from __future__ import absolute_import, division, print_function import os from libtbx import easy_run pdb_str_1 = ''' CRYST1 230.463 123.139 153.201 90.00 131.05 90.00 C 1 2 1 SCALE1 0.004339 0.000000 0.003779 0.00000 SCALE2 0.000000 0.008121 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008655 0.00000 ATOM 1 N CYS A 861 -12.347 -25.689 76.808 1.00127.20 N ATOM 2 CA CYS A 861 -13.104 -25.567 78.048 1.00133.90 C ATOM 3 C CYS A 861 -14.052 -26.748 78.202 1.00134.10 C ATOM 4 O CYS A 861 -14.691 -27.168 77.239 1.00131.28 O ATOM 5 CB CYS A 861 -13.889 -24.252 78.073 1.00135.25 C ATOM 6 SG CYS A 861 -14.037 -23.445 79.699 1.00155.43 S ATOM 7 N CYS A 864 -17.542 -24.913 77.978 1.00139.78 N ATOM 8 CA CYS A 864 -17.949 -24.175 76.780 1.00132.76 C ATOM 9 C CYS A 864 -17.994 -25.041 75.522 1.00125.77 C ATOM 10 O CYS A 864 -18.762 -24.765 74.604 1.00125.97 O ATOM 11 CB CYS A 864 -17.017 -22.980 76.533 1.00134.20 C ATOM 12 SG CYS A 864 -16.835 -21.826 77.907 1.00126.17 S ATOM 13 N CYS A1054 -20.150 -20.841 82.906 1.00100.48 N ATOM 14 CA CYS A1054 -18.688 -20.783 82.915 1.00101.74 C ATOM 15 C CYS A1054 -18.182 -19.501 83.572 1.00103.40 C ATOM 16 O CYS A1054 -18.656 -18.409 83.261 1.00107.65 O ATOM 17 CB CYS A1054 -18.128 -20.893 81.493 1.00111.10 C ATOM 18 SG CYS A1054 -16.308 -20.868 81.398 1.00 99.22 S ATOM 19 N HIS A1060 -13.988 -16.716 77.115 1.00102.85 N ATOM 20 CA HIS A1060 -14.171 -17.807 76.158 1.00107.46 C ATOM 21 C HIS A1060 -14.871 -17.324 74.890 1.00101.11 C ATOM 22 O HIS A1060 -14.674 -17.888 73.814 1.00 96.36 O ATOM 23 CB HIS A1060 -14.975 -18.973 76.754 1.00122.04 C ATOM 24 CG HIS A1060 -14.199 -19.831 77.706 1.00131.75 C ATOM 25 ND1 HIS A1060 -14.110 -19.567 79.055 1.00134.67 N ATOM 26 CD2 HIS A1060 -13.424 -20.921 77.487 1.00136.31 C ATOM 27 CE1 HIS A1060 -13.342 -20.474 79.633 1.00135.85 C ATOM 28 NE2 HIS A1060 -12.911 -21.303 78.702 1.00135.21 N TER HETATM 29 ZN ZN A2083 -15.163 -21.423 79.459 1.00340.34 Zn END ''' pdb_str_2 = """ ATOM 41609 N ARG L 107 336.348 327.647 268.798 1.00 73.69 N ATOM 41610 CA ARG L 107 336.367 326.308 269.396 1.00 76.13 C ATOM 41611 C ARG L 107 337.373 325.330 268.764 1.00 75.15 C ATOM 41612 O ARG L 107 337.457 324.176 269.202 1.00 76.91 O ATOM 41613 CB ARG L 107 334.965 325.692 269.478 1.00 75.62 C ATOM 41614 CG ARG L 107 334.342 325.248 268.174 1.00 76.45 C ATOM 41615 CD ARG L 107 333.520 324.002 268.423 1.00 80.59 C ATOM 41616 NE ARG L 107 332.567 323.744 267.356 1.00 87.69 N ATOM 41617 CZ ARG L 107 331.720 322.715 267.332 1.00 