from __future__ import absolute_import, division, print_function import iotbx.pdb import mmtbx.utils import mmtbx.refinement.group pdb_answer_str = """\n CRYST1 21.937 4.866 23.477 90.00 107.08 90.00 P 1 21 1 2 ATOM 1 N GLY A 1 -9.009 4.612 6.102 1.00 15.00 N ATOM 2 CA GLY A 1 -9.052 4.207 4.651 1.00 15.00 C ATOM 3 C GLY A 1 -8.015 3.140 4.419 1.00 15.00 C ATOM 4 O GLY A 1 -7.523 2.521 5.381 1.00 15.00 O ATOM 5 N ASN A 2 -7.656 2.923 3.155 1.00 15.00 N ATOM 6 CA ASN A 2 -6.522 2.038 2.831 1.00 15.00 C ATOM 7 C ASN A 2 -5.241 2.537 3.427 1.00 15.00 C ATOM 8 O ASN A 2 -4.978 3.742 3.426 1.00 15.00 O ATOM 9 CB ASN A 2 -6.346 1.881 1.341 1.00 15.00 C ATOM 10 CG ASN A 2 -7.584 1.342 0.692 1.00 15.00 C ATOM 11 OD1 ASN A 2 -8.025 0.227 1.016 1.00 15.00 O ATOM 12 ND2 ASN A 2 -8.204 2.155 -0.169 1.00 15.00 N ATOM 13 N ASN A 3 -4.438 1.590 3.905 1.00 15.00 N ATOM 14 CA ASN A 3 -3.193 1.904 4.589 1.00 15.00 C ATOM 15 C ASN A 3 -1.955 1.332 3.895 1.00 15.00 C ATOM 16 O ASN A 3 -1.872 0.119 3.648 1.00 15.00 O ATOM 17 CB ASN A 3 -3.259 1.378 6.042 1.00 15.00 C ATOM 18 CG ASN A 3 -2.006 1.739 6.861 1.00 15.00 C ATOM 19 OD1 ASN A 3 -1.702 2.925 7.072 1.00 15.00 O ATOM 20 ND2 ASN A 3 -1.271 0.715 7.306 1.00 15.00 N ATOM 21 N GLN A 4 -1.005 2.228 3.598 1.00 15.00 N ATOM 22 CA GLN A 4 0.384 1.888 3.199 1.00 15.00 C ATOM 23 C GLN A 4 1.435 2.606 4.088 1.00 15.00 C ATOM 24 O GLN A 4 1.547 3.843 4.115 1.00 15.00 O ATOM 25 CB GLN A 4 0.656 2.148 1.711 1.00 15.00 C ATOM 26 CG GLN A 4 1.944 1.458 1.213 1.00 15.00 C ATOM 27 CD GLN A 4 2.504 2.044 -0.089 1.00 15.00 C ATOM 28 OE1 GLN A 4 2.744 3.268 -0.190 1.00 15.00 O ATOM 29 NE2 GLN A 4 2.750 1.161 -1.091 1.00 15.00 N ATOM 30 N GLN A 5 2.154 1.821 4.871 1.00 15.00 N ATOM 31 CA GLN A 5 3.270 2.361 5.640 1.00 15.00 C ATOM 32 C GLN A 5 4.594 1.768 5.172 1.00 15.00 C ATOM 33 O GLN A 5 4.768 0.546 5.054 1.00 15.00 O ATOM 34 CB GLN A 5 3.056 2.183 7.147 1.00 15.00 C ATOM 35 CG GLN A 5 1.829 2.950 7.647 1.00 15.00 C ATOM 36 CD GLN A 5 1.344 2.414 8.954 1.00 15.00 C ATOM 37 OE1 GLN A 5 0.774 1.325 9.002 1.00 15.00 O ATOM 38 NE2 GLN A 5 1.549 3.187 10.039 1.00 15.00 N ATOM 39 N ASN A 6 5.514 2.664 4.856 1.00 15.00 N ATOM 40 CA ASN A 6 6.831 2.310 4.318 1.00 15.00 C ATOM 41 C ASN A 6 7.854 2.761 5.324 1.00 15.00 C ATOM 42 O ASN A 6 8.219 3.943 5.374 1.00 15.00 O ATOM 43 CB ASN A 6 7.065 3.016 