[Bioperl-l] convert xyz coordinates to distance

ni_psis ni_psis at hotmail.com
Wed Mar 22 11:42:47 EST 2006


Hi,

I am new to perl, but I would like write a perl script that can convert xyz
cordinates from a pdb file to distances using the formula:  distance =
SQRT[(X1-X2)^2  +  (Y1-Y2)^2 + (Z1-Z2)^2]

eg: The atoms of HELIX 1 with all the atoms of HELIX 2 and 3

the atom[0] of  1 with the atom[0] of 2
the atom[0] of  1 with the atom[1] of 2
the atom[0] of  1 with the atom[2] of 2
the atom[0] of  1 with the atom[3] of 2
.
.
.
.
.
.
the atom[1] of  1 with the atom[0] of 2
the atom[1] of  1 with the atom[1] of 2
the atom[1] of  1 with the atom[2] of 2
the atom[1] of  1 with the atom[3] of 2


I want a good idea of how to do it 
Please HELP ME 
thanks


The pdb file format look like this

HEADER    PHEROMONE                               20-DEC-95   2ERL              
HELIX 1	H1		ASP	1	GLN	9
HELIX 2	H2		GLU	12	LEU	18
HELIX 3	H3		GLU	23	ASN	35
ATOM      1  N   ASP     1      -1.115   8.537   7.075 
ATOM      2  CA  ASP     1      -1.925   7.470   6.547 
ATOM      3  C   ASP     1      -2.009   6.333   7.522 
ATOM      4  O   ASP     1      -1.467   6.394   8.624 
ATOM      5  CB  ASP     1      -1.526   6.993   5.163 
ATOM      6  CG  ASP     1      -0.189   6.261   5.135 
ATOM      7  OD1 ASP     1       0.337   6.017   6.212 
ATOM      8  OD2 ASP     1       0.306   6.000   3.954 
ATOM      9 1H   ASP     1      -1.462   8.819   7.844 
ATOM     10 2H   ASP     1      -0.287   8.240   7.214 
ATOM     11 3H   ASP     1      -1.095   9.210   6.493 
ATOM     12  HA  ASP     1      -2.833   7.829   6.464 
ATOM     13 1HB  ASP     1      -2.216   6.400   4.825 
ATOM     14 2HB  ASP     1      -1.478   7.758   4.569 
ATOM     15  N   ALA     2      -2.745   5.280   7.165 
ATOM     16  CA  ALA     2      -2.945   4.152   7.987 
ATOM     17  C   ALA     2      -1.606   3.448   8.305 
ATOM     18  O   ALA     2      -1.440   3.010   9.454 
ATOM     19  CB  ALA     2      -3.966   3.256   7.436 
ATOM     20  H   ALA     2      -3.119   5.289   6.390 
ATOM     21  HA  ALA     2      -3.296   4.485   8.839 
ATOM     22 1HB  ALA     2      -4.765   3.756   7.251 
ATOM     23 2HB  ALA     2      -3.640   2.861   6.624 
ATOM     24 3HB  ALA     2      -4.162   2.564   8.072 
ATOM     25  N   CYS     3      -0.777   3.267   7.329 
ATOM     26  CA  CYS     3       0.570   2.624   7.511 
ATOM     27  C   CYS     3       1.328   3.308   8.626 
ATOM     28  O   CYS     3       1.802   2.679   9.562 
ATOM     29  CB  CYS     3       1.351   2.667   6.209 
ATOM     30  SG  CYS     3       2.981   1.901   6.318 
ATOM     31  H   CYS     3      -1.006   3.526   6.542 
ATOM     32  HA  CYS     3       0.434   1.686   7.759 
ATOM     33 1HB  CYS     3       0.838   2.216   5.521 
ATOM     34 2HB  CYS     3       1.457   3.593   5.938 
ATOM     35  N   GLU     4       1.508   4.617   8.489 
ATOM     36  CA  GLU     4       2.255   5.404   9.498 
ATOM     37  C   GLU     4       1.610   5.225  10.885 
ATOM     38  O   GLU     4       2.334   5.109  11.842 
ATOM     39  CB  GLU     4       2.244   6.852   9.036 
ATOM     40  CG  GLU     4       2.997   7.867   9.820 