96.82 C ATOM 41618 NH1 ARG L 107 330.884 322.582 266.304 1.00102.01 N ATOM 41619 NH2 ARG L 107 331.701 321.815 268.320 1.00 97.76 N ATOM 41620 N CYS L 108 338.113 325.778 267.745 1.00 68.92 N ATOM 41621 CA CYS L 108 339.312 325.068 267.300 1.00 64.76 C ATOM 41622 C CYS L 108 340.555 325.418 268.121 1.00 66.03 C ATOM 41623 O CYS L 108 341.588 324.784 267.939 1.00 66.50 O ATOM 41624 CB CYS L 108 339.571 325.286 265.807 1.00 60.82 C ATOM 41625 SG CYS L 108 338.793 324.031 264.774 1.00 56.51 S ATOM 41680 N ASN L 116 342.905 314.996 273.851 1.00112.83 N ATOM 41681 CA ASN L 116 344.311 315.272 274.097 1.00113.37 C ATOM 41682 C ASN L 116 344.432 316.763 274.355 1.00106.26 C ATOM 41683 O ASN L 116 343.923 317.563 273.570 1.00102.97 O ATOM 41684 CB ASN L 116 345.154 314.869 272.887 1.00121.54 C ATOM 41685 CG ASN L 116 346.648 315.017 273.127 1.00128.12 C ATOM 41686 OD1 ASN L 116 347.393 315.391 272.221 1.00132.40 O ATOM 41687 ND2 ASN L 116 347.094 314.722 274.346 1.00130.54 N ATOM 41688 N GLY L 117 345.092 317.133 275.451 1.00102.26 N ATOM 41689 CA GLY L 117 345.198 318.535 275.858 1.00101.43 C ATOM 41690 C GLY L 117 345.994 319.377 274.878 1.00 98.56 C ATOM 41691 O GLY L 117 347.182 319.633 275.090 1.00103.03 O ATOM 41692 N SER L 118 345.330 319.796 273.801 1.00 90.19 N ATOM 41693 CA SER L 118 345.968 320.564 272.726 1.00 84.20 C ATOM 41694 C SER L 118 344.932 321.312 271.890 1.00 75.48 C ATOM 41695 O SER L 118 343.741 321.265 272.172 1.00 77.84 O ATOM 41696 CB SER L 118 346.801 319.635 271.828 1.00 86.49 C ATOM 41697 OG SER L 118 345.989 318.943 270.892 1.00 87.95 O ATOM 41698 N THR L 119 345.406 321.995 270.860 1.00 68.21 N ATOM 41699 CA THR L 119 344.565 322.769 269.955 1.00 65.80 C ATOM 41700 C THR L 119 344.114 321.858 268.822 1.00 59.53 C ATOM 41701 O THR L 119 344.560 320.717 268.754 1.00 59.27 O ATOM 41702 CB THR L 119 345.388 323.979 269.462 1.00 72.06 C ATOM 41703 OG1 THR L 119 345.624 324.869 270.569 1.00 76.28 O ATOM 41704 CG2 THR L 119 344.722 324.746 268.346 1.00 72.28 C ATOM 41705 N CYS L 120 343.196 322.319 267.971 1.00 57.56 N ATOM 41706 CA CYS L 120 342.863 321.598 266.735 1.00 57.89 C ATOM 41707 C CYS L 120 344.051 321.463 265.784 1.00 59.16 C ATOM 41708 O CYS L 120 344.945 322.303 265.759 1.00 57.82 O ATOM 41709 CB CYS L 120 341.697 322.250 265.986 1.00 56.77 C ATOM 41710 SG CYS L 120 341.374 321.502 264.369 1.00 53.53 S ATOM 41711 N ILE L 121 344.035 320.383 265.006 1.00 61.55 N ATOM 41712 CA ILE L 121 345.070 320.108 264.011 1.00 62.65 C ATOM 41713 C ILE