I would like to generate a symm def file with octahedral symmetry, based on a PDB file, for use with fixbb. According to the PLoS paper by DiMaio et al http://dx.doi.org/10.1371/journal.pone.0020450 tetrahedral, octahedral and icosahedral point symmetries are not properly supported by make_symmdef_file.pl. The instructions for making a symm def file http://www.rosettacommons.org/manuals/archive/rosetta3.1_user_guide/symmetry.html#How_to_adopt_your_protocol_to_use_symmetry also note, that these symmetries are not fully supported.
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?
Thanks, tartrate.
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