from __future__ import absolute_import, division, print_function import iotbx.pdb from cctbx import miller from cctbx import maptbx from libtbx.test_utils import approx_equal from cctbx.maptbx import resolution_from_map_and_model pdb_str_box = """ CRYST1 46.014 46.587 51.149 90.00 90.00 90.00 P 1 SCALE1 0.021733 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021465 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019551 0.00000 ATOM 1 N MET A 1 8.989 25.311 35.844 1.00 55.86 N ATOM 2 CA MET A 1 10.212 24.965 36.614 1.00 51.72 C ATOM 3 C MET A 1 10.661 26.174 37.411 1.00 46.27 C ATOM 4 O MET A 1 10.536 27.310 36.941 1.00 45.16 O ATOM 5 CB MET A 1 11.351 24.546 35.668 1.00 53.97 C ATOM 6 CG MET A 1 11.560 23.056 35.505 1.00 60.99 C ATOM 7 SD MET A 1 13.341 22.661 35.464 1.00 68.34 S ATOM 8 CE MET A 1 13.263 20.867 35.618 1.00 67.72 C ATOM 9 N THR A 2 11.186 25.930 38.612 1.00 43.01 N ATOM 10 CA THR A 2 11.594 27.021 39.490 1.00 40.71 C ATOM 11 C THR A 2 12.921 27.574 38.997 1.00 40.79 C ATOM 12 O THR A 2 13.738 26.869 38.391 1.00 39.70 O ATOM 13 CB THR A 2 11.702 26.615 41.004 1.00 41.37 C ATOM 14 OG1 THR A 2 12.738 25.639 41.197 1.00 42.89 O ATOM 15 CG2 THR A 2 10.358 26.062 41.530 1.00 42.18 C ATOM 16 N VAL A 3 13.110 28.862 39.223 1.00 39.13 N ATOM 17 CA VAL A 3 14.389 29.465 38.976 1.00 40.22 C ATOM 18 C VAL A 3 15.412 28.627 39.747 1.00 39.03 C ATOM 19 O VAL A 3 16.456 28.254 39.190 1.00 41.08 O ATOM 20 CB VAL A 3 14.376 30.996 39.344 1.00 41.84 C ATOM 21 CG1 VAL A 3 15.777 31.541 39.575 1.00 45.27 C ATOM 22 CG2 VAL A 3 13.658 31.801 38.239 1.00 42.05 C ATOM 23 N GLU A 4 15.093 28.285 40.994 1.00 38.38 N ATOM 24 CA GLU A 4 16.000 27.484 41.821 1.00 40.46 C ATOM 25 C GLU A 4 16.451 26.224 41.057 1.00 40.45 C ATOM 26 O GLU A 4 17.648 26.028 40.825 1.00 40.05 O ATOM 27 CB GLU A 4 15.369 27.101 43.170 1.00 41.73 C ATOM 28 CG GLU A 4 16.361 26.345 44.075 1.00 48.81 C ATOM 29 CD GLU A 4 15.918 26.181 45.520 1.00 55.24 C ATOM 30 OE1 GLU A 4 16.040 25.045 46.035 1.00 61.84 O ATOM 31 OE2 GLU A 4 15.486 27.176 46.149 1.00 57.03 O ATOM 32 N GLN A 5 15.483 25.407 40.645 1.00 39.24 N ATOM 33 CA GLN A 5 15.787 24.163 39.936 1.00 41.50 C ATOM 34 C GLN A 5 16.425 24.396 38.567 1.00 41.35 C ATOM 35 O GLN A 5 17.343 23.659 38.201 1.00 40.60 O ATOM 36 CB GLN A 5 14.543 23.275 39.802 1.00 42.26 C ATOM 37 CG GLN A 5 14.061 22.661 41.141 1.00 47.54 C ATOM 38 CD GLN A 5 14.893 21.447 41.602 1.00 51.54 C ATOM 39 OE1 GLN A 5 15.936 21.117 41.025 1.00 49.52 O ATOM 40 NE2 GLN A 5 14.420 20.787 42.648 1.00 58.93 N ATOM 41 N MET A 6 15.973 25.422 37.830 1.00 41.22 N ATOM 42 CA MET A 6 16.519 25.678 36.488 1.00 44.06 C ATOM 43 C MET A 6 17.996 26.061 36.530 1.00 45.57 C ATOM 44 O MET A 6 18.796 25.628 35.679 1.00 48.61 O ATOM 45 CB MET A 6 15.735 26.780 35.777 1.00 46.25 C ATOM 46 CG MET A 6 14.421 26.312 35.209 1.00 51.71 C ATOM 47 SD MET A 6 13.513 27.625 34.359 1.00 64.51 S ATOM 48 CE MET A 6 13.144 28.725 35.720 1.00 58.26 C HETATM 49 N SME A 7 18.343 26.883 37.513 1.00 44.69 N HETATM 50 CA SME A 7 