def read_ncs_file(self, file_name=None, log=sys.stdout):
# Read in an NCS file and make sure its symmetry is similar to others
from mmtbx.ncs.ncs import ncs
ncs_object = ncs()
ncs_object.read_ncs(file_name=file_name, log=log)
if ncs_object.max_operators() < 2:
self.ncs_object.set_unit_ncs()
self.add_ncs_object(ncs_object)
def _try_as_ncs (self) :
from mmtbx.ncs.ncs import ncs
from libtbx.utils import null_out
ncs_object=ncs()
try: # see if we can read biomtr records
pdb_inp=iotbx.pdb.input(file_name=self.file_name)
ncs_object.ncs_from_pdb_input_BIOMT(pdb_inp=pdb_inp,log=null_out(),
quiet=True)
except Exception,e: # try as regular ncs object
ncs_object.read_ncs(file_name=self.file_name,log=sys.stdout,quiet=True)
def _try_as_ncs (self) :
from mmtbx.ncs.ncs import ncs
from libtbx.utils import null_out
ncs_object=ncs()
try: # see if we can read biomtr records
pdb_inp=iotbx.pdb.input(file_name=self.file_name)
ncs_object.ncs_from_pdb_input_BIOMT(pdb_inp=pdb_inp,log=null_out(),
quiet=True)
except Exception,e: # try as regular ncs object
ncs_object.read_ncs(file_name=self.file_name,log=sys.stdout,quiet=True)
def get_results(self):
from libtbx import group_args
if not self.ncs_object:
from mmtbx.ncs.ncs import ncs
self.ncs_object=ncs()
self.score=None
self.cc=None
return group_args(
cc = self.cc,
ncs_object = self.ncs_object,
ncs_name = str(self.ncs_object.get_ncs_name()),
ncs_operators = self.ncs_object.max_operators(),
score=self.score,
)
def deep_copy(self,change_of_basis_operator=None,unit_cell=None,
coordinate_offset=None,
new_unit_cell=None): # make a copy
from mmtbx.ncs.ncs import ncs
# make new ncs object with same overall params as this one:
new=ncs(exclude_h=self._exclude_h,exclude_d=self._exclude_d)
new.source_info=self.source_info
new._ncs_read=self._ncs_read
# deep_copy over all the ncs groups:
for ncs_group in self._ncs_groups:
new._ncs_groups.append(ncs_group.deep_copy(
change_of_basis_operator=change_of_basis_operator,
coordinate_offset=coordinate_offset,
unit_cell=unit_cell,new_unit_cell=new_unit_cell))
return new
def exercise(file_name=None, pdb_file_name = None, map_file_name = None ,
split_pdb_file_name = None,
out = sys.stdout):
# Set up source data
if not os.path.isfile(file_name):
raise Sorry("Missing the file: %s" %(file_name)+"\n")
print ("Reading from %s" %(file_name))
from iotbx.map_manager import map_manager
m = map_manager(file_name)
print ("Header information from %s:" %(file_name))
m.show_summary(out = out)
map_data = m.map_data().deep_copy()
crystal_symmetry = m.crystal_symmetry()
unit_cell_parameters = m.crystal_symmetry().unit_cell().parameters()
print ("\nMap origin: %s Extent %s" %( map_data.origin(), map_data.all()))
print ("Original unit cell, not just unit cell of part in this file): %s" %(
str(unit_cell_parameters)))
grid_point = (1, 2, 3)
if map_data.origin() != (0, 0, 0): # make sure it is inside
from scitbx.matrix import col
grid_point = tuple (col(grid_point)+col(map_data.origin()))
print ("\nValue of map_data at grid point %s: %.3f" %(str(grid_point),
map_data[grid_point]))
print ("Map data is %s" %(type(map_data)))
random_position = (10, 5, 7.9)
point_frac = crystal_symmetry.unit_cell().fractionalize(random_position)
value_at_point_frac = map_data.eight_point_interpolation(point_frac)
print ("Value of map_data at coordinates %s: %.3f" %(
str(random_position), value_at_point_frac))
map_data_as_float = map_data.as_float()
print ("Map data as float is %s" %(type(map_data_as_float)))
# make a little model
sites_cart = flex.vec3_double( ((8, 10, 12), (14, 15, 16)))
model = model_manager.from_sites_cart(
atom_name = ' CA ',
resname = 'ALA',
chain_id = 'A',
b_iso = 30.,
occ = 1.,
scatterer = 'C',
sites_cart = sites_cart,
crystal_symmetry = crystal_symmetry)
# Move map and a model to place origin at (0, 0, 0)
# map data is new copy but model is shifted in place.
from iotbx.map_model_manager import map_model_manager
mam = map_model_manager(
map_manager = m,
model = model.deep_copy(),
)
# Read in map and model and split up
dm = DataManager()
aa = dm.get_map_model_manager(model_file=pdb_file_name,
map_files=map_file_name)
bb = dm.get_map_model_manager(model_file=split_pdb_file_name,
map_files=map_file_name)
for selection_method in ['by_chain', 'by_segment','supplied_selections',
'boxes']:
if selection_method == 'boxes':
choices = [True, False]
else:
choices = [True]
if selection_method == 'by_chain':
mask_choices = [True,False]
else:
mask_choices = [False]
for select_final_boxes_based_on_model in choices:
for skip_empty_boxes in choices:
for mask_choice in mask_choices:
if mask_choice: # use split model
a=bb.deep_copy()
else: # usual
a=aa.deep_copy()
print ("\nRunning split_up_map_and_model with \n"+
"select_final_boxes_based_on_model="+
"%s skip_empty_boxes=%s selection_method=%s" %(
select_final_boxes_based_on_model,skip_empty_boxes,selection_method))
if selection_method == 'by_chain':
print ("Mask around unused atoms: %s" %(mask_choice))
box_info = a.split_up_map_and_model_by_chain(
mask_around_unselected_atoms=mask_choice)
elif selection_method == 'by_segment':
box_info = a.split_up_map_and_model_by_segment()
elif selection_method == 'supplied_selections':
selection = a.model().selection('all')
box_info = a.split_up_map_and_model_by_supplied_selections(
selection_list = [selection])
elif selection_method == 'boxes':
box_info = a.split_up_map_and_model_by_boxes(
skip_empty_boxes = skip_empty_boxes,
select_final_boxes_based_on_model =
select_final_boxes_based_on_model)
print (selection_method,skip_empty_boxes,
len(box_info.selection_list),
box_info.selection_list[0].count(True))
assert (selection_method,skip_empty_boxes,
len(box_info.selection_list),
box_info.selection_list[0].count(True)) in [
('by_chain',True,3,19),
("by_chain",True,1,86,),
("by_segment",True,1,86,),
("supplied_selections",True,1,86,),
("boxes",True,13,1,),
("boxes",False,36,0,),
("boxes",True,13,1,),
("boxes",False,36,0,),
]
# Change the coordinates in one box
small_model = box_info.mmm_list[0].model()
small_sites_cart = small_model.get_sites_cart()
from scitbx.matrix import col
small_sites_cart += col((1,0,0))
small_model.set_crystal_symmetry_and_sites_cart(
sites_cart = small_sites_cart,
crystal_symmetry = small_model.crystal_symmetry())
# Put everything back together
a.merge_split_maps_and_models(box_info = box_info)
mam.box_all_maps_around_model_and_shift_origin()
shifted_crystal_symmetry = mam.model().crystal_symmetry()
shifted_model = mam.model()
shifted_map_data = mam.map_data()
print ("\nOriginal map origin (grid units):", map_data.origin())
print ("Original model:\n", model.model_as_pdb())
print ("Shifted map origin:", shifted_map_data.origin())
print ("Shifted model:\n", shifted_model.model_as_pdb())
# Save the map_model manager
mam_dc=mam.deep_copy()
print ("dc",mam)
print ("dc mam_dc",mam_dc)
# Mask map around atoms
mam=mam_dc.deep_copy()
print ("dc mam_dc dc",mam_dc)
print (mam)
mam.mask_all_maps_around_atoms(mask_atoms_atom_radius = 3,
set_outside_to_mean_inside=True, soft_mask=False)
print ("Mean before masking", mam.map_data().as_1d().min_max_mean().mean)
assert approx_equal(mam.map_data().as_1d().min_max_mean().mean,
-0.0585683621466)
print ("Max before masking", mam.map_data().as_1d().min_max_mean().max)
assert approx_equal(mam.map_data().as_1d().min_max_mean().max,
-0.0585683621466)
# Mask map around atoms, with soft mask
mam=mam_dc.deep_copy()
mam.mask_all_maps_around_atoms(mask_atoms_atom_radius = 3, soft_mask = True,
soft_mask_radius = 5, set_outside_to_mean_inside=True)
print ("Mean after first masking", mam.map_data().as_1d().min_max_mean().mean)
assert approx_equal(mam.map_data().as_1d().min_max_mean().mean,
-0.00177661714805)
print ("Max after first masking", mam.map_data().as_1d().min_max_mean().max)
assert approx_equal(mam.map_data().as_1d().min_max_mean().max,
0.236853733659)
# Mask map around atoms again
mam.mask_all_maps_around_atoms(mask_atoms_atom_radius = 3,
set_outside_to_mean_inside = True, soft_mask=False)
print ("Mean after second masking", mam.map_data().as_1d().min_max_mean().mean)
assert approx_equal(mam.map_data().as_1d().min_max_mean().mean,
-0.0585683621466)
print ("Max after second masking", mam.map_data().as_1d().min_max_mean().max)
assert approx_equal(mam.map_data().as_1d().min_max_mean().max,
-0.0585683621466)
# Mask around edges
mam=mam_dc.deep_copy()
mam.mask_all_maps_around_edges( soft_mask_radius = 3)
print ("Mean after masking edges", mam.map_data().as_1d().min_max_mean().mean)
assert approx_equal(mam.map_data().as_1d().min_max_mean().mean,
0.0155055604192)
print ("Max after masking edges", mam.map_data().as_1d().min_max_mean().max)
assert approx_equal(mam.map_data().as_1d().min_max_mean().max,
0.249827131629)
print ("\nWriting map_data and model in shifted position (origin at 0, 0, 0)")
output_file_name = 'shifted_map.ccp4'
print ("Writing to %s" %(output_file_name))
mrcfile.write_ccp4_map(
file_name = output_file_name,
crystal_symmetry = shifted_crystal_symmetry,
map_data = shifted_map_data, )
output_file_name = 'shifted_model.pdb'
f = open(output_file_name, 'w')
print (shifted_model.model_as_pdb(), file=f)
f.close()
print ("\nWriting map_data and model in original position (origin at %s)" %(
str(mam.map_manager().origin_shift_grid_units)))
output_file_name = 'new_map_original_position.ccp4'
print ("Writing to %s" %(output_file_name))
mrcfile.write_ccp4_map(
file_name = output_file_name,
crystal_symmetry = shifted_crystal_symmetry,
map_data = shifted_map_data,
origin_shift_grid_units = mam.map_manager().origin_shift_grid_units)
print (shifted_model.model_as_pdb())
output_pdb_file_name = 'new_model_original_position.pdb'
f = open(output_pdb_file_name, 'w')
print (shifted_model.model_as_pdb(), file=f)
f.close()
# Write as mmcif
output_cif_file_name = 'new_model_original_position.cif'
f = open(output_cif_file_name, 'w')
print (shifted_model.model_as_mmcif(),file = f)
f.close()
# Read the new map and model
import iotbx.pdb
new_model = model_manager(
model_input = iotbx.pdb.input(
source_info = None,
lines = flex.split_lines(open(output_pdb_file_name).read())),
crystal_symmetry = crystal_symmetry)
assert new_model.model_as_pdb() == model.model_as_pdb()
new_model_from_cif = model_manager(
model_input = iotbx.pdb.input(
source_info = None,
lines = flex.split_lines(open(output_cif_file_name).read())),
crystal_symmetry = crystal_symmetry)
assert new_model_from_cif.model_as_pdb() == model.model_as_pdb()
# Read and box the original file again in case we modified m in any
# previous tests
m = map_manager(file_name)
mam=map_model_manager(model=model.deep_copy(),map_manager=m)
mam.box_all_maps_around_model_and_shift_origin()
file_name = output_file_name
print ("Reading from %s" %(file_name))
new_map = iotbx.mrcfile.map_reader(file_name = file_name, verbose = False)
new_map.data = new_map.data.shift_origin()
print ("Header information from %s:" %(file_name))
new_map.show_summary(out = out)
assert new_map.map_data().origin() == mam.map_manager().map_data().origin()
assert new_map.crystal_symmetry().is_similar_symmetry(mam.map_manager().crystal_symmetry())
# make a map_model_manager with lots of maps and model and ncs
from mmtbx.ncs.ncs import ncs
ncs_object=ncs()
ncs_object.set_unit_ncs()
mam = map_model_manager(
map_manager = m,
ncs_object = ncs_object,
map_manager_1 = m.deep_copy(),
map_manager_2 = m.deep_copy(),
extra_model_list = [model.deep_copy(),model.deep_copy()],
extra_model_id_list = ["model_1","model_2"],
extra_map_manager_list = [m.deep_copy(),m.deep_copy()],
extra_map_manager_id_list = ["extra_1","extra_2"],
model = model.deep_copy(),
)
# make a map_model_manager with lots of maps and model and ncs and run
# with wrapping and ignore_symmetry_conflicts on
from mmtbx.ncs.ncs import ncs
ncs_object=ncs()
ncs_object.set_unit_ncs()
m.set_ncs_object(ncs_object.deep_copy())
mam2 = map_model_manager(
map_manager = m.deep_copy(),
ncs_object = ncs_object.deep_copy(),
map_manager_1 = m.deep_copy(),
map_manager_2 = m.deep_copy(),
extra_model_list = [model.deep_copy(),model.deep_copy()],
extra_model_id_list = ["model_1","model_2"],
extra_map_manager_list = [m.deep_copy(),m.deep_copy()],
extra_map_manager_id_list = ["extra_1","extra_2"],
model = model.deep_copy(),
ignore_symmetry_conflicts = True,
wrapping = m.wrapping(),
)
assert mam.map_manager().is_similar(mam2.map_manager())
assert mam.map_manager().is_similar(mam2.map_manager_1())
for m in mam2.map_managers():
assert mam.map_manager().is_similar(m)
assert mam.model().shift_cart() == mam2.model().shift_cart()
assert mam.model().shift_cart() == mam2.get_model_by_id('model_2').shift_cart()
print ("OK")
def exercise(file_name, out=sys.stdout):
# Set up source data
if not os.path.isfile(file_name):
raise Sorry("Missing the file: %s" % (file_name) + "\n")
print("Reading from %s" % (file_name))
from iotbx.map_manager import map_manager
m = map_manager(file_name)
# make a little model
sites_cart = flex.vec3_double(((8, 10, 12), (14, 15, 16)))
model = model_manager.from_sites_cart(
atom_name=' CA ',
resname='ALA',
chain_id='A',
b_iso=30.,
occ=1.,
scatterer='C',
sites_cart=sites_cart,
crystal_symmetry=m.crystal_symmetry())
# make a map_model_manager with lots of maps and model and ncs
from iotbx.map_model_manager import map_model_manager
from mmtbx.ncs.ncs import ncs
ncs_object = ncs()
ncs_object.set_unit_ncs()
mask_mm = m.deep_copy()
mask_mm.set_is_mask(True)
mam = map_model_manager(
map_manager=m,
ncs_object=ncs_object,
map_manager_1=m.deep_copy(),
map_manager_2=m.deep_copy(),
extra_map_manager_list=[m.deep_copy(),
m.deep_copy(),
m.deep_copy()],
extra_map_manager_id_list=["extra_1", "extra_2", "map_manager_mask"],
model=model.deep_copy(),
)
print(mam.map_manager())
print(mam.model())
print(mam.map_manager_1())
print(mam.map_manager_2())
print(mam.map_manager_mask())
print(mam.map_manager().ncs_object())
all_map_names = mam.map_id_list()
for id in all_map_names:
print("Map_manager %s: %s " % (id, mam.get_map_manager_by_id(id)))
dm = DataManager(['model', 'miller_array', 'real_map', 'phil', 'ncs_spec'])
dm.set_overwrite(True)
# Create a model with ncs
from iotbx.regression.ncs.tst_ncs import pdb_str_5
file_name = 'tst_mam.pdb'
f = open(file_name, 'w')
print(pdb_str_5, file=f)
f.close()
# Generate map data from this model (it has ncs)
mmm = map_model_manager()
mmm.generate_map(box_cushion=0, file_name=file_name, n_residues=500)
ncs_mam = mmm.deep_copy()
ncs_mam_copy = mmm.deep_copy()
# Make sure this model has 126 sites (42 sites times 3-fold ncs)
assert ncs_mam.model().get_sites_cart().size() == 126
assert approx_equal(ncs_mam.model().get_sites_cart()[0],
(23.560999999999996, 8.159, 10.660000000000002))
# Get just unique part (42 sites)
unique_mam = ncs_mam.extract_all_maps_around_model(
select_unique_by_ncs=True)
assert unique_mam.model().get_sites_cart().size() == 42
assert approx_equal(unique_mam.model().get_sites_cart()[0],
(18.740916666666664, 13.1794, 16.10544))
# Make sure that the extraction did not change the original but does change
# the extracted part
assert (unique_mam.model().get_sites_cart()[0] !=
ncs_mam.model().get_sites_cart()[0]
) # it was a deep copy so original stays
# Shift back the extracted part and make sure it matches the original now
shifted_back_unique_model = mmm.get_model_from_other(
unique_mam.deep_copy())
assert approx_equal(shifted_back_unique_model.get_sites_cart()[0],
(23.560999999999996, 8.158999999999997, 10.66))
# Change the extracted model
sites_cart = unique_mam.model().get_sites_cart()
sites_cart[0] = (1, 1, 1)
unique_mam.model().get_hierarchy().atoms().set_xyz(sites_cart)
# Note; setting xyz in hierarchy does not set xrs by itself. do that now:
unique_mam.model().set_sites_cart_from_hierarchy(multiply_ncs=False)
# Make sure we really changed it
assert approx_equal(unique_mam.model().get_sites_cart()[0], (1, 1, 1))
# Now propagate all the changes in this unique part to entire original model
# using NCS
ncs_mam.propagate_model_from_other(other=unique_mam,
model_id='model',
other_model_id='model')
# ...and check that copy 1 and copy 2 both change
assert approx_equal(
ncs_mam.model().get_sites_cart()[0],
(5.820083333333333, -4.020400000000001, -4.445440000000001))
assert approx_equal(
ncs_mam.model().get_sites_cart()[42],
(38.41904613024224, 17.233251085893276, 2.5547442135142524))
# Find ncs from map or model
nn = ncs_mam_copy
nn.write_map('ncs.ccp4')
nn.write_model('ncs.pdb')
ncs_object = nn.get_ncs_from_model()
dm.write_ncs_spec_file(ncs_object, 'ncs.ncs_spec')
print("NCS from map", ncs_object)
nn.set_ncs_object(ncs_object)
print("NCS now: ", nn.ncs_object())
nn.get_ncs_from_map(ncs_object=ncs_object)
print("ncs cc:", nn.ncs_cc())
assert approx_equal(nn.ncs_cc(), 0.961915979834, eps=0.01)
# Make a deep_copy
dc = mam.deep_copy()
new_mam = mam.deep_copy()
assert mam.map_manager().map_data()[0] == new_mam.map_manager().map_data(
)[0]
# Make a customized_copy
new_mam = mam.customized_copy(model_dict={'model': mam.model()})
assert new_mam.model() is mam.model()
assert not new_mam.map_dict() is mam.map_dict()
new_mam = mam.customized_copy(model_dict={'model': mam.model()},
map_dict=mam.map_dict())
assert new_mam.model() is mam.model()
assert new_mam.map_dict() is mam.map_dict()
print(mam)
# Add a map
mam = dc.deep_copy()
print(mam.map_id_list())
assert len(mam.map_id_list()) == 6
mam.add_map_manager_by_id(mam.map_manager().deep_copy(), 'new_map_manager')
print(mam.map_id_list())
assert len(mam.map_id_list()) == 7
# duplicate a map
mam = dc.deep_copy()
print(mam.map_id_list())
assert len(mam.map_id_list()) == 6
mam.duplicate_map_manager('map_manager', 'new_map_manager')
print(mam.map_id_list())
assert len(mam.map_id_list()) == 7
# resolution_filter a map
mam = dc.deep_copy()
print(mam.map_id_list())
mam.duplicate_map_manager('map_manager', 'new_map_manager')
mam.resolution_filter(map_id='new_map_manager', d_min=3.5, d_max=6)
# Add a model
mam = dc.deep_copy()
print(mam.model_id_list())
assert len(mam.model_id_list()) == 1
mam.add_model_by_id(mam.model().deep_copy(), 'new_model')
print(mam.model_id_list())
assert len(mam.model_id_list()) == 2
# Initialize a map
mam1 = new_mam.deep_copy()
mam1.initialize_maps(map_value=6)
assert mam1.map_manager().map_data()[225] == 6
# Create mask around density and apply to all maps
mam1 = new_mam.deep_copy()
mam1.mask_all_maps_around_density(
solvent_content=0.5,
soft_mask=True,
)
s = (mam1.get_map_manager_by_id('mask').map_data() > 0.5)
assert approx_equal((s.count(True), s.size()), (1024, 2048))
# Create mask around edges and apply to all maps
mam1 = new_mam.deep_copy()
mam1.mask_all_maps_around_edges()
s = (mam1.get_map_manager_by_id('mask').map_data() > 0.5)
assert approx_equal((s.count(True), s.size()), (1176, 2048))
# Create a soft mask around model and apply to all maps
new_mam.mask_all_maps_around_atoms(mask_atoms_atom_radius=8,
soft_mask=True)
s = (new_mam.get_map_manager_by_id('mask').map_data() > 0.5)
assert approx_equal((s.count(True), s.size()), (1944, 2048))
# Create a soft mask around model and do not do anything with it
new_mam.create_mask_around_atoms(mask_atoms_atom_radius=8, soft_mask=True)
s = (new_mam.get_map_manager_by_id('mask').map_data() > 0.5)
assert approx_equal((s.count(True), s.size()), (1944, 2048))
# Create a soft mask around model and do not do anything with it, wrapping =true
dummy_mam = new_mam.deep_copy()
dummy_mam.map_manager().set_wrapping(True)
dummy_mam.create_mask_around_atoms(mask_atoms_atom_radius=8,
soft_mask=True)
s = (dummy_mam.get_map_manager_by_id('mask').map_data() > 0.5)
assert approx_equal((s.count(True), s.size()), (1944, 2048))
# Create a sharp mask around model and do not do anything with it
new_mam.create_mask_around_atoms(soft_mask=False, mask_atoms_atom_radius=8)
s = (new_mam.get_map_manager_by_id('mask').map_data() > 0.5)
assert approx_equal((s.count(True), s.size()), (138, 2048))
# Mask around edges and do not do anything with it
mam = dc.deep_copy()
mam.create_mask_around_edges()
s = (mam.get_map_manager_by_id('mask').map_data() > 0.5)
assert approx_equal((s.count(True), s.size()), (1176, 2048))
# Mask around density and to not do anything with it
mam = dc.deep_copy()
mam.create_mask_around_density(soft_mask=False)
s = (mam.get_map_manager_by_id('mask').map_data() > 0.5)
assert approx_equal((s.count(True), s.size()), (1000, 2048))
# Apply the current mask to one map
mam.apply_mask_to_map('map_manager')
s = (mam.map_manager().map_data() > 0.)
