Author(s)

• phenix.map_to_object: Tom Terwilliger

Purpose

phenix.map_to_object is a command line tool for applying a rotation and translation consistent with space-group symmetry to a PDB file in order to bring its atoms close to those in a second PDB file.

Usage

How phenix.map_to_object works:

phenix.map_to_object searches over each equivalent position in the unit cell and neighboring unit cells to find the one that places the moving_pdb atoms closest to those in fixed_pdb.

You can choose to minimize the distance between the center of mass of the PDB files, or you can minimize the distance between the closest atoms, or you can maximize the number of close contacts.

Examples

Standard run of phenix.map_to_object:

Running phenix.map_to_object is easy. You can just type:

phenix.map_to_object fixed_pdb=my_target.pdb moving_pdb=my_ligand.pdb

and phenix.map_to_object will move my_ligand.pdb as close as it can to my_target.pdb.

Run of phenix.map_to_object specifying center of mass of moving PDB is to be close to any atom of fixed PDB:

By default phenix.map_to_object will move the center of mass of moving_pdb as close as possible to any atom in fixed_pdb. You could specify this explicitly with:

phenix.map_to_object fixed_pdb=my_target.pdb moving_pdb=my_ligand.pdb \
use_moving_center_of_mass=True use_fixed_center_of_mass=False

Run of phenix.map_to_object specifying center of mass of moving PDB is to have maximum number of contacts with atoms of fixed PDB:

If you wanted instead to maximize the number of close contacts under 5 A between the center of mass of my_ligand.pdb and any atom in my_target.pdb, you could type:

phenix.map_to_object fixed_pdb=my_target.pdb moving_pdb=my_ligand.pdb \
use_moving_center_of_mass=True use_fixed_center_of_mass=False  \
use_contact_order=True contact_dist=5.

Run of phenix.map_to_object searching over additional unit cells

If you wanted additionally to search over more than just the adjacent unit cells to find the best contacts, you could add extra_cells_to_search with a value bigger than 1:

phenix.map_to_object fixed_pdb=my_target.pdb moving_pdb=my_ligand.pdb \
use_moving_center_of_mass=True use_fixed_center_of_mass=False  \
use_contact_order=True contact_dist=5. \
extra_cells_to_search=2

Possible Problems

Specific limitations and problems:

Literature

Additional information

List of all available keywords

• map_to_object
  • moving_pdb = None PDB file with coordinates to move near fixed_pdb using SG symmetry
  • fixed_pdb = None PDB file to move moving_pdb close to using SG symmetry
  • output_pdb = None Name of output (moved) PDB file
  • use_moving_center_of_mass = True You can choose to just move the center of mass of the moving PDB close to the fixed PDB (as opposed to finding the operator that puts an atom of the moving PDB closest to an atom in the fixed PDB
  • use_fixed_center_of_mass = False You can choose to just move the moving PDB close to the center of mass of the fixed PDB (as opposed to finding the operator that puts the moving PDB closest to any atom in the fixed PDB
  • use_contact_order = True You can choose to maximize the number of atoms that are within contact_dist (default=6 ) A of an atom in the other structure.
  • map_by_chains = False You can choose to move each chain individually. This is useful for taking a fragmentary model and mapping it on to a fixed model
  • one_atom_per_residue = None You can choose to use only one atom per residue for the search. Default is True if number of atoms is > 200
  • contact_dist = 6. Atoms separated by contact_dist or less are considered to be in contact
  • extra_cells_to_search = 1 You can specify how many unit cells beyond the central one to search in each direction (default=1, search -1 0 and 1 in each direction)
  • verbose = False Verbose output
  • raise_sorry = False Raise sorry if problems
  • debug = False Debugging output
  • dry_run = False Just read in and check parameter names
  • output_files
    • target_output_format = *None pdb mmcif Desired output format (if possible). Choices are None ( try to use input format), pdb, mmcif. If output model does not fit in pdb format, mmcif will be used. Default is pdb.