from __future__ import absolute_import, division, print_function from mmtbx.ions.utils import anonymize_ions from libtbx.utils import null_out from libtbx import group_args from libtbx import easy_run import iotbx.pdb import os def generate_calcium_inputs(file_base="ca_frag", anonymize=True): """ Generate both a PDB file and an MTZ file for the calcium-bound structure, with the calcium optionally replaced by solvent after F(model) was calculated. Calcium is simulated as an anomalous scatterer at 1.025 A. (This method is also a suitable template for generating any other model/data files for specific structures.) Parameters ---------- file_base : str, optional anonymize : bool, optional Replace all ions in the returned pdb file with waters. Returns ------- mtz_path : str pdb_path : str """ pdb_file = write_pdb_input_calcium_binding(file_base=file_base) mtz_file = generate_mtz_file( file_base=file_base, d_min=1.5, anomalous_scatterers=[ group_args(selection="element CA", fp=0.25, fdp=0.5) ]) assert (os.path.isfile(pdb_file)) and (os.path.isfile(mtz_file)) if anonymize: pdb_in = iotbx.pdb.input(pdb_file) hierarchy = pdb_in.construct_hierarchy() hierarchy, n = anonymize_ions(hierarchy, log=null_out()) pdb_file = file_base + "_hoh.pdb" hierarchy.write_pdb_file( file_name=pdb_file, crystal_symmetry=pdb_in.crystal_symmetry()) assert os.path.isfile(pdb_file) return os.path.abspath(mtz_file), os.path.abspath(pdb_file) def generate_cd_cl_inputs(file_base="cd_cl_frag"): """ Creates a fake model and reflection data for a structure containing cadmium and chloride ions. Parameters ---------- file_base : str, optional Returns ------- mtz_path : str pdb_path : str """ pdb_file = write_pdb_input_cd_cl(file_base=file_base) mtz_file = generate_mtz_file( file_base=file_base, d_min=1.3, anomalous_scatterers=[ group_args(selection="element CD", fp=-0.29, fdp=2.676), group_args(selection="element CL", fp=0.256, fdp=0.5), ]) assert (os.path.isfile(pdb_file)) and (os.path.isfile(mtz_file)) return mtz_file, pdb_file def generate_zinc_inputs(file_base="zn_frag", anonymize=True, wavelength=None): """ Generate both a PDB file and an MTZ file for the zinc-bound structure, with the zinc optionally replaced by solvent after F(model) was calculated. Zinc is simulated as an anomalous scatterer at 1.54 A. Parameters ---------- file_base : str, optional anonymize : bool, optional Replace all ions in the returned pdb file with waters. Returns ------- mtz_path : str pdb_path : str """ anom = None if (wavelength is None): fp = -1.3 fdp = 0.47 anom = [ group_args(selection="element ZN", fp=fp, fdp=fdp), ] pdb_file = write_pdb_input_zinc_binding(file_base=file_base) mtz_file = generate_mtz_file( file_base=file_base, d_min=1.9, anomalous_scatterers=anom, wavelength=wavelength) assert os.path.isfile(pdb_file) and os.path.isfile(mtz_file) if anonymize: pdb_in = iotbx.pdb.input(pdb_file) hierarchy = pdb_in.construct_hierarchy() hierarchy, n = anonymize_ions(hierarchy, log=null_out()) pdb_file = file_base + "_hoh.pdb" hierarchy.write_pdb_file( file_name=pdb_file, crystal_symmetry=pdb_in.crystal_symmetry()) assert os.path.isfile(pdb_file) return os.path.abspath(mtz_file), os.path.abspath(pdb_file) def generate_magnessium_inputs(file_base="mg_frag", anonymize=True): """ Creates a fake model and reflection data for a structure containing magnesium ions. Parameters ---------- file_base : str, optional anonymize : bool, optional Replace all ions in the returned pdb file with waters. Returns ------- mtz_path : str pdb_path : str """ pdb_file = write_pdb_input_magnessium_binding (file_base=file_base) mtz_file = generate_mtz_file( file_base=file_base, d_min=1.5) assert os.path.isfile(pdb_file) and os.path.isfile(mtz_file) if anonymize: pdb_in = iotbx.pdb.input(pdb_file) hierarchy = pdb_in.construct_hierarchy() hierarchy, n = anonymize_ions(hierarchy, log=null_out()) pdb_file = file_base + "_hoh.pdb" hierarchy.write_pdb_file( file_name=pdb_file, crystal_symmetry=pdb_in.crystal_symmetry()) assert os.path.isfile(pdb_file) return os.path.abspath(mtz_file), os.path.abspath(pdb_file) def generate_mtz_file(file_base, d_min, anomalous_scatterers=None, wavelength=None): """ Create an MTZ file containing amplitudes (and R-free-flags) calculated from the PDB file, at the specified resolution and with enumerated anomalous scatterer groups. Parameters ---------- file_base : str d_min : float anomalous_scatterers : group_args Returns ------- mtz_path : str Examples -------- >>> from libtbx import group_args >>> from mmtbx.regression import make_fake_anomalous_data as mfad >>> file_base = "tst_gen_file" >>> pdb_file = mfad.write_pdb_input_calcium_binding(file_base=file_base) >>> scatterers = group_args(selection="element CA", fp=0.25, fdp=0.5) >>> mtz_file = mfad.generate_mtz_file( ... file_base, 1.5, anomalous_scatterers=[scatterers] ... ) >>> assert os.path.isfile(pdb_file) and os.path.isfile(mtz_file) """ mtz_file = file_base + ".mtz" if (os.path.isfile(mtz_file)): os.remove(mtz_file) params = """ high_resolution = %g r_free_flags_fraction = 0.1 add_sigmas = True pdb_file = %s.pdb wavelength = %s output { label = F type = *real complex file_name = %s.mtz }\n""" % (d_min, file_base, wavelength, file_base) if anomalous_scatterers is not None: params += "anomalous_scatterers {\n" for group in anomalous_scatterers : params += (" group {\n" " selection = %s\n" " f_prime = %g\n" " f_double_prime = %g\n" " }\n") % (group.selection, group.fp, group.fdp) params += "}\n" eff_file = file_base + "_fmodel.eff" with open(eff_file, "w") as f: f.write(params) assert (easy_run.fully_buffered("phenix.fmodel %s" % eff_file, ).raise_if_errors().return_code == 0) return mtz_file def write_pdb_input_calcium_binding(file_base="ca_frag", write_files=True): """ Outputs a selection of atoms from a structure of a calcium-binding fold. Original data: d_min=1.4, wavelength=1.116 Parameters ---------- file_base : str, optional write_files : bool, optional If false, just return the pdb hierarchy and x-ray crystal structure, instead of writing it to a file. Returns ------- str or tuple of iotbx.pdb.hierarchy.root, cctbx.xray.structure.structure """ pdb_in = iotbx.pdb.input(source_info=None, lines="""\ ATOM 1 N ASP A 37 10.710 14.456 9.568 1.00 15.78 N ATOM 2 CA ASP A 37 9.318 14.587 9.999 1.00 18.38 C ATOM 3 C ASP A 37 8.402 13.523 9.395 1.00 15.46 C ATOM 4 O ASP A 37 7.295 13.309 9.892 1.00 16.65 O ATOM 5 CB ASP A 37 8.771 16.006 9.784 1.00 24.16 C ATOM 6 CG ASP A 37 8.900 16.478 8.357 1.00 28.30 C ATOM 7 OD1 ASP A 37 9.145 15.643 7.457 1.00 30.98 O ATOM 8 OD2 ASP A 37 8.747 17.700 8.132 1.00 36.64 O-1 ATOM 9 N LEU A 38 8.862 12.840 8.346 1.00 16.14 N ATOM 10 CA LEU A 38 8.092 11.733 7.778 1.00 16.45 C ATOM 11 C LEU A 38 7.990 10.538 8.735 1.00 15.91 C ATOM 12 O LEU A 38 7.160 9.650 8.546 1.00 16.71 O ATOM 13 CB LEU A 38 8.675 11.305 6.425 1.00 17.74 C ATOM 14 CG LEU A 38 8.715 12.386 5.345 1.00 18.16 C ATOM 15 CD1 LEU A 38 9.091 11.771 4.003 1.00 20.50 C ATOM 16 CD2 LEU A 38 7.391 13.166 5.250 1.00 19.36 C ATOM 17 N ALA A 39 8.828 10.526 9.770 1.00 13.52 N ATOM 18 CA ALA A 39 8.825 9.454 10.756 1.00 15.05 C ATOM 19 C ALA A 39 7.758 9.662 11.829 1.00 16.22 C ATOM 20 O ALA A 39 7.489 8.754 12.609 1.00 15.36 O ATOM 21 CB ALA A 39 10.201 9.341 11.405 1.00 13.76 C ATOM 22 N ILE A 40 7.164 10.855 11.883 1.00 14.32 N ATOM 23 CA ILE A 40 6.164 11.156 12.915 1.00 15.53 C ATOM 24 C ILE A 40 4.885 11.819 12.386 1.00 18.72 C ATOM 25 O ILE A 40 4.178 12.497 13.136 1.00 21.36 O ATOM 26 CB ILE A 40 6.752 12.039 14.047 1.00 17.76 C ATOM 27 CG1 ILE A 40 7.253 13.375 13.493 1.00 19.23 C ATOM 28 CG2 ILE A 40 7.871 11.314 14.773 1.00 19.67 C ATOM 29 CD1 ILE A 40 7.538 14.403 14.583 1.00 22.28 C ATOM 30 N ASP A 41 4.569 11.592 11.115 1.00 17.33 N ATOM 31 CA ASP A 41 