19.702 27.367 37.690 1.00 47.86 C HETATM 51 C SME A 7 20.552 26.208 38.098 1.00 47.33 C HETATM 52 O SME A 7 21.688 26.091 37.678 1.00 48.73 O HETATM 53 CB SME A 7 19.753 28.375 38.828 1.00 48.79 C HETATM 54 CG SME A 7 18.930 29.616 38.490 1.00 51.80 C HETATM 55 CE SME A 7 21.476 30.890 38.486 1.00 66.41 C HETATM 56 OE SME A 7 19.892 30.890 36.374 1.00 65.87 O HETATM 57 S SME A 7 19.876 30.883 37.865 1.00 64.46 S ATOM 58 N LYS A 8 19.983 25.358 38.942 1.00 45.03 N ATOM 59 CA LYS A 8 20.643 24.160 39.468 1.00 46.88 C ATOM 60 C LYS A 8 21.037 23.191 38.363 1.00 46.66 C ATOM 61 O LYS A 8 22.153 22.689 38.341 1.00 49.15 O ATOM 62 CB LYS A 8 19.688 23.464 40.441 1.00 45.97 C ATOM 63 CG LYS A 8 20.287 22.433 41.349 1.00 51.13 C ATOM 64 CD LYS A 8 19.193 21.950 42.323 1.00 55.04 C ATOM 65 CE LYS A 8 19.483 20.592 42.888 1.00 59.32 C ATOM 66 NZ LYS A 8 18.353 20.108 43.739 1.00 64.12 N ATOM 67 N SER A 9 20.102 22.936 37.452 1.00 45.05 N ATOM 68 CA SER A 9 20.318 22.019 36.330 1.00 46.72 C ATOM 69 C SER A 9 21.331 22.575 35.333 1.00 49.01 C ATOM 70 O SER A 9 22.195 21.850 34.838 1.00 50.72 O ATOM 71 CB SER A 9 18.989 21.720 35.616 1.00 46.76 C ATOM 72 OG SER A 9 19.207 21.170 34.321 1.00 50.67 O ATOM 73 N GLY A 10 21.221 23.864 35.035 1.00 36.96 N ATOM 74 CA GLY A 10 22.147 24.515 34.097 1.00 34.97 C ATOM 75 C GLY A 10 23.553 24.538 34.661 1.00 34.57 C ATOM 76 O GLY A 10 24.529 24.357 33.934 1.00 31.75 O ATOM 77 N GLU A 11 23.648 24.730 35.971 1.00 39.42 N ATOM 78 CA GLU A 11 24.915 24.561 36.658 1.00 42.55 C ATOM 79 C GLU A 11 25.414 23.126 36.611 1.00 42.05 C ATOM 80 O GLU A 11 26.581 22.892 36.335 1.00 41.32 O ATOM 81 CB GLU A 11 24.832 25.019 38.120 1.00 47.91 C ATOM 82 CG GLU A 11 25.325 26.463 38.332 1.00 54.32 C ATOM 83 CD GLU A 11 24.245 27.413 38.798 1.00 60.17 C ATOM 84 OE1 GLU A 11 23.801 27.271 39.965 1.00 62.75 O ATOM 85 OE2 GLU A 11 23.861 28.305 38.005 1.00 62.45 O ATOM 86 N MET A 12 24.529 22.172 36.914 1.00 43.46 N ATOM 87 CA MET A 12 24.862 20.738 36.866 1.00 43.08 C ATOM 88 C MET A 12 25.434 20.386 35.506 1.00 39.76 C ATOM 89 O MET A 12 26.497 19.781 35.399 1.00 40.17 O ATOM 90 CB MET A 12 23.618 19.867 37.117 1.00 44.16 C ATOM 91 CG MET A 12 23.846 18.330 36.987 1.00 44.29 C ATOM 92 SD MET A 12 23.573 17.627 35.315 1.00 40.29 S ATOM 93 CE MET A 12 21.773 17.620 35.210 1.00 39.82 C ATOM 94 N ILE A 13 24.709 20.780 34.470 1.00 37.62 N ATOM 95 CA ILE A 13 25.084 20.460 33.098 1.00 35.09 C ATOM 96 C ILE A 13 26.439 21.072 32.753 1.00 33.74 C ATOM 97 O ILE A 13 27.267 20.436 32.121 1.00 33.71 O ATOM 98 CB ILE A 13 24.015 20.912 32.103 1.00 33.70 C ATOM 99 CG1 ILE A 13 22.795 20.012 32.238 1.00 36.47 C ATOM 100 CG2 ILE A 13 24.550 20.839 30.663 1.00 31.03 C ATOM 101 CD1 ILE A 13 21.527 20.571 31.689 1.00 36.99 C ATOM 102 N ARG A 14 26.666 22.309 33.178 1.00 35.83 N ATOM 103 CA ARG A 14 27.939 22.966 32.934 1.00 34.63 C ATOM 104 C ARG A 14 29.025 22.222 33.671 1.00 35.93 C ATOM 105 O ARG A 14 30.079 22.011 33.103 1.00 34.08 O ATOM 106 CB ARG A 14 27.882 24.424 33.383 1.00 37.11 C ATOM 107 