read_only_ATOM_entries Sets whether to ignore everything except ATOM entries.
include_surfaces Sets whether or not mineral surface residues will beloaded into Rosetta. include_lipids Sets whether or not lipid residues will beloaded into Rosetta. include_sugars Sets whether or not carbohydrate residues will beloaded into Rosetta. show_all_fixes Show all residue & atom name fixes add_orbitals Will add orbitals to residues only. guarantee_no_DNA Do not rename A/C/G to DA/DC/DG even if missing their 2' hydroxyl expert knowledge says this structure has no DNA. water_type_if_unspecified The name of the water residue type to use if the specific water type is not specified in the input file. Note: HOH residues, and waters in general, are incompatible with the default solvation model (LK). ignore_waters Ignore HOH residues found in PDB file. ignore_unrecognized_res Do not abort if unknown residues are found in PDB file instead, ignore them. use_truncated_termini Will not add extra OXT/Hs at termini if not in input structure no_fconfig Do not load the config file if present. These can be in either your working directory or $HOME/.rosetta/flags directory. fconfig A list of flag configurations to look for.
