|
| Python-based Hierarchical ENvironment for Integrated Xtallography |
| Documentation Home |
Merging two models with density_outside_model
Author(s)
PurposeThis routine takes a model and map coefficients and returns new map coefficients with density set to zero near the atoms in the model UsageThe main uses of phenix.density_outside_model are:
How density_outside_model works:Density_outside_model calculates a map from the map coefficients. Then all map values at points near an atom in the model are set to zero. Then a new set of map coefficients is calulated and written out. Optionally the model can be trimmed so that that the last n_trim residues in each segment of the model are not included. Output files from density_outside_modeldensity_removed.mtz: An MTZ file with your new map coefficients. ExamplesStandard run of density_outside_model:Running density_outside_model is easy. From the command-line you can type: phenix.density_outside_model pdb_in=mask_pdb.pdb \ map_coeffs.mtz Possible ProblemsSpecific limitations and problems:LiteratureAdditional informationList of all density_outside_model 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
-------------------------------------------------------------------------------
density_outside_model
input_files
pdb_in= None Input PDB file marking region to remove from map
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)
output_files
mtz_out= density_removed.mtz Output MTZ file in sg p1 with
density_removed of density
log= density_removed.log Output log file
params_out= density_removed_params.eff Parameters file to rerun
density_removed
directories
temp_dir= "temp_dir" Optional temporary work directory
output_dir= "" Output directory where files are to be written
density_removed_region
density_removed_model_radius= 2.5 If density_removed_type is model, then
flat density will replace actual density
inside of region within
density_removed_model_radius of an atom in
pdb_in (after application of any
selections specified with atom_selection.
include_hetatm= True If True, then include HETATM atoms in input PDB
file in defining region to be included
atom_selection= None Any selection specified with atom_selection is
applied to input model before using the model.
n_trim= 0 Trim all ends of segments by n_trim residues before
calculating density
density_removed_as_map= False Return modified density as map
(alternative is map coeffs).
chain_type= PROTEIN chain type (PROTEIN RNA DNA)
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
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' "
| |