VideoTutorials
& Manual
A Sample is an item of data (technically a CcpNmr Analysis object) containing information about the physical NMR sample, e.g. pH, ionic strength etc. The Samples contained in your project are listed in the sidebar under Samples.
A Sample can contain (and thus be linked to) Sample Components in your project. Sample Components can be added to a Sample manually by double-clicking New SampleComponenet in the sidebar. However, usually for large sets of screening data, you will import your data with an Excel or NEF file and these links will be established automatically.
A Sample can also be linked to a Spectrum, indicating that the Spectrum was recorded on that Sample. You can manually associate a Spectrum with a Sample by going to the Spectrum Properties pop-up (double-click on the Spectrum in the sidebar) and in the General tab selecting a Sample from the drop-down menu (note that the Sample already has to exist - you cannot create a new one on the fly in the Spectrum Properties pop-up). Again, the link between a Sample and a Spectrum is usually established automatically when importing your screening data with an Excel or NEF file.
A Sample Component is an item of data (technically a CcpNmr Analysis object) containing information about the Substance in the physical NMR sample (e.g. concentration). The Sample Components contained in your project are listed in the sidebar under SampleComponents, nested beneath Samples.
A Sample Component must always have a corresponding Substance in your project. Either you can create the Substance first (double-click New Substance in the sidebar) and then use this to create your Sample Component (select From Substances in the New Sample Component pop-up and then select the Substance from the Current Substances drop-down menu). Alternatively, you can create your Sample Component (select New in the New Sample Component pop-up) and the program will automatically create the linked Substance for you. When importing your screening data via an Excel or NEF file, these links are established automatically.
A Substance is an item of data (technically a CcpNmr Analysis object) containing information about a molecule, (e.g. a small molecule and its general properties such as: SMILES, molecular weight etc.). The Substances contained in your project are listed in the sidebar under Substances.
A Substance can be linked to a Sample Component. Note that while a Sample Component MUST have a link to a Substance, a Substance does not have to be linked to Sample Component. The link between the two is established when you create a new SampleComponent and either create the Substance at the same time, or use a pre-existing Substance. When importing your screening data via an Excel or NEF file, these links are established automatically.
A Substance can also be linked to a Spectrum in the form of a Reference Spectrum. You can set a Reference Spectrum by going to the Substance Properties pop-up (double-click on a Substance in the sidebar) and then in the Advanced section you can select a Reference Spectrum from the drop-down menu. Typically, each Substance in a set of screening data will be linked to either a Reference Singleton Spectrum or a Reference Mixture Spectrum. When importing your screening data via an Excel or NEF file, these links are established automatically.
A Spectrum Group is a container (technically a CcpNmr Analysis object) to collect together several Spectra. You can create a Spectrum Group by selecting one or more Spectra in the sidebar, right-clicking and selecting Make Spectrum Group from selected. Alternatively, double-click on New SpectrumGroup in the sidebar and then move the spectra of your choice into the Included box by either dragging them over, or double-clicking them.
For screening data we generally recommend grouping your Reference, Control, Target and Displacer Spectra into distinct SpectrumGroups. Usually this is done automatically when importing your screening data via an Excel or NEF file.
Note that you can open Spectra in SpectrumDisplays either by dragging them from the Spectra section of the sidebar or the SpectrumGroups section. If you drag a SpectrumGroup (rather than the individual spectra within the gorup), all spectra will open like a single spectrum (with a single button in the Spectrum Toolbar). The contour colour used in this case is the Group Contour Colour specified in the General tab of the Edit Spectrum Group pop-up (opened by double-clicking on a Spectrum Group in the sidebar).
A Spectrum Group is linked to the Spectra contained within it. This link is established when the Spectrum Group is created.
A sample containing one or multiple Substances prior the addition of a biological target (or the spectrum recorded on such a sample). Typically, we would expect such spectra to be recorded each time a screen is conducted. For a large screen containing multiple samples, there will be multiple Control Samples and Spectra.
The Control Spectra are linked to Control Samples and they are grouped into the Control Spectrum Group. These links and groups are usually established automatically when importing your screening data with an Excel or NEF file.
A sample containing one or multiple Substances plus a biological target (or the spectrum recorded on such a sample). For a large screen containing multiple samples, there will be multiple Target Samples and Spectra.
The Target Spectra are linked to Target Samples and they are grouped into the Target Spectrum Group. These links and groups are usually established automatically when importing your screening data with an Excel or NEF file.
A sample containing one or multiple substances, a biological target plus a molecule known to bind the biological target (or the spectrum recorded on such a sample). For a large screen containing multiple samples, there will be multiple Displacer Samples and Spectra.
Displacers are also commonly referred to as Competitors. Typically, it is expected that the displacer/competitor compound binds the biological target molecule more strongly than any of the substances used in the screen. It is usually used to assess whether a substance that binds has done so at the site of interest. The use of Displacers is optional.
The Displacer Spectra are linked to Displacer Samples and they are grouped into the Displacer Spectrum Group. These links and groups are usually established automatically when importing your screening data with an Excel or NEF file.
A spectrum recorded on a sample containing multiple Substances. This is often a spectrum that was originally used as a Control Spectrum in a previous screen. Its peaks and their annotations are used as a template to identify Substances in future screens (which is usually more accurate than using Reference Singletons). For a large screen containing multiple samples, there will be multiple Reference Mixtures whic
The Reference Mixture spectrum will be the Reference Spectrum for all the Substances contained in the sample it was recorded on. Multiple Reference Mixture spectra are usually grouped into a Reference or ReferenceMixtures Spectrum Group. These links are usually established automatically when importing your screening data with an Excel or NEF file. If you are creating a new NEF file, these links may need to be set up first.
A spectrum recorded on only one Substance. Its peaks and their annotations can be used as a template to identify Substances in future screens but usually more accurate than using Reference Mixtures.
The Reference Singleton spectrum will be the Reference Spectrum for the corresponding Substance contained in the sample it was recorded on. Multiple Reference Singleton spectra are usually grouped into a Reference or ReferenceSingletons Spectrum Group. These links are usually established automatically when importing your screening data with an Excel or NEF file.
The Substance linked to a set of spectra (reference) whose peaks have been matched to the spectral peaks (Control - Target) denoting a binding event.
The virtual link between equivalent peaks in Reference, Control and Target Spectra (possibly also Displacer Spectra, if being used) in a Screening Dataset.