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

Author(s)
Purpose
Usage
How phenix.map_to_object works:
Examples
Standard run of phenix.map_to_object:
Run of phenix.map_to_object specifying center of mass of moving PDB is to be close to any atom of fixed PDB:
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:
Run of phenix.map_to_object searching over additional unit cells
Possible Problems
Specific limitations and problems:
Literature
Additional information
List of all map_to_object keywords

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

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 map_to_object 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
------------------------------------------------------------------------------- 
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.
   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