CARA Scopes
Scopes
Instead of a single display session in XEASY, CARA offers various specialized spectrum display tools called "scopes". Several scopes can be opened for the same project at a time with assignments and peaks synchronized.
Their original descriptions on the CARA web page are here: http://www.cara.ethz.ch/Wiki/Tools
Below are descriptions of scopes relevant for the high-throughput effort.
MonoScope
MonoScope is the simplest display tool very similar to the standard XEASY display. It is the only scope that can be used to open a spectrum without creating a project first. It is usually used for:
- Spectum format conversion (e.g. from nmrPipe or Bruker into XEASY format)
- import XEASY peaklists
- NOESY peak assignment
- NOESY peaklist integration
See it description here: http://www.cara.ethz.ch/Wiki/MonoScope
SynchroScope
SynchroScope synchronizes 3D spectra with related 2D HSQC spectra. See its original description here: http://www.cara.ethz.ch/Wiki/SynchroScope
SynchroScope requires unique spin labels in the HSQC spectrum, therefore its use is limited to displaying [15N, 1H]-HSQC and triple-resonance spectra at the initial stage of resonance assignment. This restriction is removed in PolyScope - a related display tool.
SyncroScope is typically used to:
- Calibrate spectra
- Pick spins in triple-resonance spectra
You should first open an [15N, 1H]-HSQC spectrum in SynchroScope, and then load a 3D spectrum in the strip fields. It is possible to switch between different HSQC spectra and 3D spectra from then on.
StripScope
StripScope displays 3D spectra in a fashion similar to the Xeasy strips (the gs command).
See its original description here: http://www.cara.ethz.ch/Wiki/StripScope
A maximum of 10 strips per page can be displayed (set with *View -> Set Lane Count...", default is 5). As of the time of writing, only one spectrum can be displayed in one StripScope applet. However, you can open different StripScope with different spectra.
These apparent limitations are greatly offset by the features of searching for successor and predecessor spin systems, as well as interactive mapping onto the sequence.
Successor or predecessor search is superior to Xeasy "find correlations" search, since it is looking for simultaneous matches of spins. For example, if a spins system X has CA and CB picked, only spin systems having CA-1 matching CA and CB-1 matching CB will be shown as possible predecessors, thus greatly reducing the output. It is also possible to limit the search to free spin systems, i.e. either unassigned or "free" from the corresponding side. In practice, one has to choose from a handful of strips, instead of browsing through a few pages of strips in Xeasy. No particular spin labels are required, which allows CARA to match GFT "spins", such as !CApCB with !CApCB-1.
Successor or predecessor search helps build linked fragments of spin systems. These fragments can then be matched against the sequence. The user has the option of assigning the entire fragment to the sequence if he deems the match unique. Overall this tool is especially useful in patching up incomplete automated assignments (obtained with AutoAssign, for example).
PolyScope
PolyScope is very similar to SynchcroScope, but it allows to work with all HSQC spectra and 3D spectra without a unique 2D anchor. PolyScope can also display Xeasy peaklists (they should be imported into the project first with MonoScope).
For a detailed description see here: http://www.cara.ethz.ch/Wiki/PolyScope
Typical uses are:
- Side-chain assignment
- NOESY peak picking
- Converting SpinLinks into NOESY peaklists
SystemScope
SystemScope displays two orthogonal planes from a 3D spectrum. It is used to perform side-chain assignment with HCCH-COSY (or HCCH-TOCSY) and 13C-resolved NOESY (or 15N-resolved NOESY).
A very efficient method is to concurrently use two SystemScope, one with HCCH-COSY and another with 13C-resolved NOESY. Since the spin database and scopes are synchronized, a spin assigned in one scope can be immediately verified in another.
A detailed description can be found here: http://www.cara.ethz.ch/Wiki/SystemScope
Navigation is essentially the same in all scope, but somewhat different from that of XEASY.
- Cursor movement
- Mouse click
- Keyboard arrow keys (slower)
- Shift + keyboard arrow keys (faster)
- Scrolling spectrum
- Ctrl + Mouse movement
- Ctrl + Alt + keyboard arrow keys (slower)
- Ctrl + keyboard arrow keys (faster)
- PageUp - scroll expansion up
- PageDown - scroll page down
- Ctrl + PageUp - scroll page left
- Ctrl + PageDown - scroll page right
- Going through planes
- Shift + !PageUp or fp - one plane forward
- Shift + !PageDn or bp - one plane back
- Zooming spectrum
o Ctrl + Shift + click-drag - zoom region o Ctrl + Shift + left arrow - zoom out horizontally o Ctrl + Shift + right arrow - zoom in horizontally o Ctrl + Shift + down arrow - zoom out vertically o Ctrl + Shift + up arrow - zoom out vertically o Home or ww - undoes both zoom and scrolling
For details and examples see here: http://www.cara.ethz.ch/Wiki/SpectrumNavigation
Useful Common Settings
Contour Levels
By default CARA uses automatic base level determination. It seldom works as one might prefer, plus it has the nuisance of changing the level when you zoom or scroll a spectrum.
To disable this feature:
- uncheck the box in View -> Auto Contour Level
- Go to View -> Set Contour Parameters... and set you own level
In SynchroScope and PolyScope you have do it twice: from the Plane menu for the HSQC and from the Strips menu for the 3D strips.
CARA will remember the new level for a given spectrum from then on, but the Auto Contour Level has to be unchecked every time a scope is opened.
For more details see: http://www.cara.ethz.ch/Wiki/AutoContour http://www.cara.ethz.ch/Wiki/ManualContour
Folding
Check the box View -> Show Folded. This will allow you to zoom and scroll beyond the default calibration range to see folded peaks. This box is by default unchecked.
For more details and examples see http://www.cara.ethz.ch/Wiki/FoldingAndAliasing
Strip Width
To change the width of a strip, right click on it with a mouse and select Set Peak Width from the context menu. This should work in SynchroScope, PolyScope, StripScope and SystemScope.
The default strip width is 1 ppm, which makes the spectra always look awkward the first time you open them. I usually set the width to 0.3 - 0.5 ppm for 1H and 2-3 ppm for 13C/15N.
CARA will remember the new strip width and use the same value for all scopes.
Spectrum Rotation
It is possible to open a spectrum in an orientation different than the default. Right-click on a spectrum and select Open in SomeScope (rotated)... from the context menu. Select the desired dimension mapping in the pop-up window.
Usually is only makes sense to use with StripScope and SystemScope. (H)CCH-COSY and (H)CCH-TOCSY must be opened rotated in SystemScope in order to fully utilize its functionality.
Show List
In PolyScope select View -> Show List to display a list of all spin systems to the right. In MonoScope this option displays the opened Xeasy peaklist.
-- Main.AlexEletski - 08 Mar 2007