def get_master_phil () :
from mmtbx.command_line import generate_master_phil_with_inputs
return generate_master_phil_with_inputs(
phil_string="""
clash_min = 0.2
.type = float
""")
def get_master_phil():
from mmtbx.command_line import generate_master_phil_with_inputs
return generate_master_phil_with_inputs(
enable_twin_law=True,
enable_experimental_phases=True,
enable_pdb_interpretation_params=True,
enable_stop_for_unknowns=False,
enable_full_geometry_params=True,
phil_string="""
selection = None
.type = atom_selection
target_map = 2mFo-DFc
.type = str
rsr_after_anneal = False
.type = bool
resolution_factor = 0.25
.type = float
reference_sigma = 0.5
.type = float
.help = Sigma for harmonic restraints for neighboring atoms not included \
in the selection of interest.
output {
file_name = annealed.pdb
.type = path
save_map_coeffs = False
.type = path
verbose = False
.type = bool
debug = False
.type = bool
}
simulated_annealing {
include scope mmtbx.dynamics.simulated_annealing.master_params
}
""")
def master_phil () :
from mmtbx.command_line import generate_master_phil_with_inputs
return generate_master_phil_with_inputs(
enable_automatic_twin_detection=True,
phil_string="""
hetatms_only = True
.type = bool
skip_xtal_solution_mols = False
.type = bool
.help = If True, common crystallization components such as sulfate or \
glycerol will be ignored.
skip_single_atoms = True
.type = bool
skip_alt_confs = True
.type = bool
min_acceptable_cc = 0.8
.type = float
min_acceptable_2fofc = 1.0
.type = float
max_frac_atoms_below_min = 0.5
.type = float
write_coot_script = True
.type = bool
write_maps = Auto
.type = bool
""")
def get_master_phil () :
from mmtbx.command_line import generate_master_phil_with_inputs
return generate_master_phil_with_inputs(
enable_twin_law=True,
enable_experimental_phases=True,
enable_pdb_interpretation_params=True,
enable_stop_for_unknowns=False,
enable_full_geometry_params=True,
phil_string="""
selection = None
.type = atom_selection
target_map = 2mFo-DFc
.type = str
rsr_after_anneal = False
.type = bool
resolution_factor = 0.25
.type = float
reference_sigma = 0.5
.type = float
.help = Sigma for harmonic restraints for neighboring atoms not included \
in the selection of interest.
output {
file_name = annealed.pdb
.type = path
save_map_coeffs = False
.type = path
verbose = False
.type = bool
debug = False
.type = bool
}
simulated_annealing {
include scope mmtbx.dynamics.simulated_annealing.master_params
}
""")
def __init__(self,pdb_file,hklmtz_file,
detail,high_resolution=None,mdb_document=None,pdb_code=None,
do_flips=False) :
assert detail in ['file','residue'],detail
assert type(do_flips) == bool
self.pdb_file = pdb_file
self.hklmtz_file = hklmtz_file
self.detail = detail
self.pdb_code = pdb_code
self.high_resolution = high_resolution
self.do_flips = do_flips
if not pdb_code : self.pdb_code = 'N/A'
pdb_in = file_reader.any_file(pdb_file)
self.hierarchy = pdb_in.file_object.hierarchy
args = [self.pdb_file]
if self.hklmtz_file : args.append(self.hklmtz_file)
self.cmdline = load_model_and_data(
args=args,
master_phil=generate_master_phil_with_inputs(""),
require_data=False,
create_fmodel=True,
process_pdb_file=True,
prefer_anomalous=True)
# keys are res ids and values are MDBResidue objects.
if self.detail == 'residue' :
self.initiate_residues()
self.set_mdb_document(mdb_document)
def master_phil():
from mmtbx.command_line import generate_master_phil_with_inputs
return generate_master_phil_with_inputs(
enable_automatic_twin_detection=True,
phil_string="""
hetatms_only = True
.type = bool
skip_xtal_solution_mols = False
.type = bool
.help = If True, common crystallization components such as sulfate or \
glycerol will be ignored.
