Peaks

Every peak is characterized by a great many properties and it can often be useful to inspect each peak to check and modify these properties. There are two primary tools, aside from actually visualizing peaks on spectra, for this purpose. The Peak Inspector allows a detailed view of one peak at a time. The Peak Table, presents somewhat less information about each peak, but presents all the peaks in a list at once. The Peak Inspector is displayed by choosing the Peaks - Show Peak Inspector menu item. You can have multiple Peak Inspectors operational, to add additional ones choose Peaks - Add Peak Inspector menu item. Having displayed an inspector you must next select a particular list to display. Clicking the List: triangle will bring up a menu of all currently opened peak lists. Choose one from the list and the inspector will be populated with information from the first peak in that list. You can navigate forwards and backwards through the peak list by clicking the up or down arrows next to the peak id number. Alternatively type in a peak id number and hit Return to jump directly to that peak.

The Peak Inspector can also be set to display a particular peak directly from the spectrum display. Just let the mouse pointer hover over a displayed peak and press the spacebar. If the Peak Inspector is not already displayed it will this action will also display it.

Besides the buttons for navigating through the peak list, the top row of this interface provides a button for marking peaks as deleted, and for marking them as locked so their properties can't be changed. (BAJ, verify this). Clicking the Go button will jump the currently active window to display the plane containing that peak, and position the crosshairs at the positoin of the peak.

You can select which peaks will be displayed in the Peak Inspector by selecting one of the options in the combobox on the right side of the interface. Settings include all (display all peaks), ok (display only peaks not marked for deletion), deleted (only deleted peaks), assigned (only peaks with all dimensions assigned), partial (only peaks that are partially assigned), unassigned (no dimensions assigned), ambiguous (peaks with multiple assignments), and invalid (peaks, that have assignments inconsistent with the molecular structure).

To keep the size of the Peak Inspector small, only a subset of the peak information is shown by default. This includes the peak label, the residue name, the assignment, and the chemical shift at the center of the peak. The peak intensity, peak volume and an optional comment are also displayed. Remember that peak volumes are not automatically calculated so don't be surprised if these are all set to zero.

Clicking the downward pointing arrow will expand the inspector to show additional information about the peak. This includes the peak width, bounds, coupling constant, resonance id number, user data, and an error field.

All the displayed fields are editable, with the exception of the residue name field. It will only be displayed if the peak dimension is assigned to a specific atom, and a residue sequence for the current molecule has been read in. To change an editable value type in a new value and hit the Return key. As soon as you start typing the field that displays the peak identification number will change so that its background is red, to alert you to an unsaved change. When you hit the Return key the red background will revert to the normal gray. To ignore a change just go on to the next peak without hitting Return.

The Label, RName and Assign fields require special explanation. The Label field is essentially a name given to the particular dimension of the particular peak. You can type most anything in the field, but it will generally be beneficial to use labels that conform to the syntax of NMRViewJ atom specifiers (see the Molecules chapter). This way the labels can be properly interpreted as representing a particular atom in the molecular topology.

As noted above the RName field is a derived value. If you type in a label with appropriate syntax such that the residue number can be evaluated then the name of that particular residue (if it exists) will be displayed in the RName field. For example, if you enter 46.h, and residue 46 is an Alanine, then the RName field will show ALA. If the residue number is prefixed with a single letter amino acid code, then that code is validated against the residue name and the RName field will be colored appropriately. For example, with the above example if we entered in A46.h, the RName field would be green. The single letter code "A" is consistent with the type of the residue at position 46 (ALA). But if we entered H46.h, the RName field would be rendered with a red background, indicating that the entered amino acid type H (His), is inconsistent with the residue at position 46 (Ala). If you enter a residue number that is not present in the sequence, the background will be colored orange. Entering labels with the amino acid prefix is a good idea, because you'll get immediate feedback if you attempt to label the dimension to something inconsistent with the molecular structure.

The Assign field is, like the RName field, not editable. While similar to the label field, it is a more formal linkage to an atom. The label can be entered as any string of text, ideally, but not necessarily, in a format that specifies an atom in the structure. The Assign field is populated with various assignment tools and represents an explicit linkage of that peak dimension to a specific atom in the structure. Peak lists often are set up with a certain pattern defining what types of atoms can be in what dimensions, and what are the relationships between the dimensions. If you have patterns set up, and turn-on auto-completion then you may only need to assign part of the peak to get the complete assignment done.

For example, if you have an hnco with patterns i.h i-1.c i.n and you type a "32" into the label for the carbon dimension and hit Return the labels will automatically be set to 33.h 32.c 33.n If you have a proton tocsy with i.h* and i.h* and one dimension is labeled 32.hn and you type "hb2" into the other dimension it will automatically be set to 32.hb2 Auto-completion is turned on with the checkbutton. Peak Patterns can be set up in the Peak Reference Dialog, brought up from the Peak menu, or by clicking the checkbutton, and are discussed more fully in the section on Peak Identification.

A later section of this chapter will discuss the concept of peak linking and resonances. But here we want to point out that by double-clicking on the Reson. entry for a particular dimension you can display a window with a list of all the peaks that share that resonance. That display list can be used to unlink this peak from the remaining, thereby giving it a new Resonance number by itself.