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Mapping one PDB file onto another using space-group symmetry with phenix.map_to_object
Author(s)
Purposephenix.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. UsageHow 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. ExamplesStandard 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.pdband 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 cellsphenix.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=2Possible ProblemsSpecific limitations and problems:LiteratureAdditional informationList of all map_to_object keywords
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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
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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
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