from __future__ import absolute_import, division, print_function from libtbx.test_utils import approx_equal, show_diff import iotbx.ncs as ncs import iotbx.pdb import sys, os from iotbx.ncs import ncs_group_master_phil import iotbx.phil pdb_str_1 = """ CRYST1 399.000 399.000 399.000 90.00 90.00 90.00 P 1 ATOM 1 N GLY A 34 125.208 211.886 175.417 1.00 0.00 N ATOM 2 CA GLY A 34 125.035 211.123 174.168 1.00 0.00 C ATOM 3 C GLY A 34 126.386 210.806 173.507 1.00 0.00 C ATOM 4 O GLY A 34 127.304 211.628 173.503 1.00 0.00 O TER ATOM 5 N GLY B 34 251.532 143.432 175.422 1.00 0.00 N ATOM 6 CA GLY B 34 252.120 143.948 174.173 1.00 0.00 C ATOM 7 C GLY B 34 251.212 144.998 173.512 1.00 0.00 C ATOM 8 O GLY B 34 249.986 144.872 173.510 1.00 0.00 O TER ATOM 9 N GLY C 34 189.583 273.076 175.423 1.00 0.00 N ATOM 10 CA GLY C 34 188.804 273.006 174.173 1.00 0.00 C ATOM 11 C GLY C 34 188.920 271.622 173.510 1.00 0.00 C ATOM 12 O GLY C 34 189.986 271.004 173.508 1.00 0.00 O TER """ pdb_str_2 = """ CRYST1 399.000 399.000 399.000 90.00 90.00 90.00 P 1 ATOM 1 O HOH S 1 109.583 203.076 175.423 1.00 0.00 O TER ATOM 1 N GLY A 34 125.208 211.886 175.417 1.00 0.00 N ATOM 2 CA GLY A 34 125.035 211.123 174.168 1.00 0.00 C ATOM 3 C GLY A 34 126.386 210.806 173.507 1.00 0.00 C ATOM 4 O GLY A 34 127.304 211.628 173.503 1.00 0.00 O TER ATOM 5 N GLY B 34 251.532 143.432 175.422 1.00 0.00 N ATOM 6 CA GLY B 34 252.120 143.948 174.173 1.00 0.00 C ATOM 7 C GLY B 34 251.212 144.998 173.512 1.00 0.00 C ATOM 8 O GLY B 34 249.986 144.872 173.510 1.00 0.00 O TER ATOM 9 N GLY C 34 189.583 273.076 175.423 1.00 0.00 N ATOM 10 CA GLY C 34 188.804 273.006 174.173 1.00 0.00 C ATOM 11 C GLY C 34 188.920 271.622 173.510 1.00 0.00 C ATOM 12 O GLY C 34 189.986 271.004 173.508 1.00 0.00 O TER ATOM 9 O TYR D 4 189.583 273.076 175.423 1.00 0.00 O TER """ pdb_str_5 = """ ATOM 1 N MET A 1 158.070 173.095 147.115 1.00 50.00 N ATOM 2 CA MET A 1 157.408 172.627 148.359 1.00 50.00 C ATOM 3 CB MET A 1 157.550 171.094 148.516 1.00 50.00 C ATOM 4 CG MET A 1 156.748 170.503 149.691 1.00 50.00 C ATOM 5 SD MET A 1 154.968 170.855 149.612 1.00 50.00 S ATOM 6 CE MET A 1 154.505 169.913 151.091 1.00 50.00 C ATOM 7 C MET A 1 157.958 173.331 149.563 1.00 50.00 C ATOM 8 O MET A 1 157.196 173.814 150.399 1.00 50.00 O TER ATOM 9 N MET B 1 174.781 155.306 150.054 1.00 50.00 N ATOM 10 CA MET B 1 174.332 154.630 151.298 1.00 50.00 C ATOM 11 CB MET B 1 175.016 153.251 151.453 1.00 50.00 C ATOM 12 CG MET B 1 174.481 152.410 152.628 1.00 50.00 C ATOM 13 SD MET B 1 172.693 152.099 152.550 1.00 50.00 S ATOM 14 CE MET B 1 172.601 151.052 154.028 1.00 50.00 C ATOM 15 C MET B 1 174.594 155.484 152.502 1.00 50.00 C ATOM 16 O MET B 1 173.710 155.660 153.339 1.00 50.00 O TER ATOM 17 N MET C 1 148.867 195.697 144.146 1.00 50.00 N ATOM 18 CA MET C 1 148.080 195.499 145.390 1.00 50.00 C ATOM 19 CB MET C 1 147.662 194.018 145.549 1.00 50.00 C ATOM 20 CG MET C 1 146.701 193.755 146.723 1.00 50.00 C ATOM 21 SD MET C 1 145.166 194.723 146.643 1.00 50.00 S ATOM 22 CE MET C 1 144.395 194.012 148.122 1.00 50.00 C ATOM 23 C MET C 1 148.846 195.960 146.594 1.00 50.00 C ATOM 24 O MET C 1 148.308 196.685 147.429 1.00 50.00 O TER ATOM 417 N MET 1 1 274.499 237.478 69.907 1.00 50.00 N ATOM 418 CA MET 1 1 275.223 237.861 71.146 1.00 50.00 C ATOM 419 CB MET 1 1 275.281 239.400 71.298 1.00 50.00 C ATOM 420 CG MET 1 1 276.159 239.886 72.466 1.00 50.00 C ATOM 421 SD MET 1 1 277.878 239.307 72.379 1.00 50.00 S ATOM 422 CE MET 1 1 278.468 240.186 73.852 1.00 50.00 C ATOM 423 C MET 1 1 274.593 237.238 72.356 1.00 50.00 C ATOM 424 O MET 1 1 275.291 236.663 73.190 1.00 50.00 O TER END """ pdb_str_6 = """\ CRYST1 577.812 448.715 468.790 90.00 90.00 90.00 P 1 ATOM 1 CA LYS A 151 10.766 9.333 12.905 1.00 44.22 C ATOM 2 CA LYS A 152 10.117 9.159 11.610 1.00 49.42 C ATOM 3 CA LYS A 153 9.099 8.000 11.562 1.00 46.15 C ATOM 4 CA LYS A 154 8.000 8.202 11.065 1.00 52.97 C ATOM 5 CA LYS A 155 11.146 9.065 10.474 1.00 41.68 C ATOM 6 CA LYS A 156 10.547 9.007 9.084 1.00 55.55 C TER ATOM 7 CA LYS B 157 11.545 9.413 8.000 1.00 72.27 C ATOM 8 CA LYS B 158 12.277 10.718 8.343 1.00 75.78 C ATOM 9 CA LYS B 159 11.349 11.791 8.809 1.00 75.88 C TER ATOM 7 CA LYS F 157 2.154 3.953 16.298 1.00 72.27 C ATOM 8 CA LYS F 158 2.014 3.732 17.811 1.00 75.78 C ATOM 9 CA LYS F 159 2.558 2.413 18.250 1.00 75.88 C TER ATOM 7 CA LYS D 157 4.334 10.965 12.119 1.00 72.27 C ATOM 8 CA LYS D 158 4.057 11.980 13.238 1.00 75.78 C ATOM 9 CA LYS D 159 3.177 11.427 14.310 1.00 75.88 C TER ATOM 1 CA LYS C 151 6.855 8.667 15.730 1.00 44.22 C ATOM 2 CA LYS C 152 5.891 8.459 14.655 1.00 49.42 C ATOM 3 CA LYS C 153 6.103 7.155 13.858 1.00 46.15 C ATOM 4 CA LYS C 154 5.138 6.438 13.633 1.00 52.97 C ATOM 5 CA LYS C 155 5.801 9.685 13.736 1.00 41.68 C ATOM 6 CA LYS C 156 4.731 9.594 12.667 1.00 55.55 C TER ATOM 1 CA LYS E 151 6.987 4.106 17.432 1.00 44.22 C ATOM 2 CA LYS E 152 6.017 3.539 16.502 1.00 49.42 C ATOM 3 CA LYS E 153 6.497 3.492 15.036 1.00 46.15 C ATOM 4 CA LYS E 154 6.348 2.458 14.400 1.00 52.97 C ATOM 5 CA LYS E 155 4.647 4.221 16.634 1.00 41.68 C ATOM 6 CA LYS E 156 3.552 3.605 15.788 1.00 55.55 C TER """ pdb_str_7 = """\ CRYST1 577.812 448.715 468.790 90.00 90.00 90.00 P 1 ATOM 1 CA LYS A 151 10.766 9.333 12.905 1.00 44.22 C ATOM 2 CA LYS A 152 10.117 9.159 11.610 1.00 49.42 C ATOM 3 CA LYS A 153 9.099 8.000 11.562 1.00 46.15 C ATOM 4 CA LYS A 154 8.000 8.202 11.065 1.00 52.97 C ATOM 5 CA LYS A 155 11.146 9.065 10.474 1.00 41.68 C TER ATOM 222 CA LEU X 40 94.618 -5.253 91.582 1.00 87.10 C ATOM 223 CA ARG X 41 62.395 51.344 80.786 1.00107.25 C ATOM 224 CA ARG X 42 62.395 41.344 80.786 1.00107.25 C TER ATOM 1 CA THR D 1 8.111 11.080 10.645 1.00 20.00 C ATOM 2 CA THR D 2 8.000 9.722 10.125 1.00 20.00 C ATOM 3 CA THR D 3 8.075 8.694 11.249 1.00 20.00 C ATOM 4 CA THR D 4 8.890 8.818 12.163 1.00 20.00 C TER ATOM 1 CA LYS B 151 6.855 8.667 15.730 1.00 44.22 C ATOM 2 CA LYS B 152 5.891 8.459 14.655 1.00 49.42 C ATOM 3 CA LYS B 153 6.103 7.155 13.858 1.00 46.15 C ATOM 4 CA LYS B 154 5.138 6.438 13.633 1.00 52.97 C ATOM 5 CA LYS B 155 5.801 9.685 13.736 1.00 41.68 C TER ATOM 1 CA LYS C 151 6.987 4.106 17.432 1.00 44.22 C ATOM 2 CA LYS C 152 6.017 3.539 16.502 1.00 49.42 C ATOM 3 CA LYS C 153 6.497 3.492 15.036 1.00 46.15 C ATOM 4 CA LYS C 154 6.348 2.458 14.400 1.00 52.97 C ATOM 5 CA LYS C 155 4.647 4.221 16.634 1.00 41.68 C TER ATOM 222 CA LEU Y 40 194.618 5.253 81.582 1.00 87.10 C ATOM 223 CA ARG Y 41 162.395 41.344 70.786 1.00107.25 C ATOM 224 CA ARG Y 42 162.395 31.344 70.786 1.00107.25 C TER ATOM 1 CA THR E 1 8.111 -10.645 11.080 1.00 20.00 C ATOM 2 CA THR E 2 8.000 -10.125 9.722 1.00 20.00 C ATOM 3 CA THR E 3 8.075 -11.249 8.694 1.00 20.00 C ATOM 4 CA THR E 4 8.890 -12.163 8.818 1.00 20.00 C TER """ pdb_str_8 = """\ ATOM 1 N THR A 1 13.014 18.419 8.520 1.00 20.00 N ATOM 2 CA THR A 1 12.903 17.061 8.000 1.00 20.00 C ATOM 3 C THR A 1 12.978 16.033 9.124 1.00 20.00 C ATOM 4 O THR A 1 13.793 16.157 10.038 1.00 20.00 O TER ATOM 1 N THR C 1 10.325 8.000 14.368 1.00 20.00 N ATOM 2 CA THR C 1 10.111 8.702 13.108 1.00 20.00 C ATOM 3 C THR C 1 11.313 9.570 12.750 1.00 20.00 C ATOM 4 O THR C 1 11.885 10.241 13.609 1.00 20.00 O TER ATOM 1 N THR D 1 -0.430 15.458 18.495 1.00 20.00 N ATOM 2 CA THR D 1 0.086 15.020 17.204 1.00 20.00 C ATOM 3 C THR D 1 1.440 14.334 17.355 1.00 20.00 C ATOM 4 O THR D 1 2.297 14.791 18.111 1.00 20.00 O TER ATOM 1 N THR E 1 1.895 8.366 19.752 1.00 20.00 N ATOM 2 CA THR E 1 1.682 9.068 18.491 1.00 20.00 C ATOM 3 C THR E 1 2.884 9.935 18.133 1.00 20.00 C ATOM 4 O THR E 1 3.455 10.606 18.993 1.00 20.00 O TER ATOM 1 N THR F 1 8.346 7.308 15.936 1.00 20.00 N ATOM 2 CA THR F 1 7.054 7.796 15.467 1.00 20.00 C ATOM 3 C THR F 1 6.884 9.281 15.767 1.00 20.00 C ATOM 4 O THR F 1 7.237 9.751 16.849 1.00 20.00 O TER ATOM 1 N THR G 1 0.609 -0.560 24.094 1.00 20.00 N ATOM 2 CA THR G 1 0.395 0.142 22.834 1.00 20.00 C ATOM 3 C THR G 1 1.598 1.009 22.476 1.00 20.00 C ATOM 4 O THR G 1 2.169 1.680 23.335 1.00 20.00 O TER ATOM 1 N THR H 1 7.061 -1.617 20.279 1.00 20.00 N ATOM 2 CA THR H 1 5.768 -1.130 19.810 1.00 20.00 C ATOM 3 C THR H 1 5.599 0.356 20.109 1.00 20.00 C ATOM 4 O THR H 1 5.950 0.825 21.191 1.00 20.00 O TER ATOM 1 N THR I 1 8.722 4.822 16.665 1.00 20.00 N ATOM 2 CA THR I 1 7.494 4.036 16.653 1.00 20.00 C ATOM 3 C THR I 1 6.628 4.350 17.868 1.00 20.00 C ATOM 4 O THR I 1 7.130 4.482 18.984 1.00 20.00 O TER ATOM 1 N THR B 1 8.000 15.093 13.112 1.00 20.00 N ATOM 2 CA THR B 1 8.516 14.654 11.820 1.00 20.00 C ATOM 3 C THR B 1 9.870 13.968 11.972 1.00 20.00 C ATOM 4 O THR B 1 10.727 14.426 12.727 1.00 20.00 O TER """ pdb_str_9 = """\ ATOM 45 N PHEAa 6 221.693 146.930 114.416 1.00 50.00 N ATOM 46 CA PHEAa 6 220.871 148.020 114.886 1.00 50.00 C ATOM 47 C PHEAa 6 219.413 147.628 114.926 1.00 50.00 C ATOM 48 O PHEAa 6 218.730 147.905 115.908 1.00 50.00 O ATOM 49 CB PHEAa 6 221.058 149.265 113.976 1.00 50.00 C ATOM 50 CG PHEAa 6 220.338 150.481 114.498 1.00 50.00 C ATOM 51 CD1 PHEAa 6 220.740 151.082 115.702 1.00 50.00 C ATOM 52 CD2 PHEAa 6 219.240 151.016 113.801 1.00 50.00 C ATOM 53 CE1 PHEAa 6 220.059 152.198 116.204 1.00 50.00 C ATOM 54 CE2 PHEAa 6 218.557 152.133 114.299 1.00 50.00 C ATOM 55 CZ PHEAa 6 218.965 152.723 115.500 1.00 50.00 C ATOM 56 N ASNAa 7 218.926 146.940 113.868 1.00 50.00 N ATOM 57 CA ASNAa 7 217.565 146.462 113.741 1.00 50.00 C ATOM 58 C ASNAa 7 217.229 145.425 114.782 1.00 50.00 C ATOM 59 O ASNAa 7 216.113 145.412 115.283 1.00 50.00 O ATOM 60 CB ASNAa 7 217.235 145.875 112.347 1.00 50.00 C ATOM 61 CG ASNAa 7 217.277 146.970 111.271 1.00 50.00 C ATOM 62 OD1 ASNAa 7 217.061 148.155 111.550 1.00 50.00 O ATOM 63 ND2 ASNAa 7 217.551 146.541 110.002 1.00 50.00 N ATOM 64 N LEUAa 8 218.185 144.528 115.129 1.00 50.00 N ATOM 65 CA LEUAa 8 217.998 143.485 116.117 