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Cutting density out of a map with cut_out_density
Author(s)
PurposeThis routine cuts density out of a map and writes an MTZ file in space group P1 with map coefficients for the cutout density. The density map is calculated from map coefficients supplied as an input MTZ file. The region to be cut out is specified through the center of the region and dimensions in X Y and Z of a box to be cut out (cutout_center=X,Y,Z and cutout_dimensions=a,b,c). Alternatively the region can be specified with a PDB file and optional atom selections, with all points within a specified radius of an atom included, or the region can be specified with a center and the radius of a sphere to include. The density in the region cut out can optionally be offset to have a mean density of zero. The region outside the cut out region always will have a density of zero. The cut out region can be optionally padded with flat density an additional distance beyond the box that is cut out (padding=xx). The resolution of the cutout map can also be specified (the input map will be truncated at the high-resolution limit specified, and the output map will extend to the high-resolution limit.) UsageThe main uses of phenix.cut_out_density are:
How cut_out_density works:cut_out_density assumes that you are supplying map coefficients and calculates a map. Then it creates a new unit cell in space group P1 with orthogonal axes and dimensions big enough for your cut out region and padding of zero density around it. The density in your map at the center you specify is then centered at the origin in the new map. Then new map coefficients are created and written out. You can optionally specify the region to be cut out as a box, a sphere, or a region defined by all points within a specified distance of atoms in a PDB file. You can specify the center of the region to be cut out with its coordinates, or as the centroid of a PDB file that is input. If you specify an input PDB file, you can use a selection string to select any part of that model (i.e., one domain or one chain) as the region to be cut out or as the center of the cut out region. If you specify an input PDB file, then the selected atoms from that file will be offset to match the new map and written out. As a convenience, you can re-transform a PDB file back to the original position in your original model as well. Output files from cut_out_densitycutout.mtz: An MTZ file with your cut out density in space group P1. cutout.pdb: A PDB file with your input molecule translated to match the offset used in creating cutout.mtz ExamplesStandard run of cut_out_density:Running cut_out_density is easy. From the command-line you can type: phenix.cut_out_density model.pdb map_coeffs.mtz Possible ProblemsSpecific limitations and problems:LiteratureAdditional informationList of all cut_out_density 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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cut_out_density
input_files
pdb_in= None Input PDB file marking region to cut out
mtz_in= None Input MTZ file with map coefficients
map_coeff_labels= None If map coefficients cannot be identified
automatically from your MTZ file, you can specify the
label or labels for them. (Please separate labels with
blank space, MTZ columns grouped together separated by
commas with no blanks.) You can specify:
map_coeff_labels (e.g., FWT,PHIFWT) amplitudes and
phases (e.g., FP,SIGFP PHIB) or amplitudes, phases,
weights (e.g., FP,SIGFP PHIB FOM)
pdb_to_restore_position= None You can supply a PDB file that has
previously been offset by this routine and it
will restore it to its original position. You
should specify everything else just as you did
originally, then just add these two keywords
and their values:
pdb_to_restore_position=my_offset_pdb_file_with_
edits.pdb and
pdb_restored_in_position=my_restored_pdb.pdb
Nothing will be run except your
pdb_to_restore_position will be offset by the
right amount and rewritten to
pdb_restored_in_position
pdb_to_trim= None You can supply a PDB file to trim down to the region
that is cut out of density. (Note only applicable for box
and sphere values of cutout_type)
output_files
mtz_out= cutout.mtz Output MTZ file in sg p1 with cutout of density
pdb_out= cutout.pdb Output PDB file offset to match mtz_out If
atom_selection is specified, only selected atoms are written to
cutout.pdb
pdb_restored_in_position= None Name of output PDB file restored to its
original position. You can supply a PDB file
that has previously been offset by this
routine and it will restore it to its original
position. You should specify everything else
just as you did originally, then just add
these two keywords and their values:
pdb_to_restore_position=my_offset_pdb_file_with
_edits.pdb and
pdb_restored_in_position=my_restored_pdb.pdb
Nothing will be run except your
pdb_to_restore_position will
pdb_trimmed= None Name of output PDB file trimmed to match cutout region.