CG ARG A 14 29.163 25.264 33.267 1.00 39.17 C ATOM 108 CD ARG A 14 28.913 26.636 33.966 1.00 44.41 C ATOM 109 NE ARG A 14 30.015 27.595 33.842 1.00 49.92 N ATOM 110 CZ ARG A 14 30.150 28.517 32.873 1.00 50.55 C ATOM 111 NH1 ARG A 14 29.255 28.650 31.887 1.00 46.69 N ATOM 112 NH2 ARG A 14 31.208 29.327 32.892 1.00 51.05 N ATOM 113 N SER A 15 28.776 21.846 34.936 1.00 39.02 N ATOM 114 CA SER A 15 29.757 21.091 35.714 1.00 40.95 C ATOM 115 C SER A 15 30.134 19.807 34.999 1.00 39.30 C ATOM 116 O SER A 15 31.300 19.503 34.854 1.00 42.27 O ATOM 117 CB SER A 15 29.250 20.735 37.120 1.00 45.17 C ATOM 118 OG SER A 15 28.850 21.877 37.861 1.00 50.58 O ATOM 119 N VAL A 16 29.144 19.036 34.568 1.00 37.98 N ATOM 120 CA VAL A 16 29.422 17.746 33.929 1.00 37.22 C ATOM 121 C VAL A 16 30.258 17.940 32.707 1.00 35.88 C ATOM 122 O VAL A 16 31.251 17.251 32.505 1.00 37.43 O ATOM 123 CB VAL A 16 28.132 16.957 33.616 1.00 36.91 C ATOM 124 CG1 VAL A 16 28.426 15.792 32.690 1.00 40.10 C ATOM 125 CG2 VAL A 16 27.517 16.432 34.946 1.00 38.88 C ATOM 126 N CYS A 17 29.888 18.938 31.916 1.00 33.28 N ATOM 127 CA CYS A 17 30.457 19.112 30.606 1.00 32.19 C ATOM 128 C CYS A 17 31.839 19.730 30.633 1.00 32.65 C ATOM 129 O CYS A 17 32.705 19.319 29.845 1.00 32.70 O ATOM 130 CB CYS A 17 29.484 19.882 29.729 1.00 29.99 C ATOM 131 SG CYS A 17 28.090 18.841 29.331 1.00 29.57 S ATOM 132 N LEU A 18 32.061 20.689 31.541 1.00 32.85 N ATOM 133 CA LEU A 18 33.419 21.192 31.770 1.00 33.50 C ATOM 134 C LEU A 18 34.334 20.057 32.259 1.00 37.40 C ATOM 135 O LEU A 18 35.526 20.029 31.940 1.00 38.44 O ATOM 136 CB LEU A 18 33.446 22.308 32.810 1.00 34.41 C ATOM 137 CG LEU A 18 32.901 23.703 32.531 1.00 35.31 C ATOM 138 CD1 LEU A 18 32.910 24.557 33.814 1.00 36.98 C ATOM 139 CD2 LEU A 18 33.689 24.372 31.360 1.00 34.44 C ATOM 140 N GLY A 19 33.774 19.153 33.063 1.00 40.28 N ATOM 141 CA GLY A 19 34.506 18.011 33.590 1.00 44.13 C ATOM 142 C GLY A 19 34.947 17.026 32.529 1.00 44.20 C ATOM 143 O GLY A 19 36.065 16.507 32.601 1.00 46.42 O ATOM 144 N LYS A 20 34.078 16.758 31.558 1.00 41.93 N ATOM 145 CA LYS A 20 34.367 15.761 30.513 1.00 42.83 C ATOM 146 C LYS A 20 35.376 16.242 29.482 1.00 42.66 C ATOM 147 O LYS A 20 36.147 15.443 28.952 1.00 42.05 O ATOM 148 CB LYS A 20 33.089 15.330 29.792 1.00 41.52 C ATOM 149 CG LYS A 20 32.245 14.346 30.623 1.00 46.85 C ATOM 150 CD LYS A 20 32.516 12.892 30.192 1.00 53.93 C ATOM 151 CE LYS A 20 32.342 11.903 31.321 1.00 56.45 C ATOM 152 NZ LYS A 20 33.639 11.254 31.736 1.00 64.84 N ATOM 153 N THR A 21 35.374 17.544 29.217 1.00 40.77 N ATOM 154 CA THR A 21 36.176 18.117 28.142 1.00 40.50 C ATOM 155 C THR A 21 37.378 18.992 28.602 1.00 42.78 C ATOM 156 O THR A 21 38.249 19.315 27.793 1.00 44.01 O ATOM 157 CB THR A 21 35.255 18.954 27.232 1.00 37.48 C ATOM 158 OG1 THR A 21 34.872 20.144 27.911 1.00 35.35 O ATOM 159 CG2 THR A 21 33.989 18.173 26.837 1.00 35.67 C ATOM 160 N LYS A 22 37.421 19.391 29.876 1.00 44.63 N ATOM 161 CA LYS A 22 38.514 20.235 30.393 1.00 45.73 C ATOM 162 C LYS A 22 38.768 21.527 29.585 