Python-based Hierarchical ENvironment for Integrated Xtallography
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General Procedure
Ligand hydrogen addition
Metal coordination
Neutron exchange addition
List of all ready_set keywords



Nigel W. Moriarty


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 ready_set keywords

Legend: black bold - scope names
        black - parameter names
        red - parameter values
        blue - parameter help
        blue bold - scope help
        Parameter values:
          * means selected parameter (where multiple choices are available)
          False is No
          True is Yes
          None means not provided, not predefined, or left up to the program
          "%3d" is a Python style formatting descriptor
      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
      output_file_name= None Defaults to current directory
      hydrogens= True
      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
      metals= True Generate edits file for metal coordination
      remove_waters= False Remove waters from model
      link_to_edits= True Output edits determined by LINK records
      use_default_bondlengths= True Use standard defaults for ideal
                               bondlengths. If false use the input geometry
      bond_cutoff= None
      output_angles= True
      random_seed= 03056941001