assert approx_equal((s.count(True), s.size()), (640, 2048))
s = (mam.map_manager().map_data() != 0.)
assert approx_equal((s.count(True), s.size()), (1000, 2048))
assert approx_equal((mam.map_manager().map_data()[225]), -0.0418027862906)
# Apply any mask to one map
mam.apply_mask_to_map('map_manager', mask_id='mask')
s = (mam.map_manager().map_data() > 0.)
assert approx_equal((s.count(True), s.size()), (640, 2048))
s = (mam.map_manager().map_data() != 0.)
assert approx_equal((s.count(True), s.size()), (1000, 2048))
assert approx_equal((mam.map_manager().map_data()[225]), -0.0418027862906)
# Apply the mask to all maps
mam.apply_mask_to_maps()
s = (mam.map_manager().map_data() > 0.)
assert approx_equal((s.count(True), s.size()), (640, 2048))
s = (mam.map_manager().map_data() != 0.)
assert approx_equal((s.count(True), s.size()), (1000, 2048))
assert approx_equal((mam.map_manager().map_data()[225]), -0.0418027862906)
# Apply the mask to all maps, setting outside value to mean inside
mam.apply_mask_to_maps(set_outside_to_mean_inside=True)
s = (mam.map_manager().map_data() > 0.)
assert approx_equal((s.count(True), s.size()), (1688, 2048))
s = (mam.map_manager().map_data() != 0.)
assert approx_equal((s.count(True), s.size()), (2048, 2048))
assert approx_equal((mam.map_manager().map_data()[2047]), -0.0759598612785)
s = (mam.get_map_manager_by_id('mask').map_data() > 0).as_1d()
inside = mam.map_manager().map_data().as_1d().select(s)
outside = mam.map_manager().map_data().as_1d().select(~s)
assert approx_equal(
(inside.min_max_mean().max, outside.min_max_mean().max),
(0.335603952408, 0.0239064293122))
# Make a new map and model, get mam and box with selection
mmm = map_model_manager()
mmm.generate_map(box_cushion=0, wrapping=True)
mam = mmm
mam_dc = mam.deep_copy()
new_mm_1 = mam.map_manager()
assert approx_equal((mmm.map_data().all(), new_mm_1.map_data().all()),
((18, 25, 20), (18, 25, 20)))
# Get local fsc or randomized map
dc = mam_dc.deep_copy()
dc.map_manager().set_wrapping(False)
map_coeffs = dc.map_manager().map_as_fourier_coefficients(d_min=3)
from cctbx.development.create_models_or_maps import generate_map
new_mm_1 = generate_map(map_coeffs=map_coeffs,
d_min=3,
low_resolution_real_space_noise_fraction=1,
high_resolution_real_space_noise_fraction=50,
map_manager=dc.map_manager(),
random_seed=124321)
new_mm_2 = generate_map(map_coeffs=map_coeffs,
d_min=3,
low_resolution_real_space_noise_fraction=1,
high_resolution_real_space_noise_fraction=50,
map_manager=dc.map_manager(),
random_seed=734119)
dc.add_map_manager_by_id(new_mm_1, 'map_manager_1')
dc.add_map_manager_by_id(new_mm_2, 'map_manager_2')
cc = dc.map_map_cc()
fsc_curve = dc.map_map_fsc()
dc.set_log(sys.stdout)
dc.local_fsc(n_boxes=1)
# Get map-map FSC
dc = mam_dc.deep_copy()
dc.duplicate_map_manager(map_id='map_manager', new_map_id='filtered')
dc.resolution_filter(d_min=3.5, d_max=10, map_id='filtered')
dc.create_mask_around_atoms()
fsc_curve = dc.map_map_fsc(map_id_1='map_manager',
map_id_2='filtered',
mask_id='mask',
resolution=3.5,
fsc_cutoff=0.97)
assert approx_equal(fsc_curve.d_min, 3.91175024213, eps=0.01)
assert approx_equal(fsc_curve.fsc.fsc[-1], 0.695137718033)
# Get map-map CC
dc = mam_dc.deep_copy()
dc.duplicate_map_manager(map_id='map_manager', new_map_id='filtered')
dc.resolution_filter(d_min=3.5, d_max=6, map_id='filtered')
cc = dc.map_map_cc('map_manager', 'filtered')
assert approx_equal(cc, 0.706499206126)
# Get map-map CC with mask
dc = mam_dc.deep_copy()
dc.duplicate_map_manager(map_id='map_manager', new_map_id='filtered')
dc.create_mask_around_density(mask_id='filtered')
cc = dc.map_map_cc('map_manager', 'filtered', mask_id='mask')
assert approx_equal(cc, 0.411247493741)
# box around model
mam = mam_dc.deep_copy()
mam.box_all_maps_around_model_and_shift_origin(
selection_string="resseq 221:221")
new_mm_1 = mam.map_manager()
assert approx_equal((mmm.map_data().all(), new_mm_1.map_data().all()),
((18, 25, 20), (24, 20, 20)))
# extract_around_model (get new mam)
new_mam_dc = mam_dc.extract_all_maps_around_model(
selection_string="resseq 221:221")
new_mm_1a = new_mam_dc.map_manager()
assert approx_equal((mmm.map_data().all(), new_mm_1a.map_data().all()),
((18, 25, 20), (24, 20, 20)))
assert approx_equal(new_mm_1.map_data(), new_mm_1a.map_data())
# box around_density
mam2 = mam_dc.deep_copy()
mam2.box_all_maps_around_density_and_shift_origin(box_cushion=0)
new_mm_2 = mam2.map_manager()
assert approx_equal((mmm.map_data().all(), new_mm_2.map_data().all()),
((18, 25, 20), (16, 23, 18)))
# extract_around_density (get new mam)
mam2 = mam_dc.deep_copy()
mam2_b = mam2.extract_all_maps_around_density(box_cushion=0)
new_mm_2 = mam2_b.map_manager()
assert approx_equal((mmm.map_data().all(), new_mm_2.map_data().all()),
((18, 25, 20), (16, 23, 18)))
# Repeat as map_model_manager:
mmm = mam_dc.as_map_model_manager().deep_copy()
mmm.box_all_maps_around_model_and_shift_origin(
selection_string="resseq 221:221")
new_mm_1a = mmm.map_manager()
assert approx_equal((mmm.map_data().all(), new_mm_1a.map_data().all()),
((24, 20, 20), (24, 20, 20)))
assert approx_equal(new_mm_1.map_data(), new_mm_1a.map_data())
# box around density
mam.box_all_maps_around_density_and_shift_origin(box_cushion=0)
new_mm_1 = mam.map_manager()
assert approx_equal((mmm.map_data().all(), new_mm_1.map_data().all()),
((24, 20, 20), (22, 18, 18)))
# extract around density (get new mam)
mam1 = mam_dc.deep_copy()
mam1.extract_all_maps_around_density(box_cushion=0)
new_mm_1 = mam1.map_manager()
assert approx_equal((mmm.map_data().all(), new_mm_1.map_data().all()),
((24, 20, 20), (18, 25, 20)))
# create mask around density, then box around mask (i.e., box around density)
mam.create_mask_around_density(soft_mask=False)
mam.box_all_maps_around_mask_and_shift_origin(box_cushion=3)
new_mm_1 = mam.map_manager()
assert approx_equal((mmm.map_data().all(), new_mm_1.map_data().all()),
((24, 20, 20), (22, 18, 18)))
# box with bounds
mam.box_all_maps_with_bounds_and_shift_origin(lower_bounds=(10, 10, 10),
upper_bounds=(15, 15, 15))
new_mm_1 = mam.map_manager()
assert approx_equal((mmm.map_data().all(), new_mm_1.map_data().all()),
((24, 20, 20), (6, 6, 6)))
# extract with bounds
mam = mam_dc.deep_copy()
mam_1 = mam.extract_all_maps_with_bounds(lower_bounds=(10, 10, 10),
upper_bounds=(15, 15, 15))
new_mm_1 = mam_1.map_manager()
assert approx_equal((mmm.map_data().all(), new_mm_1.map_data().all()),
((24, 20, 20), (6, 6, 6)))
# box with unique
mam = mam_dc.deep_copy()
mam.box_all_maps_around_unique_and_shift_origin(molecular_mass=2500,
resolution=3)
new_mm_1 = mam.map_manager()
assert approx_equal((mmm.map_data().all(), new_mm_1.map_data().all()),
((24, 20, 20), (18, 25, 20)))
# extract with unique
mam = mam_dc.deep_copy()
mam_1 = mam.extract_all_maps_around_unique(molecular_mass=2500,
resolution=3)
new_mm_1 = mam_1.map_manager()
assert approx_equal((mmm.map_data().all(), new_mm_1.map_data().all()),
((24, 20, 20), (18, 25, 20)))
# extract a box and then restore model into same reference as current mam
mam = mam_dc.deep_copy()
mam.box_all_maps_with_bounds_and_shift_origin(lower_bounds=(2, 2, 2),
upper_bounds=(17, 17, 17))
print("mam:",
mam.model().get_sites_cart()[0],
mam.map_manager().origin_is_zero())
# extract a box
box_mam = mam.extract_all_maps_with_bounds(lower_bounds=(10, 10, 10),
upper_bounds=(15, 15, 15))
box_model = box_mam.model()
matched_box_model = mam.get_model_from_other(box_mam)
assert approx_equal(matched_box_model.get_sites_cart()[0],
mam.model().get_sites_cart()[0])
# Convert a map to fourier coefficients
mam = mam_dc.deep_copy()
ma = mam.map_as_fourier_coefficients(d_min=3)
assert approx_equal(ma.d_min(), 3.01655042414)
mam.add_map_from_fourier_coefficients(ma, map_id='new_map_manager')
cc = flex.linear_correlation(
mam.get_map_manager_by_id('map_manager').map_data().as_1d(),
mam.get_map_manager_by_id(
'new_map_manager').map_data().as_1d()).coefficient()
assert (cc >= 0.99)
# Get map-model CC
dc = mam_dc.extract_all_maps_around_model(
selection_string="(name ca or name cb or name c or name o) " +
"and resseq 221:221",
box_cushion=0)
cc = dc.map_model_cc(resolution=3)
assert approx_equal(cc, 0.450025539936)
# Remove model outside map
dc.remove_model_outside_map(boundary=0)
assert (mam_dc.model().get_sites_cart().size(),
dc.model().get_sites_cart().size()) == (86, 4)
# shift a model to match the map
dc = mam_dc.extract_all_maps_around_model(
selection_string="(name ca or name cb or name c or name o) " +
"and resseq 221:221",
box_cushion=0)
actual_model = dc.model().deep_copy()
working_model = dc.model().deep_copy()
working_model.set_shift_cart((0, 0, 0))
working_model.set_sites_cart(working_model.get_sites_cart() -
actual_model.shift_cart())
dc.shift_any_model_to_match(working_model)
assert approx_equal(actual_model.get_sites_cart()[0],
working_model.get_sites_cart()[0])
selection = pdb_hierarchy.atom_selection_cache().selection(
string=params.selection)
if selection.size():
print_statistics.make_sub_header("atom selection", out=log)
print >> log, "Selection string: selection='%s'" % params.selection
print >> log, \
" selects %d atoms from total %d atoms."%(selection.count(True),
selection.size())
sites_cart_all = xray_structure.sites_cart()
sites_cart = sites_cart_all.select(selection)
selection = xray_structure.selection_within(radius=params.selection_radius,
selection=selection)
if not ncs_object:
from mmtbx.ncs.ncs import ncs
ncs_object = ncs()
if params.symmetry_file:
ncs_object.read_ncs(params.symmetry_file, log=log)
print >> log, "Total of %s operators read" % (
ncs_object.max_operators())
if not ncs_object or ncs_object.max_operators() < 1:
print >> log, "No symmetry available"
if ncs_object:
n_ops = max(1, ncs_object.max_operators())
else:
n_ops = 1
# Get sequence if extract_unique is set
sequence = None
if params.extract_unique:
if params.sequence_file:
def run(args, crystal_symmetry=None,
ncs_object=None,
pdb_hierarchy=None,
map_data=None,
mask_data=None,
half_map_data_list=None,
half_map_labels_list=None,
lower_bounds=None,
upper_bounds=None,
write_output_files=True,
log=None):
h = "phenix.map_box: extract box with model and map around selected atoms"
if(log is None): log = sys.stdout
print_statistics.make_header(h, out=log)
default_message="""\
%s.
