The Spectrum Graph displays your NMR spectrum as a graph of intensity vs. frequency. In addition to the simple zoom and scroll that you may be familiar with in other software, Chenomx NMR Suite includes a number of specialized tools for manipulating your view of your spectrum.
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Click and drag directly on the spectrum. A red zoom box appears to show you the region you are about to zoom in on.
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Use the horizontal and vertical scroll bars appearing at the bottom and right sides of the Spectrum Graph.
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Middle-click anywhere in the Spectrum Graph to apply an Auto Zoom.
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Select a region using the “Select Region” tool, and double-click in the region, or right-click in the region and select Expand Region. The region expands horizontally to fill the Spectrum Graph.
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Select a region using the “Select Region” tool, and middle-click in the region, or right-click in the region and select Auto Zoom Region. The region expands horizontally to fill the Spectrum Graph, and an Auto Zoom is applied.
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Place the mouse cursor anywhere in the Spectrum Graph, and use the mouse scroll wheel to adjust the Vertical Zoom.
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Place the mouse cursor anywhere in the Spectrum Graph, then hold down the Shift key and use the scroll wheel on your mouse to scroll horizontally.
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Place the mouse cursor anywhere in the Spectrum Graph, press and hold the Control key (Command for Mac OS X) and use the mouse scroll wheel to adjust the Horizontal Zoom.
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Press + (plus) or - (minus) to adjust the Vertical Zoom.
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Press * (asterisk) or / (slash) to adjust the Horizontal Zoom.
The Spectrum Thumbnail appears in the bottom right corner of modules with a Spectrum View, and displays a miniature version of the Spectrum Graph. You can interact with the Spectrum Thumbnail to change what's shown in the Spectrum Graph.
How do I toggle the display of the Spectrum Thumbnail?
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Click Show Spectrum Thumbnail.
How do I use the Spectrum Thumbnail?
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Click and drag in the Spectrum Thumbnail. A red zoom box appears to show you the region you are about to zoom in on, and remains to indicate the region currently displayed in the Spectrum Graph.
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Click and drag inside the zoom box to move it. The Spectrum Graph updates to show the new region.
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Click and drag one of the solid borders of the zoom box to move that border, or click and drag one of the corners to move the size and shape of the displayed region.
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Click or double-click anywhere in the Spectrum Thumbnail outside the zoom box to show the entire spectrum in the Spectrum Graph. The results are the same as using the “Show Entire Spectrum” zoom tool.
You can use the Select Region tool as an alternate zoom function, to specify areas with which to filter the Compound Table, and to obtain information about the selected region itself, including the region's width and the area under various lines within the region.
| Menu Location | View > Zoom > Select Region |
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How do I select a region?
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Activate Select Region.
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Click and drag across a region of the Spectrum Graph to select the region.
Tips and Tricks
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You can also activate Select Region by double-clicking anywhere in the Spectrum View.
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Double-click in the selected region to expand the region horizontally to fill the Spectrum Graph.
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Middle-click in the selected region to expand the region horizontally to fill the Spectrum Graph and apply an Auto Zoom.
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Additional information about the selected region appears in the top right corner of the Spectrum Graph. The information displayed always includes the region width in Hz and ppm. Depending on the module, the display can also include the areas under the compound line, overlay line, simulation line, spectrum line or sum line within the selected region, as well as the percentage of the selected area fit by the sum line (Profiler only).
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In Profiler, you can use the selected region to filter the contents of the Compound Table via Quick Searches. Right-click on the selected region, then click Filter for Compounds in Selected Region.
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The selected region remains in the Spectrum Graph until you click on an empty region of the Spectrum Graph, select a new region using the Select Region tool, or expand the current selected region to fill the Spectrum Graph.
Related Topics
Overlay Chenomx spectra (.cnx) in any
module with a Spectrum View. Overlaying a spectrum in Compound Builder or
Spin Simulator can aid the compound signature creation process,
while overlays in Profiler and Processor can provide useful visual
references to other spectra in a dataset.
| Menu Locations | Tools > Add Spectrum Overlays |
| Tools > Set Spectrum Overlay | |
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How do I overlay a spectrum in Compound Builder and Spin Simulator?
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Click Set Spectrum Overlay.
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Locate the folder containing the spectra that you would like to overlay, and select the spectra.
How do I overlay multiple spectra in Profiler and Processor?
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Click Tools > Add Spectrum Overlays or drag-and-drop files or directories directly into the Legend panel.
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Choose whether to Add Files or Add Folder
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Locate the files or single folder containing the spectra that you would like to overlay.
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Select the type of information to overlay: either the experimental line, the sum line or the subtraction line.
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Select whether to color all overlays as a default grey color, or whether to automatically assign different colors to each overlay using the radio buttons.
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Select how the overlays should be scaled relative to the main displayed spectra, either using the default setting (based on the intensity of the internal standard), or the total area in specified spectral regions.
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Click OK.
How do I change the scale of the overlayed spectra?
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You can rescale the overlayed spectra by choosing Scale spectrum overlays from the Tools menu or by selecting a spectral region using the Select Region tool, right-clicking in the defined region and choosing Rescale overlays to this region.
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You can also interactively modify the scaling of an individual overlay by clicking on the tiny graph icon next to the overlay line name and moving the slider. The sliders for all overlay lines can be toogle on/off by hovering the mouse over the "Overlay Lines" label at the top of the overlay lines list and selecting Hide/Show All Scaling Sliders.
The sliders are self-adjusting. They will automatically extend their scale once you drag the slider knob to the limit on either end. You can also use the mouse wheel to either shink or grow the scale of the sliders, allowing for very fine or coarse adjustments.
You can also customize the scaling ratio of the overlays by right-clicking on the overlay names and selecting Set Scaling Ratio. A window will open showing the current scaling ratio setting in a text field.
