from __future__ import absolute_import, division, print_function from scitbx.array_family import flex from libtbx import easy_run import iotbx.pdb pdb_str = """ REMARK 3 TLS DETAILS. REMARK 3 NUMBER OF TLS GROUPS: 2 REMARK 3 ORIGIN: CENTER OF MASS REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 8.7338 28.3021 16.6793 REMARK 3 T TENSOR REMARK 3 T11: 0.0695 T22: 0.0842 REMARK 3 T33: 0.0992 T12: 0.0039 REMARK 3 T13: -0.0041 T23: 0.0014 REMARK 3 L TENSOR REMARK 3 L11: 2.1725 L22: 0.5881 REMARK 3 L33: 1.1562 L12: 0.4879 REMARK 3 L13: -0.0881 L23: 0.2404 REMARK 3 S TENSOR REMARK 3 S11: 0.0512 S12: 0.0543 S13: 0.0992 REMARK 3 S21: -0.0892 S22: -0.0659 S23: -0.0441 REMARK 3 S31: -0.0042 S32: -0.0302 S33: 0.0147 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): 18.7338 48.3021 46.6793 REMARK 3 T TENSOR REMARK 3 T11: 0.0695 T22: 0.0842 REMARK 3 T33: 0.0992 T12: 0.0039 REMARK 3 T13: -0.0041 T23: 0.0014 REMARK 3 L TENSOR REMARK 3 L11: 2.1725 L22: 0.5881 REMARK 3 L33: 1.1562 L12: 0.4879 REMARK 3 L13: -0.0881 L23: 0.2404 REMARK 3 S TENSOR REMARK 3 S11: 0.0512 S12: 0.0543 S13: 0.0992 REMARK 3 S21: -0.0892 S22: -0.0659 S23: -0.0441 REMARK 3 S31: -0.0042 S32: -0.0302 S33: 0.0147 REMARK 3 CRYST1 35.050 40.500 42.370 90.00 90.00 90.00 P 21 21 21 SCALE1 0.028531 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024691 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023602 0.00000 ATOM 1 CA THR A 6 6.096 14.546 15.382 1.00 0.00 C ATOM 2 CA THR A 7 4.643 17.379 17.472 1.00 0.00 C ATOM 3 CA TYR A 8 7.031 20.308 17.626 1.00 0.00 C ATOM 4 CA LYS A 9 6.715 23.191 20.108 1.00 0.00 C ATOM 5 CA LEU A 10 7.484 26.896 19.736 1.00 0.00 C ATOM 6 CA VAL A 11 8.313 28.973 22.814 1.00 0.00 C ATOM 7 CA ILE A 12 7.745 32.666 21.951 1.00 0.00 C ATOM 8 CA ASN A 13 9.367 35.454 23.951 1.00 0.00 C ATOM 9 CA GLY A 14 8.223 38.436 21.869 1.00 0.00 C ATOM 10 CA LYS A 15 7.732 42.071 22.635 1.00 0.00 C ATOM 11 CA THR A 16 3.910 41.794 22.427 1.00 0.00 C ATOM 12 CA LEU A 17 3.328 38.080 21.651 1.00 0.00 C ATOM 13 CA LYS A 18 4.268 35.598 24.351 1.00 0.00 C ATOM 14 CA GLY A 19 3.567 31.957 25.117 1.00 0.00 C ATOM 15 CA GLU A 20 3.694 28.633 23.293 1.00 0.00 C ATOM 16 CA THR A 21 2.207 27.042 20.183 1.00 0.00 C ATOM 17 CA THR A 22 2.609 23.707 18.385 1.00 0.00 C ATOM 18 CA THR A 23 2.682 22.183 14.916 1.00 0.00 C ATOM 19 CA LYS A 24 2.823 18.625 13.556 1.00 0.00 C ATOM 20 CA ALA A 25 5.312 17.719 10.843 1.00 0.00 C ATOM 21 CA VAL A 26 7.260 14.854 9.299 1.00 0.00 C ATOM 22 CA ASP A 27 10.612 16.526 10.001 1.00 0.00 C ATOM 23 CA ALA A 28 12.142 19.541 11.794 1.00 0.00 C ATOM 24 CA GLU A 29 12.712 21.542 8.632 1.00 0.00 C ATOM 25 CA THR A 30 9.005 21.472 7.817 1.00 0.00 C ATOM 26 CA ALA A 31 8.121 22.548 11.353 1.00 0.00 C ATOM 