Usage:
phenix.map_box model.pdb map_coefficients.mtz selection="chain A and resseq 1:10"
or
phenix.map_box map.ccp4 density_select=True
Parameters:"""%h
if(len(args) == 0 and not pdb_hierarchy):
print(default_message)
master_phil.show(prefix=" ")
return
# Process inputs ignoring symmetry conflicts just to get the value of
# ignore_symmetry_conflicts...
inputs = mmtbx.utils.process_command_line_args(args = args,
cmd_cs=crystal_symmetry,
master_params = master_phil,
suppress_symmetry_related_errors=True)
params = inputs.params.extract()
# Now process inputs for real and write a nice error message if necessary.
try:
inputs = mmtbx.utils.process_command_line_args(args = args,
cmd_cs=crystal_symmetry,
master_params = master_phil,
suppress_symmetry_related_errors=params.ignore_symmetry_conflicts)
except Exception as e:
if str(e).find("symmetry mismatch ")>1:
raise Sorry(str(e)+"\nTry 'ignore_symmetry_conflicts=True'")
else:
raise e
params = inputs.params.extract()
master_phil.format(python_object=params).show(out=log)
# Overwrite params with parameters in call if available
if lower_bounds:
params.lower_bounds=lower_bounds
if upper_bounds:
params.upper_bounds=upper_bounds
# PDB file
if params.pdb_file and not inputs.pdb_file_names and not pdb_hierarchy:
inputs.pdb_file_names=[params.pdb_file]
if(len(inputs.pdb_file_names)!=1 and not params.density_select and not
params.mask_select and not
pdb_hierarchy and not params.keep_map_size and not params.upper_bounds
and not params.extract_unique and not params.bounds_match_this_file):
raise Sorry("PDB file is needed unless extract_unique, "+
"density_select, mask_select, keep_map_size \nor bounds are set .")
if (len(inputs.pdb_file_names)!=1 and not pdb_hierarchy and \
(params.mask_atoms )):
raise Sorry("PDB file is needed for mask_atoms")
if params.soft_mask and (not params.resolution) and \
(len(inputs.pdb_file_names)!=1 and not pdb_hierarchy):
raise Sorry("Need resolution for soft_mask without PDB file")
if ((params.density_select or params.mask_select) and params.keep_map_size):
raise Sorry("Cannot set both density_select/mask_select and keep_map_size")
if ((params.density_select or params.mask_select) and params.upper_bounds):
raise Sorry("Cannot set both density_select/mask_select and bounds")
if (params.keep_map_size and params.upper_bounds):
raise Sorry("Cannot set both keep_map_size and bounds")
if (params.upper_bounds and not params.lower_bounds):
raise Sorry("Please set lower_bounds if you set upper_bounds")
if (params.extract_unique):
if (not params.resolution):
raise Sorry("Please set resolution for extract_unique")
if (not params.symmetry) and (not params.symmetry_file) and \
(not ncs_object):
raise Sorry(
"Please supply a symmetry file or symmetry for extract_unique (you "+
"\ncan try symmetry=ALL if you do not know your symmetry or "+
"symmetry=C1 if \nthere is none)")
from mmtbx.ncs.ncs import ncs
ncs_object=ncs()
ncs_object.set_unit_ncs()
if params.keep_input_unit_cell_and_grid and (
(params.output_unit_cell_grid is not None ) or
(params.output_unit_cell is not None ) ):
raise Sorry("If you set keep_input_unit_cell_and_grid then you cannot "+\
"set \noutput_unit_cell_grid or output_unit_cell")
if (write_output_files) and ("mtz" in params.output_format) and (
(params.keep_origin) and (not params.keep_map_size)):
print("\nNOTE: Skipping write of mtz file as keep_origin=True and \n"+\
"keep_map_size is False\n")
params.output_format=remove_element(params.output_format,element='mtz')
if (write_output_files) and ("mtz" in params.output_format) and (
(params.extract_unique)):
print("\nNOTE: Skipping write of mtz file as extract_unique=True\n")
params.output_format=remove_element(params.output_format,element='mtz')
if params.output_origin_match_this_file or params.bounds_match_this_file:
if params.output_origin_match_this_file:
fn=params.output_origin_match_this_file
if params.bounds_match_this_file:
raise Sorry("Cannot match origin and bounds at same time")
else:
fn=params.bounds_match_this_file
if not params.ccp4_map_file:
raise Sorry(
"Need to specify your input file with ccp4_map_file=xxx if you use "+
"output_origin_match_this_file=xxxx or bounds_match_this_file=xxxx")
af = any_file(fn)
if (af.file_type == 'ccp4_map'):
origin=af.file_content.data.origin()
if params.output_origin_match_this_file:
params.output_origin_grid_units=origin
print("Origin of (%s,%s,%s) taken from %s" %(
origin[0],origin[1],origin[2],fn))
else:
all=af.file_content.data.all()
params.lower_bounds=origin
print("Lower bounds of (%s,%s,%s) taken from %s" %(
params.lower_bounds[0],params.lower_bounds[1],
params.lower_bounds[2],fn))
params.upper_bounds=list(col(origin)+col(all)-col((1,1,1)))
print("upper bounds of (%s,%s,%s) taken from %s" %(
params.upper_bounds[0],params.upper_bounds[1],
params.upper_bounds[2],fn))
params.bounds_are_absolute=True
else:
raise Sorry("Unable to interpret %s as map file" %(fn))
if params.output_origin_grid_units is not None and params.keep_origin:
params.keep_origin=False
print("Setting keep_origin=False as output_origin_grid_units is set")
print_statistics.make_sub_header("pdb model", out=log)
if len(inputs.pdb_file_names)>0:
pdb_inp = iotbx.pdb.input(file_name=inputs.pdb_file_names[0])
pdb_hierarchy = pdb_inp.construct_hierarchy()
if pdb_hierarchy:
pdb_atoms = pdb_hierarchy.atoms()
pdb_atoms.reset_i_seq()
else:
pdb_hierarchy=None
# Map or map coefficients
map_coeff = None
input_unit_cell_grid=None
input_unit_cell=None
input_map_labels=None
if (not map_data):
# read first mtz file
if ( (len(inputs.reflection_file_names) > 0) or
(params.map_coefficients_file is not None) ):
# file in phil takes precedent
if (params.map_coefficients_file is not None):
if (len(inputs.reflection_file_names) == 0):
inputs.reflection_file_names.append(params.map_coefficients_file)
else:
inputs.reflection_file_names[0] = params.map_coefficients_file
map_coeff = reflection_file_utils.extract_miller_array_from_file(
file_name = inputs.reflection_file_names[0],
label = params.label,
type = "complex",
log = log)
if not crystal_symmetry: crystal_symmetry=map_coeff.crystal_symmetry()
fft_map = map_coeff.fft_map(resolution_factor=params.resolution_factor)
fft_map.apply_sigma_scaling()
map_data = fft_map.real_map_unpadded()
map_or_map_coeffs_prefix=os.path.basename(
inputs.reflection_file_names[0][:-4])
# or read CCP4 map
elif ( (inputs.ccp4_map is not None) or
(params.ccp4_map_file is not None) ):
if (params.ccp4_map_file is not None):
af = any_file(params.ccp4_map_file)
if (af.file_type == 'ccp4_map'):
inputs.ccp4_map = af.file_content
inputs.ccp4_map_file_name = params.ccp4_map_file
print_statistics.make_sub_header("CCP4 map", out=log)
ccp4_map = inputs.ccp4_map
ccp4_map.show_summary(prefix=" ",out=log)
if not crystal_symmetry: crystal_symmetry=ccp4_map.crystal_symmetry()
map_data = ccp4_map.data #map_data()
input_unit_cell_grid=ccp4_map.unit_cell_grid
input_unit_cell=ccp4_map.unit_cell_parameters
input_map_labels=ccp4_map.get_labels()
if inputs.ccp4_map_file_name.endswith(".ccp4"):
map_or_map_coeffs_prefix=os.path.basename(
inputs.ccp4_map_file_name[:-5])
else:
map_or_map_coeffs_prefix=os.path.basename(
inputs.ccp4_map_file_name[:-4])
else: # have map_data
map_or_map_coeffs_prefix=None
if params.half_map_list and (not half_map_data_list):
if not params.extract_unique:
raise Sorry("Can only use half_map_with extract_unique")
print ("Reading half-maps",params.half_map_list)
half_map_data_list=[]
half_map_labels_list=[]
for fn in params.half_map_list:
print("Reading half map from %s" %(fn),file=log)
af = any_file(fn)
print_statistics.make_sub_header("CCP4 map", out=log)
h_ccp4_map = af.file_content
h_ccp4_map.show_summary(prefix=" ",out=log)
h_map_data = h_ccp4_map.data
half_map_data_list.append(h_map_data)
half_map_labels_list.append(h_ccp4_map.get_labels())
if params.map_scale_factor:
print("Applying scale factor of %s to map data on read-in" %(
params.map_scale_factor))
map_data=map_data*params.map_scale_factor
if params.output_origin_grid_units is not None:
origin_to_match=tuple(params.output_origin_grid_units)
else:
origin_to_match=None
if origin_to_match:
sc=[]
for x,o,a in zip(crystal_symmetry.unit_cell().parameters()[:3],
origin_to_match,
map_data.all()):
sc.append(-x*o/a)
shift_cart_for_origin_to_match=tuple(sc)
else:
origin_to_match=None
shift_cart_for_origin_to_match=None
if crystal_symmetry and not inputs.crystal_symmetry:
inputs.crystal_symmetry=crystal_symmetry
# final check that map_data exists
if(map_data is None):
raise Sorry("Map or map coefficients file is needed.")
if len(inputs.pdb_file_names)>0:
output_prefix=os.path.basename(inputs.pdb_file_names[0])[:-4]
else:
output_prefix=map_or_map_coeffs_prefix
if not pdb_hierarchy: # get an empty hierarchy
from cctbx.array_family import flex
pdb_hierarchy=iotbx.pdb.input(
source_info='',lines=flex.split_lines('')).construct_hierarchy()
xray_structure = pdb_hierarchy.extract_xray_structure(
crystal_symmetry=inputs.crystal_symmetry)
xray_structure.show_summary(f=log)
#
if not params.selection: params.selection="all"
selection = pdb_hierarchy.atom_selection_cache().selection(
string = params.selection)
if selection.size():
print_statistics.make_sub_header("atom selection", out=log)
print("Selection string: selection='%s'"%params.selection, file=log)
print(" selects %d atoms from total %d atoms."%(selection.count(True),
selection.size()), file=log)
sites_cart_all = xray_structure.sites_cart()
sites_cart = sites_cart_all.select(selection)
selection = xray_structure.selection_within(
radius = params.selection_radius,
selection = selection)
if not ncs_object:
from mmtbx.ncs.ncs import ncs
ncs_object=ncs()
if params.symmetry_file:
ncs_object.read_ncs(params.symmetry_file,log=log)
print("Total of %s operators read" %(ncs_object.max_operators()), file=log)
if not ncs_object or ncs_object.max_operators()<1:
print("No symmetry available", file=log)
if ncs_object:
n_ops=max(1,ncs_object.max_operators())
else:
n_ops=1
# Get sequence if extract_unique is set
sequence=None
if params.extract_unique or params.mask_select:
if params.sequence_file:
if n_ops > 1: # get unique part of sequence
remove_duplicates=True
else:
remove_duplicates=False
from iotbx.bioinformatics import get_sequences
sequence=(" ".join(get_sequences(file_name=params.sequence_file,
remove_duplicates=remove_duplicates)))
if params.chain_type in ['None',None]: params.chain_type=None
if sequence and not params.molecular_mass:
# get molecular mass from sequence
from iotbx.bioinformatics import text_from_chains_matching_chain_type
if params.chain_type in [None,'PROTEIN']:
n_protein=len(text_from_chains_matching_chain_type(
text=sequence,chain_type='PROTEIN'))
else:
n_protein=0
if params.chain_type in [None,'RNA']:
n_rna=len(text_from_chains_matching_chain_type(
text=sequence,chain_type='RNA'))
else:
n_rna=0
if params.chain_type in [None,'DNA']:
n_dna=len(text_from_chains_matching_chain_type(
text=sequence,chain_type='DNA'))
else:
n_dna=0
params.molecular_mass=n_ops*(n_protein*110+(n_rna+n_dna)*330)
print("\nEstimate of molecular mass is %.0f " %(params.molecular_mass), file=log)
if params.density_select or params.mask_select:
print_statistics.make_sub_header(
"Extracting box around selected density and writing output files", out=log)
else:
print_statistics.make_sub_header(
"Extracting box around selected atoms and writing output files", out=log)
#
if params.value_outside_atoms=='mean':
print("\nValue outside atoms mask will be set to mean inside mask", file=log)
if params.get_half_height_width and params.density_select:
print("\nHalf width at half height will be used to id boundaries", file=log)
if params.soft_mask and sites_cart_all.size()>0:
print("\nSoft mask will be applied to model-based mask", file=log)
elif params.soft_mask:
print ("\nSoft mask will be applied to outside of map box",file=log)
if params.keep_map_size:
print("\nEntire map will be kept (not cutting out region)", file=log)
if params.restrict_map_size:
print("\nOutput map will be within input map", file=log)
if params.lower_bounds and params.upper_bounds:
print("Bounds for cut out map are (%s,%s,%s) to (%s,%s,%s)" %(
tuple(list(params.lower_bounds)+list(params.upper_bounds))), file=log)
if mask_data:
mask_data=mask_data.as_double()
box = mmtbx.utils.extract_box_around_model_and_map(
xray_structure = xray_structure,
map_data = map_data.as_double(),
mask_data = mask_data,
box_cushion = params.box_cushion,
selection = selection,
mask_select = params.mask_select,
density_select = params.density_select,
threshold = params.density_select_threshold,
get_half_height_width = params.get_half_height_width,
mask_atoms = params.mask_atoms,
soft_mask = params.soft_mask,
soft_mask_radius = params.soft_mask_radius,
mask_atoms_atom_radius = params.mask_atoms_atom_radius,
value_outside_atoms = params.value_outside_atoms,
keep_map_size = params.keep_map_size,
restrict_map_size = params.restrict_map_size,
lower_bounds = params.lower_bounds,
upper_bounds = params.upper_bounds,
bounds_are_absolute = params.bounds_are_absolute,
zero_outside_original_map = params.zero_outside_original_map,
extract_unique = params.extract_unique,
target_ncs_au_file = params.target_ncs_au_file,
regions_to_keep = params.regions_to_keep,
box_buffer = params.box_buffer,
soft_mask_extract_unique = params.soft_mask_extract_unique,
mask_expand_ratio = params.mask_expand_ratio,
keep_low_density = params.keep_low_density,
chain_type = params.chain_type,
sequence = sequence,
solvent_content = params.solvent_content,
molecular_mass = params.molecular_mass,
resolution = params.resolution,
ncs_object = ncs_object,
symmetry = params.symmetry,
half_map_data_list = half_map_data_list,
)
ph_box = pdb_hierarchy.select(selection)
ph_box.adopt_xray_structure(box.xray_structure_box)
box.hierarchy=ph_box
if params.mask_select:
print("\nSolvent content used in mask_select: %.3f " %(
box.get_solvent_content()),file=log)
if (inputs and
inputs.crystal_symmetry and inputs.ccp4_map and
inputs.crystal_symmetry.unit_cell().parameters() and
inputs.ccp4_map.unit_cell_parameters ) and (
inputs.crystal_symmetry.unit_cell().parameters() !=
inputs.ccp4_map.unit_cell_parameters):
print("\nNOTE: Input CCP4 map is only part of unit cell:", file=log)
print("Full unit cell ('unit cell parameters'): "+\
"(%.1f, %.1f, %.1f, %.1f, %.1f, %.1f) A" %tuple(
inputs.ccp4_map.unit_cell_parameters), file=log)
print("Size of CCP4 map 'map unit cell': "+\
"(%.1f, %.1f, %.1f, %.1f, %.1f, %.1f) A" %tuple(
inputs.crystal_symmetry.unit_cell().parameters()), file=log)
print("Full unit cell as grid units: (%s, %s, %s)" %(
inputs.ccp4_map.unit_cell_grid), file=log)
print("Map unit cell as grid units: (%s, %s, %s)" %(
map_data.all()), file=log)
box.unit_cell_parameters_from_ccp4_map=inputs.ccp4_map.unit_cell_parameters
box.unit_cell_parameters_deduced_from_map_grid=\
inputs.crystal_symmetry.unit_cell().parameters()
else:
box.unit_cell_parameters_from_ccp4_map=None
box.unit_cell_parameters_deduced_from_map_grid=None
if box.pdb_outside_box_msg:
print(box.pdb_outside_box_msg, file=log)
