This panel provides controls to specify the display of peaks in the spectral windows. The window header will indicate the name of the window whose attributes are being set, and the name of the dataset currently assigned to the window. The panel is displayed by selecting the Attributes option of the Peak Menu in the Spectral Display Menu.

You can color-code your peaks, give them meaningful labels, and display them in various ways using the controls in the Peak Attributes panel of the Spectrum Attributes window (). NVJ defaults to coloring peaks according to plane, making them black if they're in the plane you're examining (which means all peaks in a 2D spectrum), and red if they're not. Thus those in the plane are called "On" and those outside are called "Off". Likewise, if you color by "Assigned," then peaks that are assigned are "On" and adopt the "On" color, and those that aren't assigned are "Off" and adopt the "Off" color. The "Plane" selection allows you to display peaks from neighboring planes, and the pulldown lets you choose how many extra planes to either side of the one you're viewing will be included. Note that only the picked-peak rectangles, crosshairs and labels get displayed this way, not the actual peaks. This is useful for a number of purposes, especially for identifying sinc wiggles flanking real peaks. In this case, you would observe two or more small peaks one or two planes away from one major peak; by looking at the peaks in neighboring planes, you could judge whether a small peak is genuine or probably a sinc wiggle. NVJ defaults to 0 extra planes. If you should select, say, 2 planes, you would see black peaks corresponding to those in your active plane, and red peaks from two planes on either side of it.

Figure 6.14. The Spectrum Attributes Peak Attributes panel, with pulldown menus

The Display pulldown lets you conveniently turn off the peak display. Just pull down the menu and select "none", then click the "Draw" button either in the Spectrum Attributes window or the Spectrum window.

The other controls are relevant only in connection with the Peak panel (Main Toolbar...Assign Peaks, ) or in the case of Draw...Simulated, a simulation routine. These will be described briefly for completeness here, more extensively later, when discussing how to assign peaks.

The "Show Mode" is a fun feature that lets you scroll through your peaklist and examine each peak on its own terms. If you select "Expand" then go to your Peak panel, which shows information about a single peak, then click in the display indicating the peak number , then hit your return key. Zing! Your spectrum display places that peak smack in the middle of your spectrum and scales your display so your peaks' rectangle occupies about 25% of your window. If, in your Peak panel, then you click the up or down arrows to examine the next or previous peak, respectively, then that peak will be displayed (in its plane) such that it occupies about a quarter of the screen in either direction. Choosing "Expand Fix" in the Show pulldown retains the size of the currently displayed region of the spectrum but still centers the peak in your widow. This feature is useful when determining whether a peak is signal or noise, as small peaks shown in Expand (not Expand Fix) mode show little of their surroundings, making it hard to gauge their relative significance. Selecting "Plane" in show mode seems like it should display the current 2D region of the spectrum but only the plane associated with the peak. When I tried it it didn't work, so this feature is probably still in development.

The Label pulldown allows you to display the peak with a variety of annotations. The default choice is the most basic, the Peak Number - which simply corresponds to the order in which the peaks were picked. Displaying the "Label" label shows the assignment (requiring your labor or that of an automated routine) of the form F2(residue number.atom) F1(residue number.atom), e.g. "12.HN 12.N" in an hsqc. If "Residue" is chosen as the label, you just see the residue number, e.g. "12." "Atom" will give the F2 and F1 atom types, e.g. "HN N". "Cluster" will show the cluster this peak to which the peak has been assigned (peak clustering will be covered in a later section of this guide). "User" corresponds to the a line in the Peak window for entering the spectroscopist who takes the credit/blame for a peak assignment. Likewise, "Comment" will display the comment associated with a peak in the Peak window. "Summary" displays the peak's intensity, number is series ("s 0" if it's not part of a series), and X-axis chemical shift.

"Links" will enable an action related to the Link A and Link B lines in the Peak panel.

With 3D and 4D spectra, only peaks whose z and/or z2 dimensions are within a specified number of planes of the planes currently displayed will appear. The range within which planes are displayed is specified with the "Plane" control on the "Peak Attributes Panel" (see below) or with the nv_win peak_off command. Peaks whose z and/or z2 dimensions are closest to the display plane appear with the color red. Those peaks that are off the display planes, but within the specified range appear with the color green. These colors may be changed with the "On Color" and "Off Color" controls on the "Peak Attributes Panel" or with the nv_win peak_col_on and nv_win peak_col_off commands. Alternatively, the color choice may be based on whether the peak has been assigned (defined as the lack of a ? in the peak label fields). This option may be selected with the "Color By" control "on the "Peak Attributes Panel" or with the nv_win peak_col_type command. The second method to display peaks is by selecting the desired peak list name