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Plotting 2D Spectra

This tutorial will illustrate how to create a post-script file of a two-dimensional gCOSY spectra using the vnmrj software. This example will specifically use data from a gCOSY experiment, but the same general protocol applies to other two-dimensional, homo-nuclear, experiments.

 

 

For this plotting procedure, begin by enabling BioPack by clicking Edit, then Applications. In the pop-up window select enabled in the drop down menu next to /vnmr/biopack then click Okay.

Click File, Open, to select the data you wish to analyze.

Define parameters of spectra by clicking in the lower left corner with the left mouse button and the upper right corner using the right mouse button. Zoom in on this region with the magnification icon in the right side toolbar.

To adjust the vertical scaling use the Scaling icons in the right hand toolbar. This will increase/decrease the vertical scale, moving towards or away from the noise floor. Adjust the vertical scale so that each resonance is clearly distinguishable from the experimental noise.

To ensure the limits are the same in both dimensions (we must set F2 equal to F1 since a homo-nuclear experiment has identical parameters in each dimension) type the following commands.

sp=sp1

wp=wp1

wc=wc2

Turn on “what you see is what you get” by typing wysiwyg=’y’ so that what is composed on the interface is exactly what will be seen in the saved file or in print, To view changes made to the 2D spectra in the interface type the command dconi.

Now begin plotting the page. Click the Plot tab, and select Plot 2D from the left side column. (From this point, it may be helpful to think about it as if each command is being sent to a temporary data file to be stored and we are assembling the plot with each stored command.)

In the Set Position (mm) section, change the parameters to center the spectra in the interface leaving enough space above and to the left to fit projections.

  1. Set the Horizontal Offset and Vertical Offset to zero
  2. Set the Horizontal Length and Vertical Length to a number around 115mm (remember to set them equal to each other in order to maintain square spectra)

To plot the spectra click Plot next to Both under the section Contour Plot.

To plot projections first click Horizontal next to the title Projection. This will show the horizontal projections on the interface. Using the center mouse wheel scroll up or down to adjust the peak scale, once you achieve desired scale click Plot next to HHHorizontal. To plot the vertical projections click Vertical, then Plot. The vertical peak scale will already be adjusted according to the horizontal projections.

To print the spectra click the red Plot Page button.

To save the spectra as a post script file that can be edited by illustrator, canvas, or any other similar software this type the command page(‘filename.ps’).

Either printing or saving the data will clear the plotting you have done so far, so you can imagine once you choose a final command, either printing or saving the .ps file, the temporary file of stored commands is deleted and you start from the beginning again. If you ever need to clear the plot manually, click clear plot.

screen shot of plotting 2d spectra

Last Updated: 11/3/16