skip_single_atoms = True
.type = bool
skip_alt_confs = True
.type = bool
min_acceptable_cc = 0.8
.type = float
min_acceptable_2fofc = 1.0
.type = float
max_frac_atoms_below_min = 0.5
.type = float
write_coot_script = True
.type = bool
write_maps = Auto
.type = bool
""")
def master_phil():
from mmtbx.command_line import generate_master_phil_with_inputs
return generate_master_phil_with_inputs(
enable_automatic_twin_detection=True,
phil_string="""\
output_file = fmodel.pkl
.type = path
""")
def master_phil () :
from mmtbx.command_line import generate_master_phil_with_inputs
return generate_master_phil_with_inputs(
enable_automatic_twin_detection=True,
phil_string="""\
output_file = fmodel.pkl
.type = path
""")
def get_master_phil () :
from mmtbx.command_line import generate_master_phil_with_inputs
return generate_master_phil_with_inputs(
enable_automatic_twin_detection=True,
phil_string="""
find_peaks
.style = auto_align
{
include scope mmtbx.find_peaks.master_params
}
map_cutoff = 3.0
.type = float
.short_caption = mFo-DFc map cutoff (sigma)
anom_map_cutoff = 3.0
.type = float
.short_caption = Anomalous map cutoff (sigma)
include_peaks_near_model = False
.type = bool
.short_caption = Don't filter peaks by distance to model
.help = By default, the program will only display peaks that map to points \
outside of the current model, ignoring those that overlap with atoms. \
Setting this option to True is equivalent to specifying a distance \
cutoff of zero for the filtering step.
.style = OnChange:toggle_min_model_peak_dist
wavelength = None
.type = float
.help = Optional parameter, if defined this will cause all atoms to be \
treated as anomalous scatterers using the standard Sasaki table to \
obtain theoretical fp and fpp values. Only really useful if the Phaser \
LLG map is being used for the anomalous map.
filter_peaks_by_2fofc = None
.type = float
.short_caption = Filter peaks by 2mFo-DFc
.help = If this is set, peaks outside 2mFo-DFc density at the \
cutoff will be discarded. (This does not apply to the analysis of \
solvent atoms.) Holes will not be changed.
use_phaser_if_available = True
.type = bool
.short_caption = Use Phaser LLG map
.help = If True, and Phaser is installed and configured, an anomalous LLG \
map will be used in place of the simple anomalous difference map. The \
wavelength should be specified for this to be maximally useful.
write_pdb = True
.type = bool
.short_caption = Write peaks to PDB file
write_maps = True
.type = bool
.short_caption = Save map coefficients
output_file_prefix = peaks_holes
.type = str
include scope libtbx.phil.interface.tracking_params
""")
def get_master_phil():
from mmtbx.command_line import generate_master_phil_with_inputs
return generate_master_phil_with_inputs(
enable_automatic_twin_detection=True,
phil_string="""
find_peaks
.style = auto_align
{
include scope mmtbx.find_peaks.master_params
}
map_cutoff = 3.0
.type = float
.short_caption = mFo-DFc map cutoff (sigma)
anom_map_cutoff = 3.0
.type = float
.short_caption = Anomalous map cutoff (sigma)
include_peaks_near_model = False
.type = bool
.short_caption = Don't filter peaks by distance to model
.help = By default, the program will only display peaks that map to points \
outside of the current model, ignoring those that overlap with atoms. \
Setting this option to True is equivalent to specifying a distance \
cutoff of zero for the filtering step.
.style = OnChange:toggle_min_model_peak_dist
wavelength = None
.type = float
.help = Optional parameter, if defined this will cause all atoms to be \
treated as anomalous scatterers using the standard Sasaki table to \
obtain theoretical fp and fpp values. Only really useful if the Phaser \
LLG map is being used for the anomalous map.
filter_peaks_by_2fofc = None
.type = float
.short_caption = Filter peaks by 2mFo-DFc
.help = If this is set, peaks outside 2mFo-DFc density at the \
cutoff will be discarded. (This does not apply to the analysis of \
solvent atoms.) Holes will not be changed.
use_phaser_if_available = True
.type = bool
.short_caption = Use Phaser LLG map
.help = If True, and Phaser is installed and configured, an anomalous LLG \
map will be used in place of the simple anomalous difference map. The \
wavelength should be specified for this to be maximally useful.