1.00 50.00 C ATOM 66 C LEUAa 8 217.846 144.051 117.505 1.00 50.00 C ATOM 67 O LEUAa 8 217.002 143.585 118.265 1.00 50.00 O ATOM 68 CB LEUAa 8 219.168 142.476 116.143 1.00 50.00 C ATOM 69 CG LEUAa 8 219.217 141.553 114.906 1.00 50.00 C ATOM 70 CD1 LEUAa 8 220.600 140.889 114.770 1.00 50.00 C ATOM 71 CD2 LEUAa 8 218.098 140.493 114.925 1.00 50.00 C ATOM 72 N LYSAa 9 218.665 145.069 117.866 1.00 50.00 N ATOM 73 CA LYSAa 9 218.573 145.769 119.133 1.00 50.00 C ATOM 74 C LYSAa 9 217.287 146.554 119.234 1.00 50.00 C ATOM 75 O LYSAa 9 216.682 146.606 120.301 1.00 50.00 O ATOM 76 CB LYSAa 9 219.751 146.744 119.364 1.00 50.00 C ATOM 77 CG LYSAa 9 221.113 146.057 119.558 1.00 50.00 C ATOM 78 CD LYSAa 9 221.257 145.305 120.891 1.00 50.00 C ATOM 79 CE LYSAa 9 222.646 144.673 121.065 1.00 50.00 C ATOM 80 NZ LYSAa 9 222.723 143.882 122.315 1.00 50.00 N TER ATOM 1244 N PHEAb 1 305.367 162.705 105.239 1.00 50.00 N ATOM 1245 CA PHEAb 1 304.396 162.991 106.331 1.00 50.00 C ATOM 1246 C PHEAb 1 304.285 164.473 106.586 1.00 50.00 C ATOM 1247 O PHEAb 1 304.837 165.292 105.851 1.00 50.00 O ATOM 1248 CB PHEAb 1 304.743 162.176 107.627 1.00 50.00 C ATOM 1249 CG PHEAb 1 305.801 162.775 108.540 1.00 50.00 C ATOM 1250 CD1 PHEAb 1 307.055 163.195 108.061 1.00 50.00 C ATOM 1251 CD2 PHEAb 1 305.501 162.973 109.900 1.00 50.00 C ATOM 1252 CE1 PHEAb 1 307.967 163.838 108.909 1.00 50.00 C ATOM 1253 CE2 PHEAb 1 306.412 163.612 110.751 1.00 50.00 C ATOM 1254 CZ PHEAb 1 307.642 164.054 110.251 1.00 50.00 C ATOM 1255 N LYSAb 2 303.607 164.838 107.696 1.00 50.00 N ATOM 1256 CA LYSAb 2 303.542 166.190 108.180 1.00 50.00 C ATOM 1257 C LYSAb 2 303.642 166.054 109.667 1.00 50.00 C ATOM 1258 O LYSAb 2 302.934 165.255 110.277 1.00 50.00 O ATOM 1259 CB LYSAb 2 302.234 166.947 107.855 1.00 50.00 C ATOM 1260 CG LYSAb 2 302.035 167.201 106.352 1.00 50.00 C ATOM 1261 CD LYSAb 2 300.842 168.117 106.023 1.00 50.00 C ATOM 1262 CE LYSAb 2 301.067 169.582 106.424 1.00 50.00 C ATOM 1263 NZ LYSAb 2 299.910 170.421 106.031 1.00 50.00 N ATOM 1264 N ALAAb 3 304.533 166.867 110.282 1.00 50.00 N ATOM 1265 CA ALAAb 3 304.840 166.840 111.692 1.00 50.00 C ATOM 1266 C ALAAb 3 303.670 167.320 112.503 1.00 50.00 C ATOM 1267 O ALAAb 3 303.399 166.803 113.583 1.00 50.00 O ATOM 1268 CB ALAAb 3 306.055 167.711 112.038 1.00 50.00 C ATOM 1269 N GLUAb 4 302.961 168.344 111.975 1.00 50.00 N ATOM 1270 CA GLUAb 4 301.784 168.942 112.560 1.00 50.00 C ATOM 1271 C GLUAb 4 300.678 167.941 112.768 1.00 50.00 C ATOM 1272 O GLUAb 4 300.094 167.886 113.848 1.00 50.00 O ATOM 1273 CB GLUAb 4 301.233 170.108 111.709 1.00 50.00 C ATOM 1274 CG GLUAb 4 302.268 171.215 111.421 1.00 50.00 C ATOM 1275 CD GLUAb 4 302.808 171.795 112.727 1.00 50.00 C ATOM 1276 OE1 GLUAb 4 304.040 171.677 112.965 1.00 50.00 O ATOM 1277 OE2 GLUAb 4 301.994 172.363 113.504 1.00 50.00 O TER ATOM 2754 N PHEAc 6 244.472 153.067 117.352 1.00 50.00 N ATOM 2755 CA PHEAc 6 243.314 153.789 117.823 1.00 50.00 C ATOM 2756 C PHEAc 6 242.094 152.900 117.864 1.00 50.00 C ATOM 2757 O PHEAc 6 241.358 152.912 118.847 1.00 50.00 O ATOM 2758 CB PHEAc 6 243.040 155.017 116.913 1.00 50.00 C ATOM 2759 CG PHEAc 6 241.932 155.894 117.436 1.00 50.00 C ATOM 2760 CD1 PHEAc 6 242.091 156.600 118.639 1.00 50.00 C ATOM 2761 CD2 PHEAc 6 240.715 155.999 116.739 1.00 50.00 C ATOM 2762 CE1 PHEAc 6 241.055 157.396 119.141 1.00 50.00 C ATOM 2763 CE2 PHEAc 6 239.676 156.795 117.237 1.00 50.00 C ATOM 2764 CZ PHEAc 6 239.846 157.493 118.439 1.00 50.00 C ATOM 2765 N ASNAc 7 241.886 152.082 116.806 1.00 50.00 N ATOM 2766 CA ASNAc 7 240.788 151.148 116.680 1.00 50.00 C ATOM 2767 C ASNAc 7 240.847 150.058 117.721 1.00 50.00 C ATOM 2768 O ASNAc 7 239.810 149.645 118.224 1.00 50.00 O ATOM 2769 CB ASNAc 7 240.690 150.481 115.286 1.00 50.00 C ATOM 2770 CG ASNAc 7 240.334 151.517 114.210 1.00 50.00 C ATOM 2771 OD1 ASNAc 7 239.707 152.544 114.490 1.00 50.00 O ATOM 2772 ND2 ASNAc 7 240.743 151.215 112.941 1.00 50.00 N ATOM 2773 N LEUAc 8 242.062 149.565 118.068 1.00 50.00 N ATOM 2774 CA LEUAc 8 242.264 148.525 119.056 1.00 50.00 C ATOM 2775 C LEUAc 8 241.919 148.999 120.443 1.00 50.00 C ATOM 2776 O LEUAc 8 241.299 148.260 121.204 1.00 50.00 O ATOM 2777 CB LEUAc 8 243.717 148.003 119.082 1.00 50.00 C ATOM 2778 CG LEUAc 8 244.094 147.160 117.844 1.00 50.00 C ATOM 2779 CD1 LEUAc 8 245.623 147.037 117.707 1.00 50.00 C ATOM 2780 CD2 LEUAc 8 243.430 145.768 117.864 1.00 50.00 C ATOM 2781 N LYSAc 9 242.317 150.242 120.804 1.00 50.00 N ATOM 2782 CA LYSAc 9 241.981 150.863 122.071 1.00 50.00 C ATOM 2783 C LYSAc 9 240.499 151.134 122.173 1.00 50.00 C ATOM 2784 O LYSAc 9 239.916 150.965 123.241 1.00 50.00 O ATOM 2785 CB LYSAc 9 242.729 152.197 122.302 1.00 50.00 C ATOM 2786 CG LYSAc 9 244.248 152.045 122.495 1.00 50.00 C ATOM 2787 CD LYSAc 9 244.653 151.394 123.828 1.00 50.00 C ATOM 2788 CE LYSAc 9 246.177 151.304 124.001 1.00 50.00 C ATOM 2789 NZ LYSAc 9 246.534 150.594 125.250 1.00 50.00 N TER ATOM 3953 N PHEAd 1 316.882 197.854 108.123 1.00 50.00 N ATOM 3954 CA PHEAd 1 315.875 197.773 109.215 1.00 50.00 C ATOM 3955 C PHEAd 1 315.239 199.116 109.471 1.00 50.00 C ATOM 3956 O PHEAd 1 315.460 200.078 108.736 1.00 50.00 O ATOM 3957 CB PHEAd 1 316.493 197.136 110.512 1.00 50.00 C ATOM 3958 CG PHEAd 1 317.265 198.076 111.424 1.00 50.00 C ATOM 3959 CD1 PHEAd 1 318.283 198.919 110.944 1.00 50.00 C ATOM 3960 CD2 PHEAd 1 316.915 198.154 112.784 1.00 50.00 C ATOM 3961 CE1 PHEAd 1 318.905 199.846 111.792 1.00 50.00 C ATOM 3962 CE2 PHEAd 1 317.536 199.077 113.635 1.00 50.00 C ATOM 3963 CZ PHEAd 1 318.525 199.932 113.135 1.00 50.00 C ATOM 3964 N LYSAd 2 314.475 199.212 110.581 1.00 50.00 N ATOM 3965 CA LYSAd 2 313.929 200.450 111.066 1.00 50.00 C ATOM 3966 C LYSAd 2 314.073 200.360 112.553 1.00 50.00 C ATOM 3967 O LYSAd 2 313.699 199.360 113.163 1.00 50.00 O ATOM 3968 CB LYSAd 2 312.437 200.687 110.742 1.00 50.00 C ATOM 3969 CG LYSAd 2 312.159 200.852 109.239 1.00 50.00 C ATOM 3970 CD LYSAd 2 310.717 201.278 108.910 1.00 50.00 C ATOM 3971 CE LYSAd 2 310.400 202.726 109.311 1.00 50.00 C ATOM 3972 NZ LYSAd 2 309.019 203.094 108.919 1.00 50.00 N ATOM 3973 N ALAAd 3 314.612 201.440 113.166 1.00 50.00 N ATOM 3974 CA ALAAd 3 314.909 201.525 114.577 1.00 50.00 C ATOM 3975 C ALAAd 3 313.646 201.552 115.389 1.00 50.00 C ATOM 3976 O ALAAd 3 313.579 200.972 116.469 1.00 50.00 O ATOM 3977 CB ALAAd 3 315.731 202.774 114.922 1.00 50.00 C ATOM 3978 N GLUAd 4 312.615 202.253 114.862 1.00 50.00 N ATOM 3979 CA GLUAd 4 311.303 202.387 115.448 1.00 50.00 C ATOM 3980 C GLUAd 4 310.630 201.057 115.656 1.00 50.00 C ATOM 3981 O GLUAd 4 310.105 200.796 116.737 1.00 50.00 O ATOM 3982 CB GLUAd 4 310.369 203.279 114.597 1.00 50.00 C ATOM 3983 CG GLUAd 4 310.938 204.683 114.308 1.00 50.00 C ATOM 3984 CD GLUAd 4 311.233 205.418 115.614 1.00 50.00 C ATOM 3985 OE1 GLUAd 4 312.425 205.752 115.850 1.00 50.00 O ATOM 3986 OE2 GLUAd 4 310.271 205.657 116.392 1.00 50.00 O TER END """ pdb_str_10 = """\ ATOM 181 CA SER L 26 43.792 -65.179 67.649 1.00 22.76 C ATOM 182 C SER L 26 43.921 -63.740 68.152 1.00 25.79 C ATOM 183 O SER L 26 44.600 -63.476 69.148 1.00 27.95 O ATOM 184 CB SER L 26 45.023 -65.575 66.834 1.00 23.39 C ATOM 185 OG SER L 26 45.013 -64.937 65.570 1.00 21.58 O ATOM 186 N GLN L 27 43.266 -62.813 67.460 1.00 23.64 N ATOM 187 CA GLN L 27 43.289 -61.405 67.832 1.00 24.84 C ATOM 188 C GLN L 27 41.869 -60.863 67.858 1.00 25.95 C ATOM 189 O GLN L 27 40.987 -61.380 67.172 1.00 26.41 O ATOM 190 CB GLN L 27 44.108 -60.589 66.830 1.00 27.09 C ATOM 191 CG GLN L 27 45.602 -60.618 67.048 1.00 35.67 C ATOM 192 CD GLN L 27 46.338 -59.767 66.033 1.00 38.53 C ATOM 193 OE1 GLN L 27 46.675 -60.228 64.942 1.00 43.32 O ATOM 194 NE2 GLN L 27 46.572 -58.507 66.380 1.00 40.19 N ATOM 195 N SER L 27A 41.653 -59.819 68.651 1.00 21.30 N ATOM 196 CA SER L 27A 40.340 -59.209 68.744 1.00 23.38 C ATOM 197 C SER L 27A 39.920 -58.676 67.377 1.00 22.05 C ATOM 198 O SER L 27A 40.712 -58.050 66.678 1.00 19.83 O ATOM 199 CB SER L 27A 40.362 -58.057 69.745 1.00 20.17 C ATOM 200 OG SER L 27A 39.122 -57.376 69.738 1.00 24.39 O ATOM 201 N LEU L 27B 38.669 -58.918 67.003 1.00 21.73 N ATOM 202 CA LEU L 27B 38.173 -58.446 65.720 1.00 20.41 C ATOM 203 C LEU L 27B 37.484 -57.089 65.854 1.00 21.13 C ATOM 204 O LEU L 27B 36.749 -56.670 64.961 1.00 21.34 O ATOM 205 CB LEU L 27B 37.212 -59.473 65.116 1.00 17.54 C ATOM 206 CG LEU L 27B 37.805 -60.882 64.938 1.00 21.70 C ATOM 207 CD1 LEU L 27B 36.800 -61.778 64.232 1.00 19.78 C ATOM 208 CD2 LEU L 27B 39.092 -60.808 64.132 1.00 17.87 C ATOM 235 N ASN L 28 36.659 -48.175 64.751 1.00 23.50 N ATOM 236 CA ASN L 28 35.418 -47.408 64.733 1.00 19.92 C ATOM 237 C ASN L 28 34.411 -48.040 65.685 1.00 22.34 C ATOM 238 O ASN L 28 33.274 -47.586 65.794 1.00 25.95 O ATOM 239 CB ASN L 28 34.831 -47.338 63.321 1.00 19.19 C ATOM 240 CG ASN L 28 34.676 -48.707 62.680 1.00 22.32 C ATOM 241 OD1 ASN L 28 34.703 -49.732 63.359 1.00 19.98 O ATOM 242 ND2 ASN L 28 34.498 -48.726 61.364 1.00 21.69 N ATOM 243 N GLY L 29 34.835 -49.093 66.374 1.00 23.30 N ATOM 244 CA GLY L 29 33.957 -49.746 67.329 1.00 23.12 C ATOM 245 C GLY L 29 33.135 -50.912 66.810 1.00 25.74 C ATOM 246 O GLY L 29 32.347 -51.500 67.555 1.00 22.95 O TER ATOM 1 CA SER H 26 46.792 -62.179 70.649 1.00 22.76 C ATOM 2 C SER H 26 46.921 -60.740 71.152 1.00 25.79 C ATOM 3 O SER H 26 47.600 -60.476 72.148 1.00 27.95 O ATOM 4 CB SER H 26 48.023 -62.575 69.834 1.00 23.39 C ATOM 5 OG SER H 26 48.013 -61.937 68.570 1.00 21.58 O ATOM 6 N GLN H 27 46.266 -59.813 70.460 1.00 23.64 N ATOM 7 CA GLN H 27 46.289 -58.405 70.832 1.00 24.84 C ATOM 8 C GLN H 27 44.869 -57.863 70.858 1.00 25.95 C ATOM 9 O GLN H 27 43.987 -58.380 70.172 1.00 26.41 O ATOM 10 CB GLN H 27 47.108 -57.589 69.830 1.00 27.09 C ATOM 11 CG GLN H 27 48.602 -57.618 70.048 1.00 35.67 C ATOM 12 CD GLN H 27 49.338 -56.767 69.033 1.00 38.53 C ATOM 13 