2.993 1.00 15.00 C ATOM 44 CG ASN A 6 5.961 2.735 2.003 1.00 15.00 C ATOM 45 OD1 ASN A 6 5.798 1.604 1.551 1.00 15.00 O ATOM 46 ND2 ASN A 6 5.195 3.747 1.679 1.00 15.00 N ATOM 47 N TYR A 7 8.292 1.817 6.147 1.00 15.00 N ATOM 48 CA TYR A 7 9.159 2.144 7.299 1.00 15.00 C ATOM 49 C TYR A 7 10.603 2.331 6.885 1.00 15.00 C ATOM 50 O TYR A 7 11.041 1.811 5.855 1.00 15.00 O ATOM 51 CB TYR A 7 9.061 1.065 8.369 1.00 15.00 C ATOM 52 CG TYR A 7 7.665 0.929 8.902 1.00 15.00 C ATOM 53 CD1 TYR A 7 6.771 0.021 8.327 1.00 15.00 C ATOM 54 CD2 TYR A 7 7.210 1.756 9.920 1.00 15.00 C ATOM 55 CE1 TYR A 7 5.480 -0.094 8.796 1.00 15.00 C ATOM 56 CE2 TYR A 7 5.904 1.649 10.416 1.00 15.00 C ATOM 57 CZ TYR A 7 5.047 0.729 9.831 1.00 15.00 C ATOM 58 OH TYR A 7 3.766 0.589 10.291 1.00 15.00 O ATOM 59 OXT TYR A 7 11.358 2.999 7.612 1.00 15.00 O END """ pdb_poor_adp_str = """\n CRYST1 21.937 4.866 23.477 90.00 107.08 90.00 P 1 21 1 2 ATOM 1 N GLY A 1 -9.009 4.612 6.102 1.00 0.01 N ATOM 2 CA GLY A 1 -9.052 4.207 4.651 1.00 0.01 C ATOM 3 C GLY A 1 -8.015 3.140 4.419 1.00 0.01 C ATOM 4 O GLY A 1 -7.523 2.521 5.381 1.00 0.01 O ATOM 5 N ASN A 2 -7.656 2.923 3.155 1.00495.00 N ATOM 6 CA ASN A 2 -6.522 2.038 2.831 1.00495.00 C ATOM 7 C ASN A 2 -5.241 2.537 3.427 1.00495.00 C ATOM 8 O ASN A 2 -4.978 3.742 3.426 1.00495.00 O ATOM 9 CB ASN A 2 -6.346 1.881 1.341 1.00495.00 C ATOM 10 CG ASN A 2 -7.584 1.342 0.692 1.00495.00 C ATOM 11 OD1 ASN A 2 -8.025 0.227 1.016 1.00495.00 O ATOM 12 ND2 ASN A 2 -8.204 2.155 -0.169 1.00495.00 N ATOM 13 N ASN A 3 -4.438 1.590 3.905 1.00 2.00 N ATOM 14 CA ASN A 3 -3.193 1.904 4.589 1.00 2.00 C ATOM 15 C ASN A 3 -1.955 1.332 3.895 1.00 2.00 C ATOM 16 O ASN A 3 -1.872 0.119 3.648 1.00 2.00 O ATOM 17 CB ASN A 3 -3.259 1.378 6.042 1.00 2.00 C ATOM 18 CG ASN A 3 -2.006 1.739 6.861 1.00 2.00 C ATOM 19 OD1 ASN A 3 -1.702 2.925 7.072 1.00 2.00 O ATOM 20 ND2 ASN A 3 -1.271 0.715 7.306 1.00 2.00 N ATOM 21 N GLN A 4 -1.005 2.228 3.598 1.00385.00 N ATOM 22 CA GLN A 4 0.384 1.888 3.199 1.00385.00 C ATOM 23 C GLN A 4 1.435 2.606 4.088 1.00385.00 C ATOM 24 O GLN A 4 1.547 3.843 4.115 1.00385.00 O ATOM 25 CB GLN A 4 0.656 2.148 1.711 1.00385.00 C ATOM 26 CG GLN A 4 1.944 1.458 1.213 1.00385.00 C ATOM 27 CD GLN A 4 2.504 2.044 -0.089 1.00385.00 C ATOM 28 OE1 GLN A 4 2.744 3.268 -0.190 1.00385.00 O ATOM 29 NE2 GLN A 4 2.750 