mmtbx.ions.build module¶
Deals with modifying a structure to include unbuilt and misidentified ions.
- mmtbx.ions.build.clean_up_ions(fmodel, model, params, log=None, verbose=True)¶
- Parameters:
fmodel (mmtbx.f_model.manager)
model (mmtbx.model.manager)
params (libtbx.phil.scope_extract)
log (file, optional)
verbose (bool, optional)
- Returns:
An updated model with ions corrected.
- Return type:
mmtbx.model.manager
- mmtbx.ions.build.find_and_build_ions(manager, fmodels, model, wavelength, params, nproc=1, elements=<libtbx.AutoType object>, out=None, run_ordered_solvent=False, occupancy_strategy_enabled=False, group_anomalous_strategy_enabled=False, use_svm=None)¶
Analyzes the water molecules in a structure and re-labels them as ions if they scatter and bind environments that we expect of that ion.
- Parameters:
manager (mmtbx.ions.identity.manager)
fmodels (mmtbx.fmodels)
model (mmtbx.model.manager)
wavelength (float)
params (libtbx.phil.scope_extract)
nproc (int, optional)
out (file, optional)
run_ordered_solvent (bool, optional)
occupancy_strategy_enabled (bool, optional)
group_anomalous_strategy_enabled (bool, optional)
use_svm (bool, optional)