Chart : Residue Interaction Matrix

Display a Density Matrix of Residue-Residue Contact Information

This popup window is based around the “Interaction Matrix” in the first tab and is designed to give a graphical representation of the residue to residue interactions that are present in NMR data. At present this informations comes from peak lists; to show assignment connectivities (e.g. NOE) and restraint lists; to show distance and H-bond restraints.

To operate this system the user opens the “Peak Lists” and “Restraint Lists” tabs and toggles the “Use?” columns to enable or disable peak and restraint lists in the analysis. After pressing the [Draw] button at the top, the interaction matrix in the first tab is redrawn to display the connectivity information form the selected sources.

The main interaction matrix is colour coded so that darker squares represent a greater number of observed interactions. The coordinates of each square represents the intersection between two residues from the axes. The residues that are used on the X- and Y-axes many be specified via the “Residues” tab, both in terms of sequence range and molecular chain. To determine the precise residues that correspond to a given interaction the user can hover the mouse cursor over a small square in the matrix and the identities of the residues are displayed on the two axes.

Tips

If the interaction matrix display is too large or too small the size of the chart can be adjusted via the [+] and [-] buttons.

A PostScript file of the density matrix can be saved via the right mouse menu of the matrix tab.

Main Panel

button Draw: Using the selected peak lists, restraint lists and residue ranges draw a colour density residue interaction matrix

button [+]: Zoom in on the matrix view; make the boxes larger

button [-]: Zoom out on the matrix view; make the boxes smaller

button Clone: Clone popup window

button Help: Show popup help document

button Close: Close popup

Interaction Matrix

The main colour density matrix that displays residue-residue interaction strength

Peak Lists

Selects which peak lists to show residue-residue interactions for

Table 1
Spectrum The experiment:spectrum name of the peak list that may be considered
PeakList The serial number of the peak lists within its spectrum
Use? Sets whether or not the peak list will be used as a source of residue interaction information (Editable)

Restraint Lists

Selects which distance restraint lists to show residue-residue interactions for

pulldown Restraint Set: Selects which set of restraints to select restraint connectivity information from

Table 2
List The serial number, within the restraint set, and name of the restraint list
Type Whether the restraint list is a Distance restraint list or an H-Bond restraint list
Use? Sets whether or not the restraint list will be used as a source of residue interaction information (Editable)

Residues

Specifies which molecular chains and residue ranges to consider on the matrix axes

pulldown X axis: Selects which molecular chain to use as the sequence along the horizontal axis of the interaction matrix

int IntEntry: Sets the number of the first residue that appears at the start (left) of the horizontal matrix axis

int to: Sets the number of the last residue that appears at the end (right) of the horizontal matrix axis

pulldown Y axis: Selects which molecular chain to use as the sequence along the vertical axis of the interaction matrix

int IntEntry: Sets the number of the first residue that appears at the start (bottom) of the vertical matrix axis

int to: Sets the number of the last residue that appears at the end (top) of the vertical matrix axis

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