27 CA GLU A 32 10.719 25.317 11.217 1.00 0.00 C ATOM 28 CA LYS A 33 9.139 26.736 8.061 1.00 0.00 C ATOM 29 CA ALA A 34 5.654 26.682 9.658 1.00 0.00 C ATOM 30 CA PHE A 35 6.940 28.471 12.774 1.00 0.00 C ATOM 31 CA LYS A 36 8.915 31.065 10.827 1.00 0.00 C ATOM 32 CA GLN A 37 5.784 31.817 8.802 1.00 0.00 C ATOM 33 CA TYR A 38 3.757 32.125 12.022 1.00 0.00 C ATOM 34 CA ALA A 39 6.322 34.523 13.495 1.00 0.00 C ATOM 35 CA ASN A 40 6.375 36.639 10.306 1.00 0.00 C ATOM 36 CA ASP A 41 2.536 36.702 10.145 1.00 0.00 C ATOM 37 CA ASN A 42 2.519 38.093 13.718 1.00 0.00 C ATOM 38 CA GLY A 43 5.296 40.638 13.264 1.00 0.00 C ATOM 39 CA VAL A 44 7.921 38.823 15.338 1.00 0.00 C ATOM 40 CA ASP A 45 11.526 39.426 14.290 1.00 0.00 C ATOM 41 CA GLY A 46 13.865 37.643 16.623 1.00 0.00 C ATOM 42 CA VAL A 47 16.614 35.096 17.081 1.00 0.00 C ATOM 43 CA TRP A 48 16.026 31.364 17.129 1.00 0.00 C ATOM 44 CA THR A 49 17.146 28.133 18.719 1.00 0.00 C ATOM 45 CA TYR A 50 16.165 24.543 17.999 1.00 0.00 C ATOM 46 CA ASP A 51 16.716 21.634 20.410 1.00 0.00 C ATOM 47 CA ASP A 52 16.413 18.270 18.691 1.00 0.00 C ATOM 48 CA ALA A 53 16.219 16.432 22.049 1.00 0.00 C ATOM 49 CA THR A 54 12.971 18.177 23.062 1.00 0.00 C ATOM 50 CA LYS A 55 11.609 19.022 19.577 1.00 0.00 C ATOM 51 CA THR A 56 11.365 22.651 20.684 1.00 0.00 C ATOM 52 CA PHE A 57 12.052 25.886 18.846 1.00 0.00 C ATOM 53 CA THR A 58 12.461 29.177 20.755 1.00 0.00 C ATOM 54 CA VAL A 59 12.275 32.720 19.421 1.00 0.00 C ATOM 55 CA THR A 60 13.202 35.851 21.380 1.00 0.00 C ATOM 56 CA GLU A 61 12.989 39.521 20.535 1.00 0.00 C TER ATOM 1 CA THR B 6 18.094 36.747 38.683 1.00 0.00 C ATOM 2 CA THR B 7 17.002 37.634 42.222 1.00 0.00 C ATOM 3 CA TYR B 8 18.786 40.734 43.451 1.00 0.00 C ATOM 4 CA LYS B 9 18.872 41.840 47.104 1.00 0.00 C ATOM 5 CA LEU B 10 18.852 45.310 48.658 1.00 0.00 C ATOM 6 CA VAL B 11 20.333 45.838 52.123 1.00 0.00 C ATOM 7 CA ILE B 12 18.910 49.102 53.545 1.00 0.00 C ATOM 8 CA ASN B 13 20.640 50.975 56.357 1.00 0.00 C ATOM 9 CA GLY B 14 18.382 54.043 56.519 1.00 0.00 C ATOM 10 CA LYS B 15 17.597 56.519 59.219 1.00 0.00 C ATOM 11 CA THR B 16 14.034 55.170 59.682 1.00 0.00 C ATOM 12 CA LEU B 17 13.836 52.292 57.150 1.00 0.00 C ATOM 13 CA LYS B 18 16.034 49.280 57.805 1.00 0.00 C ATOM 14 CA GLY B 19 16.242 45.699 56.592 1.00 0.00 C ATOM 15 CA GLU B 20 16.278 43.860 53.274 1.00 0.00 C ATOM 16 CA THR B 21 14.098 43.538 50.182 1.00 0.00 C ATOM 17 CA THR B 22 14.399 41.766 46.823 1.00 0.00 C ATOM 18 CA THR B 23 13.529 42.164 43.156 1.00 0.00 C ATOM 19 CA LYS B 24 13.775 39.919 40.086 1.00 0.00 C ATOM 20 CA ALA B 25 15.298 41.242 36.875 1.00 0.00 C ATOM 21 CA VAL B 26 17.040 40.230 33.662 1.00 0.00 C ATOM 22 CA ASP B 27 20.109 42.345 34.455 1.00 0.00 C ATOM 23 CA ALA B 28 