Compound Builder includes a variety of tools to help you build and manipulate custom signatures for your compounds. Compound signatures are comprised of clusters, which are in turn comprised of groups of peaks. Compound Builder provides a variety of tools for creating and manipulating these signatures.
| Menu Location | File > New Compound... |
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The New Compound feature creates a new compound file that contains the size, position, and shape of the clusters and peaks that make up a single compound's NMR signature. The new compound starts with default “Compound Details”, including a magnet frequency of 800 MHz and a sample concentration of 5 mM.
Tips and Tricks
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When you open or create a compound, it does not have a spectrum overlay by default. Add a spectrum overlay before you begin building the compound's signature.
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You can overlay one spectrum at a time in Compound Builder.
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You need to save the new compound (as an
.xcpdfile) to retain changes that you have made. -
Spectrum overlays are not retained when a compound is saved.
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If the compound that you've created is not always going to be a good fit when it is used to profile real NMR signatures, you might want to switch your compound's Fit Style from from peak-based to region-based (see “Compound Fit Style”).
Related Topics
Importing lets you use an existing spin simulation
(.xss) or legacy compound album
(.cca) to guide the construction of
a new compound signature.
| Menu Location | File > Import Simulation... |
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How do I import a spin simulation or compound album?
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Open the Import Compound dialog.
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Locate the folder containing the simulation or album file that you would like to import.
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Select the simulation or album file and click Open.
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Choose a calibration method.
If you are calibrating to a spectrum file (
.cnx), click the Browse button (...) and locate the spectrum file you would like to use.The spectrum that you choose is overlaid in the Spectrum View.
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Click OK.
Tips and Tricks
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You should calibrate a signature to a real spectrum for accurate results when using the signature for an analysis. This will ensure that your simulation is run at the same magnet frequency as the calibration spectrum when it is imported.
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Calibrating to the Default Environment instead of a spectrum will run the simulation at 800 MHz while importing it. It will have a pH of 7.00, and CSI settings corresponding to DSS at 0.500 mM (height of 1 si, width of 1 sw).
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The magnet frequency and spectrum pH for the current spectrum overlay appear in the status bar at the bottom of the Compound Builder window. If there is no spectrum overlay, the displayed values correspond to the default environment.
Related Topics
Add Peaks lets you add new peaks to the current compound signature by clicking on the graph. New peaks appear in the peaks list in a new cluster.
| Menu Location | Compound > Add Peaks |
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How do I add a peak to the current signature?
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Switch to Add Peaks mode. The mouse cursor changes to a large crosshair.
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Click somewhere on the spectrum to add a new peak. The point that you click defines both the position and the height of the new peak.
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Repeat as necessary. When finished, click Compound > Stop Adding Peaks.
Tips and Tricks
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All new peaks are automatically added to their own new cluster (i.e. grouping). To add a peak to the currently selected cluster, hold down the Ctrl or Cmd key while clicking to add the new peak.
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The new peak appears in the peak list in numerical order with the currently displayed peaks, not necessarily at the beginning or end of the list.
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Although the position that you click on the spectrum sets the position and height of the new peak, you are free to change both after you have added the peak.
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You can also right-click anywhere in the Spectrum Graph that does not already contain a peak and select Add Peak at x.xx ppm to add a new peak to a new cluster.
Many actions that you perform in Compound Builder require you to first select a peak or cluster to act on. There are several ways to select peaks, unassociated groups of peaks, or clusters.
You can select peaks or clusters by clicking on them in the graph, or in the Information Panel.
How do I select a cluster?
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Make sure selection by cluster is turned on, then click on the cluster in the Spectrum Graph.
OR
Click on the cluster's position in the Information Panel.
OR
Double click on the cluster.
How do I select a peak?
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Make sure selection by cluster is turned off, then click on the cluster in the Spectrum Graph.
OR
Click on the peak's position in the Information Panel.
How do I select multiple peaks or clusters?
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Turn selection by cluster on or off, as needed.
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Hold down the Ctrl or Cmd key, then click several peaks or clusters, either in the Spectrum Graph, the Information Panel, or both. You can hold down Shift instead to select a range of peaks or clusters.
Tips and Tricks
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When you have a cluster currently selected, only the peaks associated with that cluster are available to select via the Information Panel.
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When you have no clusters currently selected, no peaks are visible or available to select via the Information Panel.
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If the peak that you would like to select is not visible in the Information Panel, you may need to select a different cluster.
As you build a compound signature, you may need to delete one or more peaks from the signature to refine or simplify the signature.
| Menu Location | Compound > Delete Selected Peaks |
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How do I delete peaks?