# NOTE: box object is always shifted to place origin at (0,0,0)
# NOTE ON ORIGIN SHIFTS: The shifts are applied locally here. The box
# object is not affected and always has the origin at (0,0,0)
# output_box is copy of box with shift_cart corresponding to the output
# files. Normally this is the same as the original shift_cart. However
# if user has specified a new output origin it will differ.
# For output files ONLY:
# keep_origin==False leave origin at (0,0,0)
# keep_origin==True: we shift everything back to where it was,
# output_origin_grid_units=10,10,10: output origin is at (10,10,10)
# ncs_object is original
# box.ncs_object is shifted by shift_cart
# output_box.ncs_object is shifted back by -new shift_cart
# Additional note on output unit_cell and grid_units.
# The ccp4-style output map can specify the unit cell and grid units
# corresponding to that cell. This can be separate from the origin and
# number of grid points in the map as written. If specified, write these
# out to the output ccp4 map and also use this unit cell for writing
# any output PDB files
from copy import deepcopy
output_box=deepcopy(box) # won't use box below here except to return it
print("\nBox cell dimensions: (%.2f, %.2f, %.2f) A" %(
box.box_crystal_symmetry.unit_cell().parameters()[:3]), file=log)
if box.shift_cart:
print("Working origin moved from grid position of"+\
": (%d, %d, %d) to (0,0,0) " %(
tuple(box.origin_shift_grid_units(reverse=True))), file=log)
print("Working origin moved from coordinates of:"+\
" (%.2f, %.2f, %.2f) A to (0,0,0)\n" %(
tuple(-col(box.shift_cart))), file=log)
if (params.keep_origin):
print("\nRestoring original position for output files", file=log)
print("Origin will be at grid position of"+\
": (%d, %d, %d) " %(
tuple(box.origin_shift_grid_units(reverse=True))), file=log)
print("\nOutput files will be in same location as original", end=' ', file=log)
if not params.keep_map_size:
print("just cut out.", file=log)
else:
print("keeping entire map", file=log)
print("Note that output maps are only valid in the cut out region.\n", file=log)
else:
if origin_to_match:
output_box.shift_cart=shift_cart_for_origin_to_match
if params.output_origin_grid_units:
print("Output map origin to be shifted to match target", file=log)
print("Placing origin at grid point (%s, %s, %s)" %(
origin_to_match)+"\n"+ \
"Final coordinate shift for output files: (%.2f,%.2f,%.2f) A\n" %(
tuple(col(output_box.shift_cart)-col(box.shift_cart))), file=log)
elif box.shift_cart:
output_box.shift_cart=(0,0,0) # not shifting back
print("Final origin will be at (0,0,0)", file=log)
print("Final coordinate shift for output files: (%.2f,%.2f,%.2f) A\n" %(
tuple(col(output_box.shift_cart)-col(box.shift_cart))), file=log)
else:
print("\nOutput files are in same location as original and origin "+\
"is at (0,0,0)\n", file=log)
print("\nBox grid: (%s, %s, %s) " %(output_box.map_box.all()),file=log)
ph_output_box_output_location = ph_box.deep_copy()
if output_box.shift_cart: # shift coordinates and NCS back by shift_cart
# NOTE output_box.shift_cart could be different than box.shift_cart if
# there is a target position for the origin and it is not the same as the
# original origin.
sites_cart = output_box.shift_sites_cart_back(
output_box.xray_structure_box.sites_cart())
xrs_offset = ph_output_box_output_location.extract_xray_structure(
crystal_symmetry=output_box.xray_structure_box.crystal_symmetry()
).replace_sites_cart(new_sites = sites_cart)
ph_output_box_output_location.adopt_xray_structure(xrs_offset)
if output_box.ncs_object:
output_box.ncs_object=output_box.ncs_object.coordinate_offset(
tuple(-col(output_box.shift_cart)))
shift_back=True
else:
shift_back=False
if params.keep_input_unit_cell_and_grid and \
(input_unit_cell_grid is not None) and \
(input_unit_cell is not None):
params.output_unit_cell=input_unit_cell
params.output_unit_cell_grid=input_unit_cell_grid
print("Setting output unit cell parameters and unit cell grid to"+\
" match\ninput map file", file=log)
if params.output_unit_cell: # Set output unit cell parameters
from cctbx import crystal
output_crystal_symmetry=crystal.symmetry(
unit_cell=params.output_unit_cell, space_group="P1")
output_unit_cell=output_crystal_symmetry.unit_cell()
print("Output unit cell set to: %.2f, %.2f, %.2f, %.2f, %.2f, %.2f)" %tuple(
output_crystal_symmetry.unit_cell().parameters()), file=log)
else:
output_crystal_symmetry=None
# ============= Check/set output unit cell grid and cell parameters =======
if params.output_unit_cell_grid or output_crystal_symmetry:
if params.output_unit_cell_grid:
output_unit_cell_grid=params.output_unit_cell_grid
else:
output_unit_cell_grid=output_box.map_box.all()
print("Output unit cell grid set to: (%s, %s, %s)" %tuple(
output_unit_cell_grid), file=log)
expected_output_abc=[]
box_spacing=[]
output_spacing=[]
box_abc=output_box.xray_structure_box.\
crystal_symmetry().unit_cell().parameters()[:3]
if output_crystal_symmetry:
output_abc=output_crystal_symmetry.unit_cell().parameters()[:3]
else:
output_abc=[None,None,None]
for a_box,a_output,n_box,n_output in zip(
box_abc,
output_abc,
output_box.map_box.all(),
output_unit_cell_grid):
expected_output_abc.append(a_box*n_output/n_box)
box_spacing.append(a_box/n_box)
if output_crystal_symmetry:
output_spacing.append(a_output/n_output)
else:
output_spacing.append(a_box/n_box)
if output_crystal_symmetry: # make sure it is compatible...
r0=expected_output_abc[0]/output_abc[0]
r1=expected_output_abc[1]/output_abc[1]
r2=expected_output_abc[2]/output_abc[2]
from libtbx.test_utils import approx_equal
if not approx_equal(r0,r1,eps=0.001) or not approx_equal(r0,r2,eps=0.001):
print("WARNING: output_unit_cell and cell_grid will "+\
"change ratio of grid spacing.\nOld spacings: "+\
"(%.2f, %.2f, %.2f) A " %(tuple(box_spacing))+\
"\nNew spacings: (%.2f, %.2f, %.2f) A \n" %(tuple(output_spacing)), file=log)
else:
output_abc=expected_output_abc
from cctbx import crystal
output_crystal_symmetry=crystal.symmetry(
unit_cell=list(output_abc)+[90,90,90], space_group="P1")
print("Output unit cell will be: (%.2f, %.2f, %.2f, %.2f, %.2f, %.2f)\n"%(
tuple(output_crystal_symmetry.unit_cell().parameters())), file=log)
else:
output_unit_cell_grid = output_box.map_box.all()
output_crystal_symmetry=output_box.xray_structure_box.crystal_symmetry()
# ========== Done check/set output unit cell grid and cell parameters =====
if write_output_files:
# Write PDB file
if ph_box.overall_counts().n_residues>0:
if(params.output_file_name_prefix is None):
file_name = "%s_box.pdb"%output_prefix
else: file_name = "%s.pdb"%params.output_file_name_prefix
ph_output_box_output_location.write_pdb_file(file_name=file_name,
crystal_symmetry = output_crystal_symmetry)
print("Writing boxed PDB with box unit cell to %s" %(
file_name), file=log)
# Write NCS file if NCS
if output_box.ncs_object and output_box.ncs_object.max_operators()>0:
if(params.output_file_name_prefix is None):
output_symmetry_file = "%s_box.ncs_spec"%output_prefix
else:
output_symmetry_file = "%s.ncs_spec"%params.output_file_name_prefix
output_box.ncs_object.format_all_for_group_specification(
file_name=output_symmetry_file)
print("\nWriting symmetry to %s" %( output_symmetry_file), file=log)
# Write ccp4 map.
if("ccp4" in params.output_format):
if(params.output_file_name_prefix is None):
file_name = "%s_box.ccp4"%output_prefix
else: file_name = "%s.ccp4"%params.output_file_name_prefix
from iotbx.mrcfile import create_output_labels
if params.extract_unique:
program_name='map_box using extract_unique'
limitations=["extract_unique"]
else:
program_name='map_box'
limitations=[]
labels=create_output_labels(program_name=program_name,
input_file_name=inputs.ccp4_map_file_name,
input_labels=input_map_labels,
limitations=limitations,
output_labels=params.output_map_labels)
output_box.write_ccp4_map(file_name=file_name,
output_crystal_symmetry=output_crystal_symmetry,
output_mean=params.output_ccp4_map_mean,
output_sd=params.output_ccp4_map_sd,
output_unit_cell_grid=output_unit_cell_grid,
shift_back=shift_back,
output_map_labels=labels,
output_external_origin=params.output_external_origin)
print("Writing boxed map "+\
"to CCP4 formatted file: %s"%file_name, file=log)
if not params.half_map_list:
params.half_map_list=[]
if not output_box.map_box_half_map_list:
output_box.map_box_half_map_list=[]
if not half_map_labels_list:
half_map_labels_list=len(output_box.map_box_half_map_list)*[None]
for hm,labels,fn in zip(
output_box.map_box_half_map_list,
half_map_labels_list,
params.half_map_list): # half maps matching
labels=create_output_labels(program_name=program_name,
input_file_name=fn,
input_labels=labels,
limitations=limitations,
output_labels=params.output_map_labels)
hm_fn="%s_box.ccp4" %( ".".join(os.path.basename(fn).split(".")[:-1]))
output_box.write_ccp4_map(file_name=hm_fn,
map_data=hm,
output_crystal_symmetry=output_crystal_symmetry,
output_mean=params.output_ccp4_map_mean,
output_sd=params.output_ccp4_map_sd,
output_unit_cell_grid=output_unit_cell_grid,
shift_back=shift_back,
output_map_labels=labels,
output_external_origin=params.output_external_origin)
print ("Writing boxed half map to: %s " %(hm_fn),file=log)
# Write xplor map. Shift back if keep_origin=True
if("xplor" in params.output_format):
if(params.output_file_name_prefix is None):
file_name = "%s_box.xplor"%output_prefix
else: file_name = "%s.xplor"%params.output_file_name_prefix
output_box.write_xplor_map(file_name=file_name,
output_crystal_symmetry=output_crystal_symmetry,
output_unit_cell_grid=output_unit_cell_grid,
shift_back=shift_back,)
print("Writing boxed map "+\
"to X-plor formatted file: %s"%file_name, file=log)
# Write mtz map coeffs. Shift back if keep_origin=True
if("mtz" in params.output_format):
if(params.output_file_name_prefix is None):
file_name = "%s_box.mtz"%output_prefix
else: file_name = "%s.mtz"%params.output_file_name_prefix
print("Writing map coefficients "+\
"to MTZ file: %s"%file_name, file=log)
if(map_coeff is not None):
d_min = map_coeff.d_min()
elif params.resolution is not None:
d_min = params.resolution
else:
d_min = maptbx.d_min_from_map(map_data=output_box.map_box,
unit_cell=output_box.xray_structure_box.unit_cell())
output_box.map_coefficients(d_min=d_min,
scale_max=params.scale_max,
resolution_factor=params.resolution_factor, file_name=file_name,
shift_back=shift_back)
print(file=log)
return box
def get_ncs_info_as_spec(self,
exclude_h=None,
exclude_d=None,
stem=None,
write_ncs_domain_pdb=False,
log=None):
"""
XXX This function should be transfered to mmtbx/ncs/ncs.py:ncs class as
its classmethod, because it creates an object and this is the task of
a constructor. And it definetely should be decoupled from file creation!
Returns ncs spec object and can prints ncs info in a ncs_spec,
format_all_for_resolve or format_all_for_phenix_refine format
Note that while ncs_groups can master ncs can be comprised from several
chains, the spec groups can not. So groups with multiple chains in the
master selection are splitted
Note that spec format does not support insertions notation
for example "resseq 49" will include "resid 49" and "resid 49A"
Args:
write: (bool) when False, will not write to file or print
exclude_h,exclude_d : parameters of the ncs object
Return:
spec_object
"""
log = log or self.log
if not stem: stem = ''
else: stem += '_'
spec_object = ncs.ncs(exclude_h=exclude_h, exclude_d=exclude_d)
xyz = self.truncated_hierarchy.atoms().extract_xyz()
#===============================================================
# New implementation
# Here we have original i_seqs already in ncs_restraints_group_list,
# so we should use self.hierarchy for everything
xyz = self.hierarchy.atoms().extract_xyz()
assert self.ncs_restraints_group_list is not None
splitted_nrgl = self.ncs_restraints_group_list.split_by_chains(
hierarchy=self.hierarchy)
for i_group, group in enumerate(splitted_nrgl):
center_orth = []
rotations = []
translations = []
# chain id
chain_id_list = []
# this is [ [[1, 2] [5, 6]] ]
residue_range_list = []
rmsd_list = []
# number of residues
residues_count = []
# Putting master in:
center_orth.append(get_center_orth(xyz, group.master_iselection))
rotations.append(matrix.sqr([1, 0, 0, 0, 1, 0, 0, 0, 1]))
translations.append(matrix.col([0, 0, 0]))
chain_id, ranges, count = get_chain_and_ranges(
self.hierarchy.select(group.master_iselection))
chain_id_list.append(chain_id)
residue_range_list.append(ranges)
residues_count.append(count)
rmsd_list.append(0)
for c in group.copies:
center_orth.append(get_center_orth(xyz, c.iselection))
# in spec files transform is copy -> master, not master -> copy
r, t = inverse_transform(c.r, c.t)
rotations.append(r)
translations.append(t)
chain_id, ranges, count = get_chain_and_ranges(
self.hierarchy.select(c.iselection))
chain_id_list.append(chain_id)
residue_range_list.append(ranges)
residues_count.append(count)
rmsd_list.append(c.rmsd)
# XXX This should be consistent with full_file_name parameter in
# simple_ncs_from_pdb.py: create_ncs_domain_pdb_files()
# This is here just because we need to output filename of the domain
# into the spec file if pdb file is going to be created...
ncs_domain_pdb = None
if write_ncs_domain_pdb:
ncs_domain_pdb = stem + 'group_' + str(i_group + 1) + '.pdb'
spec_object.import_ncs_group(
center_orth=center_orth,
ncs_rota_matr=rotations,
trans_orth=translations,
rmsd_list=rmsd_list,
chain_residue_id=[chain_id_list, residue_range_list],
residues_in_common_list=residues_count,
ncs_domain_pdb=ncs_domain_pdb)
spec_object._ncs_obj = self
return spec_object
def run(args, log=sys.stdout, as_gui_program=False):
if (len(args) == 0):
parsed = defaults(log=log)
parsed.show(prefix=" ", out=log)
return
command_line = (option_parser().enable_symmetry_comprehensive().option(
"-q",
"--quiet",
action="store_true",
default=False,
help="suppress output").option("--output_plots",
action="store_true",
default=False)).process(args=args)
parsed = defaults(log=log)
processed_args = mmtbx.utils.process_command_line_args(
args=command_line.args,
cmd_cs=command_line.symmetry,
master_params=parsed,
log=log,
suppress_symmetry_related_errors=True)
processed_args.params.show(out=log)
params = processed_args.params.extract().density_modification
output_plots = command_line.options.output_plots
crystal_symmetry = crystal.symmetry(
unit_cell=params.input.unit_cell,
space_group_info=params.input.space_group)
reflection_files = {}
for rfn in (params.input.reflection_data.file_name,
params.input.experimental_phases.file_name,
params.input.map_coefficients.file_name):
if os.path.isfile(str(rfn)) and rfn not in reflection_files:
reflection_files.setdefault(
rfn,
iotbx.reflection_file_reader.any_reflection_file(
file_name=rfn, ensure_read_access=False))
# TODO is reflection_files a dict ?
server = iotbx.reflection_file_utils.reflection_file_server(
crystal_symmetry=crystal_symmetry,
reflection_files=list(reflection_files.values()))
fo = mmtbx.utils.determine_data_and_flags(
server,
parameters=params.input.reflection_data,
extract_r_free_flags=False,
log=log).f_obs
hl_coeffs = mmtbx.utils.determine_experimental_phases(
server,
params.input.experimental_phases,
log=log,
parameter_scope="",
working_point_group=None,
symmetry_safety_check=True,
ignore_all_zeros=True)
if params.input.map_coefficients.file_name is not None:
map_coeffs = server.get_phases_deg(
file_name=params.input.map_coefficients.file_name,
labels=params.input.map_coefficients.labels,
convert_to_phases_if_necessary=False,
original_phase_units=None,
parameter_scope="",
parameter_name="labels").map_to_asu()
else:
map_coeffs = None
ncs_object = None
if params.input.ncs_file_name is not None:
ncs_object = ncs.ncs()
ncs_object.read_ncs(params.input.ncs_file_name)
ncs_object.display_all(log=log)
fo = fo.map_to_asu()
hl_coeffs = hl_coeffs.map_to_asu()
fo = fo.eliminate_sys_absent().average_bijvoet_mates()
hl_coeffs = hl_coeffs.eliminate_sys_absent().average_bijvoet_mates()
model_map = None
model_map_coeffs = None
if len(processed_args.pdb_file_names):
pdb_inp = mmtbx.utils.pdb_inp_from_multiple_files(
pdb_files=processed_args.pdb_file_names, log=log)
xs = pdb_inp.xray_structure_simple()
fo_, hl_ = fo, hl_coeffs
if params.change_basis_to_niggli_cell:
change_of_basis_op = xs.change_of_basis_op_to_niggli_cell()
xs = xs.change_basis(change_of_basis_op)
fo_ = fo_.change_basis(change_of_basis_op).map_to_asu()
hl_ = hl_.change_basis(change_of_basis_op).map_to_asu()
#fo_, hl_ = fo_.common_sets(hl_)
fmodel_refined = mmtbx.utils.fmodel_simple(
f_obs=fo_,
scattering_table=
"wk1995", #XXX pva: 1) neutrons? 2) move up as a parameter.