OE1 GLN H 27 49.675 -57.228 67.942 1.00 43.32 O ATOM 14 NE2 GLN H 27 49.572 -55.507 69.380 1.00 40.19 N ATOM 15 N SER H 27A 44.653 -56.819 71.651 1.00 21.30 N ATOM 16 CA SER H 27A 43.340 -56.209 71.744 1.00 23.38 C ATOM 17 C SER H 27A 42.920 -55.676 70.377 1.00 22.05 C ATOM 18 O SER H 27A 43.712 -55.050 69.678 1.00 19.83 O ATOM 19 CB SER H 27A 43.362 -55.057 72.745 1.00 20.17 C ATOM 20 OG SER H 27A 42.122 -54.376 72.738 1.00 24.39 O ATOM 21 N LEU H 27B 41.669 -55.918 70.003 1.00 21.73 N ATOM 22 CA LEU H 27B 41.173 -55.446 68.720 1.00 20.41 C ATOM 23 C LEU H 27B 40.484 -54.089 68.854 1.00 21.13 C ATOM 24 O LEU H 27B 39.749 -53.670 67.961 1.00 21.34 O ATOM 25 CB LEU H 27B 40.212 -56.473 68.116 1.00 17.54 C ATOM 26 CG LEU H 27B 40.805 -57.882 67.938 1.00 21.70 C ATOM 27 CD1 LEU H 27B 39.800 -58.778 67.232 1.00 19.78 C ATOM 28 CD2 LEU H 27B 42.092 -57.808 67.132 1.00 17.87 C ATOM 29 N ASN H 28 39.659 -45.175 67.751 1.00 23.50 N ATOM 30 CA ASN H 28 38.418 -44.408 67.733 1.00 19.92 C ATOM 31 C ASN H 28 37.411 -45.040 68.685 1.00 22.34 C ATOM 32 O ASN H 28 36.274 -44.586 68.794 1.00 25.95 O ATOM 33 CB ASN H 28 37.831 -44.338 66.321 1.00 19.19 C ATOM 34 CG ASN H 28 37.676 -45.707 65.680 1.00 22.32 C ATOM 35 OD1 ASN H 28 37.703 -46.732 66.359 1.00 19.98 O ATOM 36 ND2 ASN H 28 37.498 -45.726 64.364 1.00 21.69 N ATOM 37 N GLY H 29 37.835 -46.093 69.374 1.00 23.30 N ATOM 38 CA GLY H 29 36.957 -46.746 70.329 1.00 23.12 C ATOM 39 C GLY H 29 36.135 -47.912 69.810 1.00 25.74 C ATOM 40 O GLY H 29 35.347 -48.500 70.555 1.00 22.95 O """ pdb_str_11 = """\ ATOM 181 CA SER L 26 43.792 -65.179 67.649 1.00 22.76 C ATOM 182 C SER L 26 43.921 -63.740 68.152 1.00 25.79 C ATOM 183 O SER L 26 44.600 -63.476 69.148 1.00 27.95 O ATOM 184 CB SER L 26 45.023 -65.575 66.834 1.00 23.39 C ATOM 185 OG SER L 26 45.013 -64.937 65.570 1.00 21.58 O ATOM 186 N AGLN L 27 43.266 -62.813 67.460 0.50 23.64 N ATOM 187 CA AGLN L 27 43.289 -61.405 67.832 0.50 24.84 C ATOM 188 C AGLN L 27 41.869 -60.863 67.858 0.50 25.95 C ATOM 189 O AGLN L 27 40.987 -61.380 67.172 0.50 26.41 O ATOM 190 CB AGLN L 27 44.108 -60.589 66.830 0.50 27.09 C ATOM 191 CG AGLN L 27 45.602 -60.618 67.048 0.50 35.67 C ATOM 192 CD AGLN L 27 46.338 -59.767 66.033 0.50 38.53 C ATOM 193 OE1AGLN L 27 46.675 -60.228 64.942 0.50 43.32 O ATOM 194 NE2AGLN L 27 46.572 -58.507 66.380 0.50 40.19 N ATOM 195 N BSER L 27 41.653 -59.819 68.651 0.50 21.30 N ATOM 196 CA BSER L 27 40.340 -59.209 68.744 0.50 23.38 C ATOM 197 C BSER L 27 39.920 -58.676 67.377 0.50 22.05 C ATOM 198 O BSER L 27 40.712 -58.050 66.678 0.50 19.83 O ATOM 199 CB BSER L 27 40.362 -58.057 69.745 0.50 20.17 C ATOM 200 OG BSER L 27 39.122 -57.376 69.738 0.50 24.39 O ATOM 235 N ASN L 28 36.659 -48.175 64.751 1.00 23.50 N ATOM 236 CA ASN L 28 35.418 -47.408 64.733 1.00 19.92 C ATOM 237 C ASN L 28 34.411 -48.040 65.685 1.00 22.34 C ATOM 238 O ASN L 28 33.274 -47.586 65.794 1.00 25.95 O ATOM 239 CB ASN L 28 34.831 -47.338 63.321 1.00 19.19 C ATOM 240 CG ASN L 28 34.676 -48.707 62.680 1.00 22.32 C ATOM 241 OD1 ASN L 28 34.703 -49.732 63.359 1.00 19.98 O ATOM 242 ND2 ASN L 28 34.498 -48.726 61.364 1.00 21.69 N TER ATOM 1 CA SER H 26 46.792 -62.179 70.649 1.00 22.76 C ATOM 2 C SER H 26 46.921 -60.740 71.152 1.00 25.79 C ATOM 3 O SER H 26 47.600 -60.476 72.148 1.00 27.95 O ATOM 4 CB SER H 26 48.023 -62.575 69.834 1.00 23.39 C ATOM 5 OG SER H 26 48.013 -61.937 68.570 1.00 21.58 O ATOM 6 N AGLN H 27 46.266 -59.813 70.460 0.50 23.64 N ATOM 7 CA AGLN H 27 46.289 -58.405 70.832 0.50 24.84 C ATOM 8 C AGLN H 27 44.869 -57.863 70.858 0.50 25.95 C ATOM 9 O AGLN H 27 43.987 -58.380 70.172 0.50 26.41 O ATOM 10 CB AGLN H 27 47.108 -57.589 69.830 0.50 27.09 C ATOM 11 CG AGLN H 27 48.602 -57.618 70.048 0.50 35.67 C ATOM 12 CD AGLN H 27 49.338 -56.767 69.033 0.50 38.53 C ATOM 13 OE1AGLN H 27 49.675 -57.228 67.942 0.50 43.32 O ATOM 14 NE2AGLN H 27 49.572 -55.507 69.380 0.50 40.19 N ATOM 15 N BSER H 27 44.653 -56.819 71.651 0.50 21.30 N ATOM 16 CA BSER H 27 43.340 -56.209 71.744 0.50 23.38 C ATOM 17 C BSER H 27 42.920 -55.676 70.377 0.50 22.05 C ATOM 18 O BSER H 27 43.712 -55.050 69.678 0.50 19.83 O ATOM 19 CB BSER H 27 43.362 -55.057 72.745 0.50 20.17 C ATOM 20 OG BSER H 27 42.122 -54.376 72.738 0.50 24.39 O ATOM 29 N ASN H 28 39.659 -45.175 67.751 1.00 23.50 N ATOM 30 CA ASN H 28 38.418 -44.408 67.733 1.00 19.92 C ATOM 31 C ASN H 28 37.411 -45.040 68.685 1.00 22.34 C ATOM 32 O ASN H 28 36.274 -44.586 68.794 1.00 25.95 O ATOM 33 CB ASN H 28 37.831 -44.338 66.321 1.00 19.19 C ATOM 34 CG ASN H 28 37.676 -45.707 65.680 1.00 22.32 C ATOM 35 OD1 ASN H 28 37.703 -46.732 66.359 1.00 19.98 O ATOM 36 ND2 ASN H 28 37.498 -45.726 64.364 1.00 21.69 N """ pdb_str_12 = """\ MODEL 1 ATOM 181 CA SER L 26 43.792 -65.179 67.649 1.00 22.76 C ATOM 182 C SER L 26 43.921 -63.740 68.152 1.00 25.79 C ATOM 183 O SER L 26 44.600 -63.476 69.148 1.00 27.95 O ATOM 184 CB SER L 26 45.023 -65.575 66.834 1.00 23.39 C ATOM 185 OG SER L 26 45.013 -64.937 65.570 1.00 21.58 O ATOM 1 CA SER H 26 46.792 -62.179 70.649 1.00 22.76 C ATOM 2 C SER H 26 46.921 -60.740 71.152 1.00 25.79 C ATOM 3 O SER H 26 47.600 -60.476 72.148 1.00 27.95 O ATOM 4 CB SER H 26 48.023 -62.575 69.834 1.00 23.39 C ATOM 5 OG SER H 26 48.013 -61.937 68.570 1.00 21.58 O ENDMDL MODEL 2 ATOM 181 CA SER L 26 43.792 -65.179 67.649 1.00 22.76 C ATOM 182 C SER L 26 43.921 -63.740 68.152 1.00 25.79 C ATOM 183 O SER L 26 44.600 -63.476 69.148 1.00 27.95 O ATOM 184 CB SER L 26 45.023 -65.575 66.834 1.00 23.39 C ATOM 185 OG SER L 26 45.013 -64.937 65.570 1.00 21.58 O ATOM 1 CA SER H 26 46.792 -62.179 70.649 1.00 22.76 C ATOM 2 C SER H 26 46.921 -60.740 71.152 1.00 25.79 C ATOM 3 O SER H 26 47.600 -60.476 72.148 1.00 27.95 O ATOM 4 CB SER H 26 48.023 -62.575 69.834 1.00 23.39 C ATOM 5 OG SER H 26 48.013 -61.937 68.570 1.00 21.58 O ENDMDL """ pdb_str_13 = """\ ATOM 1 P DG A 101 29.431 -7.266 16.571 1.00 20.00 P ATOM 2 OP1 DG A 101 28.043 -6.752 16.549 1.00 20.00 O ATOM 3 OP2 DG A 101 30.364 -6.133 16.806 1.00 20.00 O ATOM 4 O5' DG A 101 29.574 -8.346 17.739 1.00 20.00 O ATOM 5 C5' DG A 101 30.631 -9.289 17.729 1.00 20.00 C ATOM 6 C4' DG A 101 31.914 -8.737 18.342 1.00 20.00 C ATOM 7 O4' DG A 101 32.710 -7.950 17.421 1.00 20.00 O ATOM 8 C3' DG A 101 31.833 -7.757 19.494 1.00 20.00 C ATOM 9 O3' DG A 101 31.252 -8.345 20.643 1.00 20.00 O ATOM 10 C2' DG A 101 33.328 -7.516 19.649 1.00 20.00 C ATOM 11 C1' DG A 101 33.752 -7.367 18.191 1.00 20.00 C ATOM 12 P DA A 102 30.972 -7.472 21.954 1.00 20.00 P ATOM 13 OP1 DA A 102 30.002 -8.227 22.777 1.00 20.00 O ATOM 14 OP2 DA A 102 30.635 -6.106 21.501 1.00 20.00 O ATOM 15 O5' DA A 102 32.406 -7.509 22.679 1.00 20.00 O ATOM 16 C5' DA A 102 32.679 -7.422 24.091 1.00 20.00 C ATOM 17 C4' DA A 102 33.179 -6.028 24.456 1.00 20.00 C ATOM 18 O4' DA A 102 33.463 -5.302 23.221 1.00 20.00 O ATOM 19 C3' DA A 102 32.175 -5.184 25.252 1.00 20.00 C ATOM 20 O3' DA A 102 32.792 -4.407 26.338 1.00 20.00 O ATOM 21 C2' DA A 102 31.466 -4.398 24.138 1.00 20.00 C ATOM 22 C1' DA A 102 32.655 -4.152 23.209 1.00 20.00 C TER ATOM 298 P DGaA 101 49.431 12.734 36.571 1.00 20.00 P ATOM 299 OP1 DGaA 101 48.043 13.248 36.549 1.00 20.00 O ATOM 300 OP2 DGaA 101 50.364 13.867 36.806 1.00 20.00 O ATOM 301 O5' DGaA 101 49.574 11.654 37.739 1.00 20.00 O ATOM 302 C5' DGaA 101 50.631 10.711 37.729 1.00 20.00 C ATOM 303 C4' DGaA 101 51.914 11.263 38.342 1.00 20.00 C ATOM 304 O4' DGaA 101 52.710 12.050 37.421 1.00 20.00 O ATOM 305 C3' DGaA 101 51.833 12.243 39.494 1.00 20.00 C ATOM 306 O3' DGaA 101 51.252 11.655 40.643 1.00 20.00 O ATOM 307 C2' DGaA 101 53.328 12.484 39.649 1.00 20.00 C ATOM 308 C1' DGaA 101 53.752 12.633 38.191 1.00 20.00 C ATOM 309 P DAaA 102 50.972 12.528 41.954 1.00 20.00 P ATOM 310 OP1 DAaA 102 50.002 11.773 42.777 1.00 20.00 O ATOM 311 OP2 DAaA 102 50.635 13.894 41.501 1.00 20.00 O ATOM 312 O5' DAaA 102 52.406 12.491 42.679 1.00 20.00 O ATOM 313 C5' DAaA 102 52.679 12.578 44.091 1.00 20.00 C ATOM 314 C4' DAaA 102 53.179 13.972 44.456 1.00 20.00 C ATOM 315 O4' DAaA 102 53.463 14.698 43.221 1.00 20.00 O ATOM 316 C3' DAaA 102 52.175 14.816 45.252 1.00 20.00 C ATOM 317 O3' DAaA 102 52.792 15.593 46.338 1.00 20.00 O ATOM 318 C2' DAaA 102 51.466 15.602 44.138 1.00 20.00 C ATOM 319 C1' DAaA 102 52.655 15.848 43.209 1.00 20.00 C END """ pdb_str_14 = """ CRYST1 399.000 399.000 399.000 90.00 90.00 90.00 P 1 ATOM 1 N1 XXX A 34 125.208 211.886 175.417 1.00 0.00 N ATOM 2 CT XXX A 34 125.035 211.123 174.168 1.00 0.00 C ATOM 3 C XXX A 34 126.386 210.806 173.507 1.00 0.00 C ATOM 4 K XXX A 34 127.304 211.628 173.503 1.00 0.00 K TER ATOM 5 N1 XXX B 34 251.532 143.432 175.422 1.00 0.00 N ATOM 6 CT XXX B 34 252.120 143.948 174.173 1.00 0.00 C ATOM 7 C XXX B 34 251.212 144.998 173.512 1.00 0.00 C ATOM 8 K XXX B 34 249.986 144.872 173.510 1.00 0.00 K TER ATOM 9 N1 XXX C 34 189.583 273.076 175.423 1.00 0.00 N ATOM 10 CT XXX C 34 188.804 273.006 174.173 1.00 0.00 C ATOM 11 C XXX C 34 188.920 271.622 173.510 1.00 0.00 C ATOM 12 K XXX C 34 189.986 271.004 173.508 1.00 0.00 K TER """ pdb_str_15 = """ ATOM 1 N1 XXX A 34 125.208 211.886 175.417 1.00 0.00 N ATOM 2 CT XXX A 34 125.035 211.123 174.168 1.00 0.00 C ATOM 3 C XXX A 34 126.386 210.806 173.507 1.00 0.00 C ATOM 4 K XXX A 34 127.304 211.628 173.503 1.00 0.00 K ATOM 1 O HOH A 35 135.208 211.886 175.417 1.00 0.00 O ATOM 2 O HOH A 36 135.035 211.123 174.168 1.00 0.00 O ATOM 3 O HOH A 37 136.386 210.806 173.507 1.00 0.00 O ATOM 4 O HOH A 38 137.304 211.628 173.503 1.00 0.00 O TER ATOM 5 N1 XXX B 34 251.532 143.432 175.422 1.00 0.00 N ATOM 6 CT XXX B 34 252.120 143.948 174.173 1.00 0.00 C ATOM 7 C XXX B 34 251.212 144.998 173.512 1.00 0.00 C ATOM 8 K XXX B 34 249.986 144.872 173.510 1.00 0.00 K ATOM 5 O HOH B 35 271.532 143.432 175.422 1.00 0.00 O ATOM 6 O HOH B 36 272.120 143.948 174.173 1.00 0.00 O ATOM 