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Select the peaks or clusters that you would like to delete.
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Click Delete Selected Peaks.
Tips and Tricks
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You can delete multiple peaks or clusters by selecting them via the Spectrum Graph or the Information Panel.
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You can also right-click on a selection in the Spectrum Graph or Information Panel and click Delete Selected Peaks.
Related Topics
In most cases, the initial properties of a peak do not accurately match the spectrum overlay. You need to modify the height or frequency (center position) of one or more peaks to arrive at a signature that fits the spectrum overlay shape.
| Menu Location | Compound > Edit Selected Peaks... |
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How do I set peak properties to specific values?
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Select the peaks or clusters that you would like to adjust.
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Open the Edit Selected Peaks dialog.
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Enter the desired center (position in ppm), amplitude (height in si) and width (in sw) to apply to all selected peaks or clusters.
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Click OK.
How do I adjust peak properties?
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Select the peaks or clusters that you would like to adjust.
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Do any of the following:
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Click and drag the selected peaks or clusters in the Spectrum Graph to adjust their positions and heights. Use the blue triangles on the horizontal and vertical axes for fine control over position and height, respectively.
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Click and drag the blue triangles on either side of the selected peaks and clusters, at approximately half-height, to adjust their widths.
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Use the W and S keys or the up and down arrow keys to adjust the height of the selection up and down.
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Use the A and D keys or the left and right arrow keys to adjust the position of the selection left and right.
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Use the Q and E keys to display the next or previous cluster.
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Tips and Tricks
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When you enter specific amplitudes and widths in the Edit Selected Peaks dialog, all of the selected peaks are set to the specified values, regardless of which clusters they are associated with.
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Double-click on a peak or cluster in the Information Panel to open the Edit Selected Peaks dialog for that peak or cluster.
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Right-click on a selection in the Spectrum Graph or Information Panel and select Edit Selected Peaks to edit properties for the selection.
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When you adjust the properties for a single peak, you can use mathematical functions of 'ph' instead of constant values to set the center, height and width of the peak. To insert an function expression instead of a single value, right-click in the text box that you would like to change, then click Expression....
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To view or edit an existing expression, click the expression icon (
) in the text box that you would like to change.
During the building process, and especially when you are building more complex compounds, you may need to group peaks from one or more separate clusters into a single cluster of their own. Grouping peaks into clusters ensures that all of the selected peaks move together when you use the compound signature for profiling, and that they obey the same transform window settings.
| Menu Location | Compound > Group Selected Peaks as Cluster |
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How do I group peaks as a cluster?
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Select the peaks and clusters that you would like to group as a new cluster.
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Click Group Selected Peaks as Cluster.
Tips and Tricks
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Right-click on a selection in the Spectrum Graph or Information Panel and select Group Selected Peaks as Cluster to group the selected peaks directly.
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After grouping peaks into a new cluster, you may want to use the Edit Selected Peaks dialog to set them all to a common width.
Adding peaks to a signature and adjusting them to approximately model a particular region of the spectrum is fairly simple. However, the task of fine-tuning those peaks to accurately match the lineshape in that region can be tedious. Once you have approximated the shape of a region of the spectrum, you can use Compound Builder's optimization algorithms to rapidly obtain a more refined match to that region.
| Menu Location | Tools > Optimize Selected Peak Shapes |
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How do I optimize the shape of peaks in my compound signature?
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Select the peaks and clusters that you would like to optimize.
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Click Optimize Selected Peak Shapes.
Tips and Tricks
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You must select fewer than 50 peaks to optimize.
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Optimization will generally give better results if your starting shape is reasonably close to the actual shape of the spectrum. In particular, it is important to have the right number of peaks. Simulating the compound in Spin Simulator can often give you a very good starting shape.
You may wish to build a compound signature that will let you verify that the compound is present in a spectrum, without necessarily providing the full range of flexibility that a chemically accurate signature affords. You can quickly create these limited-use signatures using automatically generated clusters. Generated clusters lack the chemical accuracy of signatures that are backed by spin simulations, but provide a quick model of the lineshape of a compound under specific conditions.
| Menu Location | Tools > Generate Cluster for Region |
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How do I generate a cluster to match a region of the spectrum?
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Select the region of the spectrum that you would like to match with a generated cluster.
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Click Generate Cluster for Region.
Tips and Tricks
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Unlike Spin Simulated clusters, generated clusters have no formal theoretical basis. They simply contain a number of Lorentzian peaks that approximate the overall shape of part of the overlaid source spectrum. These generated peaks will not let you accurately account for significant changes in the spectrum based on magnet frequency, pH or other systematic variations.