3.461 12.305 10.474 1.00 20.42 C ATOM 32 C ASP A 41 2.132 11.539 10.466 1.00 23.63 C ATOM 33 O ASP A 41 1.117 12.047 9.976 1.00 24.40 O ATOM 34 CB ASP A 41 3.852 12.742 9.051 1.00 19.02 C ATOM 35 CG ASP A 41 4.135 11.566 8.114 1.00 20.05 C ATOM 36 OD1 ASP A 41 4.047 10.386 8.529 1.00 17.79 O ATOM 37 OD2 ASP A 41 4.465 11.830 6.938 1.00 19.57 O-1 ATOM 38 N GLY A 42 2.132 10.328 11.012 1.00 19.52 N ATOM 39 CA GLY A 42 0.917 9.531 11.073 1.00 19.91 C ATOM 40 C GLY A 42 0.622 8.804 9.775 1.00 25.32 C ATOM 41 O GLY A 42 -0.390 8.104 9.659 1.00 25.73 O ATOM 42 N ASN A 43 1.505 8.967 8.794 1.00 20.57 N ATOM 43 CA ASN A 43 1.326 8.337 7.488 1.00 20.84 C ATOM 44 C ASN A 43 2.269 7.149 7.310 1.00 20.54 C ATOM 45 O ASN A 43 3.484 7.322 7.215 1.00 18.86 O ATOM 46 CB ASN A 43 1.563 9.367 6.382 1.00 20.63 C ATOM 47 CG ASN A 43 1.087 8.896 5.020 1.00 19.17 C ATOM 48 ND2 ASN A 43 1.027 9.825 4.069 1.00 24.27 N ATOM 49 OD1 ASN A 43 0.793 7.718 4.813 1.00 21.70 O ATOM 50 N PRO A 44 1.711 5.933 7.258 1.00 20.33 N ATOM 51 CA PRO A 44 2.542 4.737 7.081 1.00 20.08 C ATOM 52 C PRO A 44 3.221 4.664 5.716 1.00 20.25 C ATOM 53 O PRO A 44 4.166 3.891 5.562 1.00 26.14 O ATOM 54 CB PRO A 44 1.538 3.589 7.222 1.00 20.20 C ATOM 55 CG PRO A 44 0.211 4.201 6.901 1.00 25.57 C ATOM 56 CD PRO A 44 0.288 5.596 7.442 1.00 19.95 C ATOM 57 N ALA A 45 2.750 5.441 4.743 1.00 20.05 N ATOM 58 CA ALA A 45 3.316 5.406 3.393 1.00 23.75 C ATOM 59 C ALA A 45 4.525 6.323 3.231 1.00 25.35 C ATOM 60 O ALA A 45 5.211 6.281 2.205 1.00 26.63 O ATOM 61 CB ALA A 45 2.246 5.741 2.353 1.00 24.89 C ATOM 62 N THR A 46 4.783 7.153 4.239 1.00 19.37 N ATOM 63 CA THR A 46 5.952 8.027 4.226 1.00 19.58 C ATOM 64 C THR A 46 6.923 7.556 5.292 1.00 19.22 C ATOM 65 O THR A 46 6.516 6.968 6.298 1.00 16.37 O ATOM 66 CB THR A 46 5.588 9.477 4.547 1.00 17.37 C ATOM 67 CG2 THR A 46 4.599 10.035 3.514 1.00 21.06 C ATOM 68 OG1 THR A 46 4.999 9.537 5.849 1.00 18.86 O ATOM 69 N SER A 47 8.206 7.816 5.068 1.00 17.65 N ATOM 70 CA SER A 47 9.224 7.383 6.009 1.00 16.72 C ATOM 71 C SER A 47 10.503 8.190 5.885 1.00 17.50 C ATOM 72 O SER A 47 10.765 8.834 4.859 1.00 15.22 O ATOM 73 CB SER A 47 9.541 5.916 5.774 1.00 17.26 C ATOM 74 OG SER A 47 10.208 5.738 4.530 1.00 18.61 O ATOM 75 N TRP A 48 11.299 8.139 6.947 1.00 14.32 N ATOM 76 CA TRP A 48 12.634 8.723 6.955 1.00 13.15 C ATOM 77 C TRP A 48 13.652 7.627 6.683 1.00 13.64 C ATOM 78 O TRP A 48 13.756 6.646 7.433 1.00 12.78 O ATOM 79 CB TRP A 48 12.912 9.395 8.300 1.00 13.01 C ATOM 80 CG TRP A 48 14.327 9.861 8.482 1.00 13.43 C ATOM 81 CD1 TRP A 48 14.924 10.924 7.876 1.00 14.36 C ATOM 82 CD2 TRP A 48 15.313 9.291 9.357 1.00 13.44 C ATOM 83 CE2 TRP A 48 16.485 10.060 9.221 1.00 12.26 C ATOM 84 CE3 TRP A 48 15.315 8.202 10.239 1.00 12.49 C ATOM 85 NE1 TRP A 48 16.228 11.048 8.307 1.00 13.42 N ATOM 86 CZ2 TRP A 48 17.653 9.778 9.940 1.00 13.96 C ATOM 87 CZ3 TRP A 48 16.476 7.922 10.948 1.00 11.99 C ATOM 88 CH2 TRP A 48 17.628 8.705 10.790 1.00 13.64 C TER 89 TRP A 48 ATOM 90 N ILE A 153 12.422 4.326 8.671 1.00 13.05 N ATOM 91 CA ILE A 153 11.440 4.432 9.754 1.00 14.48 C ATOM 92 C ILE A 153 10.194 5.191 9.295 1.00 12.58 C ATOM 93 O ILE A 153 10.264 6.388 8.994 1.00 13.74 O ATOM 94 CB ILE A 153 12.019 5.189 10.975 1.00 15.38 C ATOM 95 CG1 ILE A 153 13.320 4.550 11.466 1.00 15.63 C ATOM 96 CG2 ILE A 153 10.986 5.280 12.090 1.00 15.20 C ATOM 97 CD1 ILE A 153 13.950 5.283 12.647 1.00 15.77 C ATOM 98 N SER A 154 9.051 4.511 9.278 1.00 14.97 N ATOM 99 CA SER A 154 7.820 5.135 8.801 1.00 14.50 C ATOM 100 C SER A 154 7.001 5.838 9.874 1.00 15.23 C ATOM 101 O SER A 154 6.353 6.843 9.589 1.00 15.50 O ATOM 102 CB SER A 154 6.944 4.134 8.052 1.00 16.67 C ATOM 103 OG SER A 154 6.522 3.100 8.920 1.00 16.82 O ATOM 104 N GLU A 155 7.018 5.314 11.097 1.00 15.34 N ATOM 105 CA GLU A 155 6.218 5.885 12.176 1.00 15.01 C ATOM 106 C GLU A 155 6.825 5.575 13.533 1.00 12.95 C ATOM 107 O GLU A 