7 O HOH B 37 271.212 144.998 173.512 1.00 0.00 O ATOM 8 O HOH B 38 279.986 144.872 173.510 1.00 0.00 O TER """ pdb_str_16 = """\ ATOM 181 CA SER L 26 43.792 -65.179 67.649 1.00 22.76 C ATOM 182 C SER L 26 43.921 -63.740 68.152 1.00 25.79 C ATOM 183 O SER L 26 44.600 -63.476 69.148 1.00 27.95 O ATOM 184 CB SER L 26 45.023 -65.575 66.834 1.00 23.39 C ATOM 185 OG SER L 26 45.013 -64.937 65.570 1.00 21.58 O ATOM 186 N AGLN L 27 43.266 -62.813 67.460 0.50 23.64 N ATOM 187 CA AGLN L 27 43.289 -61.405 67.832 0.50 24.84 C ATOM 188 C AGLN L 27 41.869 -60.863 67.858 0.50 25.95 C ATOM 189 O AGLN L 27 40.987 -61.380 67.172 0.50 26.41 O ATOM 190 CB AGLN L 27 44.108 -60.589 66.830 0.50 27.09 C ATOM 191 CG AGLN L 27 45.602 -60.618 67.048 0.50 35.67 C ATOM 192 CD AGLN L 27 46.338 -59.767 66.033 0.50 38.53 C ATOM 193 OE1AGLN L 27 46.675 -60.228 64.942 0.50 43.32 O ATOM 194 NE2AGLN L 27 46.572 -58.507 66.380 0.50 40.19 N ATOM 195 N BSER L 27 41.653 -59.819 68.651 0.50 21.30 N ATOM 196 CA BSER L 27 40.340 -59.209 68.744 0.50 23.38 C ATOM 197 C BSER L 27 39.920 -58.676 67.377 0.50 22.05 C ATOM 198 O BSER L 27 40.712 -58.050 66.678 0.50 19.83 O ATOM 199 CB BSER L 27 40.362 -58.057 69.745 0.50 20.17 C ATOM 200 OG BSER L 27 39.122 -57.376 69.738 0.50 24.39 O ATOM 235 N ASN L 28 36.659 -48.175 64.751 1.00 23.50 N ATOM 236 CA ASN L 28 35.418 -47.408 64.733 1.00 19.92 C ATOM 237 C ASN L 28 34.411 -48.040 65.685 1.00 22.34 C ATOM 238 O ASN L 28 33.274 -47.586 65.794 1.00 25.95 O ATOM 239 CB ASN L 28 34.831 -47.338 63.321 1.00 19.19 C ATOM 240 CG ASN L 28 34.676 -48.707 62.680 1.00 22.32 C ATOM 241 OD1 ASN L 28 34.703 -49.732 63.359 1.00 19.98 O ATOM 242 ND2 ASN L 28 34.498 -48.726 61.364 1.00 21.69 N TER ATOM 1 CA SER H -1 46.792 -62.179 70.649 1.00 22.76 C ATOM 2 C SER H -1 46.921 -60.740 71.152 1.00 25.79 C ATOM 3 O SER H -1 47.600 -60.476 72.148 1.00 27.95 O ATOM 4 CB SER H -1 48.023 -62.575 69.834 1.00 23.39 C ATOM 5 OG SER H -1 48.013 -61.937 68.570 1.00 21.58 O ATOM 6 N AGLN H 0 46.266 -59.813 70.460 0.50 23.64 N ATOM 7 CA AGLN H 0 46.289 -58.405 70.832 0.50 24.84 C ATOM 8 C AGLN H 0 44.869 -57.863 70.858 0.50 25.95 C ATOM 9 O AGLN H 0 43.987 -58.380 70.172 0.50 26.41 O ATOM 10 CB AGLN H 0 47.108 -57.589 69.830 0.50 27.09 C ATOM 11 CG AGLN H 0 48.602 -57.618 70.048 0.50 35.67 C ATOM 12 CD AGLN H 0 49.338 -56.767 69.033 0.50 38.53 C ATOM 13 OE1AGLN H 0 49.675 -57.228 67.942 0.50 43.32 O ATOM 14 NE2AGLN H 0 49.572 -55.507 69.380 0.50 40.19 N ATOM 15 N BSER H 0 44.653 -56.819 71.651 0.50 21.30 N ATOM 16 CA BSER H 0 43.340 -56.209 71.744 0.50 23.38 C ATOM 17 C BSER H 0 42.920 -55.676 70.377 0.50 22.05 C ATOM 18 O BSER H 0 43.712 -55.050 69.678 0.50 19.83 O ATOM 19 CB BSER H 0 43.362 -55.057 72.745 0.50 20.17 C ATOM 20 OG BSER H 0 42.122 -54.376 72.738 0.50 24.39 O ATOM 29 N ASN H 9 39.659 -45.175 67.751 1.00 23.50 N ATOM 30 CA ASN H 9 38.418 -44.408 67.733 1.00 19.92 C ATOM 31 C ASN H 9 37.411 -45.040 68.685 1.00 22.34 C ATOM 32 O ASN H 9 36.274 -44.586 68.794 1.00 25.95 O ATOM 33 CB ASN H 9 37.831 -44.338 66.321 1.00 19.19 C ATOM 34 CG ASN H 9 37.676 -45.707 65.680 1.00 22.32 C ATOM 35 OD1 ASN H 9 37.703 -46.732 66.359 1.00 19.98 O ATOM 36 ND2 ASN H 9 37.498 -45.726 64.364 1.00 21.69 N """ pdb_str_17 = """ ATOM 1 N ASP B 1 51.626 -66.543 62.314 1.00 34.60 N ATOM 2 CA ASP B 1 50.334 -66.083 61.819 1.00 33.86 C ATOM 3 C ASP B 1 49.224 -66.387 62.821 1.00 34.02 C ATOM 4 O ASP B 1 49.488 -66.629 63.999 1.00 32.23 O ATOM 5 CB ASP B 1 50.015 -66.728 60.469 1.00 33.99 C ATOM 6 CG ASP B 1 51.047 -66.399 59.408 1.00 36.93 C ATOM 7 OD1 ASP B 1 51.647 -65.306 59.480 1.00 36.67 O ATOM 8 OD2 ASP B 1 51.258 -67.233 58.503 1.00 38.81 O ATOM 9 N VAL B 2 47.984 -66.373 62.345 1.00 31.94 N ATOM 10 CA VAL B 2 46.833 -66.647 63.196 1.00 29.81 C ATOM 11 C VAL B 2 46.674 -68.151 63.403 1.00 28.28 C ATOM 12 O VAL B 2 46.672 -68.925 62.445 1.00 27.24 O ATOM 13 CB VAL B 2 45.547 -66.026 62.609 1.00 30.66 C ATOM 14 CG1 VAL B 2 44.320 -66.509 63.370 1.00 29.42 C ATOM 15 CG2 VAL B 2 45.429 -66.333 61.122 1.00 31.43 C ATOM 16 N GLN B 3 46.550 -68.560 64.661 1.00 25.93 N ATOM 17 CA GLN B 3 46.391 -69.970 64.997 1.00 24.46 C ATOM 18 C GLN B 3 44.959 -70.433 64.750 1.00 23.33 C ATOM 19 O GLN B 3 44.010 -69.863 65.287 1.00 20.10 O ATOM 20 CB GLN B 3 46.782 -70.222 66.455 1.00 29.74 C ATOM 21 CG GLN B 3 46.646 -71.671 66.893 1.00 39.72 C ATOM 22 CD GLN B 3 47.041 -71.883 68.341 1.00 51.31 C ATOM 23 OE1 GLN B 3 47.031 -73.007 68.841 1.00 57.11 O ATOM 24 NE2 GLN B 3 47.393 -70.799 69.023 1.00 54.00 N ATOM 25 N MET B 4 44.812 -71.472 63.933 1.00 24.27 N ATOM 26 CA MET B 4 43.496 -72.013 63.613 1.00 22.89 C ATOM 27 C MET B 4 42.969 -72.880 64.752 1.00 21.48 C ATOM 28 O MET B 4 43.379 -74.029 64.912 1.00 23.73 O ATOM 29 CB MET B 4 43.551 -72.824 62.316 1.00 22.77 C ATOM 30 CG MET B 4 43.996 -72.024 61.103 1.00 20.45 C ATOM 31 SD MET B 4 42.904 -70.635 60.747 1.00 23.95 S ATOM 32 CE MET B 4 41.353 -71.486 60.468 1.00 24.76 C ATOM 33 N THR B 5 42.057 -72.320 65.541 1.00 20.55 N ATOM 34 CA THR B 5 41.472 -73.040 66.666 1.00 20.64 C ATOM 35 C THR B 5 40.063 -73.521 66.335 1.00 20.08 C ATOM 36 O THR B 5 39.176 -72.720 66.042 1.00 20.87 O ATOM 37 CB THR B 5 41.422 -72.165 67.932 1.00 23.39 C ATOM 38 OG1 THR B 5 42.751 -71.766 68.293 1.00 30.91 O ATOM 39 CG2 THR B 5 40.798 -72.934 69.087 1.00 26.97 C TER ATOM 1 N ASP A 1 46.675 -60.355 58.113 1.00 34.60 N ATOM 2 CA ASP A 1 46.807 -61.464 59.051 1.00 33.86 C ATOM 3 C ASP A 1 45.597 -61.546 59.975 1.00 34.02 C ATOM 4 O ASP A 1 45.693 -62.048 61.095 1.00 32.23 O ATOM 5 CB ASP A 1 48.090 -61.322 59.873 1.00 33.99 C ATOM 6 CG ASP A 1 49.337 -61.310 59.010 1.00 36.93 C ATOM 7 OD1 ASP A 1 49.255 -60.851 57.851 1.00 36.67 O ATOM 8 OD2 ASP A 1 50.398 -61.759 59.491 1.00 38.81 O ATOM 9 N VAL A 2 44.460 -61.050 59.499 1.00 31.94 N ATOM 10 CA VAL A 2 43.231 -61.067 60.281 1.00 29.81 C ATOM 11 C VAL A 2 42.306 -62.174 59.789 1.00 28.28 C ATOM 12 O VAL A 2 41.817 -62.132 58.660 1.00 27.24 O ATOM 13 CB VAL A 2 42.520 -59.704 60.230 1.00 30.66 C ATOM 14 CG1 VAL A 2 41.241 -59.742 61.052 1.00 29.42 C ATOM 15 CG2 VAL A 2 43.447 -58.604 60.725 1.00 31.43 C ATOM 16 N GLN A 3 42.071 -63.165 60.643 1.00 25.93 N ATOM 17 CA GLN A 3 41.205 -64.286 60.296 1.00 24.46 C ATOM 18 C GLN A 3 40.490 -64.827 61.530 1.00 23.33 C ATOM 19 O GLN A 3 41.120 -65.383 62.430 1.00 20.10 O ATOM 20 CB GLN A 3 42.011 -65.399 59.624 1.00 29.74 C ATOM 21 CG GLN A 3 41.185 -66.611 59.227 1.00 39.72 C ATOM 22 CD GLN A 3 42.016 -67.692 58.564 1.00 51.31 C ATOM 23 OE1 GLN A 3 43.226 -67.542 58.391 1.00 57.11 O ATOM 24 NE2 GLN A 3 41.370 -68.790 58.190 1.00 54.00 N ATOM 25 N MET A 4 39.172 -64.662 61.564 1.00 24.27 N ATOM 26 CA MET A 4 38.369 -65.133 62.686 1.00 22.89 C ATOM 27 C MET A 4 37.658 -66.437 62.341 1.00 21.48 C ATOM 28 O MET A 4 37.275 -67.196 63.233 1.00 23.73 O ATOM 29 CB MET A 4 37.349 -64.070 63.100 1.00 22.77 C ATOM 30 CG MET A 4 37.968 -62.752 63.535 1.00 20.45 C ATOM 31 SD MET A 4 39.065 -62.933 64.954 1.00 23.95 S ATOM 32 CE MET A 4 37.932 -63.588 66.177 1.00 24.76 C ATOM 33 N THR A 5 37.492 -66.682 61.043 1.00 20.55 N ATOM 34 CA THR A 5 36.832 -67.882 60.528 1.00 20.64 C ATOM 35 C THR A 5 35.420 -68.037 61.091 1.00 20.08 C ATOM 36 O THR A 5 35.211 -68.701 62.108 1.00 20.87 O ATOM 37 CB THR A 5 37.647 -69.156 60.837 1.00 23.39 C ATOM 38 OG1 THR A 5 39.009 -68.964 60.435 1.00 30.91 O ATOM 39 CG2 THR A 5 37.073 -70.352 60.091 1.00 26.97 C TER """ pdb_str_18 = """ ATOM 1 N MET 1 158.070 173.095 147.115 1.00 50.00 A16S N ATOM 2 CA MET 1 157.408 172.627 148.359 1.00 50.00 A16S C ATOM 3 CB MET 1 157.550 171.094 148.516 1.00 50.00 A16S C ATOM 4 CG MET 1 156.748 170.503 149.691 1.00 50.00 A16S C ATOM 5 SD MET 1 154.968 170.855 149.612 1.00 50.00 A16S S ATOM 6 CE MET 1 154.505 169.913 151.091 1.00 50.00 A16S C ATOM 7 C MET 1 157.958 173.331 149.563 1.00 50.00 A16S C ATOM 8 O MET 1 157.196 173.814 150.399 1.00 50.00 A16S O TER ATOM 9 N MET 1 174.781 155.306 150.054 1.00 50.00 B16S N ATOM 10 CA MET 1 174.332 154.630 151.298 1.00 50.00 B16S C ATOM 11 CB MET 1 175.016 153.251 151.453 1.00 50.00 B16S C ATOM 12 CG MET 1 174.481 152.410 152.628 1.00 50.00 B16S C ATOM 13 SD MET 1 172.693 152.099 152.550 1.00 50.00 B16S S ATOM 14 CE MET 1 172.601 151.052 154.028 1.00 50.00 B16S C ATOM 15 C MET 1 174.594 155.484 152.502 1.00 50.00 B16S C ATOM 16 O MET 1 173.710 155.660 153.339 1.00 50.00 B16S O TER END """ pdb_str_19 = """ ATOM 1 N MET A 1 158.070 173.095 147.115 1.00 50.00 A16S N ATOM 2 CA MET A 1 157.408 172.627 148.359 1.00 50.00 A16S C ATOM 3 CB MET A 1 157.550 171.094 148.516 1.00 50.00 A16S C ATOM 4 CG MET A 1 156.748 170.503 149.691 1.00 50.00 A16S C ATOM 5 SD MET A 1 154.968 170.855 149.612 1.00 50.00 A16S S ATOM 6 CE MET A 1 154.505 169.913 151.091 1.00 50.00 A16S C ATOM 7 C MET A 1 157.958 173.331 149.563 1.00 50.00 A16S C ATOM 8 O MET A 1 157.196 173.814 150.399 1.00 50.00 A16S O TER ATOM 9 N MET 1 174.781 155.306 150.054 1.00 50.00 B16S N ATOM 10 CA MET 1 174.332 154.630 151.298 1.00 50.00 B16S C ATOM 11 CB MET 1 175.016 153.251 151.453 1.00 50.00 B16S C ATOM 12 CG MET 1 174.481 152.410 152.628 1.00 50.00 B16S C ATOM 13 SD MET 1 172.693 152.099 152.550 1.00 50.00 B16S S ATOM 14 CE MET 1 172.601 151.052 154.028 1.00 50.00 B16S C ATOM 15 C MET 1 174.594 155.484 152.502 1.00 50.00 B16S C ATOM 16 O MET 1 173.710 155.660 153.339 1.00 50.00 B16S O TER END """ pdb_str_20 = """ CRYST1 25.287 40.217 65.471 90.00 90.00 90.00 P 21 21 21 SCALE1 0.039546 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024865 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015274 0.00000 ATOM 1 P DA A 5 -8.062 -5.965 -15.755 1.00 42.17 P ATOM 2 OP1 DA A 5 -8.426 -7.228 -16.405 1.00 50.61 O ATOM 3 OP2 DA A 5 -8.689 -5.557 -14.457 1.00 51.75 O ATOM 4 O5' DA A 5 -6.496 -5.961 -15.638 1.00 34.89 O ATOM 