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You should only expect a compound with generated clusters to fit accurately if you are profiling spectra that have been acquired under conditions very similar to the compound's source spectrum. This restriction makes compounds with generated clusters ideal candidates for the region-based fit style (see “Compound Fit Style”.)
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Generated clusters are already optimized. Using the Optimize Selected Peak Shapes feature on them will not give any better results.
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When you generate a cluster, Compound Builder will only use up to 100 peaks to match the selected region. If the region you are trying to match cannot be accurately modeled using 100 peaks, try selecting a smaller region, adding more peaks manually, or simulating the compound in Spin Simulator and importing the simulation.
You can limit the amount that you can move individual clusters in a compound signature in Profiler using transform windows. Establishing transform windows for your own compounds improves the quality of profiles that you perform with your custom compound signatures.
If you set transform windows manually, ensure that they are wide enough to account for the degree of variability in cluster position that you expect to see in your samples. For example, if you routinely analyze spectra with widely varying pH, you will need larger transform windows than if your sample spectra are always close to the same pH.
The most common influences on the position of a cluster in a compound are pH and ion concentrations. To manually set accurate transform windows for a compound, consider acquiring spectra of the pure compound at the outer limits of the conditions you expect to encounter when profiling the compounds in experimental mixtures. This makes it easier to determine maximum extent of these effects on the cluster positions in your compounds.
In the absence of specific information about the behavior of a cluster, you can set a default transform window for the cluster. The default transform window is 0.04 ppm wide, centered on the current cluster center. For a cluster appearing at 1.000 ppm, the default transform window sets lower and upper limits of 0.98 and 1.02 ppm, respectively.
| Menu Location | Compound > Transform Window > Edit for Selected Cluster... |
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How do I set the transform window for a cluster?
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Select the cluster for which you would like to set a transform window.
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Open the Edit Transform Window dialog.
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Select Limit transforms to, and enter the new lower and upper limits for the selected cluster.
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Click OK.
How do I change the transform window for a cluster?
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Select the cluster whose transform window you would like to change.
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Open the Edit Transform Window dialog.
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Enter the new lower and upper limits for the selected cluster.
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Click OK.
| Menu Location | Compound > Transform Window > Set Default on Selected Clusters |
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| Menu Location | Compound > Transform Window > Set Default on All Clusters |
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How do I set the default transform window for a cluster?
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Select the cluster for which you would like to set the transform window.
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On the Compound menu, select Transform Window > Set Default on Selected Cluster.
How do I set the default transform window for all clusters?
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On the Compound menu, select Transform Window > Set Default on All Clusters.
| Menu Location | Compound > Transform Window > Clear for Selected Clusters |
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| Menu Location | Compound > Transform Window > Clear for All Clusters |
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How do I clear the transform window for a cluster?
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Select the cluster for which you would like to clear the transform window.
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On the Compound menu, select Transform Window > Clear for Selected Clusters.
How do I clear the transform windows for all clusters?
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On the Compound menu, select Transform Window > Clear for All Clusters.
| Menu Location | Tools > pH Sensitivities... |
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How do I set pH sensitive transform windows?
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On the Tools menu, click pH Sensitivities....
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Click Load Data Points....
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Select the signatures that you would like to use to describe pH sensitive centers and transform windows for the compound.
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Click Set Data Points.
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Click Optimize Lines.
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Review the clusters in the compound. Click Accept to apply the automatically generated expressions for cluster centers and transform windows to your compound..
Tips and Tricks
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You should always apply transform windows to any compound that you create. Compounds without transform windows will always appear in the Compound Table in Profiler when performing a Quick Search by region.
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Many of the operations described above for single clusters (setting default transform windows, clearing transform, etc.) can also be performed on multiple selected clusters at once.
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A transform window applies to the center of a cluster, not the positions of its outermost peaks. Consider only cluster centers when you manually set transform windows for your compounds.
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After you have set a transform window for a cluster, if you try to move the cluster beyond either limit of the transform window, the limit moves to accommodate the new position of the cluster. If the transform window was an expression, adjusting it in this manner will replace the expression with a constant.
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You may need to acquire multiple spectra to determine appropriate transform windows for a compound. Remember that some compounds, and some clusters within a compound, are more sensitive than others to pH changes and other matrix effects.
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When you create pH sensitive compounds, expressions (functions of 'pH') for the transform windows are calculated automatically, based on the set of spectra that you select. You can view or edit this expressions by clicking on the expression icon (
) in the text box for the transform.
