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.
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:
After interpreting the file ``distance diff.matrix" with Mathematica, one obtains the plot shown in Fig. 6.4.
Figure 6.4: Difference distance matrix.