5 C5' DA A 5 -5.791 -6.321 -16.790 1.00 30.71 C ATOM 6 C4' DA A 5 -4.355 -5.917 -16.600 1.00 34.43 C ATOM 7 O4' DA A 5 -4.303 -4.509 -16.239 1.00 33.96 O ATOM 8 C3' DA A 5 -3.630 -6.687 -15.491 1.00 35.56 C ATOM 9 O3' DA A 5 -2.407 -7.257 -16.020 1.00 33.08 O ATOM 10 C2' DA A 5 -3.531 -5.654 -14.384 1.00 32.41 C ATOM 11 C1' DA A 5 -3.435 -4.334 -15.130 1.00 28.44 C ATOM 12 N9 DA A 5 -3.904 -3.143 -14.449 1.00 28.37 N ATOM 13 C8 DA A 5 -5.187 -2.933 -14.022 1.00 27.53 C ATOM 14 N7 DA A 5 -5.401 -1.724 -13.565 1.00 29.33 N ATOM 15 C5 DA A 5 -4.187 -1.082 -13.747 1.00 23.78 C ATOM 16 C6 DA A 5 -3.761 0.226 -13.474 1.00 25.22 C ATOM 17 N6 DA A 5 -4.519 1.150 -12.896 1.00 25.69 N ATOM 18 N1 DA A 5 -2.485 0.535 -13.749 1.00 24.39 N ATOM 19 C2 DA A 5 -1.712 -0.389 -14.320 1.00 24.89 C ATOM 20 N3 DA A 5 -2.001 -1.641 -14.653 1.00 28.33 N ATOM 21 C4 DA A 5 -3.268 -1.935 -14.326 1.00 27.45 C ATOM 22 P DA A 6 -1.382 -8.057 -15.083 1.00 33.49 P ATOM 23 OP1 DA A 6 -0.596 -8.971 -15.989 1.00 35.26 O ATOM 24 OP2 DA A 6 -2.097 -8.481 -13.890 1.00 34.48 O ATOM 25 O5' DA A 6 -0.480 -6.949 -14.401 1.00 31.72 O ATOM 26 C5' DA A 6 0.398 -6.138 -15.188 1.00 28.12 C ATOM 27 C4' DA A 6 1.219 -5.272 -14.269 1.00 22.57 C ATOM 28 O4' DA A 6 0.380 -4.203 -13.784 1.00 23.34 O ATOM 29 C3' DA A 6 1.783 -5.982 -13.049 1.00 23.61 C ATOM 30 O3' DA A 6 3.202 -5.785 -13.150 1.00 22.60 O ATOM 31 C2' DA A 6 1.110 -5.289 -11.881 1.00 22.21 C ATOM 32 C1' DA A 6 0.653 -3.958 -12.418 1.00 20.89 C ATOM 33 N9 DA A 6 -0.561 -3.398 -11.831 1.00 21.71 N ATOM 34 C8 DA A 6 -1.777 -4.017 -11.666 1.00 23.62 C ATOM 35 N7 DA A 6 -2.693 -3.249 -11.139 1.00 23.57 N ATOM 36 C5 DA A 6 -2.071 -2.016 -11.029 1.00 20.29 C ATOM 37 C6 DA A 6 -2.506 -0.774 -10.519 1.00 20.33 C ATOM 38 N6 DA A 6 -3.763 -0.525 -10.122 1.00 20.36 N ATOM 39 N1 DA A 6 -1.604 0.233 -10.486 1.00 20.84 N ATOM 40 C2 DA A 6 -0.341 -0.023 -10.868 1.00 21.15 C ATOM 41 N3 DA A 6 0.174 -1.126 -11.378 1.00 22.91 N ATOM 42 C4 DA A 6 -0.746 -2.101 -11.433 1.00 20.00 C ATOM 43 P DT A 7 4.283 -6.215 -12.051 1.00 23.53 P ATOM 44 OP1 DT A 7 5.598 -6.398 -12.780 1.00 27.73 O ATOM 45 OP2 DT A 7 3.774 -7.297 -11.205 1.00 24.18 O ATOM 46 O5' DT A 7 4.350 -4.948 -11.106 1.00 22.94 O ATOM 47 C5' DT A 7 4.668 -3.709 -11.633 1.00 21.30 C ATOM 48 C4' DT A 7 4.525 -2.656 -10.580 1.00 20.84 C ATOM 49 O4' DT A 7 3.138 -2.512 -10.296 1.00 19.94 O ATOM 50 C3' DT A 7 5.205 -2.966 -9.250 1.00 20.02 C ATOM 51 O3' DT A 7 6.280 -2.035 -9.099 1.00 23.74 O ATOM 52 C2' DT A 7 4.144 -2.717 -8.200 1.00 19.47 C ATOM 53 C1' DT A 7 3.048 -2.015 -8.962 1.00 20.12 C ATOM 54 N1 DT A 7 1.641 -2.197 -8.524 1.00 20.27 N ATOM 55 C2 DT A 7 0.957 -1.108 -8.030 1.00 18.61 C ATOM 56 O2 DT A 7 1.430 0.017 -7.926 1.00 19.56 O ATOM 57 N3 DT A 7 -0.344 -1.365 -7.721 1.00 18.89 N ATOM 58 C4 DT A 7 -1.018 -2.563 -7.836 1.00 21.94 C ATOM 59 O4 DT A 7 -2.200 -2.640 -7.497 1.00 23.57 O ATOM 60 C5 DT A 7 -0.226 -3.674 -8.271 1.00 18.09 C ATOM 61 C7 DT A 7 -0.860 -5.022 -8.351 1.00 19.35 C ATOM 62 C6 DT A 7 1.065 -3.446 -8.562 1.00 17.66 C ATOM 63 P DT A 8 7.284 -1.980 -7.857 1.00 26.43 P ATOM 64 OP1 DT A 8 8.611 -1.444 -8.278 1.00 28.45 O ATOM 65 OP2 DT A 8 7.248 -3.298 -7.198 1.00 27.17 O ATOM 66 O5' DT A 8 6.613 -0.927 -6.882 1.00 25.09 O ATOM 67 C5' DT A 8 6.357 0.403 -7.340 1.00 24.67 C ATOM 68 C4' DT A 8 5.543 1.125 -6.301 1.00 23.10 C ATOM 69 O4' DT A 8 4.228 0.541 -6.229 1.00 23.60 O ATOM 70 C3' DT A 8 6.127 1.057 -4.884 1.00 25.21 C ATOM 71 O3' DT A 8 6.507 2.380 -4.493 1.00 28.93 O ATOM 72 C2' DT A 8 5.018 0.434 -4.050 1.00 23.32 C ATOM 73 C1' DT A 8 3.795 0.667 -4.883 1.00 22.06 C ATOM 74 N1 DT A 8 2.713 -0.291 -4.689 1.00 19.79 N ATOM 75 C2 DT A 8 1.466 0.223 -4.414 1.00 18.40 C ATOM 76 O2 DT A 8 1.263 1.399 -4.157 1.00 20.56 O ATOM 77 N3 DT A 8 0.484 -0.716 -4.337 1.00 19.20 N ATOM 78 C4 DT A 8 0.588 -2.075 -4.597 1.00 18.45 C ATOM 79 O4 DT A 8 -0.397 -2.789 -4.538 1.00 21.38 O ATOM 80 C5 DT A 8 1.920 -2.549 -4.859 1.00 17.02 C ATOM 81 C7 DT A 8 2.126 -4.006 -5.116 1.00 20.50 C ATOM 82 C6 DT A 8 2.895 -1.634 -4.959 1.00 19.29 C TER ATOM 83 P DA B 17 -10.220 1.260 -1.207 1.00 27.94 P ATOM 84 OP1 DA B 17 -11.370 2.143 -0.856 1.00 34.83 O ATOM 85 OP2 DA B 17 -10.221 0.599 -2.553 1.00 31.17 O ATOM 86 O5' DA B 17 -8.842 2.020 -1.098 1.00 26.12 O ATOM 87 C5' DA B 17 -8.558 2.683 0.094 1.00 25.41 C ATOM 88 C4' DA B 17 -7.407 3.619 -0.107 1.00 26.38 C ATOM 89 O4' DA B 17 -6.208 2.886 -0.440 1.00 24.41 O ATOM 90 C3' DA B 17 -7.600 4.631 -1.214 1.00 27.57 C ATOM 91 O3' DA B 17 -6.972 5.834 -0.764 1.00 29.89 O ATOM 92 C2' DA B 17 -6.902 3.980 -2.406 1.00 26.29 C ATOM 93 C1' DA B 17 -5.771 3.225 -1.781 1.00 23.13 C ATOM 94 N9 DA B 17 -5.444 1.986 -2.460 1.00 22.66 N ATOM 95 C8 DA B 17 -6.295 0.942 -2.750 1.00 23.38 C ATOM 96 N7 DA B 17 -5.700 -0.094 -3.288 1.00 20.62 N ATOM 97 C5 DA B 17 -4.344 0.242 -3.234 1.00 20.59 C ATOM 98 C6 DA B 17 -3.178 -0.447 -3.603 1.00 17.89 C ATOM 99 N6 DA B 17 -3.184 -1.685 -4.072 1.00 20.22 N ATOM 100 N1 DA B 17 -1.995 0.205 -3.497 1.00 19.61 N ATOM 101 C2 DA B 17 -1.992 1.465 -3.030 1.00 20.38 C ATOM 102 N3 DA B 17 -3.021 2.207 -2.621 1.00 20.80 N ATOM 103 C4 DA B 17 -4.182 1.540 -2.774 1.00 19.17 C ATOM 104 P DA B 18 -6.994 7.132 -1.670 1.00 32.91 P ATOM 105 OP1 DA B 18 -6.817 8.281 -0.798 1.00 37.55 O ATOM 106 OP2 DA B 18 -8.060 7.037 -2.636 1.00 31.04 O ATOM 107 O5' DA B 18 -5.659 7.052 -2.535 1.00 30.20 O ATOM 108 C5' DA B 18 -4.377 7.074 -1.958 1.00 30.19 C ATOM 109 C4' DA B 18 -3.354 6.838 -3.036 1.00 28.09 C ATOM 110 O4' DA B 18 -3.424 5.481 -3.484 1.00 26.27 O ATOM 111 C3' DA B 18 -3.545 7.708 -4.286 1.00 29.73 C ATOM 112 O3' DA B 18 -2.469 8.627 -4.273 1.00 34.73 O ATOM 113 C2' DA B 18 -3.566 6.715 -5.433 1.00 27.32 C ATOM 114 C1' DA B 18 -3.010 5.448 -4.841 1.00 24.83 C ATOM 115 N9 DA B 18 -3.488 4.196 -5.410 1.00 23.72 N ATOM 116 C8 DA B 18 -4.794 3.799 -5.530 1.00 20.51 C ATOM 117 N7 DA B 18 -4.937 2.581 -5.985 1.00 22.85 N ATOM 118 C5 DA B 18 -3.636 2.147 -6.189 1.00 20.87 C ATOM 119 C6 DA B 18 -3.111 0.950 -6.675 1.00 19.34 C ATOM 120 N6 DA B 18 -3.852 -0.099 -7.028 1.00 21.88 N ATOM 121 N1 DA B 18 -1.767 0.849 -6.776 1.00 19.77 N ATOM 122 C2 DA B 18 -1.023 1.872 -6.374 1.00 21.42 C ATOM 123 N3 DA B 18 -1.392 3.050 -5.910 1.00 22.19 N ATOM 124 C4 DA B 18 -2.734 3.129 -5.836 1.00 21.41 C ATOM 125 P DT B 19 -2.064 9.546 -5.497 1.00 40.82 P ATOM 126 OP1 DT B 19 -1.281 10.615 -4.939 1.00 44.52 O ATOM 127 OP2 DT B 19 -3.292 9.787 -6.271 1.00 44.69 O ATOM 128 O5' DT B 19 -1.119 8.619 -6.355 1.00 30.72 O ATOM 129 C5' DT B 19 0.059 8.093 -5.804 1.00 29.16 C ATOM 130 C4' DT B 19 0.704 7.195 -6.832 1.00 26.15 C ATOM 131 O4' DT B 19 -0.129 6.045 -7.087 1.00 26.00 O ATOM 132 C3' DT B 19 0.941 7.859 -8.188 1.00 25.98 C ATOM 133 O3' DT B 19 2.343 7.877 -8.376 1.00 30.07 O ATOM 134 C2' DT B 19 0.207 6.968 -9.181 1.00 26.77 C ATOM 135 C1' DT B 19 0.036 5.665 -8.443 1.00 25.87 C ATOM 136 N1 DT B 19 -1.122 4.839 -8.816 1.00 24.60 N ATOM 137 C2 DT B 19 -0.906 3.556 -9.283 1.00 22.21 C ATOM 138 O2 DT B 19 0.197 3.084 -9.451 1.00 22.06 O ATOM 139 N3 DT B 19 -2.038 2.833 -9.519 1.00 22.04 N ATOM 140 C4 DT B 19 -3.339 3.262 -9.380 1.00 21.81 C ATOM 141 O4 DT B 19 -4.247 2.495 -9.615 1.00 24.16 O ATOM 142 C5 DT B 19 -3.499 4.613 -8.891 1.00 22.25 C ATOM 143 C7 DT B 19 -4.879 5.143 -8.663 1.00 23.26 C ATOM 144 C6 DT B 19 -2.396 5.327 -8.640 1.00 22.85 C ATOM 145 P DT B 20 3.005 8.456 -9.725 1.00 32.03 P ATOM 146 OP1 DT B 20 4.339 8.958 -9.284 1.00 35.31 O ATOM 147 OP2 DT B 20 2.027 9.351 -10.442 1.00 33.99 O ATOM 148 O5' DT B 20 3.144 7.102 -10.543 1.00 31.33 O ATOM 149 C5' DT B 20 3.894 5.979 -10.032 1.00 28.60 C ATOM 150 C4' DT B 20 3.851 4.840 -11.020 1.00 28.63 C ATOM 151 O4' DT B 20 2.494 4.361 -11.145 1.00 26.47 O ATOM 152 C3' DT B 20 4.300 5.211 -12.437 1.00 31.59 C ATOM 153 O3' DT B 20 5.260 4.256 -12.875 1.00 39.07 O ATOM 154 C2' DT B 20 3.027 5.147 -13.257 1.00 26.06 C ATOM 155 C1' DT B 20 2.211 4.120 -12.529 1.00 24.42 C ATOM 156 N1 DT B 20 0.757 4.123 -12.660 1.00 23.79 N ATOM 157 C2 DT B 20 0.138 2.932 -12.972 1.00 25.04 C ATOM 158 O2 DT B 20 0.741 1.921 -13.262 1.00 24.66 O ATOM 159 N3 DT B 20 -1.229 2.977 -12.959 1.00 25.84 N ATOM 160 C4 DT B 20 -2.022 4.071 -12.671 1.00 25.98 C ATOM 161 O4 DT B 20 -3.234 3.948 -12.646 1.00 28.14 O ATOM 162 C5 DT B 20 -1.311 5.298 -12.387 1.00 22.81 C ATOM 163 C7 DT B 20 -2.094 6.540 -12.092 1.00 27.47 C ATOM 164 C6 DT B 20 0.028 5.263 -12.401 1.00 26.29 C TER ATOM 165 P DA C 5 -8.062 -5.965 -15.755 1.00 42.17 P ATOM 166 OP1 DA C 5 -8.426 -7.228 -16.405 1.00 50.61 O ATOM 167 OP2 DA C 5 -8.689 -5.557 -14.457 1.00 51.75 O ATOM 168 O5' DA C 5 -6.496 -5.961 -15.638 1.00 34.89 O ATOM 169 C5' DA C 5 -5.791 -6.321 -16.790 1.00 30.71 C ATOM 170 C4' DA C 5 -4.355 -5.917 -16.600 1.00 34.43 C ATOM 171 O4' DA C 5 -4.303 -4.509 -16.239 1.00 33.96 O ATOM 172 C3' DA C 5 -3.630 -6.687 -15.491 1.00 35.56 C ATOM 173 O3' DA C 5 -2.407 -7.257 -16.020 1.00 33.08 O ATOM 174 C2' DA C 5 -3.531 -5.654 -14.384 1.00 32.41 C ATOM 175 C1' DA C 5 -3.435 -4.334 -15.130 1.00 28.44 C ATOM 176 N9 DA C 5 -3.904 -3.143 -14.449 1.00 28.37 N ATOM 177 C8 DA C 5 -5.187 -2.933 -14.022 1.00 27.53 C ATOM 178 N7 DA C 5 -5.401 -1.724 -13.565 1.00 29.33 N ATOM 179 C5 DA C 5 -4.187 -1.082 -13.747 1.00 23.78 C ATOM 180 C6 DA C 5 -3.761 0.226 -13.474 1.00 25.22 C ATOM 181 N6 DA C 5 -4.519 1.150 -12.896 1.00 25.69 N ATOM 182 N1 DA C 5 -2.485 0.535 -13.749 1.00 24.39 N ATOM 183 C2 DA C 5 -1.712 -0.389 -14.320 1.00 24.89 C ATOM 184 N3 DA C 5 -2.001 -1.641 -14.653 1.00 28.33 N ATOM 185 C4 DA C 5 -3.268 -1.935 -14.326 1.00 27.45 C ATOM 186 P DA C 6 -1.382 -8.057 -15.083 1.00 33.49 P ATOM 187 OP1 DA C 6 -0.596 -8.971 -15.989 1.00 35.26 O ATOM 188 OP2 DA C 6 -2.097 -8.481 -13.890 1.00 34.48 O ATOM 189 O5' DA C 6 -0.480 -6.949 -14.401 1.00 31.72 O ATOM 