xray_structures=[xs],
bulk_solvent_correction=True,
anisotropic_scaling=True,
r_free_flags=fo_.array(data=flex.bool(fo_.size(), False)))
fmodel_refined.update(abcd=hl_)
master_phil = mmtbx.maps.map_and_map_coeff_master_params()
map_params = master_phil.fetch(
iotbx.phil.parse("""\
map_coefficients {
map_type = 2mFo-DFc
isotropize = True
}
""")).extract().map_coefficients[0]
model_map_coeffs = mmtbx.maps.map_coefficients_from_fmodel(
fmodel=fmodel_refined, params=map_params)
model_map = model_map_coeffs.fft_map(
resolution_factor=params.grid_resolution_factor).real_map_unpadded(
)
import time
t0 = time.time()
dm = density_modify(params,
fo,
hl_coeffs,
ncs_object=ncs_object,
map_coeffs=map_coeffs,
model_map_coeffs=model_map_coeffs,
log=log,
as_gui_program=as_gui_program)
time_dm = time.time() - t0
print("Time taken for density modification: %.2fs" % time_dm, file=log)
# run cns
if 0:
from cctbx.development import cns_density_modification
cns_result = cns_density_modification.run(params, fo, hl_coeffs)
print(cns_result.modified_map.all())
print(dm.map.all())
dm_map_coeffs = dm.map_coeffs_in_original_setting
from cctbx import maptbx, miller
crystal_gridding = maptbx.crystal_gridding(
dm_map_coeffs.unit_cell(),
space_group_info=dm_map_coeffs.space_group().info(),
pre_determined_n_real=cns_result.modified_map.all())
dm_map = miller.fft_map(crystal_gridding,
dm_map_coeffs).apply_sigma_scaling()
corr = flex.linear_correlation(cns_result.modified_map.as_1d(),
dm_map.real_map_unpadded().as_1d())
print("CNS dm/mmtbx dm correlation:")
corr.show_summary()
if dm.model_map_coeffs is not None:
model_map = miller.fft_map(
crystal_gridding,
dm.miller_array_in_original_setting(
dm.model_map_coeffs)).apply_sigma_scaling()
corr = flex.linear_correlation(
cns_result.modified_map.as_1d(),
model_map.real_map_unpadded().as_1d())
print("CNS dm/model correlation:")
corr.show_summary()
if output_plots:
plots_to_make = (
"fom",
"skewness",
"r1_factor",
"r1_factor_fom",
"mean_solvent_density",
"mean_protein_density",
"f000_over_v",
"k_flip",
"rms_solvent_density",
"rms_protein_density",
"standard_deviation_local_rms",
"mean_delta_phi",
"mean_delta_phi_initial",
)
from matplotlib.backends.backend_pdf import PdfPages
from libtbx import pyplot
stats = dm.get_stats()
pdf = PdfPages("density_modification.pdf")
if len(dm.correlation_coeffs) > 1:
if 0:
start_coeffs, model_coeffs = dm.map_coeffs_start.common_sets(
model_map_coeffs)
model_phases = model_coeffs.phases(deg=True).data()
exptl_phases = nearest_phase(
model_phases,
start_coeffs.phases(deg=True).data(),
deg=True)
corr = flex.linear_correlation(exptl_phases, model_phases)
corr.show_summary()
fig = pyplot.figure()
ax = fig.add_subplot(1, 1, 1)
ax.set_title("phases start")
ax.set_xlabel("Experimental phases")
ax.set_ylabel("Phases from refined model")
ax.scatter(exptl_phases, model_phases, marker="x", s=10)
pdf.savefig(fig)
#
dm_coeffs, model_coeffs = dm.map_coeffs.common_sets(
model_map_coeffs)
model_phases = model_coeffs.phases(deg=True).data()
dm_phases = nearest_phase(model_phases,
dm_coeffs.phases(deg=True).data(),
deg=True)
corr = flex.linear_correlation(dm_phases, model_phases)
corr.show_summary()
fig = pyplot.figure()
ax = fig.add_subplot(1, 1, 1)
ax.set_title("phases dm")
ax.set_xlabel("Phases from density modification")
ax.set_ylabel("Phases from refined model")
ax.scatter(dm_phases, model_phases, marker="x", s=10)
pdf.savefig(fig)
#
data = dm.correlation_coeffs
fig = pyplot.figure()
ax = fig.add_subplot(1, 1, 1)
ax.set_title("correlation coefficient")
ax.plot(list(range(1, dm.i_cycle + 2)), data)
pdf.savefig(fig)
#
data = dm.mean_phase_errors
fig = pyplot.figure()
ax = fig.add_subplot(1, 1, 1)
ax.set_title("Mean effective phase errors")
ax.plot(list(range(1, dm.i_cycle + 2)), data)
pdf.savefig(fig)
for plot in plots_to_make:
data = [
getattr(stats.get_cycle_stats(i), plot)
for i in range(1, dm.i_cycle + 2)
]
fig = pyplot.figure()
ax = fig.add_subplot(1, 1, 1)
ax.set_title(plot.replace("_", " "))
ax.plot(list(range(1, dm.i_cycle + 2)), data)
pdf.savefig(fig)
data = [
stats.get_cycle_stats(i).rms_solvent_density /
stats.get_cycle_stats(i).rms_protein_density
for i in range(1, dm.i_cycle + 2)
]
fig = pyplot.figure()
ax = fig.add_subplot(1, 1, 1)
ax.set_title("RMS solvent/protein density ratio")
ax.plot(list(range(1, dm.i_cycle + 2)), data)
pdf.savefig(fig)
pdf.close()
dm_map_coeffs = dm.map_coeffs_in_original_setting
dm_hl_coeffs = dm.hl_coeffs_in_original_setting
# output map if requested
map_params = params.output.map
if map_params.file_name is not None:
fft_map = dm_map_coeffs.fft_map(
resolution_factor=params.grid_resolution_factor)
if map_params.scale == "sigma":
fft_map.apply_sigma_scaling()
else:
fft_map.apply_volume_scaling()
gridding_first = gridding_last = None
title_lines = []
if map_params.format == "xplor":
fft_map.as_xplor_map(file_name=map_params.file_name,
title_lines=title_lines,
gridding_first=gridding_first,
gridding_last=gridding_last)
else:
fft_map.as_ccp4_map(file_name=map_params.file_name,
gridding_first=gridding_first,
gridding_last=gridding_last,
labels=title_lines)
# output map coefficients if requested
mtz_params = params.output.mtz
# Decide if we are going to actually write the mtz
if mtz_params.file_name is not None:
orig_fom, final_fom = dm.start_and_end_fom()
if mtz_params.skip_output_if_worse and final_fom < orig_fom:
ok_to_write_mtz = False
print(
"Not writing out mtz. Final FOM (%7.3f) worse than start (%7.3f)"
% (final_fom, orig_fom))
else: # usual
ok_to_write_mtz = True
else:
ok_to_write_mtz = True
if mtz_params.file_name is not None and ok_to_write_mtz:
label_decorator = iotbx.mtz.ccp4_label_decorator()
fo = dm.miller_array_in_original_setting(
dm.f_obs_complete).common_set(dm_map_coeffs)
mtz_dataset = fo.as_mtz_dataset(column_root_label="F",
label_decorator=label_decorator)
mtz_dataset.add_miller_array(dm_map_coeffs,
column_root_label="FWT",
label_decorator=label_decorator)
phase_source = dm.miller_array_in_original_setting(
dm.phase_source).common_set(dm_map_coeffs)
mtz_dataset.add_miller_array(
phase_source.array(data=flex.abs(phase_source.data())),
column_root_label="FOM",
column_types='W',
label_decorator=label_decorator)
mtz_dataset.add_miller_array(
phase_source.array(data=phase_source.phases(deg=True).data()),
column_root_label="PHIB",
column_types='P',
label_decorator=None)
if mtz_params.output_hendrickson_lattman_coefficients:
mtz_dataset.add_miller_array(dm_hl_coeffs,
column_root_label="HL",
label_decorator=label_decorator)
mtz_dataset.mtz_object().write(mtz_params.file_name)
return result(map_file=map_params.file_name,
mtz_file=mtz_params.file_name,
stats=dm.get_stats())
def get_ncs_obj(file_name,out=sys.stdout): from mmtbx.ncs.ncs import ncs ncs_object=ncs() ncs_object.read_ncs(file_name=file_name,log=out) return ncs_object
def run(args,
crystal_symmetry=None,
ncs_object=None,
pdb_hierarchy=None,
map_data=None,
lower_bounds=None,
upper_bounds=None,
write_output_files=True,
log=None):
h = "phenix.map_box: extract box with model and map around selected atoms"
if (log is None): log = sys.stdout
print_statistics.make_header(h, out=log)
default_message = """\
%s.
Usage:
phenix.map_box model.pdb map_coefficients.mtz selection="chain A and resseq 1:10"
or
phenix.map_box map.ccp4 density_select=True
Parameters:""" % h
if (len(args) == 0 and not pdb_hierarchy):
print default_message
master_phil.show(prefix=" ")
return
inputs = mmtbx.utils.process_command_line_args(args=args,
cmd_cs=crystal_symmetry,
master_params=master_phil)
params = inputs.params.extract()
master_phil.format(python_object=params).show(out=log)
# Overwrite params with parameters in call if available
if lower_bounds:
params.lower_bounds = lower_bounds
if upper_bounds:
params.upper_bounds = upper_bounds
# PDB file
if params.pdb_file and not inputs.pdb_file_names and not pdb_hierarchy:
inputs.pdb_file_names = [params.pdb_file]
if (len(inputs.pdb_file_names) != 1 and not params.density_select
and not pdb_hierarchy and not params.keep_map_size
and not params.upper_bounds and not params.extract_unique):
raise Sorry("PDB file is needed unless extract_unique, " +
"density_select, keep_map_size \nor bounds are set .")
if (len(inputs.pdb_file_names)!=1 and not pdb_hierarchy and \
(params.mask_atoms or params.soft_mask )):
raise Sorry("PDB file is needed for mask_atoms or soft_mask")
if (params.density_select and params.keep_map_size):
raise Sorry("Cannot set both density_select and keep_map_size")
if (params.density_select and params.upper_bounds):
raise Sorry("Cannot set both density_select and bounds")
if (params.keep_map_size and params.upper_bounds):
raise Sorry("Cannot set both keep_map_size and bounds")
if (params.upper_bounds and not params.lower_bounds):
raise Sorry("Please set lower_bounds if you set upper_bounds")
if (params.extract_unique and not params.resolution):
raise Sorry("Please set resolution for extract_unique")
print_statistics.make_sub_header("pdb model", out=log)
if len(inputs.pdb_file_names) > 0:
pdb_inp = iotbx.pdb.input(file_name=inputs.pdb_file_names[0])
pdb_hierarchy = pdb_inp.construct_hierarchy()
if pdb_hierarchy:
pdb_atoms = pdb_hierarchy.atoms()
pdb_atoms.reset_i_seq()
else:
pdb_hierarchy = None
# Map or map coefficients
map_coeff = None
if (not map_data):
# read first mtz file
if ((len(inputs.reflection_file_names) > 0)
or (params.map_coefficients_file is not None)):
# file in phil takes precedent
if (params.map_coefficients_file is not None):
if (len(inputs.reflection_file_names) == 0):
inputs.reflection_file_names.append(
params.map_coefficients_file)
else:
inputs.reflection_file_names[
0] = params.map_coefficients_file
map_coeff = reflection_file_utils.extract_miller_array_from_file(
file_name=inputs.reflection_file_names[0],
label=params.label,
type="complex",
log=log)
if not crystal_symmetry:
crystal_symmetry = map_coeff.crystal_symmetry()
fft_map = map_coeff.fft_map(
resolution_factor=params.resolution_factor)
fft_map.apply_sigma_scaling()
map_data = fft_map.real_map_unpadded()
map_or_map_coeffs_prefix = os.path.basename(
inputs.reflection_file_names[0][:-4])
# or read CCP4 map
elif ((inputs.ccp4_map is not None)
or (params.ccp4_map_file is not None)):
if (params.ccp4_map_file is not None):
af = any_file(params.ccp4_map_file)
if (af.file_type == 'ccp4_map'):
inputs.ccp4_map = af.file_content
inputs.ccp4_map_file_name = params.ccp4_map_file
print_statistics.make_sub_header("CCP4 map", out=log)
ccp4_map = inputs.ccp4_map
ccp4_map.show_summary(prefix=" ", out=log)
if not crystal_symmetry:
crystal_symmetry = ccp4_map.crystal_symmetry()
map_data = ccp4_map.data #map_data()
if inputs.ccp4_map_file_name.endswith(".ccp4"):
map_or_map_coeffs_prefix = os.path.basename(
inputs.ccp4_map_file_name[:-5])
else:
map_or_map_coeffs_prefix = os.path.basename(
inputs.ccp4_map_file_name[:-4])
else: # have map_data
map_or_map_coeffs_prefix = None
if crystal_symmetry and not inputs.crystal_symmetry:
inputs.crystal_symmetry = crystal_symmetry
# final check that map_data exists
if (map_data is None):
raise Sorry("Map or map coefficients file is needed.")
if len(inputs.pdb_file_names) > 0:
output_prefix = os.path.basename(inputs.pdb_file_names[0])[:-4]
else:
output_prefix = map_or_map_coeffs_prefix
if not pdb_hierarchy: # get an empty hierarchy
from cctbx.array_family import flex
pdb_hierarchy = iotbx.pdb.input(
source_info='', lines=flex.split_lines('')).construct_hierarchy()
xray_structure = pdb_hierarchy.extract_xray_structure(
crystal_symmetry=inputs.crystal_symmetry)
xray_structure.show_summary(f=log)
#
selection = pdb_hierarchy.atom_selection_cache().selection(
string=params.selection)
if selection.size():
print_statistics.make_sub_header("atom selection", out=log)
print >> log, "Selection string: selection='%s'" % params.selection
print >> log, \
" selects %d atoms from total %d atoms."%(selection.count(True),
selection.size())
sites_cart_all = xray_structure.sites_cart()
sites_cart = sites_cart_all.select(selection)
selection = xray_structure.selection_within(radius=params.selection_radius,
selection=selection)
if not ncs_object:
from mmtbx.ncs.ncs import ncs
ncs_object = ncs()
if params.symmetry_file:
ncs_object.read_ncs(params.symmetry_file, log=log)
print >> log, "Total of %s operators read" % (
ncs_object.max_operators())
if not ncs_object or ncs_object.max_operators() < 1:
print >> log, "No symmetry available"
if ncs_object:
n_ops = max(1, ncs_object.max_operators())
else:
n_ops = 1
# Get sequence if extract_unique is set
sequence = None
if params.extract_unique:
if params.sequence_file:
if n_ops > 1: # get unique part of sequence and multiply
remove_duplicates = True
else:
remove_duplicates = False
from iotbx.bioinformatics import get_sequences
sequence = n_ops * (" ".join(
get_sequences(file_name=params.sequence_file,
remove_duplicates=remove_duplicates)))
if sequence and not params.molecular_mass:
# get molecular mass from sequence
from iotbx.bioinformatics import text_from_chains_matching_chain_type
if params.chain_type in [None, 'PROTEIN']:
n_protein = len(
text_from_chains_matching_chain_type(text=sequence,
chain_type='PROTEIN'))
else:
n_protein = 0
if params.chain_type in [None, 'RNA']:
n_rna = len(
text_from_chains_matching_chain_type(text=sequence,
chain_type='RNA'))
else:
n_rna = 0
if params.chain_type in [None, 'DNA']:
n_dna = len(
text_from_chains_matching_chain_type(text=sequence,
chain_type='DNA'))
else:
n_dna = 0
params.molecular_mass = n_protein * 110 + (n_rna + n_dna) * 330
elif not params.molecular_mass:
raise Sorry(
"Need a sequence file or molecular mass for extract_unique")
else:
molecular_mass = None
#
if params.density_select:
print_statistics.make_sub_header(
"Extracting box around selected density and writing output files",
out=log)
else:
print_statistics.make_sub_header(
"Extracting box around selected atoms and writing output files",
out=log)
#
if params.value_outside_atoms == 'mean':
print >> log, "\nValue outside atoms mask will be set to mean inside mask"
if params.get_half_height_width and params.density_select:
print >> log, "\nHalf width at half height will be used to id boundaries"
if params.soft_mask and sites_cart_all.size() > 0:
print >> log, "\nSoft mask will be applied to model-based mask"
if params.keep_map_size:
print >> log, "\nEntire map will be kept (not cutting out region)"
if params.restrict_map_size:
print >> log, "\nOutput map will be within input map"
if params.lower_bounds and params.upper_bounds:
print >> log, "Bounds for cut out map are (%s,%s,%s) to (%s,%s,%s)" % (
tuple(list(params.lower_bounds) + list(params.upper_bounds)))
box = mmtbx.utils.extract_box_around_model_and_map(
xray_structure=xray_structure,
map_data=map_data.as_double(),
box_cushion=params.box_cushion,
selection=selection,
density_select=params.density_select,
threshold=params.density_select_threshold,
get_half_height_width=params.get_half_height_width,
mask_atoms=params.mask_atoms,
soft_mask=params.soft_mask,
soft_mask_radius=params.soft_mask_radius,
mask_atoms_atom_radius=params.mask_atoms_atom_radius,
value_outside_atoms=params.value_outside_atoms,
keep_map_size=params.keep_map_size,
restrict_map_size=params.restrict_map_size,
lower_bounds=params.lower_bounds,
upper_bounds=params.upper_bounds,
extract_unique=params.extract_unique,
chain_type=params.chain_type,
sequence=sequence,
solvent_content=params.solvent_content,
molecular_mass=params.molecular_mass,
resolution=params.resolution,
ncs_object=ncs_object,
symmetry=params.symmetry,
)
ph_box = pdb_hierarchy.select(selection)
ph_box.adopt_xray_structure(box.xray_structure_box)
box.hierarchy = ph_box
if (inputs and inputs.crystal_symmetry and inputs.ccp4_map
and inputs.crystal_symmetry.unit_cell().parameters()
and inputs.ccp4_map.unit_cell_parameters) and (
inputs.crystal_symmetry.unit_cell().parameters() !=
inputs.ccp4_map.unit_cell_parameters):
print >> log, "\nNOTE: Mismatch of unit cell parameters from CCP4 map:"
print >>log,"Unit cell from CCP4 map 'unit cell parameters': "+\
"%.1f, %.1f, %.1f, %.1f, %.1f, %.1f)" %tuple(
inputs.ccp4_map.unit_cell_parameters)
print >>log,"Unit cell from CCP4 map 'map grid': "+\
"%.1f, %.1f, %.1f, %.1f, %.1f, %.1f)" %tuple(
inputs.crystal_symmetry.unit_cell().parameters())
print >>log,"\nInterpreting this as the 'unit cell parameters' was "+\
"original map \ndimension and 'map grid' is the "+\
"portion actually in the map that was supplied here.\n"
box.unit_cell_parameters_from_ccp4_map = inputs.ccp4_map.unit_cell_parameters
box.unit_cell_parameters_deduced_from_map_grid=\
inputs.crystal_symmetry.unit_cell().parameters()
else:
box.unit_cell_parameters_from_ccp4_map = None
box.unit_cell_parameters_deduced_from_map_grid = None
# ncs_object is original
# box.ncs_object is shifted by shift_cart
print >> log, "Box cell dimensions: (%.2f, %.2f, %.2f) A" % (
box.box_crystal_symmetry.unit_cell().parameters()[:3])
if params.keep_origin:
print >> log, "Box origin is at grid position of : (%d, %d, %d) " % (
tuple(box.origin_shift_grid_units(reverse=True)))
print >> log, "Box origin is at coordinates: (%.2f, %.2f, %.2f) A" % (
tuple(-col(box.shift_cart)))
if box.pdb_outside_box_msg:
print >> log, box.pdb_outside_box_msg
# NOTE: box object is always shifted to place origin at (0,0,0)
# For output files ONLY:
# keep_origin==False leave origin at (0,0,0)
# keep_origin==True: we shift everything back to where it was,
if (not params.keep_origin):
if box.shift_cart:
print >>log,\
"Final coordinate shift for output files: (%.2f,%.2f,%.2f) A" %(
tuple(box.shift_cart))
else:
print >>log,"\nOutput files are in same location as original: origin "+\
"is at (0,0,0)"
else: # keep_origin
print >> log, "\nOutput files are in same location as original, just cut out."
