When I run make_symmdef_file.pl with the PDB containing an octahedral assembly, the output PDB contains only 6 monomers (instead of the expected? 24). Additionally, the energy term in the symmdef file contains E = 2*VRT_0_0_0_0_base + ….. I would expect here 24*VRT, since there are 24 monomers and the energy is computed for the whole system (as in the C4 example in the paper quoted above) – or at least 6 if the script assumes I have only 6 monomers per symmetric complex?
How do I create a proper symm def file for octahedral symmetry?
Additional question: The make_symmdef_file script produces two lines per monomer of virtual coordinates. What does the second line with _base suffix indicate?