1.00 44.09 C ATOM 163 O LYS A 22 39.916 21.969 29.460 1.00 48.05 O ATOM 164 CB LYS A 22 39.815 19.414 30.482 1.00 47.71 C TER END """ pdb_str_5 = """ CRYST1 46.014 46.587 51.149 90.00 90.00 90.00 P 1 SCALE1 0.021733 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021465 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019551 0.00000 ATOM 1 N MET A 1 12.998 26.982 38.701 1.00 55.86 N ATOM 2 CA MET A 1 12.064 26.130 39.371 1.00 51.72 C ATOM 3 C MET A 1 12.541 25.824 40.765 1.00 46.27 C ATOM 4 O MET A 1 13.020 26.753 41.457 1.00 45.16 O ATOM 5 CB MET A 1 11.841 24.824 38.573 1.00 53.97 C ATOM 6 CG MET A 1 10.387 24.301 38.632 1.00 60.99 C ATOM 7 SD MET A 1 10.319 22.528 38.121 1.00 68.34 S ATOM 8 CE MET A 1 11.465 22.592 36.754 1.00 67.72 C ATOM 9 N THR A 2 12.430 24.571 41.223 1.00 43.01 N ATOM 10 CA THR A 2 12.760 24.214 42.608 1.00 40.71 C ATOM 11 C THR A 2 14.263 24.195 42.844 1.00 40.79 C ATOM 12 O THR A 2 15.054 23.955 41.944 1.00 39.70 O ATOM 13 CB THR A 2 12.183 22.840 42.995 1.00 41.37 C ATOM 14 OG1 THR A 2 12.764 21.861 42.123 1.00 42.89 O ATOM 15 CG2 THR A 2 10.699 22.856 42.865 1.00 42.18 C ATOM 16 N VAL A 3 14.641 24.412 44.125 1.00 39.13 N ATOM 17 CA VAL A 3 16.065 24.373 44.476 1.00 40.22 C ATOM 18 C VAL A 3 16.650 23.058 44.005 1.00 39.03 C ATOM 19 O VAL A 3 17.804 22.963 43.597 1.00 41.08 O ATOM 20 CB VAL A 3 16.274 24.578 46.008 1.00 41.84 C ATOM 21 CG1 VAL A 3 17.646 24.086 46.466 1.00 45.27 C ATOM 22 CG2 VAL A 3 16.040 26.047 46.395 1.00 42.05 C ATOM 23 N GLU A 4 15.842 22.007 44.046 1.00 38.38 N ATOM 24 CA GLU A 4 16.317 20.733 43.565 1.00 40.46 C ATOM 25 C GLU A 4 16.749 20.835 42.111 1.00 40.45 C ATOM 26 O GLU A 4 17.915 20.605 41.763 1.00 40.05 O ATOM 27 CB GLU A 4 15.245 19.679 43.726 1.00 41.73 C ATOM 28 CG GLU A 4 15.722 18.284 43.201 1.00 48.81 C ATOM 29 CD GLU A 4 15.580 17.239 44.253 1.00 55.24 C ATOM 30 OE1 GLU A 4 16.517 17.091 45.034 1.00 61.84 O ATOM 31 OE2 GLU A 4 14.519 16.594 44.350 1.00 57.03 O ATOM 32 N GLN A 5 15.802 21.158 41.231 1.00 39.24 N ATOM 33 CA GLN A 5 16.045 21.191 39.789 1.00 41.50 C ATOM 34 C GLN A 5 17.171 22.167 39.405 1.00 41.35 C ATOM 35 O GLN A 5 17.958 21.904 38.491 1.00 40.60 O ATOM 36 CB GLN A 5 14.722 21.505 39.053 1.00 42.26 C ATOM 37 CG GLN A 5 13.640 20.538 39.435 1.00 47.54 C ATOM 38 CD GLN A 5 14.002 19.109 39.010 1.00 51.54 C ATOM 39 OE1 GLN A 5 14.738 18.953 38.045 1.00 49.52 O ATOM 40 NE2 GLN A 5 13.449 18.086 39.660 1.00 58.93 N ATOM 41 N MET A 6 17.241 23.302 40.078 1.00 41.22 N ATOM 42 CA MET A 6 18.256 24.283 39.690 1.00 44.06 C ATOM 43 C MET A 6 19.628 23.887 40.196 1.00 45.57 C ATOM 44 O MET A 6 20.616 23.937 39.409 1.00 48.61 O ATOM 45 CB MET A 6 17.943 25.686 40.233 1.00 46.25 C ATOM 46 CG MET A 6 16.602 26.222 39.848 1.00 51.71 C ATOM 47 SD MET A 6 15.994 27.653 40.808 1.00 64.51 S ATOM 48 CE MET A 6 16.951 29.028 40.150 1.00 58.26 C HETATM 49 N SME A 7 19.727 23.474 41.452 1.00 44.69 N HETATM 50 CA SME A 7 21.022 23.098 42.112 1.00 47.86 C HETATM 51 C SME A 7 21.613 21.859 41.495 1.00 47.33 C HETATM 52 O