155 7.234 4.443 13.789 1.00 15.35 O ATOM 108 CB GLU A 155 4.780 5.346 12.139 1.00 17.13 C ATOM 109 CG GLU A 155 3.862 6.037 11.124 1.00 22.41 C ATOM 110 CD GLU A 155 3.866 7.552 11.272 1.00 24.24 C ATOM 111 OE1 GLU A 155 3.618 8.050 12.389 1.00 26.14 O ATOM 112 OE2 GLU A 155 4.132 8.250 10.271 1.00 23.46 O-1 ATOM 113 N ILE A 156 6.882 6.596 14.382 1.00 13.75 N ATOM 114 CA ILE A 156 7.220 6.440 15.788 1.00 12.29 C ATOM 115 C ILE A 156 6.066 7.007 16.602 1.00 11.05 C ATOM 116 O ILE A 156 5.584 8.113 16.320 1.00 13.14 O ATOM 117 CB ILE A 156 8.506 7.196 16.147 1.00 11.71 C ATOM 118 CG1 ILE A 156 9.714 6.573 15.433 1.00 12.75 C ATOM 119 CG2 ILE A 156 8.742 7.158 17.657 1.00 12.85 C ATOM 120 CD1 ILE A 156 10.932 7.490 15.398 1.00 13.97 C TER 121 ILE A 156 HETATM 122 CA CA S 1 5.334 8.357 8.032 1.00 5.89 CA+2 HETATM 123 O HOH S 2 5.396 15.243 10.734 1.00 22.95 O HETATM 124 O HOH S 3 3.629 8.994 14.414 1.00 25.28 O END""") xrs = pdb_in.xray_structure_simple(cryst1_substitution_buffer_layer=5) if (write_files): pdb_file = file_base + ".pdb" if (os.path.exists(pdb_file)): os.remove(pdb_file) f = open(pdb_file, "w") f.write(pdb_in.construct_hierarchy().as_pdb_string(crystal_symmetry=xrs)) f.close() return pdb_file else : return pdb_in, xrs def write_pdb_input_cd_cl(file_base="cd_cl_frag"): """ Outputs a selection of atoms from a structure crystallized in cadmium cloride. Original data: d_min=1.37, wavelength=1.116 Parameters ---------- file_base : str, optional Returns ------- str """ pdb_in = iotbx.pdb.input(source_info=None, lines="""\ ATOM 1 N GLU A 18 -13.959 12.159 -6.598 1.00 10.08 N ATOM 2 CA GLU A 18 -13.297 13.465 -6.628 1.00 9.83 C ATOM 3 C GLU A 18 -11.946 13.282 -7.309 1.00 9.18 C ATOM 4 CB GLU A 18 -13.128 14.035 -5.210 1.00 11.96 C ATOM 5 CG GLU A 18 -14.455 14.401 -4.522 1.00 13.56 C ATOM 6 CD GLU A 18 -14.291 15.239 -3.242 1.00 14.89 C ATOM 7 OE1 GLU A 18 -14.172 14.646 -2.143 1.00 14.24 O ATOM 8 OE2 GLU A 18 -14.309 16.498 -3.306 1.00 14.37 O1- ATOM 9 N PRO A 19 -11.418 14.350 -7.928 1.00 9.57 N ATOM 10 CD PRO A 19 -12.043 15.673 -8.082 1.00 11.94 C ATOM 11 CB SER A 20 -7.426 14.613 -4.832 1.00 12.48 C ATOM 12 CG ASP A 21 -12.019 9.806 -4.306 1.00 11.79 C ATOM 13 OD1 ASP A 21 -11.866 9.680 -3.077 1.00 12.53 O ATOM 14 OD2 ASP A 21 -13.123 10.103 -4.806 1.00 14.00 O1- TER 15 ASP A 21 ATOM 16 C GLU C 16 -17.717 21.556 1.133 1.00 9.93 C ATOM 17 O GLU C 16 -17.663 20.929 0.078 1.00 13.55 O ATOM 18 N VAL C 17 -16.747 21.509 2.043 1.00 9.02 N ATOM 19 CA VAL C 17 -15.504 20.772 1.813 1.00 10.30 C ATOM 20 C VAL C 17 -15.061 20.062 3.080 1.00 10.37 C ATOM 21 O VAL C 17 -15.568 20.347 4.166 1.00 12.61 O ATOM 22 CB VAL C 17 -14.357 21.714 1.368 1.00 11.35 C ATOM 23 CG1 VAL C 17 -14.653 22.284 -0.019 1.00 14.25 C ATOM 24 CG2 VAL C 17 -14.155 22.832 2.385 1.00 11.46 C ATOM 25 N GLU C 18 -14.120 19.134 2.943 1.00 10.25 N ATOM 26 CA GLU C 18 -13.458 18.521 4.087 1.00 9.78 C ATOM 27 C GLU C 18 -12.108 19.210 4.277 1.00 9.04 C ATOM 28 O GLU C 18 -11.528 19.727 3.312 1.00 10.29 O ATOM 29 CB GLU C 18 -13.263 17.016 3.870 1.00 11.44 C ATOM 30 CG GLU C 18 -14.568 16.219 3.805 1.00 14.22 C ATOM 31 CD GLU C 18 -14.339 14.700 3.837 1.00 18.19 C ATOM 32 OE1 GLU C 18 -14.090 14.093 2.769 1.00 17.19 O ATOM 33 OE2 GLU C 18 -14.408 14.090 4.930 1.00 18.29 O1- ATOM 34 N PRO C 19 -11.589 19.217 5.512 1.00 8.64 N ATOM 35 N SER C 20 -9.117 18.227 4.541 1.00 8.92 N ATOM 36 CA SER C 20 -8.002 17.726 3.740 1.00 9.11 C ATOM 37 C SER C 20 -8.323 17.664 2.251 1.00 10.30 C ATOM 38 O SER C 20 -7.579 17.059 1.490 1.00 12.39 O ATOM 39 N ASP C 21 -9.424 18.283 1.826 1.00 9.10 N ATOM 40 CA ASP C 21 -9.687 18.394 0.390 1.00 8.68 C ATOM 41 C ASP C 21 -8.518 19.104 -0.299 1.00 8.06 C ATOM 42 O ASP C 21 -7.956 20.072 0.240 1.00 9.29 O ATOM 43 CB ASP C 21 -10.987 19.165 0.130 1.00 9.00 C ATOM 44 CG ASP C 21 -12.175 18.250 -0.151 1.00 12.21 C ATOM 45 OD1 ASP C 21 -11.996 