def _load_model_and_mtz(self, pdb_file, mtz_file):
import os
if (not os.path.isfile(pdb_file)) or (not os.path.isfile(mtz_file)):
raise RuntimeError('One or more output files not found: \n'
'{}\n{}'.format(pdb_file, mtz_file))
self.clear_refinement()
from chimerax.open_command.cmd import provider_open
m = self._current_model = provider_open(self.session, [pdb_file])[0]
self.isolde.add_xtal_data(mtz_file, model=m)
self.set_default_atom_coloring()
self.isolde.change_selected_model(m)
def show_start_model(self, file_name):
'''
Load the starting model from file. Takes the filename (including full
path) as an argument.
'''
if self._start_model is not None and not self._start_model.deleted:
self.session.models.close([self._start_model])
from chimerax.open_command.cmd import provider_open
m = self._start_model = provider_open(self.session, [file_name])[0]
m.bonds.radii=0.05
from chimerax.clipper.symmetry import get_symmetry_handler
get_symmetry_handler(m)
self.set_default_atom_coloring()
return True
def test_xtal_mgr(session):
from chimerax.open_command.cmd import provider_open
m = provider_open(session, [os.path.join(_basedir, '3io0.pdb')])[0]
from ..clipper_mtz import ReflectionDataContainer
from .. import atom_list_from_sel
from ..clipper_python.ext import Xtal_mgr
rdc = ReflectionDataContainer(session,
os.path.join(_basedir, '3io0-sf.mtz'))
xm = Xtal_mgr(rdc.hklinfo, rdc.free_flags.data, rdc.grid_sampling,
rdc.experimental_data.datasets['FOBS, SIGFOBS'].data)
xm.generate_fcalc(atom_list_from_sel(m.atoms))
print("Rfree: {}".format(xm.rfree))
print("Rwork: {}".format(xm.rwork))
return xm, rdc
def test_clipper_sym(session, radius=12):
import os
from chimerax.open_command.cmd import provider_open
libdir = os.path.abspath(os.path.dirname(__file__))
m = provider_open(session, [os.path.join(libdir, '3io0.pdb')])[0]
m.atoms.displays = True
from chimerax.std_commands import cofr
cofr.cofr(session, method='center of view', show_pivot=True)
from chimerax.clipper import symmetry
sym_handler = symmetry.get_symmetry_handler(m, create=True)
sym_handler.spotlight_radius = radius
sym_handler.map_mgr.add_xmapset_from_mtz(os.path.join(
libdir, '3io0_combined.mtz'),
oversampling_rate=1.5)
sym_handler.map_mgr.nxmapset.add_nxmap_handler_from_file(
os.path.join(libdir, '3io0_real_space.ccp4'))
return sym_handler
def load_model(session, file_path: 'string'):
'''
Load a model from a single PDB or mmCIF file. Multi-model files are not
supported.
Args:
file_path: the full path to a single PDB or mmCIF file
Returns:
{'manager': model id for the top-level Clipper manager for the model,
'model': model id for the atomic structure itself.
}
'''
from chimerax.open_command.cmd import provider_open
from chimerax.clipper import get_symmetry_handler
m = provider_open(session, [file_path])[0]
sh = get_symmetry_handler(m, create=True, auto_add_to_session=True)
return {'manager': sh.id_string, 'model id': m.id_string}
def count_matches_for_pdb_list(session,
pdb_ids,
identity_cutoff=0.3,
evalue_cutoff=1,
log_file='pdb_matches.log'):
from chimerax.open_command.cmd import provider_open
with open(log_file, 'wt') as log:
log.write('PDB ID,Chain ID,Match count,Matching ids\n')
for pdb_id in pdb_ids:
try:
models = provider_open(session, [pdb_id])
m = models[0]
except:
print(f'Failed on {pdb_id}!')
continue
matches = get_wwpdb_matches_for_all_chains(m, identity_cutoff,
evalue_cutoff)
for c, matching in matches.items():
num_matches = len(matching)
log.write(f'{pdb_id},{c},{num_matches},{" ".join(matching)}\n')
log.flush()
session.models.close(models)
import numpy
import os
dpath = os.path.dirname(os.path.abspath(__file__))
from chimerax.open_command.cmd import provider_open
m = provider_open(session, [os.path.join(dpath, '5f4y.pdb')])[0]
from chimerax.clipper import CrystalStructure
cs = CrystalStructure(session, m, os.path.join('5f4y_map_coeffs.mtz')
from chimerax.clipper.crystal import _find_box_corner
box_corner_grid, box_corner_xyz = _find_box_corner(cs._sym_box_center, cs.cell, cs.grid, 25)
dim = numpy.array([50,50,50], numpy.int32)
symops = symops = cs.unit_cell.all_symops_in_box(box_corner_xyz, dim, True)
tfs = symops.all_matrices_orth(cs.cell)
from chimerax.clipper import geometry
m.atoms.displays = True
results = geometry.sym_transforms_in_sphere(m.atoms, tfs, session.view.center_of_rotation, 50)