SME A 7 22.746 21.693 41.056 1.00 48.73 O HETATM 53 CB SME A 7 20.891 22.855 43.631 1.00 48.79 C HETATM 54 CG SME A 7 21.759 23.780 44.433 1.00 51.80 C HETATM 55 CE SME A 7 23.144 23.218 46.623 1.00 66.41 C HETATM 56 OE SME A 7 23.168 21.603 44.662 1.00 65.87 O HETATM 57 S SME A 7 23.313 23.075 44.898 1.00 64.46 S ATOM 58 N LYS A 8 20.731 20.865 41.492 1.00 45.03 N ATOM 59 CA LYS A 8 21.070 19.546 40.953 1.00 46.88 C ATOM 60 C LYS A 8 21.261 19.557 39.429 1.00 46.66 C ATOM 61 O LYS A 8 22.108 18.821 38.908 1.00 49.15 O ATOM 62 CB LYS A 8 19.969 18.606 41.300 1.00 45.97 C ATOM 63 CG LYS A 8 20.352 17.127 41.054 1.00 51.13 C ATOM 64 CD LYS A 8 19.846 16.355 42.252 1.00 55.04 C ATOM 65 CE LYS A 8 19.359 15.012 41.841 1.00 59.32 C ATOM 66 NZ LYS A 8 18.937 14.155 42.951 1.00 64.12 N ATOM 67 N SER A 9 20.455 20.367 38.737 1.00 45.05 N ATOM 68 CA SER A 9 20.578 20.448 37.300 1.00 46.72 C ATOM 69 C SER A 9 21.860 21.145 36.916 1.00 49.01 C ATOM 70 O SER A 9 22.612 20.643 36.083 1.00 50.72 O ATOM 71 CB SER A 9 19.369 21.146 36.679 1.00 46.76 C ATOM 72 OG SER A 9 19.636 21.471 35.301 1.00 50.67 O ATOM 73 N GLY A 10 22.149 22.269 37.591 1.00 36.96 N ATOM 74 CA GLY A 10 23.376 22.991 37.285 1.00 34.97 C ATOM 75 C GLY A 10 24.607 22.198 37.667 1.00 34.57 C ATOM 76 O GLY A 10 25.600 22.163 36.948 1.00 31.75 O ATOM 77 N GLU A 11 24.560 21.578 38.828 1.00 39.42 N ATOM 78 CA GLU A 11 25.646 20.707 39.311 1.00 42.55 C ATOM 79 C GLU A 11 25.867 19.512 38.405 1.00 42.05 C ATOM 80 O GLU A 11 27.003 19.115 38.124 1.00 41.32 O ATOM 81 CB GLU A 11 25.293 20.265 40.733 1.00 47.91 C ATOM 82 CG GLU A 11 26.384 19.458 41.398 1.00 54.32 C ATOM 83 CD GLU A 11 27.716 20.215 41.418 1.00 60.17 C ATOM 84 OE1 GLU A 11 27.680 21.418 41.701 1.00 62.75 O ATOM 85 OE2 GLU A 11 28.758 19.607 41.203 1.00 62.45 O ATOM 86 N MET A 12 24.801 18.925 37.938 1.00 43.46 N ATOM 87 CA MET A 12 24.927 17.820 36.992 1.00 43.08 C ATOM 88 C MET A 12 25.546 18.283 35.671 1.00 39.76 C ATOM 89 O MET A 12 26.514 17.688 35.206 1.00 40.17 O ATOM 90 CB MET A 12 23.541 17.186 36.751 1.00 44.16 C ATOM 91 CG MET A 12 23.467 15.758 36.225 1.00 44.29 C ATOM 92 SD MET A 12 21.833 15.045 35.960 1.00 40.29 S ATOM 93 CE MET A 12 22.311 13.286 35.717 1.00 39.82 C ATOM 94 N ILE A 13 24.984 19.335 35.038 1.00 37.62 N ATOM 95 CA ILE A 13 25.466 19.762 33.721 1.00 35.09 C ATOM 96 C ILE A 13 26.898 20.240 33.800 1.00 33.74 C ATOM 97 O ILE A 13 27.756 19.815 33.008 1.00 33.71 O ATOM 98 CB ILE A 13 24.535 20.872 33.187 1.00 33.70 C ATOM 99 CG1 ILE A 13 23.089 20.349 33.073 1.00 36.47 C ATOM 100 CG2 ILE A 13 25.065 21.380 31.842 1.00 31.03 C ATOM 101 CD1 ILE A 13 22.120 21.142 32.100 1.00 36.99 C ATOM 102 N ARG A 14 27.184 21.101 34.798 1.00 35.83 N ATOM 103 CA ARG A 14 28.542 21.611 35.053 1.00 34.63 C ATOM 104 C ARG A 14 29.486 20.441 35.298 1.00 35.93 C ATOM 105 O ARG A 14 30.409 20.244 34.514 1.00 34.08 O ATOM 106 CB ARG A 14 28.500 22.648 36.199 1.00 37.11 C ATOM 107 CG ARG A 14 29.810 22.934 36.869 1.00 39.17 C ATOM 108 CD ARG A 14 29.598 23.433 38.323 1.00 44.41 