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Hi all, I am very new to nmrPipe. I want to achieve the following steps. It would be very kind if somebody helps.

I have a 2D bruker data (t2= 4k points, t1= 32 points) and I want to do Fourier transform in the F2 dimension,phase etc. (2) and then extract the 32 spectra as 1Ds and also convert these 32 spectra in ascii format. (3) fit the peaks with a gaussian or Lorentzian function. (4) integrate the peak and save the integrals and time points as an ascii file.

I only managed till the 1st step. Please help..!!

asked Oct 05 '10 at 02:40

RSnmr's gravatar image

RSnmr
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updated Oct 28 '10 at 09:44

Evgeny%20Fadeev's gravatar image

Evgeny Fadeev
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3 Answers:
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An example of this kind of 1D series analysis using NMRPipe is included in the demo data archive "dosy.tar.Z" posted at the bottom of the NMRPipe download site:

http://spin.niddk.nih.gov/NMRPipe/install

The example includes scripts which extract and save 1D slices from a 2D as a series, scripts which fit the evolution of 1D peaks over the series, and scripts which display the fitted model along with the original data.

link

answered Oct 13 '10 at 11:44

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delaglio
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nmrPipe itself does not fit or integrate the peaks, but there are separate programs and .tcl scripts that are shipped with nmrPipe which do that.

nlinLS - program that does data fitting, usually called from autoFit.tcl (type autoFit.tcl -help to see what options are available)

So in the end to automate all of that you'll have to create a script that calls nmrPipe and either autoFit.tcl or nlinLS.

One way to extract a 1D vector from nmrPipe is to use COADD function, which is quite cumbersome with many FID's tucked into the 2nd dimension (you'll need to type lot's of zeroes in your case):

nmrPipe -fn COADD -axis Y -clist 1 0 0 0 ...#(31 zeroes to get the 1st vector)

COADD will add up the data vectors using the coefficients given with the -clist argument.

Maybe there is a way to achieve the same result with EXT function, which would look like so (I've never tested this, please leave a note if it works for you).

nmrPipe -fn EXT -x1 5  -xn 5  #assuming you need 5th FID.
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answered Oct 05 '10 at 10:19

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Evgeny Fadeev
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updated Oct 05 '10 at 11:08

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hi i am sashi,new to this software, previously i was using topspin 2.1 to process 2-D data ,when we try to process same data in nmrpipe and topspin (keeping same phase valves) unfortunately we didnt get same spectra in these two softwares (topspin showing more peaks than nmrpipe).Though we followed each and every command in manual(we used basic 2D in nmrpipe).Can anybody help in this regards thankyou in advance.

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answered Oct 28 '10 at 06:24

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saship21
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Sashi, could you repost this as a separate question? Since this is a Q&A forum, answer area should not be used for questions, just because it makes things easier to follow. Also - if you post images it will be easier to understand your problem. I'm guessing that the problem may be in the data mode. - Evgeny Fadeev (Oct 28 '10 at 09:28)

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