How do I remove a single spectrum overlay?
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In the Legend view of the Sidebar, click the X beside the overlay that you would like to remove.
| Menu Locations | Tools > Remove Spectrum Overlays |
| Tools > Remove Spectrum Overlay | |
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How do I remove all spectrum overlays in Profiler and Processor?
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Click Tools > Remove Spectrum Overlays.
How do I automatically set the overlay colors?
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Click the Automatic Coloring (
)
icon in the Legend Sidebar panel.
This will assign a different color to each spectrum overlay. Clicking it again will set all overlays back to the default color.
| Menu Locations | Tools > Stack Spectrum Overlays... |
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How do I stack overlaid spectra in Profiler or Processor?
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Click the Stack Spectrum Overlays... menu item in the Tools menu.
This will open a dialog for you to input the height of all overlays.
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Or you can use the stack overlay widget on the left hand side of the graph to manually adjust the stack height.
Tips and Tricks
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You can drag cnx files (even directories) from your desktop or the Files panel directly into the Legend panel to automatically overlay their respective spectra.
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Double-click on a listed overlay line to load the corresponding file.
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You can also remove all spectrum overlays by clicking on the X beside the Overlay Lines section in the Legend.
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You can only overlay spectra in the Chenomx NMR Suite format (
.cnx). If the spectrum you would like to use is in a different, supported format, you need to import and save it in Processor before using it as an overlay. -
In Compound Builder and Spin Simulator, you can only have one spectrum overlay at a time. In Profiler and Processor, you can have up to one hundred spectrum overlays.
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In Compound Builder, if you overlay a spectrum whose frequency does not match the magnet frequency specified in the Compound Details, you are notified of the mismatch, and given the chance to update the Compound Details to match the spectrum overlay.
Related Topics
Displaying specific ranges can be useful for preparing illustrations or focusing on a particular area of the Spectrum Graph.
| Menu Location | View > Zoom > Set Zoom |
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Open the Set Zoom dialog.
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Enter the horizontal (X-Axis) in ppm, and vertical range (Y-Axis) in standard intensity (si) that you would like to display, or select Entire Axis to zoom out to the full spectrum height/width. NOTE: When you open the Set Zoom dialog, the values that appear initially correspond to your current view. If you change the values in only one dimension, your current settings in the other dimension remain intact.
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Click OK.
Just as Undo and Redo let you recall recent actions, Undo Zoom and Redo Zoom let you recall recent views of the spectrum.
| Menu Location | View > Zoom > Undo Zoom |
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| Menu Location | View > Zoom > Redo Zoom |
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Increase/Decrease Vertical/Horizontal Zoom lets you incrementally adjust the vertical/horizontal scale of the current view, without changing the displayed frequency range.
| Menu Location | View > Zoom > Increase Vertical Zoom |
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| Menu Location | View > Zoom > Decrease Vertical Zoom |
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| Menu Location | View > Zoom > Increase Horizontal Zoom |
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| Menu Location | View > Zoom > Decrease Horizontal Zoom |
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Increase/Decrease Horizontal Zoom lets you incrementally adjust the horizontal scale of the current view, without changing the displayed intensity range.
Auto Zoom lets you quickly adjust the vertical scale of the current view so that the tallest peak in the currently displayed frequency range fits nicely in the viewing pane.
| Menu Location | View > Zoom > Auto Zoom |
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Tips and Tricks
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You can apply Auto Zoom to the Spectrum Graph at any time by clicking anywhere on the spectrum with the middle mouse button.
View settings an easily be saved and recalled at any point in time. The view settings are global (shared across all modules) and are rememered between different sessions with the software. Up to 5 different view settings can be saved. Only the limits on the ppm axis get stored.
To save a view, press and hold the mouse for at least two seconds on one of the five view setting buttons on the toolbar. After two seconds, the icon will change to a flashing camera. You can then release the mouse to save the view setting. A camera shutter sound will be emitted to signify that the view has been saved in the corresponding slot. A text notification will also appear in the module's' status bar at the bottom left of the module window.
To recall a view, simply process with a regular click on one of the five view setting buttons in the module's toolbar or via the View menu.
| Menu Location | View > Zoom > Recall view setting | |
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When you prepare publications or presentations based on your work in Chenomx NMR Suite, you may need to include images illustrating the fitting process or particular regions of the spectrum. You can export spectrum images from any module with a Spectrum Graph into a variety of image formats.
| Menu Location | File > Export > Spectrum Image... |
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How do I export an image of the current spectrum?
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Start the Export Spectrum Image wizard.
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Choose a file format. You can choose a from a variety of vector or raster image formats, including portable network graphics (
.png), graphics interchange format (.gif), scalable vector graphics (.svg), or portable document format (.pdf). -
Choose a folder and filename for the exported image.
Tips and Tricks
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Choose Do not shade area under lines to ensure that none of the peak shading effects are retained in the exported image. Disabling shading can be useful when you export an image of an area containing many clusters, as shading can create a very heavy look.
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If you are exporting the graph image for display on another computer (in an email or webpage, for example), you should use a raster format like
.pngor.giffor the best results. -
If you are exporting the graph image to be embedded as a small figure in a paper document or on a large wall poster, you should use a vector format like
.svg.
Related Topics
| Menu Location | Edit > Copy Spectrum Image to Clipboard |
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You can use Copy Spectrum Image to Clipboard to quickly make an image of the current spectrum available to paste directly into another application, without creating an intermediary file.
Tips and Tricks
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The resolution and size of the spectrum image copied to the clipboard is the same as the Spectrum Graph on your screen. If adjusting combinations of your module window size and/or screen resolution do not let you produce images of a high enough quality, consider using Export Spectrum Image.
Related Topics