Author

Nigel W. Moriarty

Purpose

ReadySet! is a program designed to prepare a PDB file for refinement as in ReadySet! Refine!!!. It will add hydrogens to the protein model using phenix.reduce and to the ligands using eLBOW. The appropriate restraints are also written to disk. Hydrogens can also be added to water molecules. Deuterium atoms can be added to facilitate dual xray-neutron refinement. Metal coordination files are also generated.

General Procedure

Ligand hydrogen addition

Including hydrogens in a refinement leads to better models. ReadySet! will add hydrogens to the ligands using eLBOW and PDB Chemical Components. The input PDB file is divided into 'standard' residues including the standard aminoacids and RNA/DNA bases. The other residues (usually ligands) are tested using the three-letter and atomic names against the PHENIX monomer library and the PDB Chemical Components database.

If the ligand is determined to be in the PHENIX monomer library then the hydrogens are added with the atom naming from the library. This is done using a SMILES string taken from the PDB Chemical Components database and the atom names from the monomer library. In this case, the hydrogens are added to the output PDB file but there is no restraints written because phenix.refine will use the library restraints.

If the ligand is determined to be in the PDB Chemical Components database, the SMILES string and the atom names are used to generate a molecule that represents the ligand. The atomic naming is determined using either the version 2 or version 3 PDB names. The restraints are written to disk.

If no match is found in the PHENIX monomer library or PDB Chemical Components database, the residue atoms are used to generate the ligand. The restraints are written to disk.

Once there is a ligand representation including hydrogens, the ligand must be included in the output. For each copy of the ligand in the model the presentation is pruned to match the number of non-hydrogen atoms and overlayed onto the ligand orientation. Hydrogens are added in an optimised geometry for each copy of the ligand.

Covalently bound ligands are handled and two files, the CIF link restraints file and the atom selection file, are output.

Metal coordination

Any metals in the model are coordinated and the results output in an "edits" for phenix.refine. The distances and angles in the PDB file are used in the output.

Neutron exchange addition

Deuteriums are added to aminoacids that exhibit exchangeable sites. The hydrogens are placed in alternative location "A" and the corresponding deuteriums are placed in "B".

List of all available keywords

• ready_set
  • input
    • pdb_file_name = None PDB filename containing protein model, ligands, metal centres and water molecules
    • cif_file_name = None CIF restraints file to provide chemical information for ligands
    • cif_dir_name = None directory containing CIF restraints file to provide chemical information for ligands
    • ligand_cache_directory = None
    • output_dir = None
    • output_file_name = None
  • actions
    • hydrogens = True
    • histidine_nitrogen_protonation = False
    • neutron_option = *all_h all_d hd_and_h hd_and_d all_hd
    • add_h_to_water = False
    • add_d_to_water = False
    • neutron_exchange_hydrogens = False Add deuteriums in exchangeable sites
    • perdeuterate = False Add deuteriums in all possible sites
    • ligands = True
    • optimise_ligand_geometry = False Perform an AM1 geometry optimisation on each ligand
    • trust_residue_code_is_chemical_components_code = False
    • metals = False Generate edits file for metal coordination
    • remove_waters = False Remove waters from model
    • link_to_edits = False Output edits determined by LINK records
    • optimise_final_geometry_of_hydrogens = True
  • metal_coordination
    • use_default_bondlengths = True Use standard defaults for ideal bondlengths. If false use the input geometry values.
    • bond_cutoff = None
    • output_angles = False
  • run_options
    • random_seed = 03056941001
    • run_within_refine = False