I am using the shape complementarity filter to evaluate noncanonical amino acids. For several noncanonicals that contain Chlorine and Fluorine atoms the sc value is -1. I suspect this is due to the code for sc not being compatible with atom types that are not C,N,O,S,and P. Does anyone have a solution or suggestion on how to get sc updated to work with all NCAA's?
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There's a `use_rosetta_radii` option on the ShapeComplementarity filter. If you set that to true, it will use the same radii as used for the LJ potential (fa_atr & fa_rep). This might give slightly different results for proteins with only the 20 canonical amino acids, but it should support any structure which Rosetta is able to support.