write_pdb = True
.type = bool
.short_caption = Write peaks to PDB file
write_maps = True
.type = bool
.short_caption = Save map coefficients
output_file_prefix = peaks_holes
.type = str
include scope libtbx.phil.interface.tracking_params
""")
def master_phil () :
from mmtbx.command_line import generate_master_phil_with_inputs
return generate_master_phil_with_inputs(
enable_automatic_twin_detection=True,
enable_pdb_interpretation_params=True,
enable_stop_for_unknowns=False,
phil_string="""
include scope mmtbx.ions.identify.ion_master_phil
debug = True
.type = bool
nproc = Auto
.type = int
""")
def get_master_phil () :
from mmtbx.command_line import generate_master_phil_with_inputs
return generate_master_phil_with_inputs(
enable_automatic_twin_detection=True,
phil_string="""
prune {
%s
}
output {
file_name = None
.type = path
}
""" % model_prune_master_phil)
def master_phil():
from mmtbx.command_line import generate_master_phil_with_inputs
return generate_master_phil_with_inputs(
enable_automatic_twin_detection=True,
enable_pdb_interpretation_params=True,
enable_stop_for_unknowns=False,
phil_string="""
include scope mmtbx.ions.identify.ion_master_phil
debug = True
.type = bool
nproc = Auto
.type = int
""")
def get_master_phil():
from mmtbx.command_line import generate_master_phil_with_inputs
return generate_master_phil_with_inputs(
enable_automatic_twin_detection=True,
phil_string="""
prune {
%s
}
output {
file_name = None
.type = path
}
""" % model_prune_master_phil)
def master_phil () :
from mmtbx.command_line import generate_master_phil_with_inputs
return generate_master_phil_with_inputs(
enable_stop_for_unknowns=False,
enable_pdb_interpretation_params=True,
phil_string="""
ignore_inconsistent_occupancy = True
.type = bool
pickle = False
.type = bool
verbose = False
.type = bool
""")
def master_phil():
from mmtbx.command_line import generate_master_phil_with_inputs
return generate_master_phil_with_inputs(
enable_stop_for_unknowns=False,
enable_pdb_interpretation_params=True,
phil_string="""
ignore_inconsistent_occupancy = True
.type = bool
pickle = False
.type = bool
verbose = False
.type = bool
""")
def master_phil () :
from mmtbx.command_line import generate_master_phil_with_inputs
return generate_master_phil_with_inputs(
enable_automatic_twin_detection=True,
phil_string="""
ligand_code = None
.type = str
.multiple = True
reference_structure = None
.type = path
only_segid = None
.type = str
verbose = False
.type = bool
""")
def master_phil():
from mmtbx.command_line import generate_master_phil_with_inputs
return generate_master_phil_with_inputs(
enable_automatic_twin_detection=True,
phil_string="""
ligand_code = None
.type = str
.multiple = True
reference_structure = None
.type = path
only_segid = None
.type = str
verbose = False
.type = bool
""")
def master_phil():
from mmtbx.command_line import generate_master_phil_with_inputs
return generate_master_phil_with_inputs(phil_string="""
selection = None
.type = atom_selection
nproc = Auto
.type = int
output {
file_name = alternates.pdb
.type = path
verbose = False
.type = bool
debug = False
.type = bool
}
include scope mmtbx.building.alternate_conformations.single_residue.master_phil_str
""")
def master_phil () :
from mmtbx.command_line import generate_master_phil_with_inputs
return generate_master_phil_with_inputs(
phil_string="""
selection = None
.type = atom_selection
nproc = Auto
.type = int
output {
file_name = alternates.pdb
.type = path
verbose = False
.type = bool
debug = False
.type = bool
}
include scope mmtbx.building.alternate_conformations.single_residue.master_phil_str
""")
def master_phil () :
from mmtbx.command_line import generate_master_phil_with_inputs
return generate_master_phil_with_inputs(
phil_string="""
alt_confs {
selection = None
.type = atom_selection
macro_cycles = 1
.type = int(value_min=1)
.optional = False
include scope libtbx.easy_mp.parallel_phil_str_no_threading
include scope mmtbx.building.alternate_conformations.single_residue.master_phil_str
# sliding_window {
# include scope mmtbx.building.alternate_conformations.sliding_window.master_params_str
# }
refinement {
include scope phenix.automation.refinement.refine_hires_phil_str
constrain_correlated_occupancies = True
.type = bool
}
merging {
include scope mmtbx.building.alternate_conformations.rejoin_phil
}
}
output {
prefix = alternates
.type = str
output_dir = None
.type = path
create_dir = True
.type = bool
directory_number = None
.type = int
debug = 0
.type = int
verbose = True
.type = bool
remove_hydrogens = False
.type = bool
}
""")
def get_master_phil () :
from mmtbx.command_line import generate_master_phil_with_inputs
return generate_master_phil_with_inputs(
enable_automatic_twin_detection=True,
enable_pdb_interpretation_params=True,
enable_stop_for_unknowns=False,
enable_unmerged_data=True,
enable_cdl=Auto,
phil_string="""
molprobity {
outliers_only = True
.type = bool
keep_hydrogens = Auto
.type = bool
.help = Keep hydrogens in input file (instead of re-generating them with \
Reduce). If set to Auto, the behavior will depend on whether the \
neutron scattering table is used (regardless of whether we actually \
have experimental data).