17.207 -0.825 1.00 13.40 O ATOM 46 OD2 ASP C 21 -13.298 18.562 0.293 1.00 14.53 O1- ATOM 47 N THR C 22 -8.134 18.619 -1.473 1.00 7.93 N ATOM 48 CA THR C 22 -7.123 19.287 -2.268 1.00 8.33 C ATOM 49 C THR C 22 -7.719 20.485 -2.992 1.00 8.59 C ATOM 50 O THR C 22 -8.935 20.600 -3.185 1.00 7.86 O ATOM 51 OG1 THR C 22 -7.612 17.883 -4.158 1.00 8.83 O TER 52 THR C 22 ATOM 53 N ASN C 25 -9.688 19.311 -5.824 1.00 7.73 N ATOM 54 CA ASN C 25 -11.065 18.970 -5.481 1.00 8.22 C ATOM 55 C ASN C 25 -11.961 20.210 -5.409 1.00 7.89 C ATOM 56 O ASN C 25 -13.107 20.192 -5.859 1.00 8.41 O ATOM 57 CB ASN C 25 -11.124 18.234 -4.145 1.00 8.10 C ATOM 58 CG ASN C 25 -10.667 16.786 -4.233 1.00 8.60 C ATOM 59 ND2 ASN C 25 -10.637 16.128 -3.077 1.00 11.20 N ATOM 60 OD1 ASN C 25 -10.352 16.264 -5.306 1.00 9.78 O ATOM 61 N VAL C 26 -11.433 21.291 -4.843 1.00 7.87 N ATOM 62 CA VAL C 26 -12.169 22.548 -4.780 1.00 8.48 C ATOM 63 CG2 VAL C 26 -11.277 23.116 -2.518 1.00 13.29 C TER 64 VAL C 26 ATOM 65 CB LYS C 29 -16.653 22.060 -5.667 1.00 9.82 C ATOM 66 CG LYS C 29 -16.565 20.717 -4.972 1.00 12.48 C ATOM 67 CD LYS C 29 -16.305 20.909 -3.485 1.00 16.22 C ATOM 68 CE LYS C 29 -16.187 19.579 -2.753 1.00 22.76 C ATOM 69 NZ LYS C 29 -17.525 18.994 -2.465 1.00 26.67 N1+ TER 70 LYS C 29 ATOM 71 CD1 LEU C 56 -10.613 22.962 1.772 1.00 12.91 C TER 72 LEU C 56 HETATM 73 O HOH S 4 -10.355 10.447 0.977 1.00 18.33 O HETATM 74 O HOH S 12 -14.439 17.636 -5.803 1.00 14.31 O HETATM 75 O HOH S 19 -13.395 12.091 -1.881 1.00 18.37 O HETATM 76 O HOH S 28 -13.593 15.089 0.608 1.00 19.93 O HETATM 77 O HOH S 41 -10.275 12.953 -2.172 1.00 18.72 O HETATM 78 O HOH S 121 -18.485 11.552 -2.969 1.00 23.16 O HETATM 79 O HOH S 124 -16.053 16.459 -7.803 1.00 32.54 O HETATM 80 O HOH S 134 -10.338 14.782 1.447 1.00 18.96 O HETATM 81 O HOH S 162 -17.702 13.108 -4.810 1.00 41.20 O HETATM 82 O HOH S 204 -17.671 15.077 -3.159 1.00 42.64 O HETATM 84 CD CD X 2 -14.095 16.409 -0.841 1.00 15.00 ION CD2+ HETATM 86 CL CL Y 3 -16.374 16.899 -0.285 1.00 10.22 ION CL1- END""") xrs = pdb_in.xray_structure_simple(cryst1_substitution_buffer_layer=5) pdb_file = file_base + ".pdb" if (os.path.exists(pdb_file)): os.remove(pdb_file) f = open(pdb_file, "w") f.write("""REMARK 200 WAVELENGTH OR RANGE (A) : 1.116\n""") f.write(pdb_in.construct_hierarchy().as_pdb_string(crystal_symmetry=xrs)) f.close() return pdb_file def write_pdb_input_zinc_binding(file_base="zn_frag", write_files=True): """ Outputs a selection of atoms from a structure crystallized with zinc. Parameters ---------- file_base : str, optional write_files : bool, optional If false, just return the pdb hierarchy and x-ray crystal structure, instead of writing it to a file. Returns ------- str or tuple of iotbx.pdb.hierarchy.root, cctbx.xray.structure.structure """ # XXX extracted from 2whz (thermolysin, wavelength = 1.54A), but with an # incomplete coordination shell pdb_in = iotbx.pdb.input(source_info=None, lines="""\ ATOM 1 OD1 ASN A 112 34.902 38.381 -2.709 1.00 12.10 O ATOM 2 C ALA A 113 31.533 40.581 -3.237 1.00 12.06 C ATOM 3 O ALA A 113 32.560 40.184 -3.842 1.00 12.75 O ATOM 4 N PHE A 114 30.551 41.251 -3.854 1.00 11.88 N ATOM 5 CA PHE A 114 30.707 41.621 -5.277 1.00 12.52 C ATOM 6 C PHE A 114 29.633 42.613 -5.705 1.00 12.63 C ATOM 7 CB PHE A 114 30.665 40.371 -6.202 1.00 12.72 C ATOM 8 N TRP A 115 29.933 43.311 -6.794 1.00 13.30 N ATOM 9 CA TRP A 115 28.968 44.084 -7.575 1.00 13.94 C ATOM 10 O TRP A 115 29.375 42.549 -9.378 1.00 15.06 O ATOM 11 CB TRP A 115 29.646 45.329 -8.137 1.00 14.57 C ATOM 13 O VAL A 139 33.773 47.006 -1.063 1.00 11.73 O ATOM 15 N HIS A 142 34.994 49.588 -2.455 1.00 13.21 N ATOM 16 CA HIS A 142 35.593 48.855 -3.582 1.00 11.38 C ATOM 17 C HIS A 142 34.455 48.358 -4.484 1.00 12.11 C ATOM 18 O HIS A 142 34.468 48.596 -5.693 1.00 11.57 O ATOM 19 CB HIS A 142 36.442 47.680 -3.082 1.00 11.93 C ATOM 20 CG HIS A 142 36.945 46.756 -4.150 