log= cutout.log Output log file
params_out= cutout_params.eff Parameters file to rerun cutout
directories
temp_dir= "temp_dir" Optional temporary work directory
output_dir= "" Output directory where files are to be written
cutout_region
high_resolution= None Resolution of output map coeffs (default is
high_resolution_scale times resolution of input map
coeffs.) Purpose is to miminize truncation errors.
high_resolution_scale= 0.95 Resolution of output map coeffs will be
high_resolution_scale* resolution of input map
coeffs if high_resolution is None
cutout_center= None Center of region to be cut out. If
cutout_center=None and pdb_in is specified, the center
will be the molecular center of the molecule in pdb_in
(after applying any atom selections specified with
atom_selection.) If None and no pdb_in is specified, the
center will be (0,0,0).
cutout_fix_position= False If True, then do not translate the density to
the origin. Instead leave it in original position.
cutout_dimensions= None Dimensions (A) of region to be cut out. If None
and pdb_in is specified, the region will be the the
molecular dimensions of the molecule in pdb_in (after
applying any atom selections specified with
atom_selection.), plus a distance
cutout_model_radius. If box_scale is not defined, the
unit cell for the cutout density will have dimensions
specified by cutout_dimensions, increased by the
distance padding=xxx on each side. If
cutout_dimensions=10,10,10 and padding=5, then the
unit cell will be (20,20,20). Otherwise if box_scale
is defined, the unit cell will be box_scale times
cutout_dimensions.
box_scale= None If defined, make the dimensions of the final cell
box_scale times cutout_dimensions.
padding= 5 Padding of flat density to add around cutout density. The
unit cell for the cutout density will have dimensions specified
by cutout_dimensions, increased by the distance padding=xxx on
each side. If cutout_dimensions is None, then the unit cell
will be the molecular dimensions of the molecule in pdb_in,
increased by padding on each side. If
cutout_dimensions=10,10,10 and padding=5, then the unit cell
will be approximately (20,20,20). Note that the unit cell
dimensions may differ from this slightly as each must fall on
an exact grid multiple of 12 and the cutout region will
determine the grid.
cutout_type= *box sphere model If box and cutout_dimensions are
specified, actual density will be replaced with flat
density added outside the box defined with
cutout_dimensions. If box and pdb_in are specified then the
cut out region will be a box defined by the model plus a
distance cutout_model_radius. If sphere is specified, then
flat density will replace actual density outside of a
sphere with radius cutout_sphere_radius. Cutout_dimensions
will be the dimensions of the sphere. If model and pdb_in
are specified then the cut out region will be the region
defined by the model plus a distance cutout_model_radius.
Flat density will replace actual density outside of region
within cutout_model_radius of an atom in pdb_in.
cutout_sphere_radius= 10. If cutout_type is sphere, then flat density
will replace actual density outside of a sphere
with radius cutout_sphere_radius.
cutout_model_radius= 5. If cutout_type is model, then flat density will
replace actual density outside of region within
cutout_model_radius of an atom in pdb_in (after
application of any selections specified with
atom_selection.
cutout_subtract_mean= False If True, then mean density in cutout region
will be calculated and subtracted from all the
density in that region, yielding a mean of 0. This
is recommended if the density is to be used in
molecular replacement.
include_hetatm= True If True, then include HETATM atoms in input PDB
file in defining density to be included (e.g., if
cutout_type is model)
atom_selection= None Any selection specified with atom_selection is
applied to input model before using the model.
cutout_as_map= False Return cut out region as map (alternative is map
coeffs).
control
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
for_phaser= False Set defaults for phaser
resolve_command_list= None You can supply any resolve command here NOTE:
for command-line usage you need to enclose the
whole set of commands in double quotes (")
and each individual command in single quotes (')
like this: resolve_command_list="'no_build'
'b_overall 23' "
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