Spectrum windows

Window components and views

Once the three spectra have loaded, two windows will automatically be created. One is a two-dimensional window "window1" containing the HSQC and the other "window2" is three-dimensional for the NOESY and TOCSY. Note that if you minimise a window you can get it back again by going to M: Windows: HN: window1 (or equivalent).

You can move around the spectra within the windows using several different inputs. To zoom in and out use the 'PgUp' and 'PgDn' keys, the middle mouse wheel (if you have one), or hold 'Shift', click the middle mouse button, and move the mouse up and down. If you zoom out from your spectra so that you can see their edge you will notice a dotted line which denotes their border.

You cannot zoom out further than the maximum size allowed in each dimension. To change this size open up M: Window: Axes and select the {Axis Types} tab (if it is not already selected). Each axis type has a region (|Region|), which can be edited by double clicking on the relevant cell:

To pan around the spectra you can click and drag the scrollbars at the edges of the windows, use the arrow keys, or click and drag on the spectra with the middle mouse button.

Note that you can change the way in which the arrow keys move the spectra by going to M: Project: Preferences User Options and select the {Main Options} tab if it is not already selected:

In the row with parameter "Keys Pan Window View?", setting the corresponding |Value| to True means that the keys act as if to move the view, rather than the background.

Go to "window2" and move the extra scrollbar at the very bottom of the window. - Left click and drag. This scrollbar is present on the 3D window to change the depth or plane of the spectra being viewed. On a 4D window there would be yet another scrollbar. To change the thickness of the displayed planes click and drag the side of the depth slider with the middle mouse button.

To move to a specific coordinate in depth (so z) dimension you can type a location into the "15N" box (and press 'Return') at the bottom left of the window. To center the screen (so xy) axes at a given position you place the cursor at the location and type 'c' (if the window is in focus) or click on the coordinates button at the top bar of the window (to the right of "Strips") to get a dialog box, where you can type in an explicit position.

Staying in window2, click on "Spectra" at the top of the window. Here you will see two colored buttons, one for each of the 3D spectra. If you click the buttons you can independently toggle the contour displays for the two spectra on and off, for example:

Window options

There are various parameters that you can manipulate to change the way in which windows and spectra are displayed. Firstly we will make a new window which we can play with, whilst leaving the others alone. So go to M: Windows: New Window. Select "1H" in the z1 pulldown menu and use "window1" as the "Template window:" to make a 3D window which is orthogonal to the current window. Note that such a window is capable of displaying all three spectra because the X-Y (screen) plane has 1H and 15N axes and this is valid for the HSQC as will as the 3D spectra. Toggle some of the spectra to be visible by double clicking in the second column of the table and then click [Create Window!].

We will manipulate this window via M: Window: Windows, in the {Window & Axes} tab. For the "window3" row of the top table try changing the aspect ratio by double clicking on the |Aspect Ratio| column. Also try adding 'Crosshair Traces' (top table) or 'Side Traces' (lower table) to the axes. Note that if you really don't like the scrollbars in the window you can turn them off here.

Slice panels (1-dimensional cross sections) can also be added to and removed from the windows via the mouse-menu (accessed with right click over the window), selecting the options in R: Window; Remove or Add side traces. To change the intensity scale of the spectra in the slice panels use the 'Home' and 'End' keys. Short keys for those kind of functionalities are set in the {Macros} tab, accessible through M: Project: Preferences: User Options:

Setting contours

Now we will investigate changing the contours. Firstly change the contour colours by going to M: Experiment: Spectra, selecting the {Display Options} tab and double-clicking in the |Positive colours| or in the |Negative colours| column. To set the contour levels, within a spectrum window. Go to the spectrum window and click on the top [Contours] button (shown below). The green arrows will raise or lower the contouring floor, while the +1/-1 will change the number of contours.

To alter more of the contour settings now click on [More]:

In the popup that appears, select an appropriate spectrum and set the levels as desired. You can quickly adjust the bottom most or "Base level:" contour with the "/2" (divide by two) and "*2" (multiply by two) buttons. Note that any changes you make in the 'Auto contour levels' panel will create the specified number of levels in a geometric series (e.g. 1, 2, 4, 8, ...), starting at the base level using the specified multiplier. If the "Add levels" option is on, the levels will be created by the addition of an increment, rather than by multiplication.

To add negative contours, set the "Negative" option on. If you wish to have a only one negative contour, for example to give an indication of truncation artifacts without negative contours generally, then select (with a mouse click and drag) the unwanted contour values in the 'Negative levels' panel and press 'del' then click [Apply Manual Edits] or press 'Return'.

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