1.00 9.54 C ATOM 21 CD2 HIS A 142 36.303 45.839 -4.912 1.00 9.50 C ATOM 22 ND1 HIS A 142 38.289 46.628 -4.440 1.00 11.23 N ATOM 23 CE1 HIS A 142 38.446 45.706 -5.381 1.00 14.08 C ATOM 24 NE2 HIS A 142 37.258 45.206 -5.676 1.00 14.47 N ATOM 25 N GLU A 143 33.448 47.732 -3.879 1.00 11.17 N ATOM 26 CA GLU A 143 32.363 47.129 -4.683 1.00 12.04 C ATOM 27 C GLU A 143 31.546 48.215 -5.395 1.00 12.79 C ATOM 28 O GLU A 143 31.237 48.078 -6.584 1.00 12.97 O ATOM 29 CB GLU A 143 31.461 46.221 -3.834 1.00 11.99 C ATOM 30 CG GLU A 143 32.199 45.096 -3.030 1.00 12.94 C ATOM 31 CD GLU A 143 32.974 44.075 -3.867 1.00 15.46 C ATOM 32 OE1 GLU A 143 33.029 44.153 -5.112 1.00 16.48 O ATOM 33 OE2 GLU A 143 33.563 43.175 -3.251 1.00 16.80 O1- ATOM 35 C THR A 145 33.305 50.876 -8.608 1.00 12.68 C ATOM 36 N HIS A 146 33.071 49.560 -8.540 1.00 12.36 N ATOM 37 CA HIS A 146 32.869 48.794 -9.756 1.00 13.33 C ATOM 38 CB HIS A 146 32.643 47.318 -9.470 1.00 12.80 C ATOM 39 CG HIS A 146 33.919 46.567 -9.214 1.00 14.00 C ATOM 40 CD2 HIS A 146 34.290 45.747 -8.206 1.00 12.81 C ATOM 41 ND1 HIS A 146 34.992 46.623 -10.084 1.00 12.00 N ATOM 42 CE1 HIS A 146 35.970 45.863 -9.617 1.00 15.40 C ATOM 43 NE2 HIS A 146 35.552 45.289 -8.506 1.00 11.49 N ATOM 45 CG TYR A 157 36.255 42.005 -14.146 1.00 19.06 C ATOM 46 CD1 TYR A 157 36.607 43.119 -13.385 1.00 20.01 C ATOM 47 CD2 TYR A 157 36.279 40.754 -13.542 1.00 19.69 C ATOM 48 CE1 TYR A 157 36.970 42.993 -12.047 1.00 18.89 C ATOM 49 CE2 TYR A 157 36.645 40.612 -12.193 1.00 20.96 C ATOM 50 CZ TYR A 157 36.971 41.732 -11.462 1.00 20.87 C ATOM 51 OH TYR A 157 37.304 41.604 -10.142 1.00 21.10 O ATOM 53 O GLY A 162 40.788 44.717 -13.313 1.00 13.40 O ATOM 55 CA ASN A 165 39.280 47.961 -13.045 1.00 11.01 C ATOM 56 C ASN A 165 39.422 47.647 -11.555 1.00 11.21 C ATOM 57 O ASN A 165 38.940 48.402 -10.709 1.00 10.60 O ATOM 58 CB ASN A 165 38.414 46.889 -13.730 1.00 12.11 C ATOM 59 CG ASN A 165 36.977 46.958 -13.330 1.00 13.51 C ATOM 60 ND2 ASN A 165 36.082 46.882 -14.307 1.00 12.19 N ATOM 61 OD1 ASN A 165 36.661 47.056 -12.155 1.00 13.28 O ATOM 62 N GLU A 166 40.119 46.539 -11.250 1.00 11.43 N ATOM 63 CA GLU A 166 40.413 46.155 -9.851 1.00 10.59 C ATOM 64 C GLU A 166 41.166 47.218 -9.055 1.00 10.24 C ATOM 65 O GLU A 166 40.744 47.581 -7.940 1.00 9.90 O ATOM 66 CB GLU A 166 41.140 44.803 -9.783 1.00 10.41 C ATOM 67 CG GLU A 166 40.169 43.654 -9.741 1.00 11.01 C ATOM 68 CD GLU A 166 39.267 43.743 -8.537 1.00 15.78 C ATOM 69 OE1 GLU A 166 39.745 43.921 -7.380 1.00 14.70 O ATOM 70 OE2 GLU A 166 38.063 43.637 -8.765 1.00 12.05 O1- ATOM 71 N ALA A 167 42.243 47.759 -9.628 1.00 11.39 N ATOM 72 C ILE A 168 39.558 51.420 -8.190 1.00 10.98 C ATOM 73 N SER A 169 39.076 50.192 -8.040 1.00 10.62 N ATOM 74 CA SER A 169 38.198 49.860 -6.904 1.00 11.23 C ATOM 75 C SER A 169 38.998 49.850 -5.589 1.00 11.38 C ATOM 76 O SER A 169 38.484 50.325 -4.547 1.00 11.01 O ATOM 77 CB SER A 169 37.462 48.529 -7.144 1.00 12.04 C ATOM 78 OG SER A 169 36.259 48.790 -7.899 1.00 11.91 O ATOM 79 N ASP A 170 40.233 49.353 -5.645 1.00 11.74 N ATOM 80 CA ASP A 170 41.142 49.411 -4.436 1.00 11.68 C ATOM 81 CB ASP A 170 42.424 48.581 -4.612 1.00 11.14 C ATOM 82 CG ASP A 170 42.166 47.082 -4.475 1.00 10.59 C ATOM 83 OD1 ASP A 170 41.076 46.659 -3.990 1.00 11.83 O ATOM 84 OD2 ASP A 170 43.010 46.278 -4.909 1.00 12.10 O1- ATOM 86 NE ARG A 203 42.877 43.716 -3.830 1.00 12.26 N ATOM 87 CZ ARG A 203 41.692 43.111 -3.748 1.00 11.93 C ATOM 88 NH1 ARG A 203 41.631 41.782 -3.754 1.00 12.22 N1+ ATOM 89 NH2 ARG A 203 40.579 43.829 -3.675 1.00 11.99 N ATOM 91 C VAL A 230 43.021 41.431 -10.925 1.00 14.80 C ATOM 92 O VAL A 230 43.311 42.599 -10.716 1.00 14.05 O ATOM 93 CB VAL A 230 41.294 41.138 -12.775 1.00 14.48 C ATOM 94 CG2 VAL A 230 40.404 40.176 -11.957 1.00 14.82 C ATOM 95 N HIS A 231 42.923 40.503 -9.959 1.00 15.61 N ATOM 96 CA HIS A 231 43.233 40.790 -8.542 1.00 15.70 C ATOM 97 CB