1.161 -1.091 1.00385.00 N ATOM 30 N GLN A 5 2.154 1.821 4.871 1.00 0.03 N ATOM 31 CA GLN A 5 3.270 2.361 5.640 1.00 0.03 C ATOM 32 C GLN A 5 4.594 1.768 5.172 1.00 0.03 C ATOM 33 O GLN A 5 4.768 0.546 5.054 1.00 0.03 O ATOM 34 CB GLN A 5 3.056 2.183 7.147 1.00 0.03 C ATOM 35 CG GLN A 5 1.829 2.950 7.647 1.00 0.03 C ATOM 36 CD GLN A 5 1.344 2.414 8.954 1.00 0.03 C ATOM 37 OE1 GLN A 5 0.774 1.325 9.002 1.00 0.03 O ATOM 38 NE2 GLN A 5 1.549 3.187 10.039 1.00 0.03 N ATOM 39 N ASN A 6 5.514 2.664 4.856 1.00290.00 N ATOM 40 CA ASN A 6 6.831 2.310 4.318 1.00290.00 C ATOM 41 C ASN A 6 7.854 2.761 5.324 1.00290.00 C ATOM 42 O ASN A 6 8.219 3.943 5.374 1.00290.00 O ATOM 43 CB ASN A 6 7.065 3.016 2.993 1.00290.00 C ATOM 44 CG ASN A 6 5.961 2.735 2.003 1.00290.00 C ATOM 45 OD1 ASN A 6 5.798 1.604 1.551 1.00290.00 O ATOM 46 ND2 ASN A 6 5.195 3.747 1.679 1.00290.00 N ATOM 47 N TYR A 7 8.292 1.817 6.147 1.00 0.00 N ATOM 48 CA TYR A 7 9.159 2.144 7.299 1.00 0.00 C ATOM 49 C TYR A 7 10.603 2.331 6.885 1.00 0.00 C ATOM 50 O TYR A 7 11.041 1.811 5.855 1.00 0.00 O ATOM 51 CB TYR A 7 9.061 1.065 8.369 1.00 0.00 C ATOM 52 CG TYR A 7 7.665 0.929 8.902 1.00 0.00 C ATOM 53 CD1 TYR A 7 6.771 0.021 8.327 1.00 0.00 C ATOM 54 CD2 TYR A 7 7.210 1.756 9.920 1.00 0.00 C ATOM 55 CE1 TYR A 7 5.480 -0.094 8.796 1.00 0.00 C ATOM 56 CE2 TYR A 7 5.904 1.649 10.416 1.00 0.00 C ATOM 57 CZ TYR A 7 5.047 0.729 9.831 1.00 0.00 C ATOM 58 OH TYR A 7 3.766 0.589 10.291 1.00 0.00 O ATOM 59 OXT TYR A 7 11.358 2.999 7.612 1.00 0.00 O END """ pdb_poor_occ_str = """\n CRYST1 21.937 4.866 23.477 90.00 107.08 90.00 P 1 21 1 2 ATOM 1 N GLY A 1 -9.009 4.612 6.102 0.01 15.00 N ATOM 2 CA GLY A 1 -9.052 4.207 4.651 0.01 15.00 C ATOM 3 C GLY A 1 -8.015 3.140 4.419 0.01 15.00 C ATOM 4 O GLY A 1 -7.523 2.521 5.381 0.01 15.00 O ATOM 5 N ASN A 2 -7.656 2.923 3.155 0.91 15.00 N ATOM 6 CA ASN A 2 -6.522 2.038 2.831 0.91 15.00 C ATOM 7 C ASN A 2 -5.241 2.537 3.427 0.91 15.00 C ATOM 8 O ASN A 2 -4.978 3.742 3.426 0.91 15.00 O ATOM 9 CB ASN A 2 -6.346 1.881 1.341 0.91 15.00 C ATOM 10 CG ASN A 2 -7.584 1.342 0.692 0.91 15.00 C ATOM 11 OD1 ASN A 2 -8.025 0.227 1.016 0.91 15.00 O ATOM 12 ND2 ASN A 2 -8.204 2.155 -0.169 0.91 15.00 N ATOM 13 N ASN A 3 -4.438 1.590 3.905 0.00 15.00 N ATOM 14 CA ASN A 3 -3.193 1.904 4.589 0.00 15.00 C ATOM 15 C ASN A 3 -1.955 1.332 3.895 0.00 15.00 