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map_util.py
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map_util.py
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from __future__ import division
from scitbx.array_family import flex
from cctbx import maptbx, uctbx, crystal
from cctbx.maptbx import non_crystallographic_eight_point_interpolation
from mmtbx.command_line.real_space_diff_map import scale_k1, scale_two_real_maps_in_fourier_space
from mmtbx.maps.fem import ccp4_map
from libtbx.utils import Sorry
def get_density_at_position(position, frac_matrix, mapdata):
"""generic function for computing the density at a single point"""
# raise Sorry if the position doesn't appear to be within the bounds of the map.
# this may mean the user supplied a model that was not centered in the map.
try:
density = non_crystallographic_eight_point_interpolation(
map=mapdata,
gridding_matrix=frac_matrix,
site_cart=position)
except RuntimeError as e:
raise Sorry("Could not compute map density at the requested position. "+\
"Please check that model is entirely within map bounds.")
return density
def neutralize_scatterers(xrs):
scatterers = xrs.scatterers()
for sc in scatterers:
neutralized_scatterer = filter(lambda x: x.isalpha(), sc.scattering_type)
sc.scattering_type = neutralized_scatterer
def get_fcalc_map(model, symmetry, d_min, emmap, scatterer="electron"):
"""Fcalc map generation borrowed from EMRinger"""
xrs = model.input.xray_structure_simple(crystal_symmetry=symmetry)
if scatterer == "electron":
# until ions are added to the electron scattering tables
neutralize_scatterers(xrs)
xrs.scattering_type_registry(
d_min=d_min,
table=scatterer)
fc = xrs.structure_factors(d_min=d_min).f_calc()
cg = maptbx.crystal_gridding(
unit_cell=symmetry.unit_cell(),
space_group_info=symmetry.space_group_info(),
pre_determined_n_real=emmap.data.all())
fc_map = fc.fft_map(
crystal_gridding=cg).apply_sigma_scaling().real_map_unpadded()
scale = len(fc_map)/flex.sum(flex.abs(fc_map))
fc_map_scaled = fc_map * scale
return fc_map_scaled
def get_diff_map(symmetry, fcalc_map, expt_map, d_min):
"""Compute a difference map between the calculated and experimental maps.
Modified from mmtbx.command_line.real_space_diff_map class compdiff."""
scale = scale_k1(x=expt_map, y=fcalc_map)
scaled_fcalc_map = fcalc_map * scale # should already be scaled but okay
origin = expt_map.origin()
shifted_expt_map = expt_map.shift_origin()
shifted_diff_map = flex.double(flex.grid(expt_map.all()))
diff_map = flex.double(flex.grid(expt_map.origin(), expt_map.focus()))
ucell_params = symmetry.unit_cell().parameters()
boxes = maptbx.boxes_by_dimension(
n_real = expt_map.all(),
dim = 30,
abc = ucell_params[:3])
i_box = 0
test_map_box_obs_all = None
for start, end in zip(boxes.starts, boxes.ends):
i_box += 1
map_box_obs = maptbx.copy(shifted_expt_map, start, end)
map_box_calc = maptbx.copy(scaled_fcalc_map, start, end)
map_box_obs.reshape(flex.grid(map_box_obs.all()))
map_box_calc.reshape(flex.grid(map_box_calc.all()))
# abc = [ucell_params[i]/expt_map.all()[i] for i in range(3)]
# ucb = uctbx.unit_cell(parameters=(
# abc[0],abc[1],abc[2],ucell_params[3],ucell_params[4],ucell_params[5]))
# cs = crystal.symmetry(unit_cell=ucb, space_group="P1")
cs = symmetry
diff_map_part = scale_two_real_maps_in_fourier_space(
m1 = map_box_obs,
m2 = map_box_calc,
cs = cs,
d_min = d_min,
vector_map = True) # this means yes, use the phases from fcalc
maptbx.set_box(
map_data_from = diff_map_part,
map_data_to = shifted_diff_map,
start = start,
end = end)
# skip this additional scaling step -- it explodes everything
# sd = diff_map.sample_standard_deviation()
# if(sd!=0):
# diff_map = diff_map/sd
# somehow put the contents of shifted_diff_map into diff_map but keep origin?
for i in xrange(len(shifted_diff_map)):
diff_map[i] = shifted_diff_map[i]
# FIXME SUPER SLOW but it should work for now
return diff_map
def write_ccp4_map(mapdata, symmetry, filename):
cg = maptbx.crystal_gridding(
unit_cell=symmetry.unit_cell(),
space_group_info=symmetry.space_group_info(),
pre_determined_n_real=mapdata.all())
return ccp4_map(cg, filename, map_data=mapdata)