def write_phenix_refine_cmd(session,
model,
model_file_name=None,
param_file_name=None,
restrain_coordination_sites=False,
include_hydrogens=False,
num_processors=1,
num_macrocycles=6,
nqh_flips=True,
scattering_type='xray'):
from chimerax.clipper import get_symmetry_handler
sh = get_symmetry_handler(model, create=False)
crystal_error_str = 'Model must be a crystal structure initialised in Clipper with experimental data!'
if sh is None:
raise UserError(crystal_error_str)
if not len(sh.map_mgr.xmapsets):
raise UserError(crystal_error_str)
xmapset = sh.map_mgr.xmapsets[0]
from .refine_input import write_phenix_refine_defaults
write_phenix_refine_defaults(
session,
model,
xmapset,
model_file_name=model_file_name,
param_file_name=param_file_name,
restrain_coordination_sites=restrain_coordination_sites,
include_hydrogens=include_hydrogens,
num_processors=num_processors,
num_macrocycles=num_macrocycles,
nqh_flips=nqh_flips,
scattering_type=scattering_type)
def close_models(session, models: 'string or list'):
'''
Close one or more models and/or maps. Behaviour varies depending on the
types of models specified. If the model is an atomic structure or a Clipper
top-level manager, the manager and all maps associated with the model will
be deleted. If a map, just that map will be deleted. If a map manager, all
maps handled by that manager will be deleted.
Args:
models: a single model ID or a list of model IDs.
'''
from chimerax.atomic import AtomicStructure
if not isinstance(models, list):
models = [models]
to_close = []
not_found = []
for mid in models:
m = _model_from_id(session, mid, error_if_not_found=False)
if not m:
session.logger.warning('Model ID {} not found!'.format(mid))
not_found.append(mid)
continue
if isinstance(m, AtomicStructure):
from chimerax.clipper import get_symmetry_handler
m = get_symmetry_handler(m)
to_close.append(m)
ret = {
'closed': [m.id_string for m in to_close],
'not_found': not_found,
}
session.models.close(to_close)
return ret
def _get_symmetry_handler(model):
from chimerax.atomic import AtomicStructure
from chimerax.clipper import get_symmetry_handler
from chimerax.clipper.symmetry import SymmetryManager
if isinstance(model, AtomicStructure):
return get_symmetry_handler(model)
elif isinstance(model, SymmetryManager):
return model
else:
err_string = (
'The ID {} corresponds to an incompatible model type: {}'.format(
model.id_string, type(model)))
raise TypeError(err_string)
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 load_structure_factors(session, file_path: 'string', model_id: 'string'):
'''
Load a set of structure factors in MTZ or CIF format, generate maps and
associate them with an existing atomic model. Data may be provided as any
of the following:
F / sigF
I / sigI
F+ / sigF+ / F- / sigF-
I+ / sigI+ / I- / sigI-
Free flags
F / phi
Only one experimental dataset should be provided, but any number of F/phi
maps many be provided. If experimental data is provided, three "live" maps
will be calculated: a standard 2mFo-DFc map; a second 2mFo-DFc map with a
resolution-dependent sharpening or smoothing B-factor applied (sharpened
at resolutions worse than 2.5A, smoothed otherwise); and a mFo-DFc map. For
best results, the experimental reflections should already be corrected for
anisotropy and any artefacts such as ice rings or beamstop shadows.
Anomalous data will be automatically merged, and intensities converted to
amplitudes using the method of Read & McCoy.
CAUTION: if no free flags are provided, a new set will be automatically
generated.
Any of the generated maps may be closed using close_model() on its id, or
the whole set may be closed at once by closing the map_mgr.
Args:
file_path: the full path to a single .mtz or .cif file
model_id: id string (e.g. as returned by load_model()) of the atomic
structure to associate the structure factors with, or its
top-level Clipper manager.
Returns:
{'manager': model id for the top-level Clipper manager for the model/maps,
'model': model id for the atomic structure,
'map_mgr': model id for the manager of all maps associated with the structure,
'mapset': model id for the container holding the maps resulting from this call,
'maps': {
'map 1 column names': map 1 model id,
...
}
}
'''
from chimerax.clipper.symmetry import SymmetryManager
from chimerax.atomic import AtomicStructure
m = _model_from_id(session, model_id)
if isinstance(m, AtomicStructure):
from chimerax.clipper import get_symmetry_handler
sh = get_symmetry_handler(m, create=True, auto_add_to_session=True)
elif isinstance(m, SymmetryManager):
sh = m
else:
err_string = (
'Model ID {} has unrecognised type: {}. '
'Should be one of AtomicStructure or SymmetryManager.').format(
model_id, type(m))
raise TypeError(err_string)
mmgr = sh.map_mgr
xmapset = mmgr.add_xmapset_from_file(file_path)
return {
'manager': sh.id_string,
'model': sh.structure.id_string,
'map_mgr': mmgr.id_string,
'mapset': xmapset.id_string,
'maps': {x.name: x.id_string
for x in xmapset},
}