Mapping one PDB file onto another using space-group symmetry with phenix.map_to_object

Author(s)

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

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