C ATOM 109 NE ARG A 14 30.848 23.570 39.045 1.00 49.92 N ATOM 110 CZ ARG A 14 31.706 24.587 38.876 1.00 50.55 C ATOM 111 NH1 ARG A 14 31.419 25.497 37.982 1.00 46.69 N ATOM 112 NH2 ARG A 14 32.804 24.741 39.586 1.00 51.05 N ATOM 113 N SER A 15 29.184 19.566 36.265 1.00 39.02 N ATOM 114 CA SER A 15 30.148 18.527 36.626 1.00 40.95 C ATOM 115 C SER A 15 30.376 17.566 35.480 1.00 39.30 C ATOM 116 O SER A 15 31.528 17.249 35.111 1.00 42.27 O ATOM 117 CB SER A 15 29.602 17.741 37.825 1.00 45.17 C ATOM 118 OG SER A 15 29.743 18.374 39.100 1.00 50.58 O ATOM 119 N VAL A 16 29.306 17.091 34.890 1.00 37.98 N ATOM 120 CA VAL A 16 29.452 16.039 33.860 1.00 37.22 C ATOM 121 C VAL A 16 30.109 16.586 32.595 1.00 35.88 C ATOM 122 O VAL A 16 31.077 16.065 32.082 1.00 37.43 O ATOM 123 CB VAL A 16 28.113 15.374 33.553 1.00 36.91 C ATOM 124 CG1 VAL A 16 28.291 14.431 32.371 1.00 40.10 C ATOM 125 CG2 VAL A 16 27.613 14.599 34.763 1.00 38.88 C ATOM 126 N CYS A 17 29.572 17.693 32.090 1.00 33.28 N ATOM 127 CA CYS A 17 30.128 18.251 30.858 1.00 32.19 C ATOM 128 C CYS A 17 31.535 18.829 31.061 1.00 32.65 C ATOM 129 O CYS A 17 32.359 18.795 30.135 1.00 32.70 O ATOM 130 CB CYS A 17 29.203 19.340 30.353 1.00 29.99 C ATOM 131 SG CYS A 17 27.835 18.668 29.321 1.00 29.57 S ATOM 132 N LEU A 18 31.796 19.377 32.240 1.00 32.85 N ATOM 133 CA LEU A 18 33.128 19.914 32.524 1.00 33.50 C ATOM 134 C LEU A 18 34.169 18.799 32.677 1.00 37.40 C ATOM 135 O LEU A 18 35.349 18.974 32.398 1.00 38.44 O ATOM 136 CB LEU A 18 33.083 20.741 33.779 1.00 34.41 C ATOM 137 CG LEU A 18 34.371 21.301 34.321 1.00 35.31 C ATOM 138 CD1 LEU A 18 35.057 22.222 33.327 1.00 36.98 C ATOM 139 CD2 LEU A 18 34.173 21.979 35.744 1.00 34.44 C ATOM 140 N GLY A 19 33.779 17.627 33.161 1.00 40.28 N ATOM 141 CA GLY A 19 34.635 16.474 33.045 1.00 44.13 C ATOM 142 C GLY A 19 34.730 15.975 31.615 1.00 44.20 C ATOM 143 O GLY A 19 35.681 15.250 31.269 1.00 46.42 O ATOM 144 N LYS A 20 33.735 16.258 30.773 1.00 41.93 N ATOM 145 CA LYS A 20 33.819 15.832 29.374 1.00 42.83 C ATOM 146 C LYS A 20 34.745 16.718 28.549 1.00 42.66 C ATOM 147 O LYS A 20 35.427 16.243 27.638 1.00 42.05 O ATOM 148 CB LYS A 20 32.431 15.789 28.727 1.00 41.52 C ATOM 149 CG LYS A 20 31.613 14.516 28.974 1.00 46.85 C ATOM 150 CD LYS A 20 32.440 13.297 28.518 1.00 53.93 C ATOM 151 CE LYS A 20 32.197 12.935 27.029 1.00 56.45 C ATOM 152 NZ LYS A 20 33.346 13.503 26.261 1.00 64.84 N ATOM 153 N THR A 21 34.805 18.007 28.797 1.00 40.77 N ATOM 154 CA THR A 21 35.593 18.896 27.954 1.00 40.50 C ATOM 155 C THR A 21 36.842 19.399 28.654 1.00 42.78 C ATOM 156 O THR A 21 37.823 19.657 27.983 1.00 44.01 O ATOM 157 CB THR A 21 34.758 20.107 27.476 1.00 37.48 C ATOM 158 OG1 THR A 21 33.429 19.990 28.020 1.00 35.35 O ATOM 159 CG2 THR A 21 34.672 20.088 25.972 1.00 35.67 C ATOM 160 N LYS A 22 36.815 19.486 29.974 1.00 44.63 N ATOM 161 CA LYS A 22 37.951 19.848 30.817 1.00 45.73 C ATOM 162 C LYS A 22 38.543 21.187 30.359 1.00 44.09 C ATOM 163 O LYS A 22 39.660 21.265 29.818 1.00 48.05 O ATOM 164 CB LYS A 22 39.014 