This popup allows the user to create residue interaction charts. This type of chart is useful for inspecting the residues with which a residue is interacting, either based on peak assignments or based on restraint lists. Typical patterns of interacting residues can be observed for alpha helices, and parallel or anti-paralell beta sheets in proteins. The chart is useful for assessing the number of interactions found between pairs of residues, which can be an indication of the reliability of the assignments in a particular region.

Draw

This button updates the plot in the {Interaction Matrix} tab.

[+]

This button zooms in in the plot in the {Interaction Matrix} tab.

[-]

This button zooms out in the plot in the {Interaction Matrix} tab.

Interaction Matrix

The {Interaction Matrix} tab shows the interaction matrix, based on the setting in the other tabs of this popup. X and Y axes both are based on the selected residues in the {Residues} tab, and coordinates are coloured where interactions between different residues are found. The intensity of the color depends on the number of interaction found, as indicated in the legend of the plot. Moving the mouse over the plot causes the residues at the particular x and y coordinates to be indicated by lines and highlighted residue number and names. The plot can be printed as a postscript file with the right mouse button menu: R:Print to file, which opens the Print canvas to file popup.

The Charts: Residue Interaction Matrix popup (Interaction Matrix).

Peak Lists

The {Peak Lists} tab allows the user to specify which peak lists should be used for displaying interactions in the plot in the {Interaction Matrix} tab. After changing the |Use?| option, the plot can be updated with the [Draw] button.

The Charts: Residue Interaction Matrix popup (Peak Lists).

Peak Lists table

This table contains all the peak lists in the project that can be used for the interaction matrix plot.

Spectrum

The spectrum name.

PeakList

The peak list number for the given spectrum.

Use?

Specifies whether to use the peak list for the interaction matrix plot.

Restraint Lists

The {Restraint Lists} tab allows the user to specify which restraint lists should be used for displaying interactions in the plot in the {Interaction Matrix} tab. After changing the |Use?| option, the plot can be updated with the [Draw] button.

The Charts: Residue Interaction Matrix popup (Restraint Lists).

Constraint Set

Specifies which constraint set to use.

Restraint Lists table

Lists all the restraint lists in the selected constraint set.

List

The name of the list.

Type

The type of the restraints for the list, e.g. Distance.

Use?

Specifies whether to use the restraint list for the interaction matrix plot.

Residues

The {Residues} tab allows the user to specify which residues the X and Y axes should include in the plot in the {Interaction Matrix} tab. After changing the selected residues the plot can be updated with the [Draw] button.

The Charts: Residue Interaction Matrix popup (Residues).

X axis

Specifies the residue range on the X axis of the plot for the selected molecular chain.

Y axis

Specifies the residue range on the Y axis of the plot for the selected molecular chain.