Heya Giacomo Quilici,
I don't really know a whole lot about NUS in Topspin, but as I
understand, you would probably have had to reconstruct the data
(presumably within Topspin), to get a much higher resolution
spectrum than normal sampling would. When you compare your NUS
spectrum to the standard spectrum - are you comparing the same
number of increments (i.e. 2k x 128 x 128) or is your NUS spectrum
higher (2k x 1k x 1k)? A simple way to check this is just look at
the size of the file of 3rrr between your NUS sample and the
conventional sampled file.
If this is the issue, the problem is largely hardware related as
your computer has to try and read gigabytes of data in from the
hard drive to display a single plane and even modern computers
aren't the best at this.
Possible work arounds:
1) Use contour files rather than raw processed data. This was
mentioned a few weeks ago by one of the developers. Basically, you
get the spectrum to an appropriate S/N ratio that you want to work
at, and you can then record a reduced data file that is much
quicker to display the contours than recalculating them every time
you move through a 2D plane. Only issue is that you can't increase
or decrease contour levels as you go (you need to recalculate the
contour file or turn it off). To use them you get to the dialogue
box in the spectra window at the bottom ("contour files"), then
create a contour file for each of your spectra. Be sure to select
the two dimensions you are going to be looking at (i.e. usually 1H
and 13C for the HNCA, etc). This will take a long time especially
if your 3D data file is huge. You then set 'use contour files' as
'yes' in the spectra window. Check out
http://www2.ccpn.ac.uk/documentation/analysis/popups/CreateContourFilePopup.html
and the archive of this discussion board for more information. As
I said, I think it was only a few weeks ago this was discussed.
2) Use something like nmrPipe and order your data in the planes
you expect to view the spectrum in. This is more involved, and I
suspect that you wouldn't bother with this if you are going with
the contour file approach, but if you have your NMR data stored as
f3f2 planes (i.e. 1H15N usually for Bruker stuff at least), you
need to read each plane to plot a new 2D trace in f3f1 (1H13C).
You significantly reduce the work the computer has to do if you
store 1H13C planes as it only has to find the right one and
display it, not read each plane. If you don't quite get what I
mean, it is probably more hassle than the speed improvement would
be. There is no improvement using this method if you use contour
files.
If the size of your processed data is not any bigger than the
conventionally sampled stuff, perhaps there is another issue here,
but you would need advice from the developers on that one.
All the best,
Tom
On 10/10/13 7:09 PM, Giacomo Quilici wrote:
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Good morning,
I have recently acquired 3D spectra (HNCa and HNCO) on a Bruker
spectrometer in Non Uniform Sampling (NUS) way.
I loaded them on a CCPNMR analysis (2.1) project. The spectra
visualization is ok, but it is extremely slow (almost impossible
to manage) to navigate through the spectra with respect to same
spectra acquired without NUS.
I loaded them in "bruker" format selecting (as usual) the entire
processing folder. I have already checked if the dimension of
3irr-3rrr files is greater with respect to the homologues
spectra aqcuired in standard way, but this is not the case.
any suggestions?
best regards
Giacomo Quilici
--
Thomas J Carruthers
Structural Biology and Biophysics
Research School of Chemistry
Australian National University
Building 137-1.17
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P: (+61) 2 612 56506