| Menu Location | View > Show Left Sidebar |
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| Menu Location | View > Show Right Sidebar |
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The Sidebars are used to display frequently-used information, available on both the left and right side of the screen. Several views are available in each Sidebar, including: Legend (all modules except Library Manager), Files (all modules except Library Manager), Reference Card Panel (Profiler, Compound Builder and Library Manager), Compound Sets (Profiler and Library Manager), Simulation (Spin Simulator) and Processing History (Processor).
Tips and Tricks
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You can open and close the left and right sidebars independently, to display as much or as little extra information as you like.
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Use the drop-down menu at the top of a Sidebar to choose which view you would like available in that Sidebar.
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A Sidebar must be opened before you can access any particular view in it.
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If you set the contents of one Sidebar to be the same as the other Sidebar, the contents of the Sidebars will simply swap sides.
Related Topics
The Legend is an interactive display of the various lines currently appearing in the Spectrum Graph. You can use the Legend to toggle the display of each line, change their colors, or even remove overlays or individual compound lines from the display completely.
| Menu Location | View > Sidebars > Left Sidebar > Legend |
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How do I toggle the display of a line?
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Switch to the Legend view in the Sidebar.
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Select the check box next to a line to display it, or clear the check box to remove it from the Spectrum Graph.
| Menu Location | View > Sidebars > Right Sidebar > Legend |
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How do I change a line color using the Legend?
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Click the colored box beside an entry in the Legend.
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Click one of the preconfigured colors in the color chooser, or click More... to choose from a larger selection of colors.
How do I remove an overlay using the Legend?
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Click the X beside an overlay entry in the Legend.
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Or click Remove All Overlays in the dropdown menu for the Overlay Lines section.
How do I automatically set the colors for all the current overlays or pinned compounds?
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Click Set All to Different Colors or Set All to Default Color (
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in the dropdown menu for the Overlay Lines
or Compound Lines section.
Tips and Tricks
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Items in the legend are organized into sections. Many of these sections have a dropdown menu in the top right corner. If you click on this dropdown, you can see additional actions that can be performed on all the items in that section.
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The topmost section of the Legend contains the default lines that are always available in the current module.
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You can change the colors of the default lines in a module using the preferences for that module.
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Each of the default lines for a module can be toggled on or off temporarily using the Legend. To change the default state of these lines, use the Preferences for the module that you would like to change.
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Changing the color of a compound line using the Legend in Profiler is equivalent to setting a custom color using the Compound Table. The custom color is saved with the spectrum, and will be used when the spectrum is reopened.
The Files view is an interactive display of other files appearing in the same folder as your currently open file.
| Menu Location | View > Sidebars > Left Sidebar > Files |
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| Menu Location | View > Sidebars > Right Sidebar > Files |
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Tips and Tricks
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Click Next or Previous to open a file adjacent to the currently open file.
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There is a dropdown menu next to the Next and Previous buttons that allows you to control which aspects of the current display will be preserved whenever you click on either button. For example, you can choose whether to maintain the current zoom level in the newly opened file, or the current selected compounds, or the current spectrum overlays.
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You can open a file in a new window by right-clicking on the entry in the Files view and selecting Open in New Window....
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You can still use the Next and Previous buttons when the Files view is not open. Simply press Ctrl-Shift-R or Ctrl-Shift-W to open the next or previous file, respectively, or click the appropriate option in the File menu.
| Menu Location | View > Sidebars > Left Sidebar > Reference Card |
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| Menu Location | View > Sidebars > Right Sidebar > Reference Card |
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The Reference Card Panel Sidebar view displays information about specific compounds including structure image, molecular formula and weight, alternate names and links to external reference sites. Use this information to verify the identity of the compound that you are fitting and better understand the signature and behaviour of the compound in your sample.
The compound represented in the Reference Card Panel in Profiler and Library Manager is the compound that you currently have selected in the Compound Table. In Compound Builder, it is the compound matching the Chenomx Compound ID that you have specified in the Compound Details dialog.
The structure image for all Chenomx reference compounds have been annotated to show the atoms that contribute to each compound's NMR signature. In Profiler and Compound Builder, you can click on an atom in the structure image, and the clusters associated with it will be be selected. Likewise, when you select a cluster, the associated atoms on the structure will become highlighted.
Tips and Tricks
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Some sections in the Reference Card Panel are collapsed by default, including Alternate Names and Alternate CAS Registry. To expand them, click the button next to the section name. Click the button again to collapse the section.
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Each of the External Database References are links to the indicated database. Click a link to open the associated database entry in your system's web browser.
Related Topics
Quick Searches let you temporarily limit the number of compounds appearing in the Compound Table based on search criteria in order to locate a particular compound in large, or numerous Compound Sets. The search criteria can include text searches based on compound name, location, compound IDs, compound comments or all of these. You can also search by frequency, listing all compounds appearing at a specific frequency, or within a frequency range.
How to perform Quick Search
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Locate the search box at the top right of the Compound Table or press Ctrl-L to automatically focus the search field.
Click the binoculars icon at the left edge of the search box to choose the type of search to use (Compound Name, Compound Comment, Compound ID, Location or All). If you do not specify a search type, the default is All.
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Type your search terms in the Quick Search box. The contents of the Compound Table update to show all matches to your current entry.
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Click the X at the right edge of the search box to cancel the search and restore the full list of compounds. Clearing the search field also resets the search type to All.
Search for compounds near a single or multiple frequencies using the Spectrum View
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Right-click on the spectrum, and click Search for Compounds Near x.xx ppm to initiate a single location search, or Add x.xx ppm to search locations to append the current location to the existing search location(s).
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Click the X at the right edge of the search box to cancel the search and restore the full list of compounds.