C ATOM 16 O ASN A 3 -1.872 0.119 3.648 0.00 15.00 O ATOM 17 CB ASN A 3 -3.259 1.378 6.042 0.00 15.00 C ATOM 18 CG ASN A 3 -2.006 1.739 6.861 0.00 15.00 C ATOM 19 OD1 ASN A 3 -1.702 2.925 7.072 0.00 15.00 O ATOM 20 ND2 ASN A 3 -1.271 0.715 7.306 0.00 15.00 N ATOM 21 N GLN A 4 -1.005 2.228 3.598 7.00 15.00 N ATOM 22 CA GLN A 4 0.384 1.888 3.199 7.00 15.00 C ATOM 23 C GLN A 4 1.435 2.606 4.088 7.00 15.00 C ATOM 24 O GLN A 4 1.547 3.843 4.115 7.00 15.00 O ATOM 25 CB GLN A 4 0.656 2.148 1.711 7.00 15.00 C ATOM 26 CG GLN A 4 1.944 1.458 1.213 7.00 15.00 C ATOM 27 CD GLN A 4 2.504 2.044 -0.089 7.00 15.00 C ATOM 28 OE1 GLN A 4 2.744 3.268 -0.190 7.00 15.00 O ATOM 29 NE2 GLN A 4 2.750 1.161 -1.091 7.00 15.00 N ATOM 30 N GLN A 5 2.154 1.821 4.871 0.01 15.00 N ATOM 31 CA GLN A 5 3.270 2.361 5.640 0.01 15.00 C ATOM 32 C GLN A 5 4.594 1.768 5.172 0.01 15.00 C ATOM 33 O GLN A 5 4.768 0.546 5.054 0.01 15.00 O ATOM 34 CB GLN A 5 3.056 2.183 7.147 0.01 15.00 C ATOM 35 CG GLN A 5 1.829 2.950 7.647 0.01 15.00 C ATOM 36 CD GLN A 5 1.344 2.414 8.954 0.01 15.00 C ATOM 37 OE1 GLN A 5 0.774 1.325 9.002 0.01 15.00 O ATOM 38 NE2 GLN A 5 1.549 3.187 10.039 0.01 15.00 N ATOM 39 N ASN A 6 5.514 2.664 4.856 -1.00 15.00 N ATOM 40 CA ASN A 6 6.831 2.310 4.318 -1.00 15.00 C ATOM 41 C ASN A 6 7.854 2.761 5.324 -1.00 15.00 C ATOM 42 O ASN A 6 8.219 3.943 5.374 -1.00 15.00 O ATOM 43 CB ASN A 6 7.065 3.016 2.993 -1.00 15.00 C ATOM 44 CG ASN A 6 5.961 2.735 2.003 -1.00 15.00 C ATOM 45 OD1 ASN A 6 5.798 1.604 1.551 -1.00 15.00 O ATOM 46 ND2 ASN A 6 5.195 3.747 1.679 -1.00 15.00 N ATOM 47 N TYR A 7 8.292 1.817 6.147 5.00 15.00 N ATOM 48 CA TYR A 7 9.159 2.144 7.299 5.00 15.00 C ATOM 49 C TYR A 7 10.603 2.331 6.885 5.00 15.00 C ATOM 50 O TYR A 7 11.041 1.811 5.855 5.00 15.00 O ATOM 51 CB TYR A 7 9.061 1.065 8.369 5.00 15.00 C ATOM 52 CG TYR A 7 7.665 0.929 8.902 5.00 15.00 C ATOM 53 CD1 TYR A 7 6.771 0.021 8.327 5.00 15.00 C ATOM 54 CD2 TYR A 7 7.210 1.756 9.920 5.00 15.00 C ATOM 55 CE1 TYR A 7 5.480 -0.094 8.796 5.00 15.00 C ATOM 56 CE2 TYR A 7 5.904 1.649 10.416 5.00 15.00 C ATOM 57 CZ TYR A 7 5.047 0.729 9.831 5.00 15.00 C ATOM 58 OH TYR A 7 3.766 0.589 10.291 5.00 15.00 O ATOM 59 OXT TYR A 7 11.358 2.999 7.612 5.00 15.00 O END """ def run(refine, target, residues_per_window = 1): if(refine == "refine_adp"): refine_adp=True refine_occ=False