190 C5' DA C 6 0.398 -6.138 -15.188 1.00 28.12 C ATOM 191 C4' DA C 6 1.219 -5.272 -14.269 1.00 22.57 C ATOM 192 O4' DA C 6 0.380 -4.203 -13.784 1.00 23.34 O ATOM 193 C3' DA C 6 1.783 -5.982 -13.049 1.00 23.61 C ATOM 194 O3' DA C 6 3.202 -5.785 -13.150 1.00 22.60 O ATOM 195 C2' DA C 6 1.110 -5.289 -11.881 1.00 22.21 C ATOM 196 C1' DA C 6 0.653 -3.958 -12.418 1.00 20.89 C ATOM 197 N9 DA C 6 -0.561 -3.398 -11.831 1.00 21.71 N ATOM 198 C8 DA C 6 -1.777 -4.017 -11.666 1.00 23.62 C ATOM 199 N7 DA C 6 -2.693 -3.249 -11.139 1.00 23.57 N ATOM 200 C5 DA C 6 -2.071 -2.016 -11.029 1.00 20.29 C ATOM 201 C6 DA C 6 -2.506 -0.774 -10.519 1.00 20.33 C ATOM 202 N6 DA C 6 -3.763 -0.525 -10.122 1.00 20.36 N ATOM 203 N1 DA C 6 -1.604 0.233 -10.486 1.00 20.84 N ATOM 204 C2 DA C 6 -0.341 -0.023 -10.868 1.00 21.15 C ATOM 205 N3 DA C 6 0.174 -1.126 -11.378 1.00 22.91 N ATOM 206 C4 DA C 6 -0.746 -2.101 -11.433 1.00 20.00 C ATOM 207 P DT C 7 4.283 -6.215 -12.051 1.00 23.53 P ATOM 208 OP1 DT C 7 5.598 -6.398 -12.780 1.00 27.73 O ATOM 209 OP2 DT C 7 3.774 -7.297 -11.205 1.00 24.18 O ATOM 210 O5' DT C 7 4.350 -4.948 -11.106 1.00 22.94 O ATOM 211 C5' DT C 7 4.668 -3.709 -11.633 1.00 21.30 C ATOM 212 C4' DT C 7 4.525 -2.656 -10.580 1.00 20.84 C ATOM 213 O4' DT C 7 3.138 -2.512 -10.296 1.00 19.94 O ATOM 214 C3' DT C 7 5.205 -2.966 -9.250 1.00 20.02 C ATOM 215 O3' DT C 7 6.280 -2.035 -9.099 1.00 23.74 O ATOM 216 C2' DT C 7 4.144 -2.717 -8.200 1.00 19.47 C ATOM 217 C1' DT C 7 3.048 -2.015 -8.962 1.00 20.12 C ATOM 218 N1 DT C 7 1.641 -2.197 -8.524 1.00 20.27 N ATOM 219 C2 DT C 7 0.957 -1.108 -8.030 1.00 18.61 C ATOM 220 O2 DT C 7 1.430 0.017 -7.926 1.00 19.56 O ATOM 221 N3 DT C 7 -0.344 -1.365 -7.721 1.00 18.89 N ATOM 222 C4 DT C 7 -1.018 -2.563 -7.836 1.00 21.94 C ATOM 223 O4 DT C 7 -2.200 -2.640 -7.497 1.00 23.57 O ATOM 224 C5 DT C 7 -0.226 -3.674 -8.271 1.00 18.09 C ATOM 225 C7 DT C 7 -0.860 -5.022 -8.351 1.00 19.35 C ATOM 226 C6 DT C 7 1.065 -3.446 -8.562 1.00 17.66 C ATOM 227 P DT C 8 7.284 -1.980 -7.857 1.00 26.43 P ATOM 228 OP1 DT C 8 8.611 -1.444 -8.278 1.00 28.45 O ATOM 229 OP2 DT C 8 7.248 -3.298 -7.198 1.00 27.17 O ATOM 230 O5' DT C 8 6.613 -0.927 -6.882 1.00 25.09 O ATOM 231 C5' DT C 8 6.357 0.403 -7.340 1.00 24.67 C ATOM 232 C4' DT C 8 5.543 1.125 -6.301 1.00 23.10 C ATOM 233 O4' DT C 8 4.228 0.541 -6.229 1.00 23.60 O ATOM 234 C3' DT C 8 6.127 1.057 -4.884 1.00 25.21 C ATOM 235 O3' DT C 8 6.507 2.380 -4.493 1.00 28.93 O ATOM 236 C2' DT C 8 5.018 0.434 -4.050 1.00 23.32 C ATOM 237 C1' DT C 8 3.795 0.667 -4.883 1.00 22.06 C ATOM 238 N1 DT C 8 2.713 -0.291 -4.689 1.00 19.79 N ATOM 239 C2 DT C 8 1.466 0.223 -4.414 1.00 18.40 C ATOM 240 O2 DT C 8 1.263 1.399 -4.157 1.00 20.56 O ATOM 241 N3 DT C 8 0.484 -0.716 -4.337 1.00 19.20 N ATOM 242 C4 DT C 8 0.588 -2.075 -4.597 1.00 18.45 C ATOM 243 O4 DT C 8 -0.397 -2.789 -4.538 1.00 21.38 O ATOM 244 C5 DT C 8 1.920 -2.549 -4.859 1.00 17.02 C ATOM 245 C7 DT C 8 2.126 -4.006 -5.116 1.00 20.50 C ATOM 246 C6 DT C 8 2.895 -1.634 -4.959 1.00 19.29 C TER ATOM 247 P DA D 17 -10.220 1.260 -1.207 1.00 27.94 P ATOM 248 OP1 DA D 17 -11.370 2.143 -0.856 1.00 34.83 O ATOM 249 OP2 DA D 17 -10.221 0.599 -2.553 1.00 31.17 O ATOM 250 O5' DA D 17 -8.842 2.020 -1.098 1.00 26.12 O ATOM 251 C5' DA D 17 -8.558 2.683 0.094 1.00 25.41 C ATOM 252 C4' DA D 17 -7.407 3.619 -0.107 1.00 26.38 C ATOM 253 O4' DA D 17 -6.208 2.886 -0.440 1.00 24.41 O ATOM 254 C3' DA D 17 -7.600 4.631 -1.214 1.00 27.57 C ATOM 255 O3' DA D 17 -6.972 5.834 -0.764 1.00 29.89 O ATOM 256 C2' DA D 17 -6.902 3.980 -2.406 1.00 26.29 C ATOM 257 C1' DA D 17 -5.771 3.225 -1.781 1.00 23.13 C ATOM 258 N9 DA D 17 -5.444 1.986 -2.460 1.00 22.66 N ATOM 259 C8 DA D 17 -6.295 0.942 -2.750 1.00 23.38 C ATOM 260 N7 DA D 17 -5.700 -0.094 -3.288 1.00 20.62 N ATOM 261 C5 DA D 17 -4.344 0.242 -3.234 1.00 20.59 C ATOM 262 C6 DA D 17 -3.178 -0.447 -3.603 1.00 17.89 C ATOM 263 N6 DA D 17 -3.184 -1.685 -4.072 1.00 20.22 N ATOM 264 N1 DA D 17 -1.995 0.205 -3.497 1.00 19.61 N ATOM 265 C2 DA D 17 -1.992 1.465 -3.030 1.00 20.38 C ATOM 266 N3 DA D 17 -3.021 2.207 -2.621 1.00 20.80 N ATOM 267 C4 DA D 17 -4.182 1.540 -2.774 1.00 19.17 C ATOM 268 P DA D 18 -6.994 7.132 -1.670 1.00 32.91 P ATOM 269 OP1 DA D 18 -6.817 8.281 -0.798 1.00 37.55 O ATOM 270 OP2 DA D 18 -8.060 7.037 -2.636 1.00 31.04 O ATOM 271 O5' DA D 18 -5.659 7.052 -2.535 1.00 30.20 O ATOM 272 C5' DA D 18 -4.377 7.074 -1.958 1.00 30.19 C ATOM 273 C4' DA D 18 -3.354 6.838 -3.036 1.00 28.09 C ATOM 274 O4' DA D 18 -3.424 5.481 -3.484 1.00 26.27 O ATOM 275 C3' DA D 18 -3.545 7.708 -4.286 1.00 29.73 C ATOM 276 O3' DA D 18 -2.469 8.627 -4.273 1.00 34.73 O ATOM 277 C2' DA D 18 -3.566 6.715 -5.433 1.00 27.32 C ATOM 278 C1' DA D 18 -3.010 5.448 -4.841 1.00 24.83 C ATOM 279 N9 DA D 18 -3.488 4.196 -5.410 1.00 23.72 N ATOM 280 C8 DA D 18 -4.794 3.799 -5.530 1.00 20.51 C ATOM 281 N7 DA D 18 -4.937 2.581 -5.985 1.00 22.85 N ATOM 282 C5 DA D 18 -3.636 2.147 -6.189 1.00 20.87 C ATOM 283 C6 DA D 18 -3.111 0.950 -6.675 1.00 19.34 C ATOM 284 N6 DA D 18 -3.852 -0.099 -7.028 1.00 21.88 N ATOM 285 N1 DA D 18 -1.767 0.849 -6.776 1.00 19.77 N ATOM 286 C2 DA D 18 -1.023 1.872 -6.374 1.00 21.42 C ATOM 287 N3 DA D 18 -1.392 3.050 -5.910 1.00 22.19 N ATOM 288 C4 DA D 18 -2.734 3.129 -5.836 1.00 21.41 C ATOM 289 P DT D 19 -2.064 9.546 -5.497 1.00 40.82 P ATOM 290 OP1 DT D 19 -1.281 10.615 -4.939 1.00 44.52 O ATOM 291 OP2 DT D 19 -3.292 9.787 -6.271 1.00 44.69 O ATOM 292 O5' DT D 19 -1.119 8.619 -6.355 1.00 30.72 O ATOM 293 C5' DT D 19 0.059 8.093 -5.804 1.00 29.16 C ATOM 294 C4' DT D 19 0.704 7.195 -6.832 1.00 26.15 C ATOM 295 O4' DT D 19 -0.129 6.045 -7.087 1.00 26.00 O ATOM 296 C3' DT D 19 0.941 7.859 -8.188 1.00 25.98 C ATOM 297 O3' DT D 19 2.343 7.877 -8.376 1.00 30.07 O ATOM 298 C2' DT D 19 0.207 6.968 -9.181 1.00 26.77 C ATOM 299 C1' DT D 19 0.036 5.665 -8.443 1.00 25.87 C ATOM 300 N1 DT D 19 -1.122 4.839 -8.816 1.00 24.60 N ATOM 301 C2 DT D 19 -0.906 3.556 -9.283 1.00 22.21 C ATOM 302 O2 DT D 19 0.197 3.084 -9.451 1.00 22.06 O ATOM 303 N3 DT D 19 -2.038 2.833 -9.519 1.00 22.04 N ATOM 304 C4 DT D 19 -3.339 3.262 -9.380 1.00 21.81 C ATOM 305 O4 DT D 19 -4.247 2.495 -9.615 1.00 24.16 O ATOM 306 C5 DT D 19 -3.499 4.613 -8.891 1.00 22.25 C ATOM 307 C7 DT D 19 -4.879 5.143 -8.663 1.00 23.26 C ATOM 308 C6 DT D 19 -2.396 5.327 -8.640 1.00 22.85 C ATOM 309 P DT D 20 3.005 8.456 -9.725 1.00 32.03 P ATOM 310 OP1 DT D 20 4.339 8.958 -9.284 1.00 35.31 O ATOM 311 OP2 DT D 20 2.027 9.351 -10.442 1.00 33.99 O ATOM 312 O5' DT D 20 3.144 7.102 -10.543 1.00 31.33 O ATOM 313 C5' DT D 20 3.894 5.979 -10.032 1.00 28.60 C ATOM 314 C4' DT D 20 3.851 4.840 -11.020 1.00 28.63 C ATOM 315 O4' DT D 20 2.494 4.361 -11.145 1.00 26.47 O ATOM 316 C3' DT D 20 4.300 5.211 -12.437 1.00 31.59 C ATOM 317 O3' DT D 20 5.260 4.256 -12.875 1.00 39.07 O ATOM 318 C2' DT D 20 3.027 5.147 -13.257 1.00 26.06 C ATOM 319 C1' DT D 20 2.211 4.120 -12.529 1.00 24.42 C ATOM 320 N1 DT D 20 0.757 4.123 -12.660 1.00 23.79 N ATOM 321 C2 DT D 20 0.138 2.932 -12.972 1.00 25.04 C ATOM 322 O2 DT D 20 0.741 1.921 -13.262 1.00 24.66 O ATOM 323 N3 DT D 20 -1.229 2.977 -12.959 1.00 25.84 N ATOM 324 C4 DT D 20 -2.022 4.071 -12.671 1.00 25.98 C ATOM 325 O4 DT D 20 -3.234 3.948 -12.646 1.00 28.14 O ATOM 326 C5 DT D 20 -1.311 5.298 -12.387 1.00 22.81 C ATOM 327 C7 DT D 20 -2.094 6.540 -12.092 1.00 27.47 C ATOM 328 C6 DT D 20 0.028 5.263 -12.401 1.00 26.29 C TER END """ pdb_AB = '''\ ATOM 1 CB MET B 1 52.886 1.976 9.011 1.00 41.44 C ATOM 2 CG MET B 1 53.271 0.996 10.102 1.00 47.36 C ATOM 3 SD MET B 1 55.066 1.105 10.320 1.00 54.87 S ATOM 4 CE MET B 1 55.198 1.758 11.963 1.00 52.95 C ATOM 5 C MET B 1 51.257 3.002 7.473 1.00 32.90 C ATOM 6 O MET B 1 51.643 3.028 6.297 1.00 33.11 O ATOM 7 N MET B 1 51.320 0.535 7.805 1.00 38.36 N ATOM 8 CA MET B 1 51.486 1.834 8.434 1.00 36.79 C TER ATOM 1 CB MET A 1 0.115 20.271 3.107 1.00 41.44 C ATOM 2 CG MET A 1 0.717 21.085 1.978 1.00 47.36 C ATOM 3 SD MET A 1 1.424 22.584 2.709 1.00 54.87 S ATOM 4 CE MET A 1 3.156 22.361 2.406 1.00 52.95 C ATOM 5 C MET A 1 -1.177 18.359 3.971 1.00 32.90 C ATOM 6 O MET A 1 -2.072 18.689 4.760 1.00 33.11 O ATOM 7 N MET A 1 -1.968 19.642 1.989 1.00 38.36 N ATOM 8 CA MET A 1 -0.810 19.133 2.704 1.00 36.79 C ''' pdb_space = '''\ ATOM 1 CB MET 1 52.886 1.976 9.011 1.00 41.44 C ATOM 2 CG MET 1 53.271 0.996 10.102 1.00 47.36 C ATOM 3 SD MET 1 55.066 1.105 10.320 1.00 54.87 S ATOM 4 CE MET 1 55.198 1.758 11.963 1.00 52.95 C ATOM 5 C MET 1 51.257 3.002 7.473 1.00 32.90 C ATOM 6 O MET 1 51.643 3.028 6.297 1.00 33.11 O ATOM 7 N MET 1 51.320 0.535 7.805 1.00 38.36 N ATOM 8 CA MET 1 51.486 1.834 8.434 1.00 36.79 C TER ATOM 1 CB MET A 1 0.115 20.271 3.107 1.00 41.44 C ATOM 2 CG MET A 1 0.717 21.085 1.978 1.00 47.36 C ATOM 3 SD MET A 1 1.424 22.584 2.709 1.00 54.87 S ATOM 4 CE MET A 1 3.156 22.361 2.406 1.00 52.95 C ATOM 5 C MET A 1 -1.177 18.359 3.971 1.00 32.90 C ATOM 6 O MET A 1 -2.072 18.689 4.760 1.00 33.11 O ATOM 7 N MET A 1 -1.968 19.642 1.989 1.00 38.36 N ATOM 8 CA MET A 1 -0.810 19.133 2.704 1.00 36.79 C ''' pdb_stars = '''\ ATOM 1 CB MET** 1 52.886 1.976 9.011 1.00 41.44 C ATOM 2 CG MET** 1 53.271 0.996 10.102 1.00 47.36 C ATOM 3 SD MET** 1 55.066 1.105 10.320 1.00 54.87 S ATOM 4 CE MET** 1 55.198 1.758 11.963 1.00 52.95 C ATOM 5 C MET** 1 51.257 3.002 7.473 1.00 32.90 C ATOM 6 O MET** 1 51.643 3.028 6.297 1.00 33.11 O ATOM 7 N MET** 1 51.320 0.535 7.805 1.00 38.36 N ATOM 8 CA MET** 1 51.486 1.834 8.434 1.00 36.79 C TER ATOM 1 CB MET A 1 0.115 20.271 3.107 1.00 41.44 C ATOM 2 CG MET A 1 0.717 21.085 1.978 1.00 47.36 C ATOM 3 SD MET A 1 1.424 22.584 2.709 1.00 54.87 S ATOM 4 CE MET A 1 3.156 22.361 2.406 1.00 52.95 C ATOM 5 C MET A 1 -1.177 18.359 3.971 1.00 32.90 C ATOM 6 O MET A 1 -2.072 18.689 4.760 1.00 33.11 O ATOM 7 N MET A 1 -1.968 19.642 1.989 1.00 