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 # LIBTBX_SET_DISPATCHER_NAME xfel.map_height_at_atoms  from __future__ import division from libtbx.str_utils import make_sub_header from libtbx.utils import Sorry import..."

2014-08-22T06:04:14Z

Created page with "<pre> # LIBTBX_SET_DISPATCHER_NAME xfel.map_height_at_atoms from __future__ import division from libtbx.str_utils import make_sub_header from libtbx.utils import Sorry import..."

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<pre>
# LIBTBX_SET_DISPATCHER_NAME xfel.map_height_at_atoms

from __future__ import division
from libtbx.str_utils import make_sub_header
from libtbx.utils import Sorry
import sys

master_phil_str = """
map_type = anom
.type = str
exclude_free_r_reflections = False
.type = bool
fill_missing_f_obs = False
.type = bool
resolution_factor = 0.25
.type = float
selection = element CA or element ZN
.type = atom_selection
"""

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=False)

def run (args, out=sys.stdout) :
usage_string = """\
xfel.map_height_at_atoms model.pdb data.mtz [map_type=MAP_TYPE] \\
[selection=ATOM_SELECTION]
"""
import mmtbx.command_line
cmdline = mmtbx.command_line.load_model_and_data(
update_f_part1_for="map",
args=args,
master_phil=master_phil(),
process_pdb_file=False,
prefer_anomalous=True,
usage_string=usage_string,
#set_wavelength_from_model_header=True,
#set_inelastic_form_factors="sasaki",
out=out)
params = cmdline.params
fmodel = cmdline.fmodel
xray_structure = fmodel.xray_structure
pdb_hierarchy = cmdline.pdb_hierarchy
sel_cache = pdb_hierarchy.atom_selection_cache()
selection = sel_cache.selection(params.selection).iselection()
if (len(selection) == 0) :
raise Sorry("No atoms selected!")
params = cmdline.params
map_coeffs = fmodel.map_coefficients(
map_type=params.map_type,
exclude_free_r_reflections=params.exclude_free_r_reflections,
fill_missing=params.fill_missing_f_obs)
fft_map = map_coeffs.fft_map(
resolution_factor=params.resolution_factor).apply_sigma_scaling()
real_map = fft_map.real_map_unpadded()
make_sub_header("Map analysis", out=out)
from scitbx.array_family import flex
print >> out, "Maximum grid point value: %6.2f sigma" % \
flex.max(real_map.as_1d())
print >> out, ""
for i_seq in selection :
sc = xray_structure.scatterers()[i_seq]
map_value = real_map.tricubic_interpolation(sc.site)
print >> out, "%s : %6.2f sigma" % (sc.label, map_value)

if (__name__ == "__main__") :
run(sys.argv[1:])
</pre>

Map height at atoms.py - Revision history

Nicksauter: Created page with "
# LIBTBX_SET_DISPATCHER_NAME xfel.map_height_at_atoms from future import division from libtbx.str_utils import make_sub_header from libtbx.utils import Sorry import..."