L 121 345.134 321.190 262.946 1.00 61.66 C ATOM 41714 O ILE L 121 346.214 321.514 262.462 1.00 61.29 O ATOM 41715 CB ILE L 121 344.869 318.724 263.337 1.00 64.79 C ATOM 41716 CG1 ILE L 121 346.106 318.329 262.529 1.00 65.49 C ATOM 41717 CG2 ILE L 121 343.629 318.694 262.442 1.00 64.60 C ATOM 41718 CD1 ILE L 121 346.129 316.868 262.147 1.00 66.90 C ATOM 41719 N CYS L 122 343.982 321.748 262.588 1.00 64.24 N ATOM 41720 CA CYS L 122 343.921 322.801 261.579 1.00 68.72 C ATOM 41721 C CYS L 122 344.962 323.861 261.847 1.00 69.64 C ATOM 41722 O CYS L 122 345.597 324.371 260.927 1.00 73.06 O ATOM 41723 CB CYS L 122 342.536 323.448 261.549 1.00 70.95 C ATOM 41724 SG CYS L 122 342.155 324.561 262.930 1.00 73.02 S ATOM 41725 N ARG L 123 345.126 324.175 263.124 1.00 71.15 N ATOM 41726 CA ARG L 123 346.136 325.116 263.575 1.00 74.71 C ATOM 41727 C ARG L 123 347.595 324.736 263.284 1.00 70.94 C ATOM 41728 O ARG L 123 348.470 325.599 263.344 1.00 71.25 O ATOM 41729 CB ARG L 123 345.940 325.391 265.069 1.00 79.46 C ATOM 41730 CG ARG L 123 344.986 326.540 265.348 1.00 80.30 C ATOM 41731 CD ARG L 123 345.803 327.781 265.628 1.00 83.36 C ATOM 41732 NE ARG L 123 345.075 329.006 265.380 1.00 86.55 N ATOM 41733 CZ ARG L 123 344.805 329.490 264.173 1.00 92.39 C ATOM 41734 NH1 ARG L 123 345.154 328.845 263.060 1.00 94.43 N ATOM 41735 NH2 ARG L 123 344.154 330.635 264.076 1.00 96.56 N ATOM 41736 N VAL L 124 347.862 323.475 262.971 1.00 67.83 N ATOM 41737 CA VAL L 124 349.189 323.082 262.551 1.00 69.08 C ATOM 41738 C VAL L 124 349.362 323.546 261.125 1.00 69.73 C ATOM 41739 O VAL L 124 348.516 323.247 260.286 1.00 71.78 O ATOM 41740 CB VAL L 124 349.425 321.564 262.597 1.00 75.61 C ATOM 41741 CG1 VAL L 124 350.888 321.265 262.304 1.00 80.89 C ATOM 41742 CG2 VAL L 124 349.064 320.966 263.952 1.00 79.12 C ATOM 41743 N PRO L 125 350.451 324.280 260.839 1.00 74.22 N ATOM 41744 CA PRO L 125 350.681 324.672 259.444 1.00 79.19 C ATOM 41745 C PRO L 125 350.948 323.471 258.534 1.00 83.23 C ATOM 41746 O PRO L 125 351.794 322.636 258.864 1.00 79.01 O ATOM 41747 CB PRO L 125 351.903 325.605 259.516 1.00 78.87 C ATOM 41748 CG PRO L 125 352.460 325.483 260.892 1.00 76.89 C ATOM 41749 CD PRO L 125 351.408 324.899 261.776 1.00 74.88 C ATOM 41750 N ARG L 126 350.215 323.391 257.417 1.00 93.23 N ATOM 41751 CA ARG L 126 350.373 322.321 256.404 1.00103.77 C ATOM 41752 C ARG L 126 351.818 321.836 256.299 1.00108.83 C ATOM 41753 O ARG L 126 352.072 320.632 256.279 1.00107.99 O ATOM 41754 CB ARG L 126 349.884 322.789 