Navigation and strips

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 (You might need to open window2 again if you have closed it earlier). Note that there were 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] button 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 buttons for the 15N scrollbars. Which depth dimensions are moved depends upon which strip is active. The active strip is indicated by an asterisk "*" (see figure below) 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 vertical and/or horizontal buttons 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 ("window1") and click R: Strip: Peak Location Strips:1H-15N in window2. The result is three strips located at the amide positions corresponding to the HSQC peaks:

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Next: Assigning peaks to resonances and spin systems