print >> log, "Note that output maps are only valid in the cut out region.\n"
if params.keep_origin:
ph_box_original_location = ph_box.deep_copy()
sites_cart = box.shift_sites_cart_back(
box.xray_structure_box.sites_cart())
xrs_offset = ph_box_original_location.extract_xray_structure(
crystal_symmetry=box.xray_structure_box.crystal_symmetry(
)).replace_sites_cart(new_sites=sites_cart)
ph_box_original_location.adopt_xray_structure(xrs_offset)
box.hierarchy_original_location = ph_box_original_location
else:
box.hierarchy_original_location = None
if write_output_files:
# Write PDB file
if ph_box.overall_counts().n_residues > 0:
if (params.output_file_name_prefix is None):
file_name = "%s_box.pdb" % output_prefix
else:
file_name = "%s.pdb" % params.output_file_name_prefix
if params.keep_origin: # Keeping origin
print >> log, "Writing boxed PDB with box unit cell and in "+\
"original\n position to: %s"%(
file_name)
ph_box_original_location.write_pdb_file(
file_name=file_name,
crystal_symmetry=box.xray_structure_box.crystal_symmetry())
else: # write box PDB in box cell
print >> log, "Writing shifted boxed PDB to file: %s" % file_name
ph_box.write_pdb_file(
file_name=file_name,
crystal_symmetry=box.xray_structure_box.crystal_symmetry())
# Write NCS file if NCS
if ncs_object and ncs_object.max_operators() > 0:
if (params.output_file_name_prefix is None):
output_symmetry_file = "%s_box.ncs_spec" % output_prefix
else:
output_symmetry_file = "%s.ncs_spec" % params.output_file_name_prefix
if params.keep_origin:
if params.symmetry_file:
print >> log, "\nDuplicating symmetry in %s and writing to %s" % (
params.symmetry_file, output_symmetry_file)
else:
print >> log, "\nWriting symmetry to %s" % (
output_symmetry_file)
ncs_object.format_all_for_group_specification(
file_name=output_symmetry_file)
else:
print >> log, "\nOffsetting symmetry in %s and writing to %s" % (
params.symmetry_file, output_symmetry_file)
box.ncs_object.format_all_for_group_specification(
file_name=output_symmetry_file)
# Write ccp4 map. Shift back to original location if keep_origin=True
if ("ccp4" in params.output_format):
if (params.output_file_name_prefix is None):
file_name = "%s_box.ccp4" % output_prefix
else:
file_name = "%s.ccp4" % params.output_file_name_prefix
if params.keep_origin:
print >> log, "Writing boxed map with box unit_cell and "+\
"original\n position to CCP4 formatted file: %s"%file_name
else:
print >> log, "Writing box map shifted to (0,0,0) to CCP4 "+\
"formatted file: %s"%file_name
box.write_ccp4_map(file_name=file_name,
shift_back=params.keep_origin)
# Write xplor map. Shift back if keep_origin=True
if ("xplor" in params.output_format):
if (params.output_file_name_prefix is None):
file_name = "%s_box.xplor" % output_prefix
else:
file_name = "%s.xplor" % params.output_file_name_prefix
if params.keep_origin:
print >> log, "Writing boxed map with box unit_cell and original "+\
"position\n to X-plor formatted file: %s"%file_name
else:
print >> log, "Writing box_map shifted to (0,0,0) to X-plor "+\
"formatted file: %s"%file_name
box.write_xplor_map(file_name=file_name,
shift_back=params.keep_origin)
# Write mtz map coeffs. Shift back if keep_origin=True
if ("mtz" in params.output_format):
if (params.output_file_name_prefix is None):
file_name = "%s_box.mtz" % output_prefix
else:
file_name = "%s.mtz" % params.output_file_name_prefix
if params.keep_origin:
print >> log, "Writing map coefficients with box_map unit_cell"+\
" but position matching\n "+\
" original position to MTZ file: %s"%file_name
else:
print >> log, "Writing box_map coefficients shifted to (0,0,0) "+\
"to MTZ file: %s"%file_name
if (map_coeff is not None):
d_min = map_coeff.d_min()
elif params.resolution is not None:
d_min = params.resolution
else:
d_min = maptbx.d_min_from_map(
map_data=box.map_box,
unit_cell=box.xray_structure_box.unit_cell())
box.map_coefficients(d_min=d_min,
resolution_factor=params.resolution_factor,
file_name=file_name,
shift_back=params.keep_origin)
print >> log
return box
def run(args, crystal_symmetry=None,
ncs_object=None,
pdb_hierarchy=None,
map_data=None,
lower_bounds=None,
upper_bounds=None,
write_output_files=True,
log=None):
h = "phenix.map_box: extract box with model and map around selected atoms"
if(log is None): log = sys.stdout
print_statistics.make_header(h, out=log)
default_message="""\
%s.
Usage:
phenix.map_box model.pdb map_coefficients.mtz selection="chain A and resseq 1:10"
or
phenix.map_box map.ccp4 density_select=True
Parameters:"""%h
if(len(args) == 0 and not pdb_hierarchy):
print default_message
master_phil.show(prefix=" ")
return
inputs = mmtbx.utils.process_command_line_args(args = args,
cmd_cs=crystal_symmetry,
master_params = master_phil)
params = inputs.params.extract()
master_phil.format(python_object=params).show(out=log)
# Overwrite params with parameters in call if available
if lower_bounds:
params.lower_bounds=lower_bounds
if upper_bounds:
params.upper_bounds=upper_bounds
# PDB file
if params.pdb_file and not inputs.pdb_file_names and not pdb_hierarchy:
inputs.pdb_file_names=[params.pdb_file]
if(len(inputs.pdb_file_names)!=1 and not params.density_select and not
pdb_hierarchy and not params.keep_map_size and not params.upper_bounds
and not params.extract_unique):
raise Sorry("PDB file is needed unless extract_unique, "+
"density_select, keep_map_size \nor bounds are set .")
if (len(inputs.pdb_file_names)!=1 and not pdb_hierarchy and \
(params.mask_atoms or params.soft_mask )):
raise Sorry("PDB file is needed for mask_atoms or soft_mask")
if (params.density_select and params.keep_map_size):
raise Sorry("Cannot set both density_select and keep_map_size")
if (params.density_select and params.upper_bounds):
raise Sorry("Cannot set both density_select and bounds")
if (params.keep_map_size and params.upper_bounds):
raise Sorry("Cannot set both keep_map_size and bounds")
if (params.upper_bounds and not params.lower_bounds):
raise Sorry("Please set lower_bounds if you set upper_bounds")
if (params.extract_unique and not params.resolution):
raise Sorry("Please set resolution for extract_unique")
if (write_output_files) and ("mtz" in params.output_format) and (
(params.keep_origin) and (not params.keep_map_size)):
raise Sorry("Please set output_format=ccp4 to skip mtz or set "+\
"keep_origin=False or keep_map_size=True")
if params.keep_input_unit_cell_and_grid and (
(params.output_unit_cell_grid is not None ) or
(params.output_unit_cell is not None ) ):
raise Sorry("If you set keep_input_unit_cell_and_grid then you cannot "+\
"set \noutput_unit_cell_grid or output_unit_cell")
if params.output_origin_grid_units is not None and params.keep_origin:
params.keep_origin=False
print "Setting keep_origin=False as output_origin_grid_units is set"
print_statistics.make_sub_header("pdb model", out=log)
if len(inputs.pdb_file_names)>0:
pdb_inp = iotbx.pdb.input(file_name=inputs.pdb_file_names[0])
pdb_hierarchy = pdb_inp.construct_hierarchy()
if pdb_hierarchy:
pdb_atoms = pdb_hierarchy.atoms()
pdb_atoms.reset_i_seq()
else:
pdb_hierarchy=None
# Map or map coefficients
map_coeff = None
input_unit_cell_grid=None
input_unit_cell=None
if (not map_data):
# read first mtz file
if ( (len(inputs.reflection_file_names) > 0) or
(params.map_coefficients_file is not None) ):
# file in phil takes precedent
if (params.map_coefficients_file is not None):
if (len(inputs.reflection_file_names) == 0):
inputs.reflection_file_names.append(params.map_coefficients_file)
else:
inputs.reflection_file_names[0] = params.map_coefficients_file
map_coeff = reflection_file_utils.extract_miller_array_from_file(
file_name = inputs.reflection_file_names[0],
label = params.label,
type = "complex",
log = log)
if not crystal_symmetry: crystal_symmetry=map_coeff.crystal_symmetry()
fft_map = map_coeff.fft_map(resolution_factor=params.resolution_factor)
fft_map.apply_sigma_scaling()
map_data = fft_map.real_map_unpadded()
map_or_map_coeffs_prefix=os.path.basename(
inputs.reflection_file_names[0][:-4])
# or read CCP4 map
elif ( (inputs.ccp4_map is not None) or
(params.ccp4_map_file is not None) ):
if (params.ccp4_map_file is not None):
af = any_file(params.ccp4_map_file)
if (af.file_type == 'ccp4_map'):
inputs.ccp4_map = af.file_content
inputs.ccp4_map_file_name = params.ccp4_map_file
print_statistics.make_sub_header("CCP4 map", out=log)
ccp4_map = inputs.ccp4_map
ccp4_map.show_summary(prefix=" ",out=log)
if not crystal_symmetry: crystal_symmetry=ccp4_map.crystal_symmetry()
map_data = ccp4_map.data #map_data()
input_unit_cell_grid=ccp4_map.unit_cell_grid
input_unit_cell=ccp4_map.unit_cell_parameters
if inputs.ccp4_map_file_name.endswith(".ccp4"):
map_or_map_coeffs_prefix=os.path.basename(
inputs.ccp4_map_file_name[:-5])
else:
map_or_map_coeffs_prefix=os.path.basename(
inputs.ccp4_map_file_name[:-4])
else: # have map_data
map_or_map_coeffs_prefix=None
if params.output_origin_grid_units is not None:
origin_to_match=tuple(params.output_origin_grid_units)
else:
origin_to_match=None
if origin_to_match:
sc=[]
for x,o,a in zip(crystal_symmetry.unit_cell().parameters()[:3],
origin_to_match,
map_data.all()):
sc.append(-x*o/a)
shift_cart_for_origin_to_match=tuple(sc)
else:
origin_to_match=None
shift_cart_for_origin_to_match=None
if crystal_symmetry and not inputs.crystal_symmetry:
inputs.crystal_symmetry=crystal_symmetry
# final check that map_data exists
if(map_data is None):
raise Sorry("Map or map coefficients file is needed.")
if len(inputs.pdb_file_names)>0:
output_prefix=os.path.basename(inputs.pdb_file_names[0])[:-4]
else:
output_prefix=map_or_map_coeffs_prefix
if not pdb_hierarchy: # get an empty hierarchy
from cctbx.array_family import flex
pdb_hierarchy=iotbx.pdb.input(
source_info='',lines=flex.split_lines('')).construct_hierarchy()
xray_structure = pdb_hierarchy.extract_xray_structure(
crystal_symmetry=inputs.crystal_symmetry)
xray_structure.show_summary(f=log)
#
selection = pdb_hierarchy.atom_selection_cache().selection(
string = params.selection)
if selection.size():
print_statistics.make_sub_header("atom selection", out=log)
print >> log, "Selection string: selection='%s'"%params.selection
print >> log, \
" selects %d atoms from total %d atoms."%(selection.count(True),
selection.size())
sites_cart_all = xray_structure.sites_cart()
sites_cart = sites_cart_all.select(selection)
selection = xray_structure.selection_within(
radius = params.selection_radius,
selection = selection)
if not ncs_object:
from mmtbx.ncs.ncs import ncs
ncs_object=ncs()
if params.symmetry_file:
ncs_object.read_ncs(params.symmetry_file,log=log)
print >>log,"Total of %s operators read" %(ncs_object.max_operators())
if not ncs_object or ncs_object.max_operators()<1:
print >>log,"No symmetry available"
if ncs_object:
n_ops=max(1,ncs_object.max_operators())
else:
n_ops=1
# Get sequence if extract_unique is set
sequence=None
if params.extract_unique:
if params.sequence_file:
if n_ops > 1: # get unique part of sequence and multiply
remove_duplicates=True
else:
remove_duplicates=False
from iotbx.bioinformatics import get_sequences
sequence=n_ops * (" ".join(get_sequences(file_name=params.sequence_file,
remove_duplicates=remove_duplicates)))
if sequence and not params.molecular_mass:
# get molecular mass from sequence
from iotbx.bioinformatics import text_from_chains_matching_chain_type
if params.chain_type in [None,'PROTEIN']:
n_protein=len(text_from_chains_matching_chain_type(
text=sequence,chain_type='PROTEIN'))
else:
n_protein=0
if params.chain_type in [None,'RNA']:
n_rna=len(text_from_chains_matching_chain_type(
text=sequence,chain_type='RNA'))
else:
n_rna=0
if params.chain_type in [None,'DNA']:
n_dna=len(text_from_chains_matching_chain_type(
text=sequence,chain_type='DNA'))
else:
n_dna=0
params.molecular_mass=n_protein*110+(n_rna+n_dna)*330
elif not params.molecular_mass:
raise Sorry("Need a sequence file or molecular mass for extract_unique")
else:
molecular_mass=None
#
if params.density_select:
print_statistics.make_sub_header(
"Extracting box around selected density and writing output files", out=log)
else:
print_statistics.make_sub_header(
"Extracting box around selected atoms and writing output files", out=log)
#
if params.value_outside_atoms=='mean':
print >>log,"\nValue outside atoms mask will be set to mean inside mask"
if params.get_half_height_width and params.density_select:
print >>log,"\nHalf width at half height will be used to id boundaries"
if params.soft_mask and sites_cart_all.size()>0:
print >>log,"\nSoft mask will be applied to model-based mask"
if params.keep_map_size:
print >>log,"\nEntire map will be kept (not cutting out region)"
if params.restrict_map_size:
print >>log,"\nOutput map will be within input map"
if params.lower_bounds and params.upper_bounds:
print >>log,"Bounds for cut out map are (%s,%s,%s) to (%s,%s,%s)" %(
tuple(list(params.lower_bounds)+list(params.upper_bounds)))
box = mmtbx.utils.extract_box_around_model_and_map(
xray_structure = xray_structure,
map_data = map_data.as_double(),
box_cushion = params.box_cushion,
selection = selection,
density_select = params.density_select,
threshold = params.density_select_threshold,
get_half_height_width = params.get_half_height_width,
mask_atoms = params.mask_atoms,
soft_mask = params.soft_mask,
soft_mask_radius = params.soft_mask_radius,
mask_atoms_atom_radius = params.mask_atoms_atom_radius,
value_outside_atoms = params.value_outside_atoms,
keep_map_size = params.keep_map_size,
restrict_map_size = params.restrict_map_size,
lower_bounds = params.lower_bounds,
upper_bounds = params.upper_bounds,
extract_unique = params.extract_unique,
chain_type = params.chain_type,
sequence = sequence,
solvent_content = params.solvent_content,
molecular_mass = params.molecular_mass,
resolution = params.resolution,
ncs_object = ncs_object,
symmetry = params.symmetry,
)
ph_box = pdb_hierarchy.select(selection)
ph_box.adopt_xray_structure(box.xray_structure_box)
box.hierarchy=ph_box
if (inputs and # XXX fix or remove this
inputs.crystal_symmetry and inputs.ccp4_map and
inputs.crystal_symmetry.unit_cell().parameters() and
inputs.ccp4_map.unit_cell_parameters ) and (
inputs.crystal_symmetry.unit_cell().parameters() !=
inputs.ccp4_map.unit_cell_parameters):
print >>log,"\nNOTE: Mismatch of unit cell parameters from CCP4 map:"
print >>log,"Unit cell from CCP4 map 'unit cell parameters': "+\
"%.1f, %.1f, %.1f, %.1f, %.1f, %.1f)" %tuple(
inputs.ccp4_map.unit_cell_parameters)
print >>log,"Unit cell from CCP4 map 'map grid': "+\
"%.1f, %.1f, %.1f, %.1f, %.1f, %.1f)" %tuple(
inputs.crystal_symmetry.unit_cell().parameters())
print >>log,"\nInterpreting this as the 'unit cell parameters' was "+\
"original map \ndimension and 'map grid' is the "+\
"portion actually in the map that was supplied here.\n"
box.unit_cell_parameters_from_ccp4_map=inputs.ccp4_map.unit_cell_parameters
box.unit_cell_parameters_deduced_from_map_grid=\
inputs.crystal_symmetry.unit_cell().parameters()
else:
box.unit_cell_parameters_from_ccp4_map=None
box.unit_cell_parameters_deduced_from_map_grid=None
if box.pdb_outside_box_msg:
print >> log, box.pdb_outside_box_msg
# NOTE: box object is always shifted to place origin at (0,0,0)
# NOTE ON ORIGIN SHIFTS: The shifts are applied locally here. The box
# object is not affected and always has the origin at (0,0,0)
# output_box is copy of box with shift_cart corresponding to the output
# files. Normally this is the same as the original shift_cart. However
# if user has specified a new output origin it will differ.
# For output files ONLY:
# keep_origin==False leave origin at (0,0,0)
# keep_origin==True: we shift everything back to where it was,
# output_origin_grid_units=10,10,10: output origin is at (10,10,10)
# ncs_object is original
# box.ncs_object is shifted by shift_cart
# output_box.ncs_object is shifted back by -new shift_cart
# Additional note on output unit_cell and grid_units.
# The ccp4-style output map can specify the unit cell and grid units
# corresponding to that cell. This can be separate from the origin and
# number of grid points in the map as written. If specified, write these
# out to the output ccp4 map and also use this unit cell for writing
# any output PDB files
from copy import deepcopy
output_box=deepcopy(box) # won't use box below here except to return it
print >>log,"\nBox cell dimensions: (%.2f, %.2f, %.2f) A" %(
box.box_crystal_symmetry.unit_cell().parameters()[:3])
if box.shift_cart:
print>>log,"Working origin moved from grid position of"+\
": (%d, %d, %d) to (0,0,0) " %(
tuple(box.origin_shift_grid_units(reverse=True)))
print>>log,"Working origin moved from coordinates of:"+\
" (%.2f, %.2f, %.2f) A to (0,0,0)\n" %(
tuple(-col(box.shift_cart)))
if (params.keep_origin):
print >>log,"\nRestoring original position for output files"
print >>log,"Origin will be at grid position of"+\
": (%d, %d, %d) " %(
tuple(box.origin_shift_grid_units(reverse=True)))
print >>log,\
"\nOutput files will be in same location as original",
if not params.keep_map_size:
print >>log,"just cut out."
