To understand basic input options, complete this tutorial.
Here is a list of common used input options. For most of these options, the option groups (in:path etc) do not need to be given. The option groups need to be given only for options that have the same name as other options in other option groups. Rosetta will warn you if this is the case.
-in:ignore_unrecognized_res Do not abort if unknown residues are found in PDB file; instead, ignore them. default='false' [Boolean]. -ignore_zero_occupancy By default, Rosetta will ignore atoms in input PDB files whose occupancy is 0. To read those atoms/residues anyway, pass false to this option. default='true' [Boolean]. -in:ignore_waters Ignore only WAT water molecules. Default=false. [Boolean]. -in:path:database Database file input search paths. If the database option is not given or the database is not found, the ROSETTA3_DB environment variable is tried [PathVector] -in:file:residue_type_set ResidueTypeSet for input files', default = 'fa_standard. [String]
-in:file:s Name(s) of single PDB file(s) to process. [FileVector] -in:file:l File(s) containing list(s) of PDB files to process. [FileVector] -in:path Paths to search for input files. Useful in combination with PDB lists that do not have full paths. [FileVector] -in:file:native Native PDB filename. [File] -in:file:native_exclude_res Residue numbers to be excluded from RMS calculation. [IntegerVector] -in:file:no_detect_pseudobonds By default, Rosetta automatically detects pseudobonds on file import. If this is set to true, this auto-detection is disabled. False by default. [Boolean] -in:file:fullatom Enable full-atom input of PDB or centroid structures. Usually not needed for already full-atom PDB structures [Boolean] -in:file:centroid_input Enable centroid inputs of PDBs. default = 'false' [Boolean] -in:auto_setup_metals Enable automatic setup of covalent bonds to metal ions and appropriate constraints on PDB import. -in:read_only_ATOM_entries Read only the ATOM entries from the PDB. Skip all others. Works for PDB and mmCIF, not silent files.
See also Residue Params file
-in:file:extra_res_fa Full atom "params" files for small molecules or non-standard residues [FileVector] -in:file:extra_res_path Directory containing non-standard residue params files. [PathVector] -in:file:extra_res_cen Centroid-mode "params" files for small molecules or non-standard residues [FileVector] -in:file:remap_pdb_atom_names_for When reading PDBs, use geometry to load atoms (instead of atom names) for the residues with the given three letter codes [StringVector]
See here for more info
-in:use_database Indicate that structures should be read from the given database -in:select_structures_from_database An sql query to select which structures should be extracted. ex: "SELECT tag FROM structures WHERE tag = '7rsa';"
-in:file:fasta Fasta-formatted sequence file. [FileVector] -in:file:frag3 Fragments file with residue length of 3 [String] -in:file:frag9 Fragments file with residue length of 9 [String]
-in:file:silent Silent input filename(s). [FileVector] -in:file:silent_list Silent input filename list(s) - like -l is to -s. [FileVector] -in:file:tags Instead of using all the structures in the input silent file(s) use just the listed structures. [StringVector] -in:file:tagfile Like -in:file:tags, but instead of listing the tags on the command line, read the tags from the specified file. [FileName] -in:file:silent_optH Call optH when reading a silent file. [Boolean] -in:file:silent_structure_type Type of SilentStruct object to use in silent-file input'. Default='protein', [String] -in:file:silent_read_through_errors Try to salvage damaged silent files -in:file:silent_score_prefix Prefix that is appended to all scores read in from a silent-file', default='' [String]
-in:file:repair_sidechains Attempt a repack/minmize to repair sidechain problems. Such as proline geometry and his tautomerization' default = 'false' [Boolean]
An alternative Job Inputter in the framework of JD2( The current Job Distribution system) that is specifically for working with an ensemble of input structures. Simple. Two modes. Seed Ensemble and Grid Ensemble.
Author - Jared Adolf-Bryfogle (email@example.com); PI : William Schief
Randomly choose the starting files using the list of structures given by -s and -l
#name weight ALL 1 awesome_model.pdb 3
Use the input files given in -s and -l and nstruct to cover a grid.
NOTE: The Ensemble Job Inputter Does not currently work with silent files.