255.015 1.00107.19 C ATOM 41755 CG ARG L 126 348.492 322.304 254.586 1.00105.56 C ATOM 41756 CD ARG L 126 347.848 323.272 253.583 1.00104.23 C ATOM 41757 NE ARG L 126 346.983 322.636 252.583 1.00101.59 N ATOM 41758 CZ ARG L 126 346.272 323.292 251.657 1.00 98.80 C ATOM 41759 NH1 ARG L 126 346.287 324.629 251.594 1.00 95.11 N ATOM 41760 NH2 ARG L 126 345.523 322.604 250.788 1.00 94.57 N ATOM 41761 N ALA L 127 352.743 322.794 256.242 1.00117.75 N ATOM 41762 CA ALA L 127 354.185 322.535 256.247 1.00128.16 C ATOM 41763 C ALA L 127 354.633 321.442 257.215 1.00132.82 C ATOM 41764 O ALA L 127 355.367 320.538 256.817 1.00139.14 O ATOM 41765 CB ALA L 127 354.945 323.821 256.551 1.00130.58 C ATOM 41766 N GLN L 128 354.181 321.515 258.468 1.00132.72 N ATOM 41767 CA GLN L 128 354.740 320.669 259.528 1.00136.88 C ATOM 41768 C GLN L 128 354.199 319.249 259.411 1.00142.70 C ATOM 41769 O GLN L 128 354.960 318.259 259.431 1.00147.09 O ATOM 41770 CB GLN L 128 354.424 321.259 260.902 1.00132.51 C ATOM 41771 CG GLN L 128 355.284 320.701 262.024 1.00132.58 C ATOM 41772 CD GLN L 128 355.031 321.381 263.359 1.00135.91 C ATOM 41773 OE1 GLN L 128 354.731 322.576 263.421 1.00136.01 O ATOM 41774 NE2 GLN L 128 355.158 320.620 264.440 1.00139.88 N ATOM 41775 N LEU L 129 352.879 319.186 259.255 1.00144.90 N ATOM 41776 CA LEU L 129 352.165 317.909 259.079 1.00148.05 C ATOM 41777 C LEU L 129 352.701 317.176 257.861 1.00160.65 C ATOM 41778 O LEU L 129 352.972 315.965 257.917 1.00169.37 O ATOM 41779 CB LEU L 129 350.666 318.131 258.881 1.00138.19 C ATOM 41780 CG LEU L 129 349.894 318.599 260.107 1.00131.29 C ATOM 41781 CD1 LEU L 129 348.548 319.171 259.692 1.00128.46 C ATOM 41782 CD2 LEU L 129 349.732 317.471 261.115 1.00131.02 C ATOM 41783 N GLU L 130 352.842 317.937 256.779 1.00168.55 N ATOM 41784 CA GLU L 130 353.342 317.410 255.501 1.00178.63 C ATOM 41785 C GLU L 130 354.727 316.810 255.692 1.00178.61 C ATOM 41786 O GLU L 130 355.008 315.700 255.213 1.00181.96 O ATOM 41787 CB GLU L 130 353.390 318.514 254.439 1.00192.08 C ATOM 41788 CG GLU L 130 353.832 318.059 253.052 1.00205.27 C ATOM 41789 CD GLU L 130 353.694 319.147 251.999 1.00216.41 C ATOM 41790 OE1 GLU L 130 353.991 320.324 252.301 1.00219.33 O ATOM 41791 OE2 GLU L 130 353.295 318.822 250.860 1.00221.86 O ATOM 41792 N GLU L 131 355.564 317.567 256.392 1.00184.22 N ATOM 41793 CA GLU L 131 356.945 317.166 256.684 1.00195.20 C ATOM 41794 C GLU L 131 356.957 315.838 257.434 1.00193.99 C ATOM 41795 O GLU L 131 357.723 314.922 257.095 1.00195.22 