else:
print >>log,"keeping entire map"
print >>log,"Note that output maps are only valid in the cut out region.\n"
else:
if origin_to_match:
output_box.shift_cart=shift_cart_for_origin_to_match
if params.output_origin_grid_units:
print >>log,"Output map origin to be shifted to match target"
print >>log, "Placing origin at grid point (%s, %s, %s)" %(
origin_to_match)+"\n"+ \
"Final coordinate shift for output files: (%.2f,%.2f,%.2f) A\n" %(
tuple(col(output_box.shift_cart)-col(box.shift_cart)))
elif box.shift_cart:
output_box.shift_cart=(0,0,0) # not shifting back
print >>log,"Final origin will be at (0,0,0)"
print >>log,\
"Final coordinate shift for output files: (%.2f,%.2f,%.2f) A\n" %(
tuple(col(output_box.shift_cart)-col(box.shift_cart)))
else:
print >>log,\
"\nOutput files are in same location as original and origin "+\
"is at (0,0,0)\n"
ph_output_box_output_location = ph_box.deep_copy()
if output_box.shift_cart: # shift coordinates and NCS back by shift_cart
# NOTE output_box.shift_cart could be different than box.shift_cart if
# there is a target position for the origin and it is not the same as the
# original origin.
sites_cart = output_box.shift_sites_cart_back(
output_box.xray_structure_box.sites_cart())
xrs_offset = ph_output_box_output_location.extract_xray_structure(
crystal_symmetry=output_box.xray_structure_box.crystal_symmetry()
).replace_sites_cart(new_sites = sites_cart)
ph_output_box_output_location.adopt_xray_structure(xrs_offset)
if output_box.ncs_object:
output_box.ncs_object=output_box.ncs_object.coordinate_offset(
tuple(-col(output_box.shift_cart)))
shift_back=True
else:
shift_back=False
if params.keep_input_unit_cell_and_grid and \
(input_unit_cell_grid is not None) and \
(input_unit_cell is not None):
params.output_unit_cell=input_unit_cell
params.output_unit_cell_grid=input_unit_cell_grid
print >>log,"Setting output unit cell parameters and unit cell grid to"+\
" match\ninput map file"
if params.output_unit_cell: # Set output unit cell parameters
from cctbx import crystal
output_crystal_symmetry=crystal.symmetry(
unit_cell=params.output_unit_cell, space_group="P1")
output_unit_cell=output_crystal_symmetry.unit_cell()
print >>log,\
"Output unit cell set to: %.2f, %.2f, %.2f, %.2f, %.2f, %.2f)" %tuple(
output_crystal_symmetry.unit_cell().parameters())
else:
output_crystal_symmetry=None
# ============= Check/set output unit cell grid and cell parameters =======
if params.output_unit_cell_grid or output_crystal_symmetry:
if params.output_unit_cell_grid:
output_unit_cell_grid=params.output_unit_cell_grid
else:
output_unit_cell_grid=output_box.map_box.all()
print >>log,\
"Output unit cell grid set to: (%s, %s, %s)" %tuple(
output_unit_cell_grid)
expected_output_abc=[]
box_spacing=[]
output_spacing=[]
box_abc=output_box.xray_structure_box.\
crystal_symmetry().unit_cell().parameters()[:3]
if output_crystal_symmetry:
output_abc=output_crystal_symmetry.unit_cell().parameters()[:3]
else:
output_abc=[None,None,None]
for a_box,a_output,n_box,n_output in zip(
box_abc,
output_abc,
output_box.map_box.all(),
output_unit_cell_grid):
expected_output_abc.append(a_box*n_output/n_box)
box_spacing.append(a_box/n_box)
if output_crystal_symmetry:
output_spacing.append(a_output/n_output)
else:
output_spacing.append(a_box/n_box)
if output_crystal_symmetry: # make sure it is compatible...
r0=expected_output_abc[0]/output_abc[0]
r1=expected_output_abc[1]/output_abc[1]
r2=expected_output_abc[2]/output_abc[2]
from libtbx.test_utils import approx_equal
if not approx_equal(r0,r1,eps=0.001) or not approx_equal(r0,r2,eps=0.001):
print >>log,"WARNING: output_unit_cell and cell_grid will "+\
"change ratio of grid spacing.\nOld spacings: "+\
"(%.2f, %.2f, %.2f) A " %(tuple(box_spacing))+\
"\nNew spacings: (%.2f, %.2f, %.2f) A \n" %(tuple(output_spacing))
else:
output_abc=expected_output_abc
from cctbx import crystal
output_crystal_symmetry=crystal.symmetry(
unit_cell=list(output_abc)+[90,90,90], space_group="P1")
print >>log, \
"Output unit cell will be: (%.2f, %.2f, %.2f, %.2f, %.2f, %.2f)\n"%(
tuple(output_crystal_symmetry.unit_cell().parameters()))
else:
output_unit_cell_grid = map_data=output_box.map_box.all()
output_crystal_symmetry=output_box.xray_structure_box.crystal_symmetry()
# ========== Done check/set output unit cell grid and cell parameters =====
if write_output_files:
# Write PDB file
if ph_box.overall_counts().n_residues>0:
if(params.output_file_name_prefix is None):
file_name = "%s_box.pdb"%output_prefix
else: file_name = "%s.pdb"%params.output_file_name_prefix
ph_output_box_output_location.write_pdb_file(file_name=file_name,
crystal_symmetry = output_crystal_symmetry)
print >> log, "Writing boxed PDB with box unit cell to %s" %(
file_name)
# Write NCS file if NCS
if output_box.ncs_object and output_box.ncs_object.max_operators()>0:
if(params.output_file_name_prefix is None):
output_symmetry_file = "%s_box.ncs_spec"%output_prefix
else:
output_symmetry_file = "%s.ncs_spec"%params.output_file_name_prefix
output_box.ncs_object.format_all_for_group_specification(
file_name=output_symmetry_file)
print >>log,"\nWriting symmetry to %s" %( output_symmetry_file)
# Write ccp4 map.
if("ccp4" in params.output_format):
if(params.output_file_name_prefix is None):
file_name = "%s_box.ccp4"%output_prefix
else: file_name = "%s.ccp4"%params.output_file_name_prefix
output_box.write_ccp4_map(file_name=file_name,
output_crystal_symmetry=output_crystal_symmetry,
output_unit_cell_grid=output_unit_cell_grid,
shift_back=shift_back)
print >> log, "Writing boxed map "+\
"to CCP4 formatted file: %s"%file_name
# Write xplor map. Shift back if keep_origin=True
if("xplor" in params.output_format):
if(params.output_file_name_prefix is None):
file_name = "%s_box.xplor"%output_prefix
else: file_name = "%s.xplor"%params.output_file_name_prefix
output_box.write_xplor_map(file_name=file_name,
output_crystal_symmetry=output_crystal_symmetry,
output_unit_cell_grid=output_unit_cell_grid,
shift_back=shift_back,)
print >> log, "Writing boxed map "+\
"to X-plor formatted file: %s"%file_name
# Write mtz map coeffs. Shift back if keep_origin=True
if("mtz" in params.output_format):
if(params.output_file_name_prefix is None):
file_name = "%s_box.mtz"%output_prefix
else: file_name = "%s.mtz"%params.output_file_name_prefix
print >> log, "Writing map coefficients "+\
"to MTZ file: %s"%file_name
if(map_coeff is not None):
d_min = map_coeff.d_min()
elif params.resolution is not None:
d_min = params.resolution
else:
d_min = maptbx.d_min_from_map(map_data=output_box.map_box,
unit_cell=output_box.xray_structure_box.unit_cell())
output_box.map_coefficients(d_min=d_min,
resolution_factor=params.resolution_factor, file_name=file_name,
shift_back=shift_back)
print >> log
return box
def run(args, log = sys.stdout, as_gui_program=False):
if(len(args)==0):
parsed = defaults(log=log)
parsed.show(prefix=" ", out=log)
return
command_line = (option_parser()
.enable_symmetry_comprehensive()
.option("-q", "--quiet",
action="store_true",
default=False,
help="suppress output")
.option("--output_plots",
action="store_true",
default=False)
).process(args=args)
parsed = defaults(log=log)
processed_args = mmtbx.utils.process_command_line_args(
args=command_line.args,
cmd_cs=command_line.symmetry,
master_params=parsed,
log=log,
suppress_symmetry_related_errors=True)
processed_args.params.show(out=log)
params = processed_args.params.extract().density_modification
output_plots = command_line.options.output_plots
crystal_symmetry = crystal.symmetry(
unit_cell=params.input.unit_cell,
space_group_info=params.input.space_group)
reflection_files = {}
for rfn in (params.input.reflection_data.file_name,
params.input.experimental_phases.file_name,
params.input.map_coefficients.file_name):
if os.path.isfile(str(rfn)) and rfn not in reflection_files:
reflection_files.setdefault(
rfn, iotbx.reflection_file_reader.any_reflection_file(
file_name=rfn, ensure_read_access=False))
server = iotbx.reflection_file_utils.reflection_file_server(
crystal_symmetry=crystal_symmetry,
reflection_files=reflection_files.values())
fo = mmtbx.utils.determine_data_and_flags(
server,
parameters=params.input.reflection_data,
extract_r_free_flags=False,log=log).f_obs
hl_coeffs = mmtbx.utils.determine_experimental_phases(
server,
params.input.experimental_phases,
log=log,
parameter_scope="",
working_point_group=None,
symmetry_safety_check=True,
ignore_all_zeros=True)
if params.input.map_coefficients.file_name is not None:
map_coeffs = server.get_phases_deg(
file_name=params.input.map_coefficients.file_name,
labels=params.input.map_coefficients.labels,
convert_to_phases_if_necessary=False,
original_phase_units=None,
parameter_scope="",
parameter_name="labels").map_to_asu()
else:
map_coeffs = None
ncs_object = None
if params.input.ncs_file_name is not None:
ncs_object = ncs.ncs()
ncs_object.read_ncs(params.input.ncs_file_name)
ncs_object.display_all(log=log)
fo = fo.map_to_asu()
hl_coeffs = hl_coeffs.map_to_asu()
fo = fo.eliminate_sys_absent().average_bijvoet_mates()
hl_coeffs = hl_coeffs.eliminate_sys_absent().average_bijvoet_mates()
model_map = None
model_map_coeffs = None
if len(processed_args.pdb_file_names):
pdb_file = mmtbx.utils.pdb_file(
pdb_file_names=processed_args.pdb_file_names)
xs = pdb_file.pdb_inp.xray_structure_simple()
fo_, hl_ = fo, hl_coeffs
if params.change_basis_to_niggli_cell:
change_of_basis_op = xs.change_of_basis_op_to_niggli_cell()
xs = xs.change_basis(change_of_basis_op)
fo_ = fo_.change_basis(change_of_basis_op).map_to_asu()
hl_ = hl_.change_basis(change_of_basis_op).map_to_asu()
#fo_, hl_ = fo_.common_sets(hl_)
fmodel_refined = mmtbx.utils.fmodel_simple(
f_obs=fo_,
scattering_table="wk1995",#XXX pva: 1) neutrons? 2) move up as a parameter.
xray_structures=[xs],
bulk_solvent_correction=True,
anisotropic_scaling=True,
r_free_flags=fo_.array(data=flex.bool(fo_.size(), False)))
fmodel_refined.update(abcd=hl_)
master_phil = mmtbx.maps.map_and_map_coeff_master_params()
map_params = master_phil.fetch(iotbx.phil.parse("""\
map_coefficients {
map_type = 2mFo-DFc
isotropize = True
}
""")).extract().map_coefficients[0]
model_map_coeffs = mmtbx.maps.map_coefficients_from_fmodel(
fmodel=fmodel_refined, params=map_params)
model_map = model_map_coeffs.fft_map(
resolution_factor=params.grid_resolution_factor).real_map_unpadded()
import time
t0 = time.time()
dm = density_modify(
params,
fo,
hl_coeffs,
ncs_object=ncs_object,
map_coeffs=map_coeffs,
model_map_coeffs=model_map_coeffs,
log=log,
as_gui_program=as_gui_program)
time_dm = time.time()-t0
print >> log, "Time taken for density modification: %.2fs" %time_dm
# run cns
if 0:
from cctbx.development import cns_density_modification
cns_result = cns_density_modification.run(params, fo, hl_coeffs)
print cns_result.modified_map.all()
print dm.map.all()
dm_map_coeffs = dm.map_coeffs_in_original_setting
from cctbx import maptbx, miller
crystal_gridding = maptbx.crystal_gridding(
dm_map_coeffs.unit_cell(),
space_group_info=dm_map_coeffs.space_group().info(),
pre_determined_n_real=cns_result.modified_map.all())
dm_map = miller.fft_map(crystal_gridding, dm_map_coeffs).apply_sigma_scaling()
corr = flex.linear_correlation(cns_result.modified_map.as_1d(), dm_map.real_map_unpadded().as_1d())
print "CNS dm/mmtbx dm correlation:"
corr.show_summary()
if dm.model_map_coeffs is not None:
model_map = miller.fft_map(
crystal_gridding,
dm.miller_array_in_original_setting(dm.model_map_coeffs)).apply_sigma_scaling()
corr = flex.linear_correlation(cns_result.modified_map.as_1d(), model_map.real_map_unpadded().as_1d())
print "CNS dm/model correlation:"
corr.show_summary()
if output_plots:
plots_to_make = (
"fom", "skewness",
"r1_factor", "r1_factor_fom", "mean_solvent_density", "mean_protein_density",
"f000_over_v", "k_flip", "rms_solvent_density", "rms_protein_density",
"standard_deviation_local_rms", "mean_delta_phi", "mean_delta_phi_initial",
)
from matplotlib.backends.backend_pdf import PdfPages
from libtbx import pyplot
stats = dm.get_stats()
pdf = PdfPages("density_modification.pdf")
if len(dm.correlation_coeffs) > 1:
if 0:
start_coeffs, model_coeffs = dm.map_coeffs_start.common_sets(model_map_coeffs)
model_phases = model_coeffs.phases(deg=True).data()
exptl_phases = nearest_phase(
model_phases, start_coeffs.phases(deg=True).data(), deg=True)
corr = flex.linear_correlation(exptl_phases, model_phases)
corr.show_summary()
fig = pyplot.figure()
ax = fig.add_subplot(1,1,1)
ax.set_title("phases start")
ax.set_xlabel("Experimental phases")
ax.set_ylabel("Phases from refined model")
ax.scatter(exptl_phases,
model_phases,
marker="x", s=10)
pdf.savefig(fig)
#
dm_coeffs, model_coeffs = dm.map_coeffs.common_sets(model_map_coeffs)
model_phases = model_coeffs.phases(deg=True).data()
dm_phases = nearest_phase(
model_phases, dm_coeffs.phases(deg=True).data(), deg=True)
corr = flex.linear_correlation(dm_phases, model_phases)
corr.show_summary()
fig = pyplot.figure()
ax = fig.add_subplot(1,1,1)
ax.set_title("phases dm")
ax.set_xlabel("Phases from density modification")
ax.set_ylabel("Phases from refined model")
ax.scatter(dm_phases,
model_phases,
marker="x", s=10)
pdf.savefig(fig)
#
data = dm.correlation_coeffs
fig = pyplot.figure()
ax = fig.add_subplot(1,1,1)
ax.set_title("correlation coefficient")
ax.plot(range(1, dm.i_cycle+2), data)
pdf.savefig(fig)
#
data = dm.mean_phase_errors
fig = pyplot.figure()
ax = fig.add_subplot(1,1,1)
ax.set_title("Mean effective phase errors")
ax.plot(range(1, dm.i_cycle+2), data)
pdf.savefig(fig)
for plot in plots_to_make:
data = [getattr(stats.get_cycle_stats(i), plot) for i in range(1, dm.i_cycle+2)]
fig = pyplot.figure()
ax = fig.add_subplot(1,1,1)
ax.set_title(plot.replace("_", " "))
ax.plot(range(1, dm.i_cycle+2), data)
pdf.savefig(fig)
data = [stats.get_cycle_stats(i).rms_solvent_density/
stats.get_cycle_stats(i).rms_protein_density
for i in range(1, dm.i_cycle+2)]
fig = pyplot.figure()
ax = fig.add_subplot(1,1,1)
ax.set_title("RMS solvent/protein density ratio")
ax.plot(range(1, dm.i_cycle+2), data)
pdf.savefig(fig)
pdf.close()
dm_map_coeffs = dm.map_coeffs_in_original_setting
dm_hl_coeffs = dm.hl_coeffs_in_original_setting
# output map if requested
map_params = params.output.map
if map_params.file_name is not None:
fft_map = dm_map_coeffs.fft_map(resolution_factor=params.grid_resolution_factor)
if map_params.scale == "sigma":
fft_map.apply_sigma_scaling()
else:
fft_map.apply_volume_scaling()
gridding_first = gridding_last = None
title_lines = []
if map_params.format == "xplor":
fft_map.as_xplor_map(
file_name = map_params.file_name,
title_lines = title_lines,
gridding_first = gridding_first,
gridding_last = gridding_last)
else :
fft_map.as_ccp4_map(
file_name = map_params.file_name,
gridding_first = gridding_first,
gridding_last = gridding_last,
labels=title_lines)
# output map coefficients if requested
mtz_params = params.output.mtz
# Decide if we are going to actually write the mtz
if mtz_params.file_name is not None:
orig_fom,final_fom=dm.start_and_end_fom()
if mtz_params.skip_output_if_worse and final_fom < orig_fom:
ok_to_write_mtz=False
print "Not writing out mtz. Final FOM (%7.3f) worse than start (%7.3f)" %(
final_fom,orig_fom)
else: # usual
ok_to_write_mtz=True
else:
ok_to_write_mtz=True
if mtz_params.file_name is not None and ok_to_write_mtz:
label_decorator=iotbx.mtz.ccp4_label_decorator()
fo = dm.miller_array_in_original_setting(dm.f_obs_complete).common_set(dm_map_coeffs)
mtz_dataset = fo.as_mtz_dataset(
column_root_label="F",
label_decorator=label_decorator)
mtz_dataset.add_miller_array(
dm_map_coeffs,
column_root_label="FWT",
label_decorator=label_decorator)
phase_source = dm.miller_array_in_original_setting(dm.phase_source).common_set(dm_map_coeffs)
mtz_dataset.add_miller_array(
phase_source.array(data=flex.abs(phase_source.data())),
column_root_label="FOM",
column_types='W',
label_decorator=label_decorator)
mtz_dataset.add_miller_array(
phase_source.array(data=phase_source.phases(deg=True).data()),
column_root_label="PHIB",
column_types='P',
label_decorator=None)
if mtz_params.output_hendrickson_lattman_coefficients:
mtz_dataset.add_miller_array(
dm_hl_coeffs,
column_root_label="HL",
label_decorator=label_decorator)
mtz_dataset.mtz_object().write(mtz_params.file_name)
return result(
map_file=map_params.file_name,
mtz_file=mtz_params.file_name,
stats=dm.get_stats())
def run(args, crystal_symmetry=None, log=None):
h = "phenix.map_box: extract box with model and map around selected atoms"
if(log is None): log = sys.stdout
print_statistics.make_header(h, out=log)
default_message="""\
%s.
