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Distance Matrix Analysis

In the next example, a distance matrix is produced among the mass-weighted centroids of all residues of the protein.

A file “distance.matrix" is produced, which can be interpreted by Mathematica using the following statements:

The resulting density plot of the distance matrix is shown in Fig. 6.3.

**Figure 6.3:** Distance matrix.
$\begin{figure}{\epsfxsize =300pt \noindent\epsffile{geomanal___distance_plot.eps} }\end{figure}$

The pick bond statement is used to produce the distance matrix. It can be replaced by any other statement or series of statements in X-PLOR. For example, one could compute the interaction energy between the pair of residues using the constraints interaction and the energy statements (see Section 4.7). In the next example, a distance difference matrix is produced between two coordinate sets:

distance_diff_plot.inp

After interpreting the file “distance diff.matrix" with Mathematica, one obtains the plot shown in Fig. 6.4.

**Figure 6.4:** Difference distance matrix.
$\begin{figure}{\epsfxsize =300pt \noindent\epsffile{geomanal___distance_diff_plot.eps} }\end{figure}$

Xplor-NIH 2025-03-21