This chapter covers basic software operations including: file operations, navigation, display options and preferences that directly affect your day-to-day use of Chenomx NMR Suite.
You can open Chenomx NMR Suite spectra files (.cnx) in
Processor and Profiler, and you can use them as overlays in Processor, Profiler,
Compound Builder and Spin Simulator. You can open Chenomx compound files
(.xcpd) in Compound Builder, and you can open Chenomx
spin simulation files (.xss) in Spin Simulator, or
import them in Compound Builder.
Tips and Tricks
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When you open the next or previous file, the zoom settings, selected compound and selected compound sets, where applicable, are preserved.
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You can also open files using the Files Sidebar Panel (see “Files”). This is especially useful for skimming through sets of spectra.
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If you want to open a Agilent spectrum named
Example.fid, the raw data is stored in the file namedExample.fid\fid, while the processed data is stored in the file namedExample.fid\datdir\phasefile. -
If you want to open a Bruker spectrum named
Example\1, the raw data is stored in the file namedExample\1\fid, while the processed data is stored in the file namedExample\1\pdata\1\1r.
When you import a spectrum from a supported format (see “Spectral Data Processing”) in Processor or Profiler, you can choose from a number of import options.
Table 10.1. Import NMR Data Options
| Sample contains a Chemical Shape Indicator (CSI) | Indicate whether a Chemical Shape Indicator (CSI) is present in the sample. Specify the CSI used, and enter its concentration in millimoles per litre (mM). You can choose DSS, TSP, Formate, or a Custom CSI (see “Define Custom CSI”). |
| Sample contains one or more pH Indicators | Indicate whether any pH indicators are present in the sample. If they are, Processor will attempt to automatically detect the pH of the sample, subject to the specified uncertainty, using signals from imidazole, creatinine and DFTMP. You must have at least one of these pH indicators present in the sample to attempt automatic pH detection. If the pH is not detected, it will be set to 7.00. You can change the pH manually after the spectrum is imported. |
| Phase Correction | Automatically apply phase adjustments to your spectrum. When importing Agilent
raw data (fid), you are given two options:
Auto applies automatically-determined phase angles, while
Import from VNMR imports the phase angles found in the VNMR
procpar file.
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| Automatic Baseline Correction | Automatically apply baseline correction to your spectrum. Linear (Drift) applies a simple two-point linear baseline correction, while Spline applies a cubic spline baseline correction based on automatically-determined breakpoints. |
| Automatic Shim Correction | Automatically apply shim correction to your spectrum. You can set a target linewidth in the Linewidth (Hz) field. |
| Reverse Spectrum (Bruker only) | Reverse your spectrum horizontally. Only available when you import Bruker
raw spectrum files (fid).
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| Line Broadening (Hz) | Apply an exponential FID weighting (line broadening) function to your data. Enter a positive value in Hz. |
| Delete Water Region | Automatically remove the water region from the spectrum during the import process. |
| Zero Fill To (FIDs only) | Enable zero-filling. Automatic zero-fills to the nearest power
of two that is at least twice as large as the number of points acquired in your
spectrum. This is normally the correct choice. You can also choose a specific
number of data points, if you prefer. This option is only available when you
import raw spectrum data (e.g. fid files).
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| Defaults | Restore all import settings for this type of imported spectrum to their default values. |
Tips and Tricks
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Saving compound files in Compound Builder or simulation files in Spin Simulator preserves only the mathematical peak descriptions created during the fitting process. Compound Builder and Spin Simulator do not retain spectrum overlays in the saved files.
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In the event that Chenomx NMR Suite stops running unexpectedly, (due to, for example, a power outage or system crash) the next time you run the software you may be given the option to restore your unsaved data. Restoring your data is not always possible, however, so it is still highly recommended that you save your work frequently.
Tips and Tricks
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You cannot close a file that has unsaved changes without having the option of saving the changes. If there are no unsaved changes, the file is simply closed without further interaction.
You can undo recent changes to the currently open file, and redo recently undone changes.
| Menu Location | Edit > Undo |
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| Menu Location | Edit > Redo |
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Tips and Tricks
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You can only redo changes that you have just undone. If you undo a change, then make other changes, you can no longer redo the change that was undone.