# nuclear = False # redundant parameter, same as
# .type = bool # pdb_interpretation.use_neutron_distances
# .short_caption = "Use nuclear hydrogen positions"
min_cc_two_fofc = 0.8
.type = float
.short_caption = "CC threshold"
.help = Values for real-space correlations below the CC threshold are \
considered outliers
n_bins = 10
.type = int
.short_caption = Number of resolution bins
use_pdb_header_resolution_cutoffs = False
.type = bool
.short_caption = Use resolution cutoffs in PDB header
count_anomalous_pairs_separately = False
.type = bool
.expert_level = 2
rotamer_library = 500 *8000
.type = choice
.help = Library of rotamer probabilities (Top500 or Top8000)
.expert_level = 2
flags
.expert_level = 3
{
include scope mmtbx.validation.molprobity.master_phil_str
}
ligand_selection = None
.type = atom_selection
.expert_level = 3
}
polygon {
include scope mmtbx.polygon.polygon_params_str
}
output {
quiet = False
.type = bool
probe_dots = True
.type = bool
.short_caption = Save Probe dots for Coot
kinemage = False
.type = bool
.short_caption = Save Kinemage file for KiNG
percentiles = False
.type = bool
.help = Show percentile rankings for summary statistics
coot = True
.type = bool
.help = Write Coot script
maps = Auto
.type = bool
.short_caption = Save map coefficients
.help = Write map coefficients (if experimental data supplied)
map_options
.short_caption = Advanced options for map coefficients
{
fill_missing_f_obs = True
.type = bool
exclude_free_r_reflections = False
.type = bool
}
prefix = None
.type = str
.style = hidden
pickle = False
.type = bool
.style = hidden
wxplots = False
.type = bool
.help = Display plots in wxPython
.style = hidden
gui_dir = None
.type = path
.short_caption = Output directory
.help = Output directory (Phenix GUI only).
.style = output_dir
include scope libtbx.phil.interface.tracking_params
}
""")
def master_phil () :
from mmtbx.command_line import generate_master_phil_with_inputs
return generate_master_phil_with_inputs(
phil_string=master_phil_str,
enable_automatic_twin_detection=True)
def get_master_phil():
from mmtbx.command_line import generate_master_phil_with_inputs
return generate_master_phil_with_inputs(
enable_twin_law=True,
enable_experimental_phases=True,
enable_pdb_interpretation_params=True,
enable_stop_for_unknowns=False,
enable_full_geometry_params=True,
phil_string="""
selection = None
.type = atom_selection
whole_residues = False
.type = bool
.help = If the initial selection includes partial residues, expand it to \
include each residue in its entirety.
selection_delete = None
.type = atom_selection
.help = Designates atoms to be removed from the structure before \
calculating the target map.
target_map = *mFo-DFc 2mFo-DFc
.type = choice
occ = 0.5
.type = float
.help = Partial occupancy for selected atoms for map calculation.
rsr_after_anneal = False
.type = bool
resolution_factor = 0.25
.type = float
negate_surrounding_sites = False
.type = bool
.help = Set map values to negative around atoms outside of the target \
selection.
reference_sigma = 0.5
.type = float
.help = Sigma for harmonic restraints for neighboring atoms not included \
in the selection of interest.
