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Hi

I have recently moved to a lab which has a varian magnet, in the past I have only used brukers. The people here use NMRpipe for processing which I am not a fan of. Is there a simple way to process Varian data in topspin? I know this is relatively simple for 1D but I am told it cant be done easily for 2D or 3D data? is this the case?

Any answer would be appreciated

asked Dec 27 '10 at 10:10

Thomas%20Garner's gravatar image

Thomas Garner
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4 Answers:
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Thomas, you just need to adjust a few more parameters. For phase sensitive data make sure that ph_mod is not set to mc or ps, but pk or no. The apodization function WDW probably also needs to be set.

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answered Dec 29 '10 at 17:48

Clemens%20Anklin's gravatar image

Clemens Anklin
406

Hi Clemens, thank you for your response, I had previously tried changing the ph_mod and ended up with what looks like coupling (these are gCOSY and TOCSY spectra), using anything other than mc in f1 (f2 is set to pk) gives spectra that look like dqf-cosy. The adipization is set to sine. thanks again - Thomas Garner (Dec 30 '10 at 10:52)

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Hi Thomas, assuming this is phase-sensitive data, you want a cosine rather than a sine window function (i.e. window function starts at 1 and goes to zero, rather than starts and ends at zero). The SINE window function uses the value of the parameter SSB and has the form:

SINE(t)= sin( (PI-PHI)*(t/AQ) + PHI)

where PHI = PI/SSB, and t runs from zero to AQ.

If SSB = 1 (or 0), this is a sine finction, if SSB=2 this is a cosine function. For phase-sensitive data you want the cosine function, or you will get odd looking data, sort of "antiphase" and thus a bit like DQF cosy. I would also use the QSIN (squared sine/cosine) window for phase sensitive data, but it's the SSB value that's more critical. This should be 2 in both dimensions.

The sine window function with SSB=1 is used to narrow the base of the broad lines in magnitude-mode spectra - for magnitude mode data use WDW=SINE, SSB=1 and PHMOD=MC in F1, PHMOD=NO in F2.

Hope that helps!

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answered Jan 13 '11 at 04:34

Pete%20Gierth's gravatar image

Pete Gierth
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Topspin has a command vconv that imports the varian data. Once the data file is imported, you can do the usual topspin processing.

A minor issue we found is that sometimes the quad detection mode is set incorrectly for the multidimensional experiments, which can be adjusted in the eda window.

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answered Dec 27 '10 at 11:34

Evgeny%20Fadeev's gravatar image

Evgeny Fadeev
5571

Hi, Thanks for the response I tried that and I can open up a 2D data set but it comes up bright green (Maybe negative??)and I cant phase it. I get the 'error magnitude data can not be phased'. I can rser1 and phase that 1d but not the 2D. any ideas? - Thomas Garner (Dec 28 '10 at 14:42)

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Hi I am using Bruker Tpospin for brain spectroscopy analysis. I am new to this software. My question is how do I make spectral lines dotted or thicker instead of colors. Any hint is highly appreciated. Thanks Surya

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answered Feb 28 '11 at 06:28

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surya
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