Edit detail for SpectrumNavigation revision 1 of 6

changed:
-
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...

   1. Start CARA and use *Tools > Open Spectrum*<br>

   2. 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":http://www.cara.ethz.ch/Tracker/0393)

    - CARA xxx.nmr<br />

   3. CARA displays the selected spectrum in a MonoScope Window. The Window is composed of 4 major parts: the main spectrum window, two slices along the x- and y-dimensions and an overview window in the lower right corner.
<br /><img src="tut_1.gif" /><br><br>

   4. 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*..., shortcut: *cp*). One can also display the spectrum in intensity mode using *View > Show Intensity* 

    - Shortcut: *si* to switch intensity on/off

    - Shortcut: *sc* to switch contours on/off<br>

   5. Click on an NMR cross peak in the main spectrum window. Yellow crosshairs appear and the x- and y-slices are updated.
<br /><img src="tut_2.gif" /><br />

   6.  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.

   7. 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*.
<br /><img src="tut_3.gif" /><br />

   8.  To move the selected expansion, you can use the mouse by *click-dragging* 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.

   9. 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.

  10. To change the expansion size, use *Ctrl+Shift+Arrow* keys. This will enlarge or shrink your selected window. The *Home* key (or *View > Fit Window* or text shortcut *ww* returns to full spectrum view.

3D-spectra:

  The third dimension is represented by an additional slice to the right. You can use this slice to change the currently displayed plane by clicking at a new position in the slice or by using the arrow keys (small movements) after activating 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

Return to GettingStarted

Return to FrontPage