Navigating in a spectrum
To begin with we will use the Tool "Open Spectrum" to learn how to view and navigate in a spectrum. After mastering the basics we will create a project, load spectra and use the more advanced features of Cara. Once we start working with projects the Open Spectrum tool can still be used to have a look at an external spectrum (e.g. for processing). So lets get started...
- Start CARA and use Tools > Open Spectrum
- Open an NMR spectrum. Formats available:
- XEASY xxx.param
- Bruker processed file rr / rrr (the procs files must be in the same directory as the rr files)
- Sparky xxx.ucsf
- nmrPipe xxx.pipe (3d spectra: all planes must be in one file)
- CARA xxx.nmr
- CARA displays the selected spectrum in a MonoScope Window. The Window is composed of 4 major parts: the main spectrum window, two 1D slices along the x- and y-dimensions of the main spectrum window, and an overview window in the lower right corner. If you open spectra with more than two dimensions, there will be additional vertical 1D slices along the axes orthogonal to the x- and y-dimensions.
- CARA displays the spectrum in AutoContour mode which sets the contour level in each spectrum automatically (View > Auto Contour Level) but you can also set contour parameters manually (View > Set contour parameters...).One can also display the spectrum in intensity mode using View > Show Intensity
Keyboard shortcuts:
- ac switches between auto contour/manual contour mode
- cp set manual contour parameters
- si to switch intensity on/off
- sc to switch contours on/off
- Click on an NMR cross peak in the main spectrum window. Yellow crosshairs appear and the x- and y-slices are updated.
- The crosshairs can be moved with a mouseclick. For small changes, the arrow keys on the keyboard can be used. Combining the arrow keys with the Shift-key produces larger movements.
- Zoom into an area around the peak. You can either press Ctrl+Shift while click-drag selecting a region in the spectrum with the mouse or use the small overview window at the bottom. Simply select a rectangular region with a click-drag.
- To move the selected expansion, you can use the mouse by click-dragging in the main spectrum window with a pressed Ctrl-key like pushing a piece of paper with your finger. Alternatively, you can use the overview window. Simply clicking in the Overview window moves the expansion onto the new location, a click-drag selects a new expansion in this position.
- You can use the keyboard: Ctrl+Arrow keys move the region a small distance, Page Up and Page Down move up and down by one expansion, Ctrl+Page Up and Ctrl+Page Down move left and right by one expansion.
- To change the expansion size, use Ctrl+Shift+Arrow keys. This will enlarge or shrink your selected window vertically or horizontally. The Home key (or View > Fit Window or keyboard shortcut ww returns to full spectrum view.
3D-spectra:
When displaying a 3D spectrum, the third dimension is represented by an additional slice to the right. You can use this slice to change the currently displayed plane in the main window by clicking at a new position in the slice or by using the arrow keys (small movements) after activating the slice window (hit tab until slide is highlighted with a magenta box, or control-click in the slice window), or bp / fp to go one plane backward / forward (keyboard shortcut: Shift-PageDown / Shift-PageUp).
Frequently, it is easier to navigate in a 3D by using an additional 2D spectrum. SynchroScope and PolyScope are the right tools for this.
NEXT: PeaksAndPeaklists
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