Was just wondering, are there any options I can use to force Rosetta to ignore PDB defined hydrogens and rebuild all hydrogens (including non-polar) when loading into the score, relax, rosetta_scripts Apps? I particularly need to rebuild backbone non-polar hydrogens as these are bad in the input PDB files but Rosetta generally seems to leave these untouched.
I have tried the options:
but these didn't appear to have the desired effect. I could, of course, delete these in the input file but was wondering if there was a way of doing this with some flag.
thanks for your help!