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Editor: damberger
Time: 2015/04/02 14:06:39 GMT+2 |
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Note: added description and screenshots of 3D navigation in SystemList |
changed: - Note: SpinLinks are only displayed if the checkbox "View-Show SpinLinks" (in StripScope) or "Strip-Show SpinLinks" (in PolyScope) is selected. Note: SpinLinks are only displayed if the checkbox "View-Show !SpinLinks" (in StripScope) or "Strip-Show !SpinLinks" (in PolyScope) is selected.
You can create a SpinLink to the anchor 1H spin of a strip by right-clicking on a peak in the Strip of a NOESY spectrum displayed with PolyScope? or StripScope? and selecting Propose Spin. The SpinLink will result in the appearance of a crosspeak in all NOESY spectra where the two spins can be correlated. I.e. CARA extrapolates the existence of the NOE in all relevant NOESY spectra.
Note: SpinLinks? are only displayed if the checkbox "View-Show SpinLinks" (in StripScope?) or "Strip-Show SpinLinks" (in PolyScope?) is selected.
E.g. If you picked a SpinLink for the NOE "GLU23 HA-ASN24 HN", then this NOE will appear in the GLU23 HA/CA strip of the 3D 13C-aliphatic NOESY and the ASN24 HN/N strip of the 3D 15N NOESY.
A SpinLink contains the SpinId? of the two linked spins and appears as follows in the spinbase of a project from the repository:
<pair lhs=40
rhs=1347
/>
Here lhs defines the SpinId? of the "left hand side" spin and rhs defines the SpinId? of the "right hand side" spin. Since NOEs indicate proximity of two spins but have no direction there is no particular meaning to "left" or "right".
A list of all SpinLinks from a project can be accessed from CARAs Project-explorer under Project-SpinLinks.
SpinLinks can also be displayed in the SystemList? explorer of PolyScope?. Expand a system. Each spin which has SpinLinks to other spins is represented by an expandable node. Click on it to display the SpinLinks. These can be colored by defining a ColorCode?.
In PolyScopes SystemList?, right-click the option "3D navigation".
Now by double-clicking on the SpinLink symbol you can navigate to the corresponding NOE in the displayed 3D spectrum. There will be two options in cases where both anchor pairs are possible. E.g Double-clicking on the SpinLink LEU 111 HD1-LEU 111 HB2 in a 3D 13Cali NOESY will give two choices located at strip anchors LEU 111 HD1-CD1 and LEU 111 HB2-CB:
IMPORTANT: 3D navigation will only work if you enable the display of SpinLinks in the 3D spectrum via the checkbox Strips-Show SpinLinks. Otherwise the message "Goto peak: element not found in inferred base" will appear on the status line since with the settings, the pathway simulation does not display the peak corresponding to the SpinLink.
Navigate to the partner spin of a spinlink in the SystemList? by clicking on the spinlink symbol and right-clicking Find Link partner:
SpinLink = Project:linkSpins( Spin1, Spin2 )where Project is the selected project. Spin1 is the lhs spin and Spin2 is the rhs spin. The command returns a reference to the SpinLink which can be used to manipulate it (see below).
Project:unlinkSpins( Spin1, Spin2 )
Project:setLinkParams( SpinLink, Spectrum, Rating, Code, Visible )where Spectrum is the selected spectrum where the visibility is set, Visible has either the value true or false, Rating is a real number, and Code is an integer corresponding to the color code.
SpinLink:getParams( Spectrum )which returns the values Rating, Code, Visible. Including the spectrum reference returns the values for that spectrum. Leaving it out returns the default parameters of the SpinLink.