Edit detail for SpinLinks revision 2 of 14

A spinlink represents the involvement of two spins in an NOE or through-space interaction.

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".

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.

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 list of all SpinLinks? from a project can be accessed from the Cara-explorer under Projects-SpinLinks?

SpinLinks? are created with one of the following methods:

1. In PolyScope? NOESY strip: click on a signal and then right-click on "Propose Spin". A list of spins appears ordered by the how closely the spins shift matches the current cursor position. Clicking on one of the spins followed by OK creates a spinlink between the 1H anchor spin of the strip and the chosen spin.
2. In StripScope? NOESY strip: click on an NOE signal and then right-click on "Propose Spin". Same features as in PolyScope?.
3. In the SystemList?: expand a system and click on a spin. Right-click on "Create Link". Enter the SpinId? of the spin to like the selected spin to.
4. LUA API Create a spinlink from a LUA script using the command:

   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 the spinlink.

SpinLinks? are destroyed with one of the following methods:

1. In PolyScope? NOESY strip: click on a signal and then right-click on "Delete Link". This will delete the spinlink and leave the spins themselves untouched. It is not the same as "Delete Spin" which will delete the spinlink and the linked Spin itself!
2. In StripScope? NOESY strip: click on a signal and then right-click on "Delete Link". Same considerations as for PolyScope?.
3. In the SystemList?: expand a system and click on the arrow box next to a spin. This expands the list of spins to which the currently selected spin is linked. Each spinlink is represented by o-o. Click on a spinlink and then right-click "delete" to delete it.
4. LUA API Destroy a spinlink using a LUA script with the command:

   Project:unlinkSpins( Spin1, Spin2 )

Spinlinks have several properties:

1. Visibility a boolean value. This is a list of spectra where the spinlink is visible. If the spinlink is invisible in a particular NOESY spectrum then no crosspeak will appear in that NOESY spectrum at the corresponding coordinates. This allows for example the selective removal of crosspeaks from NOESY spectra where the corresponding peak is missing due to amide proton exchange.

1. Code an integer. This allows the color of the spinlink symbol in the SystemList? to be set. Each color has a specified code. This can be useful to mark crosspeaks of signals requiring user attention. E.g. if the corresponding UPL was violated during a structure calculation the spinlink symbol could be color-coded pink.
2. Rating a real number. This allows a real value such as the value of the UPL or a value which indicates the quality of match between the UPL and a set of structures to be represented.

Spinlink properties can be manipulated in the following ways:

1. Open SystemList? from a Scope displaying a NOESY: Expand a system. Expand a Spin. Click on a Spinlink symbol o-o. Right-click "Set link parameters". A box appears where you can manipulate the visibility in the current NOESY, the color code of the o-o symbol and the rating of the spinlink. To set the color ... (I can't figure out how to do this FFD).
2. LUA API To change properties of a given spinlink from within a LUA script, use the command

   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.