21.647 44.472 37.241 1.00 0.00 C ATOM 24 CA GLU B 29 20.766 47.787 35.639 1.00 0.00 C ATOM 25 CA THR B 30 17.068 46.930 35.697 1.00 0.00 C ATOM 26 CA ALA B 31 17.284 45.873 39.341 1.00 0.00 C ATOM 27 CA GLU B 32 19.190 49.044 40.204 1.00 0.00 C ATOM 28 CA LYS B 33 16.417 51.191 38.731 1.00 0.00 C ATOM 29 CA ALA B 34 13.747 49.286 40.715 1.00 0.00 C ATOM 30 CA PHE B 35 15.711 49.704 43.961 1.00 0.00 C ATOM 31 CA LYS B 36 16.449 53.384 43.382 1.00 0.00 C ATOM 32 CA GLN B 37 12.736 53.956 42.785 1.00 0.00 C ATOM 33 CA TYR B 38 11.911 52.051 45.988 1.00 0.00 C ATOM 34 CA ALA B 39 14.398 54.150 47.965 1.00 0.00 C ATOM 35 CA ASN B 40 13.011 57.407 46.510 1.00 0.00 C ATOM 36 CA ASP B 41 9.393 56.311 47.200 1.00 0.00 C ATOM 37 CA ASN B 42 10.372 55.772 50.867 1.00 0.00 C ATOM 38 CA GLY B 43 12.371 58.965 51.313 1.00 0.00 C ATOM 39 CA VAL B 44 15.806 57.334 51.476 1.00 0.00 C ATOM 40 CA ASP B 45 18.685 59.472 50.212 1.00 0.00 C ATOM 41 CA GLY B 46 21.939 57.654 50.662 1.00 0.00 C ATOM 42 CA VAL B 47 25.055 56.218 49.087 1.00 0.00 C ATOM 43 CA TRP B 48 25.136 52.936 47.216 1.00 0.00 C ATOM 44 CA THR B 49 27.244 49.886 46.524 1.00 0.00 C ATOM 45 CA TYR B 50 26.676 46.957 44.186 1.00 0.00 C ATOM 46 CA ASP B 51 28.485 43.605 44.454 1.00 0.00 C ATOM 47 CA ASP B 52 28.165 41.547 41.287 1.00 0.00 C ATOM 48 CA ALA B 53 29.434 38.394 43.060 1.00 0.00 C ATOM 49 CA THR B 54 26.490 38.319 45.499 1.00 0.00 C ATOM 50 CA LYS B 55 23.900 40.218 43.402 1.00 0.00 C ATOM 51 CA THR B 56 23.461 42.607 46.326 1.00 0.00 C ATOM 52 CA PHE B 57 22.940 46.353 46.449 1.00 0.00 C ATOM 53 CA THR B 58 23.434 48.296 49.708 1.00 0.00 C ATOM 54 CA VAL B 59 22.228 51.780 50.588 1.00 0.00 C ATOM 55 CA THR B 60 23.245 53.732 53.695 1.00 0.00 C ATOM 56 CA GLU B 61 22.160 57.082 55.047 1.00 0.00 C TER END """ def run(file_name = "tst_tls_as_xyz.pdb"): of = open(file_name,"w") print(pdb_str, file=of) of.close() uc = iotbx.pdb.input(file_name=file_name).crystal_symmetry().unit_cell() #for n in range(10,100,10)+range(100,1000,100)+range(1000,10001,1000)+[15000,20000]: for n in [1000,]: easy_run.call("phenix.tls_as_xyz %s n_models=%s > tst_tls_as_xyz.log"%( file_name,str(n))) for i in [0,1]: u1 = iotbx.pdb.input(file_name= "tst_tls_as_xyz_u_from_ensemble_%s.pdb"%str(i) ).xray_structure_simple().scatterers().extract_u_cart(uc) u2 = iotbx.pdb.input(file_name= "tst_tls_as_xyz_u_from_tls_%s.pdb"%str(i) ).xray_structure_simple().scatterers().extract_u_cart(uc) u1, u2 = u1.as_double(), u2.as_double() cc = flex.linear_correlation(x=u1, y=u2).coefficient() r = flex.sum(flex.abs(flex.abs(u1)-flex.abs(u2)))/\ flex.sum(flex.abs(flex.abs(u1)+flex.abs(u2)))*2 print("%5d %6.4f %6.4f"%(n, cc, r)) assert cc>0.99, cc assert r<0.06, r if (__name__ == "__main__"): run()