Department of Chemistry, University of Alberta         September 2003
NMR News 2003-03
News and tips for users of the Varian NMR systems in the Department
Editor: Albin.Otter@ualberta.ca         http://nmr.chem.ualberta.ca

There are no fixed publishing dates for this newsletter; its appearance solely depends on whether there is a need to present information to the users of the spectrometers or not.


Other content of this NMR News is no longer meaningful and has been removed April 2010.

Contents 

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NMR staff changes

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FAQ 2003-03.1: How can I create 2D plots with 1D spectra on the side?

 

NMR staff changes
Mark Miskolzie joined the NMR support team. Mark replaced Gerdy Aarts who retired recently. Mark can be reached in WB-13 (492-2573).
We wish Gerdy all the best for the NMR-free part of her life and thank her for all efforts to keep magnets filled and spins spinning over many years.

FAQ 2003-03.1: How can I create 2D plots with 1D spectra on the side?
Quite a number of users mentioned that their preferred way of plotting 2D spectra is with the corresponding 1D spectra on the side. This is substantially different from a 2D plot with projections:
(1) projections are of lower quality compared to 1D spectra due to much lower digital resolution (see FAQ 99-08.1: digital resolution, what is it?);
(2) it is much more complicated to create a 2D plot with 1D spectra because data have to be obtained from 2 or even 3 different experiments: the 2D spectrum itself, the corresponding proton 1D and, for heteronuclear experiments such as GHM[Q/B]C, the corresponding APT or 1D-13C. This can be addressed by switching back and forth between individual experiments and by using the relevant plot commands in those experiments. However, this is a very cumbersome process and needs to be repeated if different expansions are desired.

The entire procedure is now available within the EZ NMR system in a much simplified form. There are two ways to achieve this: with the click of a button or by using one of two macros called pl2d1dhh or pl2d1dhx (hh for homonuclear experiments such as GCOSY, GTOCSY, TROESY etc. and hx for all heteronuclear experiments, e.g. GHSQC). If the button is used the software decides automatically which macro to call. The fundamental difference is that the macros give you a variety of options while the button does not.

To use the macros or the button it is a prerequisite and assumed that

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the 1D proton spectrum has been processed, phased and referenced correctly in a separate experiment

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the APT spectrum (where applicable) has been processed, phased and referenced correctly in a separate experiment

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the 2D experiment has been processed, referenced correctly and is the current experiment in VNMRJ

Experiment numbers can be freely selected but the use of the macro or button has to be from within the experiment that contains the 2D spectrum. In general, everything is done in the experiment that contains the 2D data!

A summary in PDF format for both the homo- and heteronuclear case can be found here. As an example, for homonuclear experiments, here is what happens when using the macro pl2d1dhh or clicking on the button 2D with 1D in the Plotting section of EZ P+P:

user input

system response

click on  2D with 1D

or type:

pl2d1dhh

This macro needs to know where the processed 1D proton spectrum is located. If you are not sure and want to start over enter 0, find out where your experiment is located, then start over by clicking on Restart 2D with 1D or by typing newpl2d1d.

Enter experiment number of the processed 1D spectrum (or 0 to quit):

2 (assuming 1D is in exp 2) plots 2D from current experiment and 1D from exp 2 at the top and on the side of 2D

After change of expansion limits in 2D spectrum

click on  2D with 1D

or type:

pl2d1dhh

plots 2D from current experiment and 1D from exp 2 at the top and on the side of 2D with spectral limits adjusted automatically, no need to re-enter location of 1D (the macro/button remembers it!)

This is the easy and most often used way for that task. More can be done but only by using the macro pl2d1dhh with arguments (a maximum of 5 arguments can be specified).

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To increase the vertical scaling of the 1D spectrum: type for example pl2d1dhh(‘x5’). Values from 2 to 99 are allowed.

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Use of a different 1D than initially specified: you have to tell the macro where to look, e.g. pl2d1dhh(6) takes the 1D spectrum from experiment 6.

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You can specify that only positive or negative contours are plotted, e.g. pl2d1dhh(‘pos’,’x3’) will plot only positive contours and triple the vertical scaling of the 1D plot.

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Example with 5 arguments: pl2d1dhh(‘neg’,’x5’,3,15,1.2)
The 1D is taken from experiment 3 and its vertical scale multiplied by 5, 15 negative contours spaced by 1.2 are plotted. If you want to specify contour level numbers and spacing you must specify the location of the 1D because the first numerical is interpreted as the location of the 1D spectrum. There is no way around this, however, there should be virtually no need to specify contour numbers and spacing; the default of 20, 1.5 covers a huge range of peak heights.

The heteronuclear version can accept up to 7 arguments and a description analogue to the one given above for the homonuclear case is in the PDF document to allow easy printout.

This may look rather overwhelming but it can be as easy as clicking on the correct button and the rest is automatic and will in nearly all cases lead to the desired result. You may want to give this a try!


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