38.36 N ATOM 8 CA MET A 1 -0.810 19.133 2.704 1.00 36.79 C ''' pdb_stars_and_spaces = '''\ ATOM 1 CB MET** 1 52.886 1.976 9.011 1.00 41.44 C ATOM 2 CG MET** 1 53.271 0.996 10.102 1.00 47.36 C ATOM 3 SD MET** 1 55.066 1.105 10.320 1.00 54.87 S ATOM 4 CE MET** 1 55.198 1.758 11.963 1.00 52.95 C ATOM 5 C MET** 1 51.257 3.002 7.473 1.00 32.90 C ATOM 6 O MET** 1 51.643 3.028 6.297 1.00 33.11 O ATOM 7 N MET** 1 51.320 0.535 7.805 1.00 38.36 N ATOM 8 CA MET** 1 51.486 1.834 8.434 1.00 36.79 C TER ATOM 1 CB MET 1 0.115 20.271 3.107 1.00 41.44 C ATOM 2 CG MET 1 0.717 21.085 1.978 1.00 47.36 C ATOM 3 SD MET 1 1.424 22.584 2.709 1.00 54.87 S ATOM 4 CE MET 1 3.156 22.361 2.406 1.00 52.95 C ATOM 5 C MET 1 -1.177 18.359 3.971 1.00 32.90 C ATOM 6 O MET 1 -2.072 18.689 4.760 1.00 33.11 O ATOM 7 N MET 1 -1.968 19.642 1.989 1.00 38.36 N ATOM 8 CA MET 1 -0.810 19.133 2.704 1.00 36.79 C ''' pdb_str_23 = """\ CRYST1 178.041 178.041 241.485 90.00 90.00 90.00 P 4 21 2 SCALE1 0.005617 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005617 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004141 0.00000 ATOM 1 N VAL A 175 4.326 -59.034 -15.595 1.00105.80 N ATOM 2 CA VAL A 175 5.525 -58.206 -15.617 1.00 86.22 C ATOM 3 C VAL A 175 6.348 -58.476 -14.358 1.00 61.80 C ATOM 4 O VAL A 175 5.879 -59.158 -13.445 1.00 58.55 O TER ATOM 2117 N THR B 174 -15.180 -65.753 -17.549 1.00113.31 N ATOM 2118 CA THR B 174 -14.857 -64.334 -17.581 1.00120.94 C ATOM 2119 C THR B 174 -15.877 -63.524 -16.808 1.00109.70 C ATOM 2120 O THR B 174 -15.828 -62.302 -16.798 1.00110.07 O TER ATOM 9373 N LYS F 30 -75.643 8.901 124.736 1.00205.41 N ATOM 9374 CA LYS F 30 -74.928 10.142 125.003 1.00200.32 C ATOM 9375 C LYS F 30 -75.558 11.283 124.229 1.00198.69 C ATOM 9376 O LYS F 30 -74.919 11.832 123.330 1.00194.89 O ATOM 9377 N THR F 31 -76.807 11.640 124.555 1.00163.49 N ATOM 9378 CA THR F 31 -77.445 12.728 123.826 1.00162.32 C ATOM 9379 C THR F 31 -76.491 13.902 123.640 1.00160.35 C ATOM 9380 O THR F 31 -76.874 15.060 123.806 1.00158.76 O TER END """ def exercise_00(prefix="iotbx_ncs_exercise_00",debug=False): pdb_file_name = "%s.pdb"%prefix ncs_params_str = """ ncs_group { reference = chain A selection = chain B selection = chain C } """ def check_result(ncs_inp, test_i): if test_i == 0: l1, l2, l3 = [0,1,2,3], [4,5,6,7], [8,9,10,11] elif test_i == 1: l1, l2, l3 = [1,2,3,4], [5,6,7,8], [9,10,11,12] else: assert 0 ncs_groups = ncs_inp.get_ncs_restraints_group_list() # ncs_groups._show() # STOP() assert len(ncs_groups) == 1, len(ncs_groups) ncs_group = ncs_groups[0] assert approx_equal(ncs_group.master_iselection, l1) assert len(ncs_group.copies) == 2 assert approx_equal(ncs_group.copies[0].iselection, l2) assert approx_equal(ncs_group.copies[1].iselection, l3) files_to_delete = [] for test_i, pdb_str in enumerate([ pdb_str_1, pdb_str_2]): of = open(pdb_file_name, "w") files_to_delete.append(pdb_file_name) print(pdb_str, file=of) of.close() pdb_inp = iotbx.pdb.input(file_name = pdb_file_name) pdb_hierarchy = iotbx.pdb.input(file_name = pdb_file_name).\ construct_hierarchy() # using pdb_hierarchy ncs_inp = ncs.input(hierarchy = pdb_hierarchy) check_result(ncs_inp,test_i) # cleanup if not debug: clean_temp_files(files_to_delete) def exercise_01(prefix="iotbx_ncs_exercise_01", debug=False): """ Make sure provided selections take precedence and are correctly respected. """ pdb_file_name = "%s.pdb"%prefix ncs_params_str = """ ncs_group { reference = chain C selection = chain A } """ def check_result(ncs_inp, test_i): if test_i == 0: l1, l2 = [8,9,10,11], [0,1,2,3] elif test_i == 1: l1, l2 = [9,10,11,12], [1,2,3,4] else: assert 0 ncs_groups = ncs_inp.get_ncs_restraints_group_list() assert len(ncs_groups) == 1 ncs_group = ncs_groups[0] # print "master sel:", list(ncs_group.master_iselection), l1 # print "copy sel:", list(ncs_group.copies[0].iselection), l2 assert approx_equal(ncs_group.master_iselection, l1) assert len(ncs_group.copies) == 1 assert approx_equal(ncs_group.copies[0].iselection, l2) files_to_delete = [] for test_i, pdb_str in enumerate([pdb_str_1, pdb_str_2]): files_to_delete.append(pdb_file_name) of = open(pdb_file_name, "w") print(pdb_str, file=of) of.close() pdb_inp = iotbx.pdb.input(file_name = pdb_file_name) # using combination of pdb_inp and Phil parameter string phil_groups = ncs_group_master_phil.fetch( iotbx.phil.parse(ncs_params_str)).extract() ncs_inp = ncs.input(hierarchy = pdb_inp.construct_hierarchy(), ncs_phil_groups=phil_groups.ncs_group) check_result(ncs_inp,test_i) if not debug: clean_temp_files(files_to_delete) def exercise_03(): """ Expect one master and 3 copies. """ pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str_5) ncs_inp = ncs.input(hierarchy = pdb_inp.construct_hierarchy()) ncs_groups = ncs_inp.get_ncs_restraints_group_list() # truncated_hierarchy also works here asc = ncs_inp.original_hierarchy.atom_selection_cache() sel_master = asc.selection(string = "chain 1") sel_copy_1 = asc.selection(string = "chain A") sel_copy_2 = asc.selection(string = "chain B") sel_copy_3 = asc.selection(string = "chain C") assert len(ncs_groups)==1 ng = ncs_groups[0] # chains are sorted by name (numbers first) assert approx_equal(sel_master.iselection(), ng.master_iselection) assert approx_equal(sel_copy_1.iselection(), ng.copies[0].iselection) assert approx_equal(sel_copy_2.iselection(), ng.copies[1].iselection) assert approx_equal(sel_copy_3.iselection(), ng.copies[2].iselection) def exercise_05(): """ Make sure that phil selection overrides ncs grouping """ phil_str = """\ ncs_group { reference = chain A selection = chain C } ncs_group { reference = chain B selection = chain D } """ phil_groups = ncs_group_master_phil.fetch( iotbx.phil.parse(phil_str)).extract() pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str_6) ncs_inp = ncs.input( hierarchy=pdb_inp.construct_hierarchy(), ncs_phil_groups=phil_groups.ncs_group) nrgl = ncs_inp.get_ncs_restraints_group_list() # print nrgl.get_array_of_str_selections() assert nrgl.get_array_of_str_selections() == \ [["chain 'A'", "chain 'C'"], ["chain 'B'", "chain 'D'"]] def exercise_06(): """ Two groups, different number of chain in each group. Two chains that are NOT ncs related """ pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str_7) ncs_inp = ncs.input(hierarchy=pdb_inp.construct_hierarchy()) nrgl = ncs_inp.get_ncs_restraints_group_list() # print nrgl.get_array_of_str_selections() assert nrgl.get_array_of_str_selections() == \ [["chain 'A'", "chain 'B'", "chain 'C'"], ["chain 'D'", "chain 'E'"]] def exercise_07(): """ Test that minimal number of chains in master ncs are selected (not the minimal number of transformations) """ pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str_8) ncs_inp = ncs.input(hierarchy=pdb_inp.construct_hierarchy()) nrgl = ncs_inp.get_ncs_restraints_group_list() # print nrgl.get_array_of_str_selections() assert nrgl.get_array_of_str_selections() == \ [["chain 'A'", "chain 'B'", "chain 'C'", "chain 'D'", "chain 'E'", "chain 'F'", "chain 'G'", "chain 'H'", "chain 'I'"]] def exercise_09(): """ Test minimal master NCS grouping make sure it does not group together similar chains that can be grouped and that NCS group and transforms created properly """ from mmtbx.ncs import ncs_search pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str_8) ph = pdb_inp.construct_hierarchy() # match_dict = ncs_search.search_ncs_relations( ph=ph,chain_similarity_threshold=0) # make sure that all possible chains compared model = ph.models()[0] chain_ids = list({x.id for x in model.chains()}) chain_ids = sorted(chain_ids) n_chains = len(chain_ids) assert n_chains==9 assert len(match_dict)==8, len(match_dict) def exercise_10(): """ Test minimal NCS operators """ from mmtbx.ncs import ncs_search pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str_8) ph = pdb_inp.construct_hierarchy() # match_dict = ncs_search.search_ncs_relations( ph=ph, chain_similarity_threshold=0) # chains_info = ncs_search.get_chains_info(ph) # nrgl = ncs_search.ncs_grouping_and_group_dict(match_dict, ph) nrgl.update_str_selections_if_needed(ph) str_sel = nrgl.get_array_of_str_selections() print(str_sel) assert str_sel == [["chain 'A'", "chain 'B'", "chain 'C'", "chain 'D'", "chain 'E'", "chain 'F'", "chain 'G'", "chain 'H'", "chain 'I'"]] def exercise_11(): """ Make sure user-provided NCS groups are preserved. Also make sure two-letter chain ID are handled correctly """ phil_str=""" ncs_group { reference = chain 'Aa' and (resseq 6:9 ) selection = chain 'Ac' and (resseq 6:9 ) } ncs_group { reference = chain 'Ab' and (resseq 1:4 ) selection = chain 'Ad' and (resseq 1:4 ) } """ asc = iotbx.pdb.input(source_info=None, lines=pdb_str_9).construct_hierarchy().atom_selection_cache() ### default pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str_9) ncs_inp = ncs.input(hierarchy=pdb_inp.construct_hierarchy()) ncs_groups = ncs_inp.get_ncs_restraints_group_list() # no more grouping, therefore groups are like in phil_str above # ncs_inp.show(format='phil') assert len(ncs_groups)==2, len(ncs_groups) assert ncs_groups[0].master_iselection.all_eq( asc.selection(string = "chain Aa").iselection()) g1_c = ncs_groups[0].copies assert len(g1_c)==1 assert g1_c[0].iselection.all_eq( asc.selection(string = "chain Ac").iselection()) assert ncs_groups[1].master_iselection.all_eq( asc.selection(string = "chain Ab").iselection()) g2_c = ncs_groups[1].copies assert len(g1_c)==1 assert g2_c[0].iselection.all_eq( asc.selection(string = "chain Ad").iselection()) # NO MORE GROUPING, therefore these are not valid # assert len(ncs_groups)==1, len(ncs_groups) # assert ncs_groups[0].master_iselection.all_eq( # asc.selection(string = "chain Aa or chain Ab").iselection()) # g1_c = ncs_groups[0].copies # assert len(g1_c)==1 # assert