You can make compound signatures that you create in Compound Builder sensitive to the pH of the spectrum that you are profiling. When used in Profiler, the clusters of pH sensitive compounds will automatically adapt their centers and transform windows based on the profiled spectrum's pH, ensuring that they start closer to their correct position and simplifying compound identification in complex regions of the spectrum.
| Menu Location | Tools > pH Sensitivities... |
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How do I make a compound signature pH sensitive?
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Make sure that you have a set of compound signatures (
.xcpdfiles) available touse as data points when calculating pH curves. You will create these signatures using Compound Builder. They must satisfy the following criteria:-
All of the compound signatures must have the same number of clusters, in the same order.
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Each signature must have its valid pH set to the pH value from the signature's originating sample, via the Compound Details dialog. Use a single value instead of a range.
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Select a signature to use as a 'master' signature. This signature will become the pH sensitive compound signature, and therefore should be very well fit to its associated spectrum file (
.cnx). The remaining signatures must have accurate cluster locations, but otherwise do not need to be perfectly fit to their associated spectra. -
Open the master signature file (
.xcpd) in Compound Builder, and overlay its associated spectrum file (.cnx). -
On the Tools menu, click pH Sensitivities....
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Click Load Data Points... and choose the your compound signatures.
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Click Optimize Lines.
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Review the resulting pH curves for each cluster by clicking the various tabs at the top of the pH Sensitivities dialog.
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Click Accept to apply the automatically generated cluster center and transform window expressions to the clusters in your master signature, and set the valid pH of the master signature to the range defined by the pH values of your individual data points.
Tips and Tricks
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Clusters that appear green in the Cluster Navigator are pH sensitive, meaning that their heights, positions, and widths all change with spectrum pH. If a compound signatures's cluster centers and transforms were set with the pH Sensitivities dialog, all of its clusters should be green.
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If you manually adjust any cluster after applying pH sensitivities to the compound, some or all of its automatically generated pH sensitivity expressions will be replaced with constant values. These clusters are no longer entirely pH sensitive, and will not appear green in the Cluster Navigator.
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If the clusters in your set of signatures appear in different orders in some of the files, use Manage Cluster IDs to rearrange the cluster IDs in the signatures so that they match.
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If the signatures you use as data points are at a different spectrometer frequency than your master signature, you may need to apply an offset to ensure accurate pH curves. Click Lock to Current Clusters in the pH Sensitivities dialog to calculate the offset before reviewing and accepting the pH curves.
Clusters have ID numbers that are normally not visible to the user. But if you create a new versions of an existing compound or multiple compound signatures for the same compound (for example, if you are going to make a pH sensitive compound) then it is important to make sure that the cluster ID for each cluster is the same in every compound signature.
| Menu Location | Tools > Manage Cluster IDs... |
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How do I change the cluster IDs in a signature?
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On the Tools menu, click Manage Cluster IDs....
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Click and drag the clusters in the list to change their order.
Or
Select a cluster in the list and use the green up and down arrows to change the position of the cluster in the list.
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Click OK.
Tips and Tricks
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Cluster IDs are used by the pH sensitivities dialog to determine which clusters should be considered as corresponding to the same signal across all of your selected data points. Make sure that the clusters appear in the proper order in each of your data points before applying pH sensitivities.
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A cluster that appears upfield from another cluster at one pH may appear downfield from the same cluster at a different pH. Consider overlaying all of your data point spectra (
.cnx) together in Processor or Profiler to more easily see the behavior of clusters across the full pH range. -
If you have already used a compound to profile spectra, replacing that compound in your library with a new version that has different cluster IDs will make your existing fits of that compound invalid.
Related Topics
The Cluster Navigator lets you quickly move among the clusters that you have created in the current compound signature. It appears in the top left corner of the Spectrum Graph as an ordered list of the approximate positions of all the clusters of the compound, in ppm. When you click on a cluster position in the navigator, the Spectrum Graph zooms to provide an optimal view of the cluster. You can also use the Cluster Navigator to move sequentially through the list of clusters in either direction.
How do I display the clusters of a compound in the Spectrum View?
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Make sure that the Cluster Navigator is visible.
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Click a cluster position to zoom directly to that cluster. Click the left or right arrow to move sequentially through the list of clusters.
Tips and Tricks
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Clusters that appear green in the Cluster Navigator are pH sensitive, meaning that their heights, positions, and widths all change with spectrum pH.
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Click on a cluster and drag along the Cluster Navigator to zoom to multiple adjacent clusters in the Spectrum Graph.