O ATOM 41796 CB GLU L 131 357.689 318.251 257.476 1.00203.89 C ATOM 41797 CG GLU L 131 359.202 318.071 257.527 1.00210.24 C ATOM 41798 CD GLU L 131 359.947 319.363 257.839 1.00211.87 C ATOM 41799 OE1 GLU L 131 359.450 320.166 258.658 1.00213.20 O ATOM 41800 OE2 GLU L 131 361.037 319.574 257.266 1.00209.81 O ATOM 41801 N GLU L 132 356.095 315.773 258.441 1.00198.20 N ATOM 41802 CA GLU L 132 355.953 314.582 259.288 1.00210.00 C ATOM 41803 C GLU L 132 355.590 313.372 258.434 1.00212.98 C ATOM 41804 O GLU L 132 356.179 312.289 258.581 1.00214.87 O ATOM 41805 CB GLU L 132 354.918 314.777 260.411 1.00219.10 C ATOM 41806 CG GLU L 132 355.523 315.116 261.768 1.00226.96 C ATOM 41807 CD GLU L 132 356.331 313.977 262.376 1.00231.60 C ATOM 41808 OE1 GLU L 132 355.887 312.810 262.305 1.00231.32 O ATOM 41809 OE2 GLU L 132 357.413 314.253 262.937 1.00234.06 O ATOM 41810 N ALA L 133 354.620 313.595 257.557 1.00219.78 N ATOM 41811 CA ALA L 133 354.121 312.563 256.643 1.00226.27 C ATOM 41812 C ALA L 133 355.263 312.032 255.779 1.00226.20 C ATOM 41813 O ALA L 133 355.428 310.813 255.617 1.00225.84 O ATOM 41814 CB ALA L 133 352.992 313.098 255.772 1.00230.45 C ATOM 41815 N ARG L 134 356.027 312.976 255.248 1.00224.89 N ATOM 41816 CA ARG L 134 357.175 312.679 254.384 1.00223.99 C ATOM 41817 C ARG L 134 358.174 311.797 255.127 1.00222.38 C ATOM 41818 O ARG L 134 358.663 310.790 254.589 1.00223.69 O ATOM 41819 CB ARG L 134 357.817 313.979 253.889 1.00227.22 C ATOM 41820 CG ARG L 134 358.955 313.807 252.896 1.00230.13 C ATOM 41821 CD ARG L 134 359.198 315.089 252.105 1.00232.93 C ATOM 41822 NE ARG L 134 360.621 315.406 251.973 1.00236.77 N ATOM 41823 CZ ARG L 134 361.384 315.953 252.924 1.00237.39 C ATOM 41824 NH1 ARG L 134 360.890 316.255 254.127 1.00233.02 N ATOM 41825 NH2 ARG L 134 362.669 316.195 252.672 1.00242.00 N ATOM 41826 N LYS L 135 358.447 312.202 256.361 1.00219.78 N ATOM 41827 CA LYS L 135 359.382 311.494 257.242 1.00219.95 C ATOM 41828 C LYS L 135 358.927 310.054 257.442 1.00216.67 C ATOM 41829 O LYS L 135 359.728 309.112 257.342 1.00217.41 O ATOM 41830 CB LYS L 135 359.537 312.198 258.597 1.00224.43 C ATOM 41831 CG LYS L 135 360.319 313.501 258.539 1.00235.13 C ATOM 41832 CD LYS L 135 361.820 313.265 258.445 1.00244.36 C ATOM 41833 CE LYS L 135 362.598 314.571 258.513 1.00250.04 C ATOM 41834 NZ LYS L 135 362.299 315.485 257.374 1.00251.38 N ATOM 41835 N LYS L 136 357.634 309.921 257.714 1.00216.69 N ATOM 41836 CA LYS L 136 357.000 308.621 257.949 1.00216.81 C ATOM 41837 C LYS