18.761 30.772 1.00 47.71 C TER END """ pdb_str_5bb = """ CRYST1 46.014 46.587 51.149 90.00 90.00 90.00 P 1 SCALE1 0.021733 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021465 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019551 0.00000 ATOM 1 N MET A 1 12.998 26.982 38.701 1.00 55.86 N ATOM 2 CA MET A 1 12.064 26.130 39.371 1.00 51.72 C ATOM 3 C MET A 1 12.541 25.824 40.765 1.00 46.27 C ATOM 4 O MET A 1 13.020 26.753 41.457 1.00 45.16 O ATOM 5 N THR A 2 12.430 24.571 41.223 1.00 43.01 N ATOM 6 CA THR A 2 12.760 24.214 42.608 1.00 40.71 C ATOM 7 C THR A 2 14.263 24.195 42.844 1.00 40.79 C ATOM 8 O THR A 2 15.054 23.955 41.944 1.00 39.70 O ATOM 9 N VAL A 3 14.641 24.412 44.125 1.00 39.13 N ATOM 10 CA VAL A 3 16.065 24.373 44.476 1.00 40.22 C ATOM 11 C VAL A 3 16.650 23.058 44.005 1.00 39.03 C ATOM 12 O VAL A 3 17.804 22.963 43.597 1.00 41.08 O ATOM 13 N GLU A 4 15.842 22.007 44.046 1.00 38.38 N ATOM 14 CA GLU A 4 16.317 20.733 43.565 1.00 40.46 C ATOM 15 C GLU A 4 16.749 20.835 42.111 1.00 40.45 C ATOM 16 O GLU A 4 17.915 20.605 41.763 1.00 40.05 O ATOM 17 N GLN A 5 15.802 21.158 41.231 1.00 39.24 N ATOM 18 CA GLN A 5 16.045 21.191 39.789 1.00 41.50 C ATOM 19 C GLN A 5 17.171 22.167 39.405 1.00 41.35 C ATOM 20 O GLN A 5 17.958 21.904 38.491 1.00 40.60 O ATOM 21 N MET A 6 17.241 23.302 40.078 1.00 41.22 N ATOM 22 CA MET A 6 18.256 24.283 39.690 1.00 44.06 C ATOM 23 C MET A 6 19.628 23.887 40.196 1.00 45.57 C ATOM 24 O MET A 6 20.616 23.937 39.409 1.00 48.61 O HETATM 25 N SME A 7 19.727 23.474 41.452 1.00 44.69 N HETATM 26 CA SME A 7 21.022 23.098 42.112 1.00 47.86 C HETATM 27 C SME A 7 21.613 21.859 41.495 1.00 47.33 C HETATM 28 O SME A 7 22.746 21.693 41.056 1.00 48.73 O ATOM 29 N LYS A 8 20.731 20.865 41.492 1.00 45.03 N ATOM 30 CA LYS A 8 21.070 19.546 40.953 1.00 46.88 C ATOM 31 C LYS A 8 21.261 19.557 39.429 1.00 46.66 C ATOM 32 O LYS A 8 22.108 18.821 38.908 1.00 49.15 O ATOM 33 N SER A 9 20.455 20.367 38.737 1.00 45.05 N ATOM 34 CA SER A 9 20.578 20.448 37.300 1.00 46.72 C ATOM 35 C SER A 9 21.860 21.145 36.916 1.00 49.01 C ATOM 36 O SER A 9 22.612 20.643 36.083 1.00 50.72 O ATOM 37 N GLY A 10 22.149 22.269 37.591 1.00 36.96 N ATOM 38 CA GLY A 10 23.376 22.991 37.285 1.00 34.97 C ATOM 39 C GLY A 10 24.607 22.198 37.667 1.00 34.57 C ATOM 40 O GLY A 10 25.600 22.163 36.948 1.00 31.75 O ATOM 41 N GLU A 11 24.560 21.578 38.828 1.00 39.42 N ATOM 42 CA GLU A 11 25.646 20.707 39.311 1.00 42.55 C ATOM 43 C GLU A 11 25.867 19.512 38.405 1.00 42.05 C ATOM 44 O GLU A 11 27.003 19.115 38.124 1.00 41.32 O ATOM 45 N MET A 12 24.801 18.925 37.938 1.00 43.46 N ATOM 46 CA MET A 12 24.927 17.820 36.992 1.00 43.08 C ATOM 47 C MET A 12 25.546 18.283 35.671 1.00 39.76 C ATOM 48 O MET A 12 26.514 17.688 35.206 1.00 40.17 O ATOM 49 N ILE A 13 24.984 19.335 35.038 1.00 37.62 N ATOM 50 CA ILE A 13 25.466 19.762 33.721 1.00 35.09 C ATOM 51 C ILE A 13 26.898 20.240 33.800 1.00 33.74 C ATOM 52 O ILE A 13 27.756 19.815 33.008 1.00 33.71 O ATOM 53 N ARG A 14 27.184 21.101 34.798 1.00 35.83 N ATOM 54 