g1_c[0].iselection.all_eq( # asc.selection(string = "chain Ac or chain Ad").iselection()) ### user-supplied phil_groups = ncs_group_master_phil.fetch( iotbx.phil.parse(phil_str)).extract() pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str_9) ncs_inp = ncs.input(hierarchy=pdb_inp.construct_hierarchy(), ncs_phil_groups=phil_groups.ncs_group) ncs_groups = ncs_inp.get_ncs_restraints_group_list() assert len(ncs_groups)==2 # group 1 assert ncs_groups[0].master_iselection.all_eq( asc.selection(string = "chain Aa and resseq 6:9").iselection()) g1_c = ncs_groups[0].copies assert len(g1_c)==1 assert g1_c[0].iselection.all_eq( asc.selection(string = "chain Ac and resseq 6:9").iselection()) # group 2 assert ncs_groups[1].master_iselection.all_eq( asc.selection(string = "chain Ab and resseq 1:4").iselection()) g1_c = ncs_groups[1].copies assert len(g1_c)==1 assert g1_c[0].iselection.all_eq( asc.selection(string = "chain Ad and resseq 1:4").iselection()) def exercise_12(): """ Test dealing with chains names that are space or **""" ncs_obj_AB = ncs.input(hierarchy=iotbx.pdb.input(source_info=None, lines=pdb_AB).construct_hierarchy()) ncs_obj_space = ncs.input(hierarchy=iotbx.pdb.input(source_info=None, lines=pdb_space).construct_hierarchy()) ncs_obj_stars = ncs.input(hierarchy=iotbx.pdb.input(source_info=None, lines=pdb_stars).construct_hierarchy()) ncs_obj_str_and_spc = ncs.input(hierarchy=iotbx.pdb.input(source_info=None, lines=pdb_stars_and_spaces).construct_hierarchy()) # for ncs_obj in [ ncs_obj_AB, ncs_obj_space, ncs_obj_stars, ncs_obj_str_and_spc]: ncs_groups = ncs_obj.get_ncs_restraints_group_list() assert len(ncs_groups) == 1 assert ncs_groups[0].master_iselection.size() == 8 assert ncs_groups[0].copies[0].iselection.size() == 8 def exercise_13(): """ PDB file with insertion codes. """ asc = iotbx.pdb.input(source_info=None, lines=pdb_str_10).construct_hierarchy().atom_selection_cache() ncs_inp = ncs.input(hierarchy=iotbx.pdb.input(source_info=None, lines=pdb_str_10).construct_hierarchy()) ncs_groups = ncs_inp.get_ncs_restraints_group_list() assert len(ncs_groups)==1 assert ncs_groups[0].master_iselection.all_eq( asc.selection(string = "chain H").iselection()) g1_c = ncs_groups[0].copies assert len(g1_c)==1 assert g1_c[0].iselection.all_eq( asc.selection(string = "chain L").iselection()) def exercise_14(): """ PDB file with alternative conformations. """ asc = iotbx.pdb.input(source_info=None, lines=pdb_str_11).construct_hierarchy().atom_selection_cache() ncs_inp = ncs.input(hierarchy=iotbx.pdb.input(source_info=None, lines=pdb_str_11).construct_hierarchy()) ncs_groups = ncs_inp.get_ncs_restraints_group_list() assert len(ncs_groups)==1 assert ncs_groups[0].master_iselection.all_eq(asc.selection( string = "chain H and not (altloc A or altloc B)").iselection()) g1_c = ncs_groups[0].copies assert len(g1_c)==1 assert g1_c[0].iselection.all_eq(asc.selection( string = "chain L and not (altloc A or altloc B)").iselection()) def exercise_15(): """ PDB file with MODEL-ENDMDL. """ exc = None try: ncs_inp = ncs.input(hierarchy=iotbx.pdb.input(source_info=None, lines=pdb_str_12).construct_hierarchy()) ncs_groups = ncs_inp.get_ncs_restraints_group_list() except Exception as e: exc = e assert str(exc)=="Multi-model PDB (with MODEL-ENDMDL) is not supported." def exercise_16(): """ PDB file with nucleic acids. """ asc = iotbx.pdb.input(source_info=None, lines=pdb_str_13).construct_hierarchy().atom_selection_cache() ncs_inp = ncs.input(hierarchy=iotbx.pdb.input(source_info=None, lines=pdb_str_13).construct_hierarchy()) ncs_groups = ncs_inp.get_ncs_restraints_group_list() assert len(ncs_groups)==1 assert ncs_groups[0].master_iselection.all_eq(asc.selection( string = "chain A").iselection()) g1_c = ncs_groups[0].copies assert len(g1_c)==1 assert g1_c[0].iselection.all_eq(asc.selection( string = "chain aA").iselection()) def exercise_17(): """ PDB file with ligands. """ asc = iotbx.pdb.input(source_info=None, lines=pdb_str_14).construct_hierarchy().atom_selection_cache() p = ncs.input.get_default_params() p.ncs_search.exclude_selection=None ncs_inp = ncs.input( hierarchy=iotbx.pdb.input(source_info=None, lines=pdb_str_14).construct_hierarchy(), params=p.ncs_search) ncs_groups = ncs_inp.get_ncs_restraints_group_list() assert len(ncs_groups)==1 assert ncs_groups[0].master_iselection.all_eq(asc.selection( string = "chain A").iselection()) g1_c = ncs_groups[0].copies assert len(g1_c)==2 assert g1_c[0].iselection.all_eq(asc.selection( string = "chain B").iselection()) assert g1_c[1].iselection.all_eq(asc.selection( string = "chain C").iselection()) def exercise_19(): """ PDB file with insertion codes, resseqs are different. """ asc = iotbx.pdb.input(source_info=None, lines=pdb_str_16).construct_hierarchy().atom_selection_cache() ncs_inp = ncs.input(hierarchy=iotbx.pdb.input(source_info=None, lines=pdb_str_16).construct_hierarchy()) ncs_groups = ncs_inp.get_ncs_restraints_group_list() assert len(ncs_groups)==1 assert ncs_groups[0].master_iselection.all_eq(asc.selection( string = "chain H and not (altloc A or altloc B)").iselection()) g1_c = ncs_groups[0].copies assert len(g1_c)==1 assert g1_c[0].iselection.all_eq(asc.selection( string = "chain L and not (altloc A or altloc B)").iselection()) def exercise_20(): """ Identical chains, too large rms difference. No NCS by default, use user siupplied NCS. """ phil_str=""" ncs_group { reference = chain A selection = chain B } """ asc = iotbx.pdb.input(source_info=None, lines=pdb_str_17).construct_hierarchy().atom_selection_cache() ### user-supplied phil_groups = ncs_group_master_phil.fetch( iotbx.phil.parse(phil_str)).extract() ncs_inp = ncs.input( hierarchy=iotbx.pdb.input(source_info=None, lines=pdb_str_17).construct_hierarchy(), ncs_phil_groups=phil_groups.ncs_group) ncs_groups = ncs_inp.get_ncs_restraints_group_list() assert len(ncs_groups)==1 # group 1 assert ncs_groups[0].master_iselection.all_eq( asc.selection(string = "chain A").iselection()) g1_c = ncs_groups[0].copies assert len(g1_c)==1 assert g1_c[0].iselection.all_eq( asc.selection(string = "chain B").iselection()) ### default ncs_inp = ncs.input(hierarchy=iotbx.pdb.input(source_info=None, lines=pdb_str_17).construct_hierarchy()) ncs_groups = ncs_inp.get_ncs_restraints_group_list() assert len(ncs_groups)==0 def exercise_21(): """ PDB file with blank chain ID and segID. XXX No support for segID in search procedure anymore. """ # both chain ID blank. segID non-blank ncs_inp = ncs.input(hierarchy=iotbx.pdb.input(source_info=None, lines=pdb_str_18).construct_hierarchy()) ncs_groups = ncs_inp.get_ncs_restraints_group_list() # STOP() assert len(ncs_groups)==0 # it does not care about segID # blank and non-blank chain ID, non-blank segID ncs_inp = ncs.input(hierarchy=iotbx.pdb.input(source_info=None, lines=pdb_str_19).construct_hierarchy()) ncs_groups = ncs_inp.get_ncs_restraints_group_list() assert len(ncs_groups)==1 asc = iotbx.pdb.input(source_info=None, lines=pdb_str_19).construct_hierarchy().atom_selection_cache() assert ncs_groups[0].master_iselection.all_eq(asc.selection( string = "chain ' '").iselection()) g1_c = ncs_groups[0].copies assert len(g1_c)==1 assert g1_c[0].iselection.all_eq(asc.selection( string = "chain 'A'").iselection()), list(g1_c[0].iselection) def exercise_22(): """ PDB file with perfectly overlapping chains. """ ncs_inp = ncs.input(hierarchy=iotbx.pdb.input(source_info=None, lines=pdb_str_20).construct_hierarchy()) ncs_groups = ncs_inp.get_ncs_restraints_group_list() assert len(ncs_groups)==1 assert len(ncs_groups[0].copies)==3 asc = iotbx.pdb.input(source_info=None, lines=pdb_str_20).construct_hierarchy().atom_selection_cache() assert ncs_groups[0].master_iselection.all_eq(asc.selection( string = "chain A").iselection()) g1_c = ncs_groups[0].copies sel_1 = g1_c[0].iselection sel_1.extend(g1_c[1].iselection) sel_1.extend(g1_c[2].iselection) sel = asc.selection( string = "chain B or chain C or chain D").iselection() assert sel_1.all_eq(sel) def exercise_23(): """ Case when reordering of chains (function update_chain_ids_search_order ncs_search.py) results in selections that doesn't match 'atom-by-atom' with each others. """ pdb_inp = iotbx.pdb.input(source_info=None,lines=pdb_str_23.split('\n')) pdb_hierarchy = pdb_inp.construct_hierarchy() pdb_hierarchy = pdb_hierarchy.expand_to_p1( crystal_symmetry=pdb_inp.crystal_symmetry()) pdb_hierarchy.write_pdb_file(file_name="m.pdb") pdb_hierarchy.atoms().reset_i_seq() ncs_inp = iotbx.ncs.input(hierarchy=pdb_hierarchy) # print dir(ncs_inp) # print ncs_inp.print_ncs_phil_param() # STOP() ncs_groups = ncs_inp.get_ncs_restraints_group_list() phil_out = ncs_inp.show_phil_format() assert not show_diff(phil_out, """\ NCS phil parameters: ----------------------- ncs_group { reference = chain Aa or chain Ab or chain Ac selection = chain Ad or chain Ae or chain Af selection = chain Ag or chain Ah or chain Ai selection = chain Aj or chain Ak or chain Al selection = chain Am or chain An or chain Ao selection = chain Ap or chain Aq or chain Ar selection = chain As or chain At or chain Au selection = chain Av or chain Aw or chain Ax }""") def clean_temp_files(file_list): """ delete files in the file_list """ for fn in file_list: if os.path.isfile(fn): os.remove(fn) if (__name__ == "__main__"): debug = ('debug' in sys.argv[1:]) exercise_00(debug=debug) exercise_01(debug=debug) exercise_03() exercise_05() exercise_06() exercise_07() exercise_09() exercise_10() exercise_11() exercise_12() exercise_13() exercise_14() exercise_15() exercise_16() exercise_17() exercise_19() exercise_20() exercise_21() # No support for segID in search procedure anymore. exercise_22() # exercise_23() # Not grouping chains anymore. Test is left to illustrate # failure of update_chain_ids_search_order in this example print("OK")