HIS A 231 42.434 39.898 -7.566 1.00 15.19 C ATOM 98 CG HIS A 231 40.955 40.000 -7.734 1.00 16.56 C ATOM 99 CD2 HIS A 231 40.056 40.844 -7.174 1.00 17.34 C ATOM 100 ND1 HIS A 231 40.241 39.168 -8.573 1.00 16.47 N ATOM 101 CE1 HIS A 231 38.960 39.505 -8.529 1.00 15.36 C ATOM 102 NE2 HIS A 231 38.825 40.518 -7.687 1.00 15.29 N HETATM 104 N ILE A1001 35.271 41.187 -4.048 1.00 16.78 N HETATM 105 CA ILE A1001 36.473 41.816 -3.412 1.00 17.77 C HETATM 106 C ILE A1001 37.764 41.046 -3.756 1.00 18.36 C HETATM 107 O ILE A1001 38.832 41.640 -3.838 1.00 16.99 O HETATM 108 CB ILE A1001 36.323 42.040 -1.875 1.00 17.98 C HETATM 109 CG1 ILE A1001 37.464 42.899 -1.320 1.00 16.76 C HETATM 110 CG2 ILE A1001 36.360 40.753 -1.098 1.00 20.77 C HETATM 111 CD1 ILE A1001 37.576 44.234 -1.913 1.00 17.79 C HETATM 112 N TYR A1002 37.653 39.739 -3.981 1.00 18.85 N HETATM 113 CA TYR A1002 38.834 38.984 -4.422 1.00 20.77 C HETATM 114 C TYR A1002 38.430 37.858 -5.360 1.00 21.31 C HETATM 115 O TYR A1002 39.302 37.219 -5.983 1.00 22.07 O HETATM 116 CB TYR A1002 39.632 38.473 -3.225 1.00 21.20 C HETATM 117 OXT TYR A1002 37.226 37.594 -5.543 1.00 22.10 O HETATM 118 O HOH A2080 32.747 43.340 -10.935 1.00 44.97 O HETATM 119 O HOH A2097 33.150 44.796 -12.822 1.00 35.29 O HETATM 120 O HOH A2190 32.628 42.780 -7.708 1.00 17.31 O HETATM 121 O HOH A2206 36.319 49.625 -10.585 1.00 16.17 O HETATM 122 O HOH A2210 33.342 47.349 -12.959 1.00 24.18 O HETATM 123 O HOH A2284 42.614 44.224 -6.731 1.00 15.85 O HETATM 125 ZN ZN A1317 36.762 44.115 -7.277 1.00 15.32 ZN+2 END """) # XXX this is the missing water #HETATM 124 O HOH A2351 36.007 42.038 -6.782 1.00 10.54 O xrs = pdb_in.xray_structure_simple(cryst1_substitution_buffer_layer=5) if write_files: pdb_file = file_base + ".pdb" if (os.path.exists(pdb_file)): os.remove(pdb_file) with open(pdb_file, "w") as f: f.write(pdb_in.construct_hierarchy().as_pdb_string(crystal_symmetry=xrs)) return pdb_file else: return pdb_in, xrs def write_pdb_input_magnessium_binding(file_base="mg_frag", write_files=True): """ Outputs a selection of atoms from a structure crystallized with magnesium. Parameters ---------- file_base : str, optional write_files : bool, optional If false, just return the pdb hierarchy and x-ray crystal structure, instead of writing it to a file. Returns ------- str or tuple of iotbx.pdb.hierarchy.root, cctbx.xray.structure.structure """ pdb_in = iotbx.pdb.input(source_info=None, lines="""\ REMARK fragment derived from 3ip0 ATOM 1 N ASP A 95 -12.581 4.250 10.804 1.00 5.08 N ATOM 2 CA ASP A 95 -11.950 3.273 9.927 1.00 5.04 C ATOM 3 C ASP A 95 -11.505 2.089 10.784 1.00 4.97 C ATOM 4 O ASP A 95 -10.680 2.251 11.678 1.00 5.43 O ATOM 5 CB ASP A 95 -10.737 3.916 9.223 1.00 5.26 C ATOM 6 CG ASP A 95 -10.103 3.032 8.160 1.00 5.03 C ATOM 7 OD1 ASP A 95 -10.879 2.437 7.372 1.00 5.23 O ATOM 8 OD2 ASP A 95 -8.836 2.949 8.149 1.00 5.44 O1- TER 9 ASP A 95 ATOM 10 N ASP A 97 -9.724 -1.416 10.219 1.00 4.47 N ATOM 11 CA ASP A 97 -8.951 -2.179 9.250 1.00 4.64 C ATOM 12 C ASP A 97 -8.480 -3.469 9.910 1.00 4.67 C ATOM 13 O ASP A 97 -7.947 -3.449 11.042 1.00 5.63 O ATOM 14 CB ASP A 97 -7.746 -1.380 8.744 1.00 5.20 C ATOM 15 CG ASP A 97 -8.132 -0.223 7.828 1.00 5.06 C ATOM 16 OD1 ASP A 97 -9.317 -0.118 7.445 1.00 5.31 O ATOM 17 OD2 ASP A 97 -7.197 0.558 7.508 1.00 5.74 O1- TER 18 ASP A 97 HETATM 19 PA APC A 171 -11.494 1.693 3.101 1.00 5.93 P HETATM 20 PB APC A 171 -8.904 2.838 3.989 1.00 5.40 P HETATM 21 PG APC A 171 -6.189 1.883 3.824 1.00 5.44 P HETATM 22 C5' APC A 171 -11.917 -0.062 1.209 1.00 6.23 C HETATM 23 O5' APC A 171 -11.907 0.228 2.621 1.00 5.98 O HETATM 24 C4' APC A 171 -12.005 -1.551 1.015 1.00 6.31 C HETATM 25 O4' APC A 171 -10.811 -2.160 1.564 1.00 6.21 O HETATM 26 C3' APC A 171 -13.142 -2.283 1.727 1.00 6.94 C HETATM 27 O3' APC A 171 -14.374 -2.203 1.097 1.00 8.42 O HETATM 28 C2' APC A 171 -12.584 -3.692 1.886 1.00 6.56 C HETATM 