FAQ 2003-03.1: How can I create 2D plots with 1D spectra on the side?
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.
Contents
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FAQ 2003-03.1: How can I create 2D plots with 1D spectra on the side? |
NMR
News: changes in distribution
The Departmental Newsletter has changed to a non-paper version and NMR News will
follow in the same direction. Since 1997, about 40 issues have been published,
first on paper only, then paper and HTML (web). All issues are available on-line
including those published before the start of the NMR web site in November 1998.
In the future, a note will be posted in the Departmental Newsletter when a
new version of NMR News is available. Of course, there will also be a link
on the main web page and under the NMR News button. If a detailed “how to”
description is provided such as the one below for 2D plots with 1D spectra on
the side, a PDF document will also be provided on the web to allow a better
printout.
NMR staff changes
Mark Miskolzie joined the NMR support team. Mark replaced Gerdy Aarts who
retired recently. Mark can be reached in WB-13 or EB-44 (2573 and 3507). 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.
Forms on the web
It has been pointed out before (NMR News 2002-04) that many NMR-related
forms are available on the web in PDF format. To facilitate locating them, a new
link has been added on the main page (right in the middle below the link to
Spectrometers Reservations and Schedules) that goes directly to the forms page.
Line frequency display: now in ppm and Hz
The menu buttons in the AO-VNMR system have been expanded. It is now
possible to display, or redisplay after threshold adjustments, the line list in
Hz or in ppm. This was always possible for hardcopies but not on
screen. The scale is always in ppm but the peak labels are selectable: Hz or ppm.
This is the direct result of user feedback!
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 in full length if different
expansions are desired.
The entire procedure is now available within the AO-VNMR 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). 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 in a separate experiment |
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the APT spectrum (where applicable) has been processed, phased and referenced in a separate experiment |
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the 2D experiment has been processed, referenced and is the current experiment in VNMR |
Experiment numbers can be freely selected but the use of the macro or button has to be 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. For homonuclear experiments such as GCOSY, GTOCSY, TROESY etc. here is what can be done and what happens.
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using the macro pl2d1dhh |
Using the button sequence 1:AO -> 2:Proc -> More -> 8:Plot2D+1D |
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User input |
System response |
User input |
System response |
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pl2d1dhh(2) |
Plotting is carried out with 1D from exp2 |
Click on button |
Plots or asks for location of 1D if not already known then, after user input, plots. |
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Change of expansion limits in 2D spectrum |
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pl2d1dhh |
Plots expansion of 2D with 1D spectra adjusted accordingly. The macro remembers where the 1D is stored, thus (2) is no longer required. |
Click on button |
Plots expansion of 2D with 1D spectra adjusted accordingly. |
The macro pl2d1dhh gives you the following features/options (a maximum of 5 arguments can be specified):
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If the macro does not know where to look for the 1D spectrum, it will ask. |
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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('negi','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.
In summary, this may look rather overwhelming but it can be as easy as clicking on the correct button and the rest is automatic. Typing pl2d1dhh or pl2d2dhx will in nearly all cases also lead to the desired result. You may want to give this a try!