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
Draw: Using the selected peak lists, restraint lists and residue ranges draw a colour density residue interaction matrix
[+]: Zoom in on the matrix view; make the boxes larger
[-]: Zoom out on the matrix view; make the boxes smaller
Clone: Clone popup window
Help: Show popup help document
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
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
X axis: Selects which molecular chain to use as the sequence along the horizontal axis of the interaction matrix
IntEntry: Sets the number of the first residue that appears at the start (left) of the horizontal matrix axis
to: Sets the number of the last residue that appears at the end (right) of the horizontal matrix axis
Y axis: Selects which molecular chain to use as the sequence along the vertical axis of the interaction matrix
IntEntry: Sets the number of the first residue that appears at the start (bottom) of the vertical matrix axis
to: Sets the number of the last residue that appears at the end (top) of the vertical matrix axis