ap_Crmsd calculates crmsd value on C-alpha coordinates. The program prints just the crmsd value.
USAGE: ap_Crmsd structureA.pdb [structureB.pdb]
If two structures are provided, the program calculates crmsd between the first model of structure A and the first model of structure B. If only one input PDB file is given, crsmd is computed for every pair of models found in the input file (each-vs-each)