L 136 357.030 307.659 256.752 1.00214.11 C ATOM 41838 O LYS L 136 357.563 306.548 256.836 1.00213.14 O ATOM 41839 CB LYS L 136 355.571 308.774 258.487 1.00220.08 C ATOM 41840 CG LYS L 136 355.512 309.381 259.888 1.00224.22 C ATOM 41841 CD LYS L 136 354.767 308.502 260.886 1.00228.88 C ATOM 41842 CE LYS L 136 353.275 308.441 260.599 1.00233.74 C ATOM 41843 NZ LYS L 136 352.538 307.685 261.651 1.00232.90 N ATOM 41844 N GLY L 137 356.456 308.128 255.646 1.00214.82 N ATOM 41845 CA GLY L 137 356.225 307.318 254.449 1.00217.82 C ATOM 41846 C GLY L 137 354.863 307.608 253.838 1.00218.27 C ATOM 41847 O GLY L 137 354.728 307.678 252.614 1.00219.44 O ATOM 41848 N THR L 138 353.856 307.771 254.700 1.00212.51 N ATOM 41849 CA THR L 138 352.483 308.087 254.276 1.00205.76 C ATOM 41850 C THR L 138 352.329 309.488 253.664 1.00189.06 C ATOM 41851 O THR L 138 353.228 310.326 253.750 1.00191.76 O ATOM 41852 CB THR L 138 351.476 307.928 255.446 1.00208.89 C ATOM 41853 OG1 THR L 138 350.135 307.982 254.942 1.00211.23 O ATOM 41854 CG2 THR L 138 351.662 309.017 256.516 1.00209.11 C ATOM 41855 N GLN L 139 351.170 309.716 253.050 1.00167.14 N ATOM 41856 CA GLN L 139 350.845 310.989 252.401 1.00156.67 C ATOM 41857 C GLN L 139 350.213 311.928 253.433 1.00153.10 C ATOM 41858 O GLN L 139 350.154 311.588 254.617 1.00150.87 O ATOM 41859 CB GLN L 139 349.913 310.752 251.202 1.00158.66 C ATOM 41860 CG GLN L 139 350.597 310.133 249.989 1.00167.24 C ATOM 41861 CD GLN L 139 350.944 308.664 250.170 1.00173.83 C ATOM 41862 OE1 GLN L 139 351.970 308.325 250.761 1.00175.13 O ATOM 41863 NE2 GLN L 139 350.095 307.784 249.648 1.00177.64 N ATOM 41864 N VAL L 140 349.758 313.106 252.995 1.00155.40 N ATOM 41865 CA VAL L 140 349.120 314.084 253.896 1.00154.21 C ATOM 41866 C VAL L 140 347.881 313.470 254.558 1.00136.02 C ATOM 41867 O VAL L 140 346.968 312.978 253.890 1.00127.48 O ATOM 41868 CB VAL L 140 348.764 315.414 253.180 1.00167.65 C ATOM 41869 CG1 VAL L 140 347.959 316.337 254.099 1.00173.32 C ATOM 41870 CG2 VAL L 140 350.031 316.121 252.705 1.00169.90 C ATOM 41871 N SER L 141 347.867 313.543 255.881 1.00123.31 N ATOM 41872 CA SER L 141 347.078 312.647 256.713 1.00119.75 C ATOM 41873 C SER L 141 345.648 313.110 256.960 1.00114.75 C ATOM 41874 O SER L 141 344.712 312.315 256.845 1.00111.46 O ATOM 41875 CB SER L 141 347.800 312.469 258.047 1.00124.39 C ATOM 41876 OG SER L 141 348.391 313.694 258.461 1.00124.59 O ATOM 41877 N PHE L 142 345.493 314.383 257.324 1.00107.21 N ATOM 41878 CA PHE L 142 344.184 314.954 