detect_disulf_tolerance disulf tolerance Note that disabling disulfides causes severe clashes for native disulfides.
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Setting '-detect_disulf false' disables all detection, even in full atom poses. Setting '-detect_disulf true' will force aggressive disulfide detection in centroid poses based on CB distance. When unspecified, rosetta conservatively detects disulfides in full atom input based on SG distance, but will not form centroid disulfides. detect_disulf Forcably enable or disable disulfide detection. detect_oops Detect oligooxopiperazines (oops) and add required constraints preserve_crystinfo Preserve information important for crystal refinement (B factors +CRYST1 line) remember_unrecognized_water Remember waters along with other unrecognized residues. remember_unrecognized_res Ignore unrecognized residues, but remember them in PDBInfo.
membrane Initialize pose as a membrane protein using specified membrane parameters. glycan_virtual_offset Apply a very small offset to the glycan virtual positions to avoid collinearity in the angle minimization. min_bond_length Sets minimum O-C distance for glycan connection search. max_bond_length Sets maximum O-C distance for glycan connection search. auto_detect_glycan_connections Sets whether to search for non-protein connections using PDB coordinates and generate LINK records. 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.