It turns out I need TopSpin 2.1 or higher to do this. I have TopSpin
1.3 on that instrument. Thanks anyway, and a little summary is added.
Bob Honeychuck
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On Jan 14, 2011, at 9:16 AM, Robert Honeychuck wrote:
> IconNMR experts:
>
> Anyone know how to get IconNMR to move integral trails off the
> spectrum baseline? I can do this in TopSpin and Plot manually, but
> IconNMR doesn't seem to have this capability. On a black and white
> printer this results in obscured peaks. I'm using a modified version
> of autoplot_6_of_6.
>
> This is for my most novice users, who are not permitted to use
> TopSpin or Plot, and are not allowed to put samples into the magnet.
> They cannot manually integrate.
>
> Thanks much.
>
> Robert V Honeychuck
> Dept of Chemistry and Biochemistry
> George Mason University
> Fairfax VA 22030
> rhoneych_at_gmu.edu
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this is a question of the layout used together with the experiment. In
the newer versions of the TopSpin plot editor (since 2.1, I think),
you can define an offset for the integral trails in the automation
settings. I include a screen shot with this option enabled. See the
last line in the automation actions window and the result on the
screen. If you can't figure it out, please contact us again.
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Hello Robert,
Modifying the automation parameters of each layout utilized in
the autoplot_6_of_6 AU program as depicted in the attached picture will
move the baseline of the integral trails from the spectrum baseline.
It is always safest to save modified layouts and AU programs using
new names
and not overwrite the Bruker files. This means modifying or adding the
parameter sets
to the Iconnmr experiment lists.
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I'm still using XWIN, so I am not sure if mu suggestion works for
'autoplot', but you ought to be able to uncheck traces from being
displayed (and only the numerical value showing) in the Edit window for
the (XWINPLOT?) template the spectra are printed from. Who needs traces
nowadays, anyway ;-))?
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a quick fix might be to change the color of the integral traces to
white?
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I don't have direct experience with the autoplot function in ICONNMR,
but I would suggest creating and saving a modified plot layout so that
the integral curves are translated (either up or down, as you like),
and then point to that modified plot layout in the parameter sets for
the novices users.
In the novice parameter sets, set the processing parameter LAYOUT =
<my modified plot layout>.xwp
and then save the modified parameter set.
I think that should work, but I am not 100% sure how the autoplot
function works in ICONNMR.
Perhaps someone else may have some suggestions. Let me know how it
works out.
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Did you try to remove it from your plotting template?
----------
You should be able to modify that in XWINPLOT and save it in XWP
format. Then call it in the process parameters for plotting. This
option is near the bottom of the PROCPAR tab. A step further that
this may be necessary. I have modified the normal Bruker parameter
file, adding in number of scans, standard pulse width for organic
compounds, standard SW, O1P and other parameters so people don't have
to type GPRO. I save these to a user parameter set called AA1H. This
may be enough to get you through.
----------
to remove integrals trails from the plot:
You have to modify the spectrum layout. Open one of your examplary
spectra in the plot editor. Open the Edit Dialog (button "Edit" on the
main menubar.
In the Edit dialog box choose the option "1D spectrum". Remove the
tick in the integral field for "Show the integrals". Click on the "ok"
button.
Save the layout using the option "save" from the "file" menu of the
main menu bar.
Or you use the attached layout (QWhich should work on TOPSPIN 1.3 and
higher).
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As you have discovered, IconNMR itself doesn't have any spectrum
manipulation options, if you are printing through autoplot then you need
to change the layout (as defined in the processing parameters of the
dataset).
In TopSpin, open the dataset & then the layout using Plot.
Edit
Automation Parameters...
Under Base lines, Check the tickbox "Keep integrals fixed on
xx % of box" & set xx to give you the offset you need. (I use 2.5% for
the zero line & 5% for the integrals)
Don't forget to re-save the layout.
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Hi Robert - To make this work in ICON-NMR/automation, you should:
(1) First create a new layout by opening the plot editor and adjust the
integral trails to where you want them. Once you are happy, save the
new
layout to disk.
(2) Once your new layout is saved, make sure the filename is specified
in
the LAYOUT parameter for the relevant parameter sets you use in ICON-
NMR.
(3) As a final step, you will need to call autoplot in your processing
macro
(specified in AUNMP) with the -n switch to disable the reset actions.
Hope this helps. Let me know if you need any additional explanations.
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Received on Fri Jan 21 2011 - 10:32:10 MST