257.656 1.00 99.09 C ATOM 41879 C PHE L 142 343.765 315.964 256.593 1.00 94.73 C ATOM 41880 O PHE L 142 344.612 316.585 255.948 1.00 92.13 O ATOM 41881 CB PHE L 142 344.212 315.598 259.057 1.00 95.68 C ATOM 41882 CG PHE L 142 344.079 317.094 259.049 1.00 92.98 C ATOM 41883 CD1 PHE L 142 345.192 317.898 258.881 1.00 93.95 C ATOM 41884 CD2 PHE L 142 342.836 317.697 259.202 1.00 93.03 C ATOM 41885 CE1 PHE L 142 345.076 319.280 258.863 1.00 94.14 C ATOM 41886 CE2 PHE L 142 342.711 319.075 259.178 1.00 92.77 C ATOM 41887 CZ PHE L 142 343.834 319.870 259.009 1.00 92.90 C ATOM 41888 N HIS L 143 342.455 316.132 256.441 1.00 97.02 N ATOM 41889 CA HIS L 143 341.885 317.071 255.482 1.00102.86 C ATOM 41890 C HIS L 143 341.237 318.249 256.187 1.00104.68 C ATOM 41891 O HIS L 143 341.656 319.391 255.994 1.00109.67 O ATOM 41892 CB HIS L 143 340.882 316.349 254.597 1.00107.27 C ATOM 41893 CG HIS L 143 341.479 315.195 253.864 1.00114.98 C ATOM 41894 ND1 HIS L 143 341.960 315.303 252.577 1.00121.22 N ATOM 41895 CD2 HIS L 143 341.709 313.919 254.249 1.00116.63 C ATOM 41896 CE1 HIS L 143 342.444 314.135 252.194 1.00125.37 C ATOM 41897 NE2 HIS L 143 342.308 313.280 253.191 1.00123.46 N ATOM 41898 N GLN L 144 340.232 317.968 257.011 1.00102.51 N ATOM 41899 CA GLN L 144 339.503 319.006 257.740 1.00102.14 C ATOM 41900 C GLN L 144 339.005 318.462 259.070 1.00 98.63 C ATOM 41901 O GLN L 144 338.713 317.270 259.190 1.00 99.59 O ATOM 41902 CB GLN L 144 338.342 319.541 256.899 1.00105.77 C ATOM 41903 CG GLN L 144 337.423 318.467 256.332 1.00110.01 C ATOM 41904 CD GLN L 144 336.457 318.994 255.283 1.00114.88 C ATOM 41905 OE1 GLN L 144 335.969 318.235 254.444 1.00115.67 O ATOM 41906 NE2 GLN L 144 336.175 320.294 255.322 1.00116.87 N ATOM 41907 N CYS L 145 338.912 319.344 260.063 1.00 94.97 N ATOM 41908 CA CYS L 145 338.541 318.949 261.422 1.00 92.47 C ATOM 41909 C CYS L 145 337.032 318.807 261.564 1.00 88.78 C ATOM 41910 O CYS L 145 336.270 319.314 260.742 1.00 89.04 O ATOM 41911 CB CYS L 145 339.074 319.959 262.435 1.00 93.38 C ATOM 41912 SG CYS L 145 338.049 321.426 262.672 1.00 97.07 S ATOM 41913 N VAL L 146 336.612 318.122 262.618 1.00 89.59 N ATOM 41914 CA VAL L 146 335.190 317.849 262.835 1.00 97.99 C ATOM 41915 C VAL L 146 334.398 319.000 263.462 1.00 96.68 C ATOM 41916 O VAL L 146 333.166 318.953 263.489 1.00 97.13 O ATOM 41917 CB VAL L 146 334.960 316.565 263.666 1.00109.04 C ATOM 41918 CG1 VAL L 146 335.631 315.371 262.988 1.00111.68 C ATOM 41919 CG2 VAL L 146 335.413 316.732 265.119 1.00111.82 