mmtbx.bulk_solvent package

Submodules

mmtbx.bulk_solvent.bulk_solvent_and_scaling module

class mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales(fmodel_kbu=None, params=None, log=None)

Bases: object

apply_back_trace_of_overall_exp_scale_matrix(xray_structure=None)
b_cart()
b_sols()
format_scale_matrix(m=None, log=None)
k_anisotropic()
k_isotropic()
k_masks()
k_sols()
r_all()
r_factor()
u_star()
mmtbx.bulk_solvent.bulk_solvent_and_scaling.k_sol_b_sol_b_cart_minimizer(fmodel_kbu, params=None, refine_k_sol=False, refine_b_sol=False, refine_u_star=False, refine_kbu=False)
mmtbx.bulk_solvent.bulk_solvent_and_scaling.kb_range(x_max, x_min, step)
class mmtbx.bulk_solvent.bulk_solvent_and_scaling.ksol_bsol_result(k_sol, b_sol, b_cart, r_factor)

Bases: object

mmtbx.bulk_solvent.scaler module

mmtbx.bulk_solvent.scaler.moving_average(x)
class mmtbx.bulk_solvent.scaler.run(f_obs, f_calc, f_mask, r_free_flags, ss, bin_selections=None, scale_method='combo', number_of_cycles=20, auto_convergence_tolerance=0.0001, log=None, auto=True, auto_convergence=True, bulk_solvent=True, try_poly=True, try_expanal=True, try_expmin=False, verbose=False)

Bases: object

anisotropic_scaling(r_start, use_highres)
apply_back_trace_of_overall_exp_scale_matrix(xray_structure=None)
apply_overall_scale()
bulk_solvent_scaling(r_start)
estimate_scale_k1(cutoff=4, width=1, min_reflections=500)
format_scale_matrix(m=None, log=None)
get_k_total(selection=None)
is_converged(r_start, tolerance=0.0001)
is_flags_good()

This function detects inadequate R-free flags.

k_anisotropic()
k_isotropic()
k_masks()
overall_isotropic_kb_estimate()
populate_bin_to_individual_k_mask_linear_interpolation(k_mask_bin)
r_all()
r_factor()
r_work()
set_k_isotropic_exp(r_start, verbose, b_lower_limit=-100)
show()
smooth(x)
try_scale(k_isotropic_exp=None, k_isotropic=None, k_mask=None, k_anisotropic=None, selection=None)
mmtbx.bulk_solvent.scaler.run_simple(fmodel_kbu, bin_selections, r_free_flags, bulk_solvent, aniso_scale)
class mmtbx.bulk_solvent.scaler.tmp(xray_structure, k_anisotropic, k_masks, ss)

Bases: object

Module contents