When this option is used, only DDs whose absolute values are greater than or equal to the user supplied minimum distance are included in the output file. Read the PDB file for the protein onto which you want to map the DDs into Insight. This should be the same protein that was used for the .seq file when running ddmrstrnt. The PDB file used should have the exact same numbering and residue names as the .seq file did. Currently, the .rstrnt file must be in the directory from which Insight was started.
Negative numbers work fine.
For instance, in characterizing the calcium-induced conformational changes in calmodulin, it was useful to count the DDs in each interhelical interface. The results of this analysis are available online . B. It also provides the most positive and most negative DDs involving residues from these two ranges. The input file for ddcounter is the MSI rstrnt file generated by ddmrstrnt . All DDs involving one residue in range a and one residue in range b with an absolute value greater than cutoff will be counted.