wc = 1
.type = float
.help = Geometry restraints weight
n_confs = 1
.type = int
nproc = Auto
.type = int
random_seed = None
.type = int
output {
file_name = disordered.pdb
.type = path
include_starting_model = True
.type = bool
map_file_name = None
.type = path
verbose = False
.type = bool
debug = False
.type = bool
}
simulated_annealing {
include scope mmtbx.dynamics.simulated_annealing.master_params
}
""")
def master_phil():
from mmtbx.command_line import generate_master_phil_with_inputs
return generate_master_phil_with_inputs(
phil_string=master_phil_str, enable_automatic_twin_detection=True)
def get_master_phil () :
from mmtbx.command_line import generate_master_phil_with_inputs
return generate_master_phil_with_inputs(
enable_automatic_twin_detection=True,
enable_pdb_interpretation_params=True,
enable_stop_for_unknowns=False,
enable_unmerged_data=True,
enable_cdl=Auto,
phil_string="""
molprobity {
outliers_only = True
.type = bool
keep_hydrogens = Auto
.type = bool
.help = Keep hydrogens in input file (instead of re-generating them with \
Reduce). If set to Auto, the behavior will depend on whether the \
neutron scattering table is used (regardless of whether we actually \
have experimental data).
nuclear = False
.type = bool
.short_caption = "Use nuclear hydrogen positions"
min_cc_two_fofc = 0.8
.type = float
.short_caption = "CC threshold"
.help = Values for real-space correlations below the CC threshold are \
considered outliers
n_bins = 10
.type = int
.short_caption = Number of resolution bins
use_pdb_header_resolution_cutoffs = False
.type = bool
.short_caption = Use resolution cutoffs in PDB header
count_anomalous_pairs_separately = False
.type = bool
.expert_level = 2
rotamer_library = 500 *8000
.type = choice
.help = Library of rotamer probabilities (Top500 or Top8000)
.expert_level = 2
flags
.expert_level = 3
{
include scope mmtbx.validation.molprobity.master_phil_str
}
ligand_selection = None
.type = atom_selection
.expert_level = 3
}
output {
quiet = False
.type = bool
probe_dots = True
.type = bool
.short_caption = Save Probe dots for Coot
kinemage = False
.type = bool
.short_caption = Save Kinemage file for KiNG
percentiles = False
.type = bool
.help = Show percentile rankings for summary statistics
coot = True
.type = bool
.help = Write Coot script
maps = Auto
.type = bool
.short_caption = Save map coefficients
.help = Write map coefficients (if experimental data supplied)
map_options
.short_caption = Advanced options for map coefficients
{
fill_missing_f_obs = True
.type = bool
exclude_free_r_reflections = False
.type = bool
}
prefix = None
.type = str
.style = hidden
pickle = False
.type = bool
.style = hidden
wxplots = False
.type = bool
.help = Display plots in wxPython
.style = hidden
gui_dir = None
.type = path
.short_caption = Output directory
.help = Output directory (Phenix GUI only).
.style = output_dir
include scope libtbx.phil.interface.tracking_params
}
""")
def get_master_phil () :
from mmtbx.command_line import generate_master_phil_with_inputs
return generate_master_phil_with_inputs(
enable_twin_law=True,
enable_experimental_phases=True,
enable_pdb_interpretation_params=True,
enable_stop_for_unknowns=False,
enable_full_geometry_params=True,
phil_string="""
selection = None
.type = atom_selection
whole_residues = False
.type = bool
.help = If the initial selection includes partial residues, expand it to \
include each residue in its entirety.
selection_delete = None
.type = atom_selection
.help = Designates atoms to be removed from the structure before \
calculating the target map.
target_map = *mFo-DFc 2mFo-DFc
.type = choice
occ = 0.5
.type = float
.help = Partial occupancy for selected atoms for map calculation.
rsr_after_anneal = False
.type = bool
resolution_factor = 0.25
.type = float
negate_surrounding_sites = False
.type = bool
.help = Set map values to negative around atoms outside of the target \
selection.
reference_sigma = 0.5
.type = float
.help = Sigma for harmonic restraints for neighboring atoms not included \
in the selection of interest.
wc = 1
.type = float
.help = Geometry restraints weight
n_confs = 1
.type = int
nproc = Auto
.type = int
random_seed = None
.type = int
output {
file_name = disordered.pdb
.type = path
include_starting_model = True
.type = bool
map_file_name = None
.type = path
verbose = False
.type = bool
debug = False
.type = bool
}
simulated_annealing {
include scope mmtbx.dynamics.simulated_annealing.master_params
}
""")
