3.0. Everything is done
automatically (e.g. level of sparsing set to 25%). Does anyone know if
there is a flexible way of manually controlling the parameters for
deciding a sampling schedule?

Thank you very much!

Yunfei Hu, Ph.D.
Beijing NMR Center, Peking University
Beijing 100871, China

[Maxim A. Dubinnyi]

We are know widely using NUS setup in Topspin 3.0 (version of August
25, 2010).

The first, in tab AcquPars change FnType from traditional (planes) to
non-uniform_sampling.
Then press large N button (switch to Nun-uniform sampling (NUS)
parameters), you will go to special GUI interface.
Here you can change AMOUNT [%] to any value (default is 25%).
Another important parameters are in T2 button. For 3D experiments
press edit and
change T2[1] and T2[2] to expected T2 values (in seconds).
THE BUG: command rga will not be executed correctly, when FnType is
non-uniform_sampling.
So, to run rga, temporary switch to traditional (planes), then run rga
and switch back to non-uniform_sampling.

Sincerely,
Maxim A. Dubinnyi,
M.M. Shemyakin and Yu.A. Ovchinnikov Institute of
Bioorganic Chemistry of the Russian Academy of Sciences (www.ibch.ru)
Department of structural biology,
Laboratory of biomolecular NMR-spectroscopy.

[Yunfei Hu]

Dear Maxim A. Dubinnyi,

Thanks for the quick response!
I see there are T2[0] to T2[7] values, and I am somewhat confused. How
do I know which T2 values (T2[1] , T2[2]) corresponds to which of the
indirect dimensions? And what does T2[0] stand for?

Thanks again!

Sincerely,
Yunfei Hu

[Maxim A. Dubinnyi]

Dear Yunfei Hu,

The notations in T2 window are realy confusing.
For 3D experiments the meaning is the following:
T2[0] refers to the relaxation in F1 dimension (carbon in triple-
resonance experiments, e.g. hncogp3d)
T2[1] refers to the relaxation in F2 dimension (nitrogen, constant-
time in triple-resonance experiments)
All others are meaningless.

It is a good idea to explore the NUS matrix after parameters setup.
To do this, press calculate button (looks like pocket calculator),
then
go to the folder of the current experiment and look for the file
nus_setup.hdr_3. This is the file with pairs of integers (for 3D), the
increments
which will be used for acquisition.
Under linux, run command gnuplot in the folder, then in gnuplot
execute command
plot "nus_setup.hdr_3", the window with NUS points will appear. Under
windows, try to open this file e.g with excel and plot graphics. For
short T2 values
the points should appear close to zero. Maximum value in each
dimension is
the half of appropriate TD value.

Sometimes an error appears like this

"
ERROR:
-- TOO few points requested (NI) with respect to maximal matrix
(NIMAX)
!! increase NI, or reduce NIMAX or maybe try another seed
"

this means that the amount[%] for the NUS matrix is too small. NI
means TD for bruker.
(the program was originaly developed for varian).

Processing of the NUS data may be done either in Topspin by the
command
ftnd 0
which will work a huge amount of time (may be several hours) and
depends on parameters
CEXP, CT_SP, NCOMP, SRSIZE, f180 or in qMDD program of Maxim Mayzel
(see in
this group). I prefer to use the qMDD.

Sincerely,
Maxim A. Dubinnyi,
M.M. Shemyakin and Yu.A. Ovchinnikov Institute of
Bioorganic Chemistry of the Russian Academy of Sciences (www.ibch.ru)
Department of structural biology,
Laboratory of biomolecular NMR-spectroscopy.