CA ARG A 14 28.542 21.611 35.053 1.00 34.63 C ATOM 55 C ARG A 14 29.486 20.441 35.298 1.00 35.93 C ATOM 56 O ARG A 14 30.409 20.244 34.514 1.00 34.08 O ATOM 57 N SER A 15 29.184 19.566 36.265 1.00 39.02 N ATOM 58 CA SER A 15 30.148 18.527 36.626 1.00 40.95 C ATOM 59 C SER A 15 30.376 17.566 35.480 1.00 39.30 C ATOM 60 O SER A 15 31.528 17.249 35.111 1.00 42.27 O ATOM 61 N VAL A 16 29.306 17.091 34.890 1.00 37.98 N ATOM 62 CA VAL A 16 29.452 16.039 33.860 1.00 37.22 C ATOM 63 C VAL A 16 30.109 16.586 32.595 1.00 35.88 C ATOM 64 O VAL A 16 31.077 16.065 32.082 1.00 37.43 O ATOM 65 N CYS A 17 29.572 17.693 32.090 1.00 33.28 N ATOM 66 CA CYS A 17 30.128 18.251 30.858 1.00 32.19 C ATOM 67 C CYS A 17 31.535 18.829 31.061 1.00 32.65 C ATOM 68 O CYS A 17 32.359 18.795 30.135 1.00 32.70 O ATOM 69 N LEU A 18 31.796 19.377 32.240 1.00 32.85 N ATOM 70 CA LEU A 18 33.128 19.914 32.524 1.00 33.50 C ATOM 71 C LEU A 18 34.169 18.799 32.677 1.00 37.40 C ATOM 72 O LEU A 18 35.349 18.974 32.398 1.00 38.44 O ATOM 73 N GLY A 19 33.779 17.627 33.161 1.00 40.28 N ATOM 74 CA GLY A 19 34.635 16.474 33.045 1.00 44.13 C ATOM 75 C GLY A 19 34.730 15.975 31.615 1.00 44.20 C ATOM 76 O GLY A 19 35.681 15.250 31.269 1.00 46.42 O ATOM 77 N LYS A 20 33.735 16.258 30.773 1.00 41.93 N ATOM 78 CA LYS A 20 33.819 15.832 29.374 1.00 42.83 C ATOM 79 C LYS A 20 34.745 16.718 28.549 1.00 42.66 C ATOM 80 O LYS A 20 35.427 16.243 27.638 1.00 42.05 O ATOM 81 N THR A 21 34.805 18.007 28.797 1.00 40.77 N ATOM 82 CA THR A 21 35.593 18.896 27.954 1.00 40.50 C ATOM 83 C THR A 21 36.842 19.399 28.654 1.00 42.78 C ATOM 84 O THR A 21 37.823 19.657 27.983 1.00 44.01 O ATOM 85 N LYS A 22 36.815 19.486 29.974 1.00 44.63 N ATOM 86 CA LYS A 22 37.951 19.848 30.817 1.00 45.73 C ATOM 87 C LYS A 22 38.543 21.187 30.359 1.00 44.09 C ATOM 88 O LYS A 22 39.660 21.265 29.818 1.00 48.05 O TER END """ def run(pdb_str, d_min, b): # pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str_box) cs = pdb_inp.crystal_symmetry() ph = pdb_inp.construct_hierarchy() xrs = ph.extract_xray_structure(crystal_symmetry=cs) xrs = xrs.set_b_iso(value=b) fc = xrs.structure_factors(d_min=d_min).f_calc() cg = maptbx.crystal_gridding( unit_cell = cs.unit_cell(), space_group_info = cs.space_group_info(), d_min = d_min) fft_map = miller.fft_map( crystal_gridding = cg, fourier_coefficients = fc) map_obs = fft_map.real_map_unpadded() # pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str) xrs = ph.extract_xray_structure(crystal_symmetry=cs) o = maptbx.resolution_from_map_and_model.run(map_data=map_obs, xray_structure=xrs) return o.d_min, o.b_iso, o.d_fsc_model if (__name__ == "__main__"): for pdb_str in [pdb_str_5bb, pdb_str_5]: for d_min in [2., 3., 4., 5.]: for b in [20,80,100,200]: if((d_min==2. or d_min==3.) and b>50.): continue result, b_result, d_fsc_model = run(pdb_str=pdb_str, d_min=d_min, b=b) print(b, d_min, "<>", b_result, result, d_fsc_model) #assert approx_equal(d_min, result) #XXX assert cc>0.9 #XXX if(not randomize): #XXX assert approx_equal(b, b_result,5.+1)