CMapper combines the protein biochemical/biophysical properties, 3D visualization capabilities of PyMol and protein contact map into a rich and intuitive tool. This tool provides several ``overlays'' that superimposes structural, physical and biochemical properties of residues on top of the contact map and communicates user selected substructures of interest to PyMol for 3D visualization. This software is freely distributed under the MIT license as a PyMol plugin and an accompanying executable for Linux, Mac OS X and Windows platforms.