Search for compounds in a single or multiple frequency ranges using a selected region
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Use the Select Region tool to select a region of the spectrum.
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Right-click on the selected region, and click Search for Compounds in this Region or Add Region to search locations.
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Click the X at the right edge of the search box to cancel the search and restore the full list of compounds.
Search for compounds containing multiplets with given peak frequencies
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Right-click on the spectrum, and click Search for multiplet with a peak at x.xx ppm to initiate a search, or Add x.xx ppm to search locations (current multiplet) to add a component to the current multiplet being searched for, or Add x.xx ppm to search locations (additional multiplet to start a new multiplet.
Search For Compounds is an alternate method for setting up a Quick Search based on a frequency or range that you type, rather than based on clicked locations in the Spectrum View.
| Menu Location | Tools > Search For Compounds... |
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Tips and Tricks
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Quick Searches temporarily limit the number of compounds displayed. Use Compound Sets created in Library Manager to define a more permanent working set of compounds for profiling a particular type of spectra.
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Reset the Quick Search box and clear all filters at any time by pressing Esc.
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Click repeatedly anywhere under the sum line (red) in the Spectrum Graph to cycle through the compounds contributing to the sum line at the frequency that you clicked.
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Right-click anywhere under the sum line (red) in the Spectrum Graph, the resulting context menu shows a list of compounds contributing to the sum line at the frequency that you clicked. Select a compound from the list to make it the active compound.
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In Profiler, you can perform frequency and frequency range searches directly from the Quick Search box. For example, type [2.89 to find compounds appearing at 2.89 ppm, or type @3.0 to 7.0 to find compounds appearing between 3.0 and 7.0 ppm.
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In Profiler, you can perform multiplet-based searches directly from the Quick Search box. For example, type [2.512 to find compounds with a multiplet containing a peak at 2.512 ppm, or type [2.512 2.542 to find compounds with a multiplet containing both a peak at 2.512 and 2.542 ppm. To append a multiplet to the search, use something like [2.51; 2.542], [2.654
The general syntax is as follow:
Multiplets must start with a left bracket [ and end with a right bracket ] (but the last multiplet can remain opened). Multiplets must be separated by a coma, and listed peak frequencies in ppm within each multiplet must be separated by semicolons.
Related Topics
| Menu Location | View > Sidebars > Left Sidebar > Spectrum Details |
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| Menu Location | View > Sidebars > Right Sidebar > Spectrum Details |
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The Spectrum Details Sidebar view displays information about your currently loaded spectrum. This information appears in three sections.
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Calibration shows a summary of the calibration parameters for the current spectrum and includes CSI, CSI concentration, and the spectrum's pH. These values can be edited in the Processor's calibration tools.
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Acquisition displays details about how your spectrum was originally acquired and imported, including the spectrum's spectral (sweep) width, magnet frequency, pulse sequence, etc. These details cannot be edited.
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Comments section is used for additional user comments about the spectrum. If any notes were imported from the original spectrum source, they'll appear in this section. You can replace or expand this text however you wish.
Tips and Tricks
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You can hide any section in the Spectrum Details view by clicking on the section's title bar. Click on the title again to restore the hidden section.
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You can only change the details in the Calibration section by using Processor's CSI and pH calibration tools.
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You must save the spectrum to retain any changes that you have made to the Comments section.
The Processing History view in Processor tracks processing effects that you add to a spectrum, recording details about each effect and letting you edit or reverse them as needed.
Related Topics
Compound sets are groups containing compounds found in your Library. You can use compound sets that you have created in Library Manager to make the task of profiling your spectra easier, by placing compounds that interest you the most at your fingertips.
The Compound Sets view lets you modify the contents of the Compound Table to include any combination of the Compound Sets that you have created in Library Manager. The panel contains a list of every compound set that is currently defined. Contents of the checked compound sets appear in the Compound Table.
| Menu Location | View > Sidebars > Left Sidebar > Compound Sets |
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| Menu Location | View > Sidebars > Right Sidebar > Compound Sets |
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How do I select multiple compound sets?
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Click the checkbox next to the Compound Sets that you want to add to the Compound Table.
How do I select a single compound set?
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Click on the name (as opposed to the checkbox) of the Compound Set that you want to select. All other Compound Sets will be deselected.
Tips and Tricks
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Reference Compound Sets, which contain any Chenomx Reference Compounds in your library, appear automatically in the Compound Sets view. If your library contains any non-Chenomx compounds, including ones that you created yourself, they will appear in a separate compound set called Custom Compounds.
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When you filter the Compound Table by frequency or range, only compounds from all the currently active compound sets are considered, since these are the only compounds in the table. You can use this, for example, by creating a compound set containing only compounds that appear in urine samples. Then, when this urine compound set is the only one active, any quick searches that you perform will only return compounds that appear in urine samples as potential hits.
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A compound set called Profiled Compounds always appears at the top of the Compound Sets view in Profiler. The Profiled Compounds set includes all compounds in the current spectrum that have modified fits, custom colors, pins or stars.
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Profiled Compounds also contains subsets that appear as you start profiling compounds. These sets are automatically updated as you work, and allow you to quickly select profiled compounds that meet specific critia. For example, you can select to view only the compounds that have a defined fit, or only the starred compounds.
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The Profiled Compounds set updates continuously, so if you clear a compound, it immediately disappears from Profiled Compounds. In this case, you can still select the compound from its original compound set.
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If you change the contents of a compound set in Library Manager, your changes immediately appear in Profiler, including modified selection rules for Smart Compound Sets, manual changes to Compound Sets by adding or removing compounds, and created or deleted compound sets.
The Simulation view in Spin Simulator lets you select, view and edit elements of the currently open spin simulation, including spin systems, spin definitions and J-modifiers.
Related Topics