I have been using the cmap.xyz to generate a contact map for my protein of interest with molecular dynamics information. I have been altering the dcut and pcut values from 10-30, and 0.25-0.75 respectively. I had anticipated that I would be reducing the community size as the pcut value became lower and the dcut value went higher, but that is not the case. The same number of communities exist from go from the pcut values of 0.50 and dcut of 15 up to a pcut of 0.75 at a dcut of 30. Is that supposed to be the case? The DCCM is altered to filter out/include more contacts in the contact map itself, but the communities aren't changed. I also have another system, that is very similar with stable MD trajectories, that has many residues in their own individual community, but they show that they are clearly within the distance cutoff to be considered in the same community in a helix. Is there a way to control how the communities themselves are formed in the analysis? How are they determined for the program?