from __future__ import absolute_import, division, print_function import iotbx.pdb import mmtbx.f_model pdb_str="""\ CRYST1 16.960 19.455 19.841 90.00 90.00 90.00 P 1 ATOM 1 N ASP A 18 14.727 11.381 11.191 1.00 21.41 N ATOM 2 CA ASP A 18 14.022 12.655 11.131 1.00 34.70 C ATOM 3 C ASP A 18 13.805 13.085 9.684 1.00 35.50 C ATOM 4 O ASP A 18 14.760 13.408 8.976 1.00 38.48 O ATOM 5 CB ASP A 18 14.798 13.731 11.893 1.00 38.15 C ATOM 6 CG ASP A 18 14.068 15.059 11.937 1.00 27.39 C ATOM 7 OD1 ASP A 18 13.282 15.275 12.883 1.00 35.78 O ATOM 8 OD2 ASP A 18 14.282 15.889 11.028 1.00 30.67 O ATOM 9 N ASN A 19 12.544 13.082 9.257 1.00 22.94 N ATOM 10 CA ASN A 19 12.169 13.463 7.896 1.00 22.82 C ATOM 11 C ASN A 19 12.886 12.623 6.841 1.00 20.25 C ATOM 12 O ASN A 19 13.859 13.069 6.233 1.00 33.24 O ATOM 13 CB ASN A 19 12.419 14.959 7.663 1.00 28.83 C ATOM 14 CG ASN A 19 11.659 15.505 6.465 1.00 26.44 C ATOM 15 OD1 ASN A 19 11.356 14.780 5.518 1.00 22.64 O ATOM 16 ND2 ASN A 19 11.350 16.797 6.504 1.00 28.91 N ATOM 17 N TYR A 20 12.397 11.404 6.631 1.00 23.81 N ATOM 18 CA TYR A 20 12.992 10.492 5.662 1.00 35.69 C ATOM 19 C TYR A 20 11.909 9.888 4.773 1.00 28.94 C ATOM 20 O TYR A 20 11.281 10.589 3.980 1.00 25.26 O ATOM 21 CB TYR A 20 13.765 9.382 6.379 1.00 33.37 C ATOM 22 CG TYR A 20 13.470 9.266 7.861 1.00 31.48 C ATOM 23 CD1 TYR A 20 12.437 8.463 8.327 1.00 36.91 C ATOM 24 CD2 TYR A 20 14.228 9.963 8.794 1.00 21.36 C ATOM 25 CE1 TYR A 20 12.169 8.355 9.678 1.00 36.56 C ATOM 26 CE2 TYR A 20 13.967 9.862 10.147 1.00 29.56 C ATOM 27 CZ TYR A 20 12.936 9.057 10.583 1.00 35.08 C ATOM 28 OH TYR A 20 12.671 8.953 11.930 1.00 38.73 O ATOM 29 N ARG A 21 11.695 8.584 4.914 1.00 38.95 N ATOM 30 CA ARG A 21 10.695 7.881 4.120 1.00 38.77 C ATOM 31 C ARG A 21 9.825 6.998 5.010 1.00 27.69 C ATOM 32 O ARG A 21 8.635 6.819 4.750 1.00 22.82 O ATOM 33 CB ARG A 21 11.373 7.048 3.027 1.00 20.00 C ATOM 34 CG ARG A 21 10.419 6.410 2.025 1.00 20.00 C ATOM 35 CD ARG A 21 10.098 4.968 2.391 1.00 20.00 C ATOM 36 NE ARG A 21 9.189 4.346 1.434 1.00 20.00 N ATOM 37 CZ ARG A 21 8.730 3.103 1.542 1.00 20.00 C ATOM 38 NH1 ARG A 21 9.094 2.347 2.569 1.00 20.00 N ATOM 39 NH2 ARG A 21 7.906 2.617 0.625 1.00 20.00 N """ def run(): # get xray_structure object from input PDB file pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str) xray_structure = pdb_inp.xray_structure_simple() # make up "F-obs" and R-free-flags f_obs = abs(xray_structure.structure_factors(d_min=1.5).f_calc()) r_free_flags = f_obs.generate_r_free_flags() # instantiate fmodel object fmodel = mmtbx.f_model.manager( f_obs = f_obs, r_free_flags = r_free_flags, xray_structure = xray_structure) # now we can caclualte R-factors and show some statistics print("r_work:", fmodel.r_work()) print("r_free:", fmodel.r_free()) fmodel.show() # we can get get 3d array of map values fft_map = fmodel.electron_density_map().fft_map(map_type = "mFobs-DFmodel") fft_map.apply_sigma_scaling() map_data = fft_map.real_map_unpadded(in_place=False) # output map in X-plor formatted file fft_map.as_xplor_map( file_name="mfo-dfm.xplor", title_lines=["mFobs-DFmodel"], gridding_first=(0,0,0), gridding_last=fft_map.n_real()) # we can compute another map map_coeffs = fmodel.electron_density_map( ).map_coefficients(map_type = "2mFobs-DFmodel") # output it as MTZ file mtz_dataset = map_coeffs.as_mtz_dataset(column_root_label="2mFoDFc") mtz_object = mtz_dataset.mtz_object() mtz_object.write(file_name = "amap.mtz") # and get actual map values fft_map = map_coeffs.fft_map(resolution_factor=0.25) fft_map.apply_volume_scaling() map_data = fft_map.real_map_unpadded() if (__name__ == "__main__"): run() print("OK")