Usage:
phenix.map_box model.pdb map_coefficients.mtz selection="chain A and resseq 1:10"
or
phenix.map_box map.ccp4 density_select=True
Parameters:"""%h
if(len(args) == 0):
print default_message
master_phil.show(prefix=" ")
return
inputs = mmtbx.utils.process_command_line_args(args = args,
cmd_cs=crystal_symmetry,
master_params = master_phil)
params = inputs.params.extract()
# PDB file
if params.pdb_file and not inputs.pdb_file_names:
inputs.pdb_file_names=[params.pdb_file]
if(len(inputs.pdb_file_names)!=1 and not params.density_select):
raise Sorry("PDB file is needed unless density_select is set.")
print_statistics.make_sub_header("pdb model", out=log)
if len(inputs.pdb_file_names)>0:
pdb_inp = iotbx.pdb.input(file_name=inputs.pdb_file_names[0])
pdb_hierarchy = pdb_inp.construct_hierarchy()
pdb_atoms = pdb_hierarchy.atoms()
pdb_atoms.reset_i_seq()
else:
pdb_hierarchy=None
# Map or map coefficients
map_coeff = None
if(inputs.ccp4_map is None):
if(len(inputs.reflection_file_names)!=1):
raise Sorry("Map or map coefficients file is needed.")
map_coeff = reflection_file_utils.extract_miller_array_from_file(
file_name = inputs.reflection_file_names[0],
label = params.label,
type = "complex",
log = log)
fft_map = map_coeff.fft_map(resolution_factor=params.resolution_factor)
fft_map.apply_sigma_scaling()
map_data = fft_map.real_map_unpadded()
map_or_map_coeffs_prefix=os.path.basename(
inputs.reflection_file_names[0][:-4])
else:
print_statistics.make_sub_header("CCP4 map", out=log)
ccp4_map = inputs.ccp4_map
ccp4_map.show_summary(prefix=" ")
map_data = ccp4_map.map_data()
if inputs.ccp4_map_file_name.endswith(".ccp4"):
map_or_map_coeffs_prefix=os.path.basename(
inputs.ccp4_map_file_name[:-5])
else:
map_or_map_coeffs_prefix=os.path.basename(
inputs.ccp4_map_file_name[:-4])
#
if len(inputs.pdb_file_names)>0:
output_prefix=os.path.basename(inputs.pdb_file_names[0])[:-4]
else:
output_prefix=map_or_map_coeffs_prefix
if not pdb_hierarchy: # get an empty hierarchy
from cctbx.array_family import flex
pdb_hierarchy=iotbx.pdb.input(
source_info='',lines=flex.split_lines('')).construct_hierarchy()
xray_structure = pdb_hierarchy.extract_xray_structure(
crystal_symmetry=inputs.crystal_symmetry)
xray_structure.show_summary(f=log)
#
selection = pdb_hierarchy.atom_selection_cache().selection(
string = params.selection)
if selection.size():
print_statistics.make_sub_header("atom selection", out=log)
print >> log, "Selection string: selection='%s'"%params.selection
print >> log, \
" selects %d atoms from total %d atoms."%(selection.count(True),
selection.size())
sites_cart_all = xray_structure.sites_cart()
sites_cart = sites_cart_all.select(selection)
selection = xray_structure.selection_within(
radius = params.selection_radius,
selection = selection)
#
if params.density_select:
print_statistics.make_sub_header(
"Extracting box around selected density and writing output files", out=log)
else:
print_statistics.make_sub_header(
"Extracting box around selected atoms and writing output files", out=log)
#
box = mmtbx.utils.extract_box_around_model_and_map(
xray_structure = xray_structure,
map_data = map_data.as_double(),
box_cushion = params.box_cushion,
selection = selection,
density_select = params.density_select,
threshold = params.density_select_threshold)
if box.initial_shift_cart:
print >>log,"\nInitial coordinate shift will be (%.1f,%.1f,%.1f)\n" %(
box.initial_shift_cart)
if box.total_shift_cart:
print >>log,"Final coordinate shift: (%.1f,%.1f,%.1f)" %(
box.total_shift_cart)
print >>log,"Final cell dimensions: (%.1f,%.1f,%.1f)\n" %(
box.box_crystal_symmetry.unit_cell().parameters()[:3])
if box.pdb_outside_box_msg:
print >> log, box.pdb_outside_box_msg
if(params.output_file_name_prefix is None):
file_name = "%s_box.pdb"%output_prefix
else: file_name = "%s.pdb"%params.output_file_name_prefix
ph_box = pdb_hierarchy.select(selection)
ph_box.adopt_xray_structure(box.xray_structure_box)
ph_box.write_pdb_file(file_name=file_name, crystal_symmetry =
box.xray_structure_box.crystal_symmetry())
if("ccp4" in params.output_format):
if(params.output_file_name_prefix is None):
file_name = "%s_box.ccp4"%output_prefix
else: file_name = "%s.ccp4"%params.output_file_name_prefix
print >> log, "writing map to CCP4 formatted file: %s"%file_name
box.write_ccp4_map(file_name=file_name)
if("xplor" in params.output_format):
if(params.output_file_name_prefix is None):
file_name = "%s_box.xplor"%output_prefix
else: file_name = "%s.xplor"%params.output_file_name_prefix
print >> log, "writing map to X-plor formatted file: %s"%file_name
box.write_xplor_map(file_name=file_name)
if("mtz" in params.output_format):
if(params.output_file_name_prefix is None):
file_name = "%s_box.mtz"%output_prefix
else: file_name = "%s.mtz"%params.output_file_name_prefix
print >> log, "writing map coefficients to MTZ file: %s"%file_name
if(map_coeff is not None): d_min = map_coeff.d_min()
else:
d_min = maptbx.d_min_from_map(map_data=box.map_box,
unit_cell=box.xray_structure_box.unit_cell())
box.map_coefficients(d_min=d_min,
resolution_factor=params.resolution_factor, file_name=file_name)
if params.ncs_file:
if(params.output_file_name_prefix is None):
output_ncs_file = "%s_box.ncs_spec"%output_prefix
else: output_ncs_file = "%s.ncs_spec"%params.output_file_name_prefix
print >>log,"\nOffsetting NCS in %s and writing to %s" %(
params.ncs_file,output_ncs_file)
from mmtbx.ncs.ncs import ncs
ncs_object=ncs()
ncs_object.read_ncs(params.ncs_file,log=log)
ncs_object.display_all(log=log)
if not ncs_object or ncs_object.max_operators()<1:
print >>log,"Skipping...no NCS available"
elif box.total_shift_cart:
from scitbx.math import matrix
print >>log,"Shifting NCS operators "+\
"based on coordinate shift of (%7.1f,%7.1f,%7.1f)" %(
tuple(box.total_shift_cart))
ncs_object=ncs_object.coordinate_offset(
coordinate_offset=matrix.col(box.total_shift_cart))
ncs_object.display_all(log=log)
ncs_object.format_all_for_group_specification(
file_name=output_ncs_file)
box.ncs_object=ncs_object
else:
box.ncs_object=None
print >> log
return box
def run(args,
crystal_symmetry=None,
pdb_hierarchy=None,
map_data=None,
write_output_files=True,
log=None):
h = "phenix.map_box: extract box with model and map around selected atoms"
if (log is None): log = sys.stdout
print_statistics.make_header(h, out=log)
default_message = """\
%s.
Usage:
phenix.map_box model.pdb map_coefficients.mtz selection="chain A and resseq 1:10"
or
phenix.map_box map.ccp4 density_select=True
Parameters:""" % h
if (len(args) == 0 and not pdb_hierarchy):
print default_message
master_phil.show(prefix=" ")
return
inputs = mmtbx.utils.process_command_line_args(args=args,
cmd_cs=crystal_symmetry,
master_params=master_phil)
params = inputs.params.extract()
# PDB file
if params.pdb_file and not inputs.pdb_file_names and not pdb_hierarchy:
inputs.pdb_file_names = [params.pdb_file]
if (len(inputs.pdb_file_names) != 1 and not params.density_select
and not pdb_hierarchy):
raise Sorry("PDB file is needed unless density_select is set.")
print_statistics.make_sub_header("pdb model", out=log)
if len(inputs.pdb_file_names) > 0:
pdb_inp = iotbx.pdb.input(file_name=inputs.pdb_file_names[0])
pdb_hierarchy = pdb_inp.construct_hierarchy()
if pdb_hierarchy:
pdb_atoms = pdb_hierarchy.atoms()
pdb_atoms.reset_i_seq()
else:
pdb_hierarchy = None
# Map or map coefficients
map_coeff = None
if (not map_data):
# read first mtz file
if ((len(inputs.reflection_file_names) > 0)
or (params.map_coefficients_file is not None)):
# file in phil takes precedent
if (params.map_coefficients_file is not None):
if (len(inputs.reflection_file_names) == 0):
inputs.reflection_file_names.append(
params.map_coefficients_file)
else:
inputs.reflection_file_names[
0] = params.map_coefficients_file
map_coeff = reflection_file_utils.extract_miller_array_from_file(
file_name=inputs.reflection_file_names[0],
label=params.label,
type="complex",
log=log)
fft_map = map_coeff.fft_map(
resolution_factor=params.resolution_factor)
fft_map.apply_sigma_scaling()
map_data = fft_map.real_map_unpadded()
map_or_map_coeffs_prefix = os.path.basename(
inputs.reflection_file_names[0][:-4])
# or read CCP4 map
elif ((inputs.ccp4_map is not None)
or (params.ccp4_map_file is not None)):
if (params.ccp4_map_file is not None):
af = any_file(params.ccp4_map_file)
if (af.file_type == 'ccp4_map'):
inputs.ccp4_map = af.file_content
inputs.ccp4_map_file_name = params.ccp4_map_file
print_statistics.make_sub_header("CCP4 map", out=log)
ccp4_map = inputs.ccp4_map
ccp4_map.show_summary(prefix=" ", out=log)
map_data = ccp4_map.data #map_data()
if inputs.ccp4_map_file_name.endswith(".ccp4"):
map_or_map_coeffs_prefix = os.path.basename(
inputs.ccp4_map_file_name[:-5])
else:
map_or_map_coeffs_prefix = os.path.basename(
inputs.ccp4_map_file_name[:-4])
else: # have map_data
map_or_map_coeffs_prefix = None
# final check that map_data exists
if (map_data is None):
raise Sorry("Map or map coefficients file is needed.")
if len(inputs.pdb_file_names) > 0:
output_prefix = os.path.basename(inputs.pdb_file_names[0])[:-4]
else:
output_prefix = map_or_map_coeffs_prefix
if not pdb_hierarchy: # get an empty hierarchy
from cctbx.array_family import flex
pdb_hierarchy = iotbx.pdb.input(
source_info='', lines=flex.split_lines('')).construct_hierarchy()
xray_structure = pdb_hierarchy.extract_xray_structure(
crystal_symmetry=inputs.crystal_symmetry)
xray_structure.show_summary(f=log)
#
selection = pdb_hierarchy.atom_selection_cache().selection(
string=params.selection)
if selection.size():
print_statistics.make_sub_header("atom selection", out=log)
print >> log, "Selection string: selection='%s'" % params.selection
print >> log, \
" selects %d atoms from total %d atoms."%(selection.count(True),
selection.size())
sites_cart_all = xray_structure.sites_cart()
sites_cart = sites_cart_all.select(selection)
selection = xray_structure.selection_within(radius=params.selection_radius,
selection=selection)
#
if params.density_select:
print_statistics.make_sub_header(
"Extracting box around selected density and writing output files",
out=log)
else:
print_statistics.make_sub_header(
"Extracting box around selected atoms and writing output files",
out=log)
#
if params.value_outside_atoms == 'mean':
print >> log, "\nValue outside atoms mask will be set to mean inside mask"
if params.get_half_height_width:
print >> log, "\nHalf width at half height will be used to id boundaries"
box = mmtbx.utils.extract_box_around_model_and_map(
xray_structure=xray_structure,
map_data=map_data.as_double(),
box_cushion=params.box_cushion,
selection=selection,
density_select=params.density_select,
threshold=params.density_select_threshold,
get_half_height_width=params.get_half_height_width,
mask_atoms=params.mask_atoms,
soft_mask=params.soft_mask,
soft_mask_radius=params.soft_mask_radius,
mask_atoms_atom_radius=params.mask_atoms_atom_radius,
value_outside_atoms=params.value_outside_atoms,
)
if box.initial_shift_cart:
print >> log, "\nInitial coordinate shift will be (%.1f,%.1f,%.1f)\n" % (
box.initial_shift_cart)
if box.total_shift_cart:
print >> log, "Final coordinate shift: (%.1f,%.1f,%.1f)" % (
box.total_shift_cart)
print >> log, "Final cell dimensions: (%.1f,%.1f,%.1f)\n" % (
box.box_crystal_symmetry.unit_cell().parameters()[:3])
if box.pdb_outside_box_msg:
print >> log, box.pdb_outside_box_msg
ph_box = pdb_hierarchy.select(selection)
ph_box.adopt_xray_structure(box.xray_structure_box)
box.hierarchy = ph_box
if not write_output_files:
return box
if (params.output_file_name_prefix is None):
file_name = "%s_box.pdb" % output_prefix
else:
file_name = "%s.pdb" % params.output_file_name_prefix
ph_box = pdb_hierarchy.select(selection)
ph_box.adopt_xray_structure(box.xray_structure_box)
ph_box.write_pdb_file(
file_name=file_name,
crystal_symmetry=box.xray_structure_box.crystal_symmetry())
if ("ccp4" in params.output_format):
if (params.output_file_name_prefix is None):
file_name = "%s_box.ccp4" % output_prefix
else:
file_name = "%s.ccp4" % params.output_file_name_prefix
print >> log, "writing map to CCP4 formatted file: %s" % file_name
box.write_ccp4_map(file_name=file_name)
if ("xplor" in params.output_format):
if (params.output_file_name_prefix is None):
file_name = "%s_box.xplor" % output_prefix
else:
file_name = "%s.xplor" % params.output_file_name_prefix
print >> log, "writing map to X-plor formatted file: %s" % file_name
box.write_xplor_map(file_name=file_name)
if ("mtz" in params.output_format):
if (params.output_file_name_prefix is None):
file_name = "%s_box.mtz" % output_prefix
else:
file_name = "%s.mtz" % params.output_file_name_prefix
print >> log, "writing map coefficients to MTZ file: %s" % file_name
if (map_coeff is not None): d_min = map_coeff.d_min()
else:
d_min = maptbx.d_min_from_map(
map_data=box.map_box,
unit_cell=box.xray_structure_box.unit_cell())
box.map_coefficients(d_min=d_min,
resolution_factor=params.resolution_factor,
file_name=file_name)
if params.ncs_file:
if (params.output_file_name_prefix is None):
output_ncs_file = "%s_box.ncs_spec" % output_prefix
else:
output_ncs_file = "%s.ncs_spec" % params.output_file_name_prefix
print >> log, "\nOffsetting NCS in %s and writing to %s" % (
params.ncs_file, output_ncs_file)
from mmtbx.ncs.ncs import ncs
ncs_object = ncs()
ncs_object.read_ncs(params.ncs_file, log=log)
ncs_object.display_all(log=log)
if not ncs_object or ncs_object.max_operators() < 1:
print >> log, "Skipping...no NCS available"
elif box.total_shift_cart:
from scitbx.math import matrix
print >>log,"Shifting NCS operators "+\
"based on coordinate shift of (%7.1f,%7.1f,%7.1f)" %(
tuple(box.total_shift_cart))
ncs_object = ncs_object.coordinate_offset(
coordinate_offset=matrix.col(box.total_shift_cart))
ncs_object.display_all(log=log)
ncs_object.format_all_for_group_specification(
file_name=output_ncs_file)
box.ncs_object = ncs_object
else:
box.ncs_object = None
print >> log
return box
orth=unit_cell.orthogonalize(frac)
trans_orth=-1.*ncs_rota_matr*orth
return ncs_rota_matr,trans_orth
#####################################################
if __name__=="__main__":
log=sys.stdout
args=sys.argv[1:]
if 'exercise' in args:
file_name='TEST.NCS'
f=open(file_name,'w')
f.write(test_ncs_info)
f.close()
ncs_object=ncs()
ncs_object.read_ncs(file_name,source_info=file_name)
ncs_object.display_all()
file2='TEST2.NCS'
text=ncs_object.format_all_for_group_specification(file_name=file2)
if not text or text != test_ncs_info:
print "NOT OK ...please compare TEST.NCS (std) vs TEST2.NCS (output)"
ff=open('txt.dat','w')
ff.write(text)
ff.close()
else:
print "OK"
elif len(args)>0 and args[0] and os.path.isfile(args[0]):
ncs_object=ncs()
ncs_object.read_ncs(args[0],source_info=args[0])