C ATOM 41920 N HIS L 147 335.088 320.021 263.962 1.00 95.17 N ATOM 41921 CA HIS L 147 334.418 321.215 264.480 1.00 96.80 C ATOM 41922 C HIS L 147 333.901 322.099 263.346 1.00 93.23 C ATOM 41923 O HIS L 147 332.735 322.503 263.326 1.00 90.92 O ATOM 41924 CB HIS L 147 335.378 322.028 265.338 1.00101.07 C ATOM 41925 CG HIS L 147 335.863 321.300 266.546 1.00105.50 C ATOM 41926 ND1 HIS L 147 335.020 320.908 267.562 1.00109.67 N ATOM 41927 CD2 HIS L 147 337.103 320.898 266.905 1.00112.15 C ATOM 41928 CE1 HIS L 147 335.721 320.292 268.496 1.00118.95 C ATOM 41929 NE2 HIS L 147 336.988 320.272 268.122 1.00120.41 N ATOM 41930 N CYS L 148 334.801 322.398 262.418 1.00 90.56 N ATOM 41931 CA CYS L 148 334.536 323.276 261.291 1.00 88.35 C ATOM 41932 C CYS L 148 335.420 322.848 260.130 1.00 93.31 C ATOM 41933 O CYS L 148 336.536 322.377 260.342 1.00 95.93 O ATOM 41934 CB CYS L 148 334.872 324.701 261.685 1.00 84.75 C ATOM 41935 SG CYS L 148 336.541 324.858 262.342 1.00 79.52 S ATOM 41936 N GLY L 149 334.935 323.001 258.906 1.00 95.38 N ATOM 41937 CA GLY L 149 335.735 322.645 257.740 1.00 98.14 C ATOM 41938 C GLY L 149 336.860 323.652 257.622 1.00101.01 C ATOM 41939 O GLY L 149 336.603 324.802 257.259 1.00104.12 O ATOM 41940 N CYS L 150 338.090 323.242 257.957 1.00 99.57 N ATOM 41941 CA CYS L 150 339.243 324.167 257.968 1.00 99.81 C ATOM 41942 C CYS L 150 340.562 323.546 257.510 1.00 98.81 C ATOM 41943 O CYS L 150 341.485 323.322 258.299 1.00 93.05 O ATOM 41944 CB CYS L 150 339.390 324.814 259.342 1.00 97.02 C ATOM 41945 SG CYS L 150 339.376 323.663 260.725 1.00 94.12 S TER HETATM63121 MG MG E1001 295.718 292.507 293.803 1.00 58.72 MG TER HETATM63122 MG MG V 201 294.595 288.583 291.518 1.00 85.44 MG TER HETATM63123 ZN ZN D1001 283.981 265.709 279.324 1.00109.36 ZN TER HETATM63156 ZN ZN L1000 337.686 325.976 263.586 1.00 31.11 ZN HETATM63157 ZN ZN L1001 340.645 325.701 261.809 1.00 38.33 ZN HETATM63158 ZN ZN L1002 340.121 322.858 263.346 1.00 15.24 ZN TER HETATM63159 ZN ZN M1000 332.230 304.393 250.913 1.00 43.73 ZN TER HETATM63160 ZN ZN N 401 334.845 288.168 279.963 1.00 74.70 ZN HETATM63161 ZN ZN N 402 347.697 291.810 270.128 1.00213.52 ZN TER END """ def main(): for i, pdb_str in enumerate([pdb_str_1, pdb_str_2]): print (i) fn = 'tst_mcl_%d.pdb'%i with open(fn, 'w') as f: f.write(pdb_str) cmd = 'phenix.pdb_interpretation %s write_geo=true'%fn print (cmd) rc = easy_run.go(cmd) assert os.path.exists('%s.geo'%fn) assert not rc.return_code if __name__ == '__main__': main() print('OK')