29 O2' APC A 171 -13.250 -4.576 0.968 1.00 8.16 O HETATM 30 C1' APC A 171 -11.120 -3.552 1.530 1.00 6.15 C HETATM 31 N1 APC A 171 -9.299 -4.552 6.318 1.00 5.61 N HETATM 32 O1A APC A 171 -12.241 2.714 2.317 1.00 6.59 O HETATM 33 O1B APC A 171 -9.519 4.202 3.986 1.00 6.49 O HETATM 34 O1G APC A 171 -5.931 1.987 5.301 1.00 5.83 O HETATM 35 C2 APC A 171 -10.353 -3.827 5.903 1.00 5.64 C HETATM 36 O2A APC A 171 -11.698 1.666 4.588 1.00 5.88 O HETATM 37 O2B APC A 171 -8.855 2.079 5.313 1.00 5.21 O HETATM 38 O2G APC A 171 -5.035 2.418 2.993 1.00 6.01 O HETATM 39 C3A APC A 171 -9.734 1.834 2.758 1.00 5.70 C HETATM 40 N3 APC A 171 -10.798 -3.610 4.683 1.00 5.70 N HETATM 41 O3B APC A 171 -7.396 2.924 3.462 1.00 5.24 O HETATM 42 O3G APC A 171 -6.675 0.503 3.400 1.00 6.98 O HETATM 43 C4 APC A 171 -10.034 -4.246 3.763 1.00 5.51 C HETATM 44 C5 APC A 171 -8.964 -5.056 4.033 1.00 5.40 C HETATM 45 C6 APC A 171 -8.569 -5.207 5.373 1.00 5.37 C HETATM 46 N6 APC A 171 -7.500 -5.912 5.734 1.00 5.71 N HETATM 47 N7 APC A 171 -8.414 -5.587 2.862 1.00 5.73 N HETATM 48 C8 APC A 171 -9.167 -5.072 1.920 1.00 6.02 C HETATM 49 N9 APC A 171 -10.168 -4.254 2.383 1.00 5.71 N HETATM 50 N1 AHHR A 181 -3.249 8.723 8.653 0.45 3.59 N HETATM 51 C2 AHHR A 181 -3.170 8.473 9.936 0.45 3.27 C HETATM 52 N2 AHHR A 181 -2.312 9.188 10.698 0.45 4.00 N HETATM 53 N3 AHHR A 181 -3.822 7.446 10.541 0.45 3.91 N HETATM 54 C4 AHHR A 181 -4.648 6.566 9.912 0.45 3.74 C HETATM 55 O4 AHHR A 181 -5.221 5.635 10.511 0.45 4.44 O HETATM 56 N5 AHHR A 181 -5.483 5.915 7.737 0.45 3.23 N HETATM 57 C6 AHHR A 181 -5.582 6.218 6.448 0.45 3.92 C HETATM 58 C6AAHHR A 181 -6.336 5.270 5.533 0.45 4.40 C HETATM 59 O6AAHHR A 181 -7.145 4.378 6.216 0.45 4.54 O HETATM 60 C7 AHHR A 181 -4.896 7.322 5.892 0.45 5.79 C HETATM 61 N8 AHHR A 181 -4.134 8.150 6.611 0.45 5.53 N HETATM 62 C9 AHHR A 181 -4.046 7.908 7.922 0.45 3.58 C HETATM 63 C10AHHR A 181 -4.762 6.791 8.479 0.45 3.12 C HETATM 64 N1 BHHS A 182 -3.604 8.719 8.748 0.55 6.49 N HETATM 65 C2 BHHS A 182 -3.478 8.455 10.036 0.55 6.53 C HETATM 66 N2 BHHS A 182 -2.673 9.243 10.809 0.55 6.01 N HETATM 67 N3 BHHS A 182 -4.109 7.429 10.645 0.55 5.05 N HETATM 68 C4 BHHS A 182 -4.896 6.564 9.963 0.55 5.93 C HETATM 69 O4 BHHS A 182 -5.536 5.719 10.560 0.55 5.29 O HETATM 70 N5 BHHS A 182 -5.756 5.984 7.764 0.55 7.30 N HETATM 71 C6 BHHS A 182 -6.698 5.438 5.588 0.55 6.59 C HETATM 72 C6ABHHS A 182 -5.887 6.282 6.483 0.55 5.89 C HETATM 73 O6ABHHS A 182 -7.411 4.466 6.183 0.55 6.94 O HETATM 74 O6BBHHS A 182 -6.769 5.796 4.398 0.55 7.23 O HETATM 75 C7 BHHS A 182 -5.274 7.421 5.955 0.55 5.00 C HETATM 76 N8 BHHS A 182 -4.530 8.228 6.695 0.55 4.94 N HETATM 77 C9 BHHS A 182 -4.383 7.927 7.998 0.55 5.58 C HETATM 78 C10BHHS A 182 -5.029 6.797 8.531 0.55 6.96 C HETATM 79 O HOH A 201 -12.056 -0.140 6.826 1.00 5.82 O HETATM 80 O HOH A 202 -10.078 -0.655 4.762 1.00 6.16 O HETATM 81 O HOH A 203 -5.851 3.057 8.110 1.00 6.43 O HETATM 82 O HOH A 205 -7.904 1.644 10.650 1.00 6.56 O HETATM 83 O HOH A 216 -13.376 -2.280 5.233 1.00 7.21 O HETATM 84 O HOH A 219 -5.353 2.683 10.917 1.00 8.33 O HETATM 85 O HOH A 243 -8.078 5.439 9.608 1.00 9.50 O HETATM 86 O HOH A 264 -14.344 0.622 4.874 1.00 14.43 O HETATM 87 O AHOH A 499 -7.735 -1.646 4.892 0.50 5.41 O HETATM 88 O BHOH A 499 -7.601 -1.751 4.259 0.50 8.56 O HETATM 89 O BHOH A 501 -13.472 3.920 6.947 0.56 7.54 O HETATM 90 O BHOH A 504 -9.634 5.594 6.224 0.25 5.98 O HETATM 91 O CHOH A 504 -9.119 6.099 7.366 0.25 7.90 O HETATM 92 MG MG A 161 -10.440 0.924 6.059 1.00 5.29 MG MG HETATM 93 MG MG A 162 -7.326 2.422 6.749 1.00 5.40 MG MG """) xrs = pdb_in.xray_structure_simple(cryst1_substitution_buffer_layer=5) if write_files: pdb_file = file_base + ".pdb" if (os.path.exists(pdb_file)): os.remove(pdb_file) with open(pdb_file, "w") as f: f.write(pdb_in.construct_hierarchy().as_pdb_string(crystal_symmetry=xrs)) return pdb_file else: return pdb_in, xrs