Picking peaks
Peak Picking and Manipulation
Focusing on the HSQC spectrum in "window1", the next task is to define some contour extrema as peaks. There are two common ways to pick peaks. One is to search for all extrema in a boxed region. Try this in the HSQC window by holding down 'Shift' and 'Ctrl' whilst clicking with the left mouse button and dragging the box to define a rectangular pick region.
Note that when the peaks are picked the contours will carry diagonal crosses to denote the peak position. Each peak will also have some annotation to the top right of the cross, which we discuss below.
Locate the contours near the point at 8.7 ppm on the 1H axis and 119.0 on the 15N axis. These contours represent two overlapping peaks where the extrema search will only pick one of the two underlying signals. To define the second peak position hold down 'Ctrl' and click on the location to pick the new peak:
Now we will select some of the peaks, e.g. artifacts or noise, for deletion. To delete peaks click with the left mouse button and drag a box over a region containing peak crosses (without holding down any keys). When the mouse button is released you will see that the peaks in the defined region are highlighted with a border around the cross. To select just a single peak click near its centre with the left mouse button. To delete the selected peaks press 'Del' or select R: Peak:Delete. selected.
If you have peaks selected and then select a different set of peaks you will see that the selection is completely substituted for a new one. You can add to an existing peak selection by holding 'Shift' while you choose. Note that you can select peaks in several different spectra, and from different windows, in this manner.
Markers and Navigation
Pick and select an isolated peak in the HSQC spectrum. Put a mark through it by holding the cursor over the peak centre and pressing 'm'. The lines produced are a multi-dimensional marker at the peak position and will be visible at the equivalent 1H-15N location in the 3D window. To go to this equivalent position in window2, with the cursor over the marked peak select R: Navigate: 1H - 15N in window2:
Note that there are also navigation options for window3. There is only one navigation option for window2 because it is an HCN window and there is only one way for the HN axes from window1 to map to it. However window3 has HHN axes and thus has two navigation options, where the second option would take you to the 1H position on the vertical axis, rather than the horizontal axis, which represents the amide proton.
Multi-dimensional marks, vertical ruler lines and horizontal ruler lines can be added to any window location, not just on peaks, using the 'm', 'v' and 'h' keys respectively. To increase the number of marks and rulers that can be displayed at one time select M:Window:Marks and Rulers or R:Markers:Options. Note that you can clear all marks and rulers with the 'n' key.
Strips and Strip Navigation
Now we will start to manipulate "strips" which are sub-divisions of a window that are connected (in terms of their view) in one of the screen dimensions, but independent in the other dimensions. Go to window2, select the [Strips] option at the top and click [+], this will add a vertical division to the window. Click and drag with the middle mouse button to move the spectra - you will see that the vertical axes of the strips are tied together, but the horizontal axis is independent. The depth dimensions are also independent, e.g. if you move the bottom most, 15N scrollbar. Which depth dimensions are moved depends upon which strip is active. The active strip is indicated by an asterisk "*" next to its strip number and is set either by double-clicking (left mouse) within a strip or by using the strip options at the top of the window; by clicking [1] or [2] or whatever. The active strip is also the one that will be removed when the [-] button is clicked. You can rearrange the strip order, moving the selected strip with the green arrows, and swap between vertical and horizontal strips with the toggle button. To remove all the strips press the buttons with vertical and/or horizontal stripes to the right of "Clear:".
Manually locating strips at interesting positions can be tedious, but there are various options to build strips from pre-defined locations, for example using peaks. To make strips using peak locations select three (picked) peaks in the HSQC spectrum and select (using the right mouse button) R: Strip: Peak Location Strips: 1H-15N in window2 (the same option is found in R:Navigate):
The result is three strips located at the amide positions corresponding to the HSQC peaks.