CARA Scopes - Revision history

Agutmana at 22:47, 9 November 2009

2009-11-09T22:47:23Z

Agutmana at 21:00, 6 November 2009

2009-11-06T21:00:23Z

← Older revision		Revision as of 21:00, 6 November 2009
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	=== Useful Common Settings ===		=== Useful Common Settings ===

	==== Contour Levels ====		==== 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.		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:		To disable this feature:

	~~   ~~ * uncheck the box in View -> Auto Contour Level~~<br>   ~~ * Go to View -> Set Contour Parameters... and set you own level		*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.		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.		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/AutoContour] [http://www.cara.ethz.ch/Wiki/ManualContour http://www.cara.ethz.ch/Wiki/ManualContour]		For more details see: [http://www.cara.ethz.ch/Wiki/AutoContour http://www.cara.ethz.ch/Wiki/AutoContour] [http://www.cara.ethz.ch/Wiki/ManualContour http://www.cara.ethz.ch/Wiki/ManualContour]

Agutmana at 20:58, 6 November 2009

2009-11-06T20:58:35Z

← Older revision		Revision as of 20:58, 6 November 2009
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	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).		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 ====

	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).		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 http://www.cara.ethz.ch/Wiki/PolyScope]		For a detailed description see here: [http://www.cara.ethz.ch/Wiki/PolyScope http://www.cara.ethz.ch/Wiki/PolyScope]

	Typical uses are:		Typical uses are:

	~~   ~~		*Side-chain assignment
	*Side-chain assignment~~<br>   ~~		*NOESY peak picking
	*NOESY peak picking~~<br>~~ ~~  ~~		*Converting SpinLinks into NOESY peaklists
	*Converting !SpinLinks into NOESY peaklists

	==== SystemScope ====		==== SystemScope ====

Agutmana at 20:58, 6 November 2009

2009-11-06T20:58:11Z

← Older revision		Revision as of 20:58, 6 November 2009
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	See it description here: [http://www.cara.ethz.ch/Wiki/MonoScope http://www.cara.ethz.ch/Wiki/MonoScope]		See it description here: [http://www.cara.ethz.ch/Wiki/MonoScope http://www.cara.ethz.ch/Wiki/MonoScope]

	==== SynchroScope ====		==== SynchroScope ====

	SynchroScope synchronizes 3D spectra with related 2D HSQC spectra. See its original description here: [http://www.cara.ethz.ch/Wiki/SynchroScope http://www.cara.ethz.ch/Wiki/SynchroScope]		SynchroScope synchronizes 3D spectra with related 2D HSQC spectra. See its original description here: [http://www.cara.ethz.ch/Wiki/SynchroScope 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.		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:		SyncroScope is typically used to:

	~~   ~~		*Calibrate spectra
	*Calibrate spectra~~<br>   ~~
	*Pick spins in triple-resonance spectra		*Pick spins in triple-resonance spectra

Agutmana at 20:57, 6 November 2009

2009-11-06T20:57:26Z

← Older revision		Revision as of 20:57, 6 November 2009
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	Below are descriptions of scopes relevant for the high-throughput effort.		Below are descriptions of scopes relevant for the high-throughput effort.

	==== MonoScope ====		==== 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:		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)~~<br>   ~~
	*import XEASY peaklists~~<br>   ~~		*Spectum format conversion (e.g. from nmrPipe or Bruker into XEASY format)
	*NOESY peak assignment~~<br>   ~~		*import XEASY peaklists
			*NOESY peak assignment
	*NOESY peaklist integration		*NOESY peaklist integration

Agutmana at 20:56, 6 November 2009

2009-11-06T20:56:53Z

← Older revision		Revision as of 20:56, 6 November 2009
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	A detailed description can be found here: [http://www.cara.ethz.ch/Wiki/SystemScope http://www.cara.ethz.ch/Wiki/SystemScope]		A detailed description can be found here: [http://www.cara.ethz.ch/Wiki/SystemScope http://www.cara.ethz.ch/Wiki/SystemScope]

	=== Navigation ===		=== Navigation ===

	Navigation is essentially the same in all scope, but somewhat different from that of XEASY.		Navigation is essentially the same in all scope, but somewhat different from that of XEASY.

	~~   ~~
	*Cursor movement<br>
	~~ooMouse click<br>         ~~
	~~ooKeyboard arrow keys (slower)<br>         ~~
	~~ooShift + keyboard arrow keys (faster)~~

	~~   ~~ * ~~Scrolling spectrum<br>          o Ctrl +~~ Mouse ~~movement<br>          o Ctrl + Alt + keyboard~~ arrow keys (slower)~~<br>          o Ctrl~~ + keyboard arrow keys (faster)<br>          o !PageUp - scroll expansion up<br>          o !PageDown - scroll page down<br>          o Ctrl + !PageUp - scroll page left<br>          o Ctrl + !PageDown - scroll page right		*Cursor movement
			**Mouse click
			**Keyboard arrow keys (slower)
			**Shift + keyboard arrow keys (faster)

	~~   ~~ * ~~Going through planes<br>          o Shift~~ + !PageUp ~~or fp~~ - ~~one plane forward<br>          o Shift~~ + ~~!PageDn or bp~~ - ~~one plane back~~		*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

	~~ ~~ * Zooming spectrum~~<br>         ~~ o Ctrl + Shift + click-drag - zoom region~~<br>         ~~ o Ctrl + Shift + left arrow - zoom out horizontally~~<br>         ~~ o Ctrl + Shift + right arrow - zoom in horizontally~~<br>         ~~ o Ctrl + Shift + down arrow - zoom out vertically~~<br>         ~~ o Ctrl + Shift + up arrow - zoom out vertically~~<br>         ~~ o Home or ww - undoes both zoom and scrolling		*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 http://www.cara.ethz.ch/Wiki/SpectrumNavigation]		For details and examples see here: [http://www.cara.ethz.ch/Wiki/SpectrumNavigation http://www.cara.ethz.ch/Wiki/SpectrumNavigation]

Agutmana: Created page with '=== 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 pr…'

2009-11-06T20:50:27Z

Created page with '=== 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 pr…'

New page

=== 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 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 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 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 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 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 http://www.cara.ethz.ch/Wiki/SystemScope]

=== Navigation ===

Navigation is essentially the same in all scope, but somewhat different from that of XEASY.

   
*Cursor movement          
ooMouse click          
ooKeyboard arrow keys (slower)          
ooShift + keyboard arrow keys (faster)

    * Scrolling spectrum           o Ctrl + Mouse movement           o Ctrl + Alt + keyboard arrow keys (slower)           o Ctrl + keyboard arrow keys (faster)           o !PageUp - scroll expansion up           o !PageDown - scroll page down           o Ctrl + !PageUp - scroll page left           o Ctrl + !PageDown - scroll page right

    * Going through planes           o Shift + !PageUp or fp - one plane forward           o 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 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/AutoContour] [http://www.cara.ethz.ch/Wiki/ManualContour 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 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