pdb_poor_str = pdb_poor_adp_str else: refine_adp=False refine_occ=True pdb_poor_str = pdb_poor_occ_str pdb_inp_poor = iotbx.pdb.input(source_info=None, lines=pdb_poor_str) ph = pdb_inp_poor.construct_hierarchy() ph.atoms().reset_i_seq() xrs_poor = pdb_inp_poor.xray_structure_simple() xrs_answer = iotbx.pdb.input(source_info=None, lines=pdb_answer_str).xray_structure_simple() f_obs = abs(xrs_answer.structure_factors(d_min=7,algorithm="direct").f_calc()) sfp=mmtbx.f_model.sf_and_grads_accuracy_master_params.extract() sfp.algorithm="direct" fmodel = mmtbx.f_model.manager( sf_and_grads_accuracy_params = sfp, xray_structure = xrs_poor, f_obs = f_obs) fmodel.show() fmodel.update(target_name=target) print("Initial r_work=%6.4f r_free=%6.4f"%(fmodel.r_work(), fmodel.r_free())) tg = mmtbx.utils.experimental_data_target_and_gradients(fmodel = fmodel) # get group gradients using internal splitting into groups result = tg.group_occupancy_grads( pdb_hierarchy = ph, residues_per_window = residues_per_window) for r in result: print("chainID_resseqs: %s occupancy_grad: %-15.6f"%tuple(r)) print() # group occupancy selections selections = ph.chunk_selections(residues_per_chunk=residues_per_window) # refine occupancies if refine_occ: print("refine occupancies:") rr = mmtbx.refinement.group.manager( fmodel = fmodel, selections = selections, max_number_of_iterations = 50, number_of_macro_cycles = 25, refine_occ = True, convergence_test = False, use_restraints = True, run_finite_differences_test = True, occupancy_max = 999, occupancy_min = -999) # refine group B-factors if refine_adp: print("refine b-factors") rr = mmtbx.refinement.group.manager( fmodel = fmodel, selections = selections, max_number_of_iterations = 50, number_of_macro_cycles = 25, convergence_test = False, run_finite_differences_test = True, refine_adp = True, use_restraints = True) print("After refinement r_work=%6.4f r_free=%6.4f"%( fmodel.r_work(), fmodel.r_free())) ph.adopt_xray_structure(fmodel.xray_structure) ph.write_pdb_file(file_name="refined_occupancies.pdb", crystal_symmetry = f_obs.crystal_symmetry()) assert rr.tested > 0, [target, refine] r_work = fmodel.r_work()*100 assert r_work < 0.1, [r_work, target] if (__name__ == "__main__"): for target in ["ml", "ls_wunit_kunit"]: for refine in ["refine_adp", "refine_occ"]: run(refine=refine, target=target)