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Hi,

Does anyone have experience using MatNMR to produce a 2D spectrum? Or know of any examples?

I'm trying to follow the instructions in the documentation: http://matnmr.sourceforge.net/manual/Processing.html#Intro for the sample data, but there are a few things I can't get to work.

I use FT from the 2D menu which seems to take the Fourier transform along the TD2 direction. In the documentation is says to then take the Fourier transform along the TD1 direction, but when I use FT it seems to take it along the TD2 direction again.

Am I supposed to take a transpose, and then Fourier transform? Or is there some other way to get it to work?

image 1

image 2

Thanks

asked Oct 27 '10 at 19:17

newToNMR's gravatar image

newToNMR
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updated Oct 29 '10 at 12:59

Evgeny%20Fadeev's gravatar image

Evgeny Fadeev
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hotlinked your images, the third one did not work for some reason. There is an "insert image" button in the editor, you can use that. It's more reliable if you upload the actual files rather than point the links. - Evgeny Fadeev (Oct 29 '10 at 13:05)

maybe to process this set you need to reverse the T1 axis. Also looks like the frequency scales are not right - the difference between peak positions (if all you see is the two diagonal peaks) should be the same in both dimensions (again assuming that you have a cosy type of dataset) - Evgeny Fadeev (Oct 29 '10 at 13:08)

It's TOCSY so they should be in the same spot, The chemical shifts are wrong too because they should be around 3ppm -- processing with spinworks verifies this. I'm worried that changing QmatNMR.Dim has affected things like scales, at this point I think I'll try looking in the source code. - newToNMR (Nov 01 '10 at 00:06)


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... maybe you need to transpose the matrix before transforming or in some other way specify the dimension to work along? Perhaps "get column" step in the manual means that?

There is a variable QmatNMR.Dim, that according to the chapter 4.2 of the manual denotes dimension number. Maybe you can set that to 2 to choose TD1?

link

answered Oct 28 '10 at 10:00

Evgeny%20Fadeev's gravatar image

Evgeny Fadeev
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Thanks for your reply. I set QmatNMR.Dim=2 for the 2nd FT and the output says that it has done an FT along the TD1 direction. I used a simple methanol fid and got this: http://tinyurl.com/2c2u34g http://tinyurl.com/2aa6ftt It seems the shift axes are wrong the original is http://tinyurl.com/25dyurn - newToNMR (Oct 28 '10 at 20:40)

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So, having re-read the documentation, I think the "get columns" step is referring the the buttons in the 2D menu specifing the row and columns currently in view. . . Once I change the column it appears that when I take the Fourier transform it is in the TD1 direction and the axes are correct. I tested it using the sample data that comes with matNMR and it works, although the methanol spectrum I have didn't work so I think there is a problem with how that particular data is being processed, but I will create a seperate thread for this issue.

link

answered Nov 04 '10 at 23:03

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newToNMR
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