ATOM     41  CD  GLU     4       2.736   9.285   9.326 
ATOM     42  OE1 GLU     4       1.708   9.575   8.697 
ATOM     43  OE2 GLU     4       3.543  10.133   9.731 
ATOM     44  H   GLU     4       1.184   5.016   7.799 
ATOM     45  HA  GLU     4       3.181   5.086   9.532 
ATOM     46 1HB  GLU     4       2.585   6.872   8.128 
ATOM     47 2HB  GLU     4       1.319   7.140   8.998 
ATOM     48 1HG  GLU     4       2.741   7.803  10.754 
ATOM     49 2HG  GLU     4       3.947   7.678   9.758 
ATOM     50  N   GLN     5       0.296   5.263  10.912 
ATOM     51  CA  GLN     5      -0.378   5.203  12.200 
ATOM     52  C   GLN     5      -0.239   3.845  12.878 
ATOM     53  O   GLN     5      -0.077   3.785  14.080 
ATOM     54  CB  GLN     5      -1.796   5.653  12.089 
ATOM     55  CG  GLN     5      -2.013   7.148  11.907 
ATOM     56  CD  GLN     5      -1.903   7.874  13.238 
ATOM     57  OE1 GLN     5      -0.839   8.347  13.647 
ATOM     58  NE2 GLN     5      -3.009   7.883  13.980 
ATOM     59  H   GLN     5      -0.156   5.321  10.182 
ATOM     60  HA  GLN     5       0.075   5.850  12.780 
ATOM     61 1HB  GLN     5      -2.203   5.194  11.338 
ATOM     62 2HB  GLN     5      -2.267   5.373  12.890 
ATOM     63 1HG  GLN     5      -1.351   7.498  11.292 
ATOM     64 2HG  GLN     5      -2.891   7.303  11.525 
ATOM     65 1HE2 GLN     5      -2.995   8.225  14.769 
ATOM     66 2HE2 GLN     5      -3.737   7.546  13.670 
ATOM     67  N   ALA     6      -0.230   2.753  12.099 
ATOM     68  CA  ALA     6       0.008   1.434  12.610 
ATOM     69  C   ALA     6       1.381   1.256  13.230 
ATOM     70  O   ALA     6       1.566   0.690  14.248 
ATOM     71  CB  ALA     6      -0.241   0.379  11.529 
ATOM     72  H   ALA     6      -0.372   2.847  11.256 
ATOM     73  HA  ALA     6      -0.650   1.279  13.320 
ATOM     74 1HB  ALA     6      -1.110   0.513  11.145 
ATOM     75 2HB  ALA     6       0.428   0.458  10.845 
ATOM     76 3HB  ALA     6      -0.196  -0.497  11.921 
ATOM     77  N   ALA     7       2.408   1.829  12.524 
ATOM     78  CA  ALA     7       3.765   1.850  13.007 
ATOM     79  C   ALA     7       3.841   2.536  14.354 
ATOM     80  O   ALA     7       4.398   2.044  15.330 
ATOM     81  CB  ALA     7       4.697   2.539  12.023 
ATOM     82  H   ALA     7       2.235   2.189  11.763 
ATOM     83  HA  ALA     7       4.066   0.924  13.117 
ATOM     84 1HB  ALA     7       4.652   2.095  11.173 
ATOM     85 2HB  ALA     7       4.432   3.456  11.919 
ATOM     86 3HB  ALA     7       5.597   2.503  12.355 
ATOM     87  N   ILE     8       3.226   3.717  14.440 
ATOM     88  CA  ILE     8       3.309   4.495  15.692 
ATOM     89  C   ILE     8       2.560   3.810  16.813 
ATOM     90  O   ILE     8       2.928   3.990  17.984 
ATOM     91  CB  ILE     8       2.843   5.950  15.428 
ATOM     92  CG1 ILE     8       3.857   6.706  14.481 
ATOM     93  CG2 ILE     8       2.577   6.751  16.654 
ATOM     94  CD1 ILE     8       3.229   8.004  13.927 
ATOM     95  H   ILE     8       2.783   4.024  13.769 
ATOM     96  HA  ILE     8       4.254   4.532  15.951 
ATOM     97  HB  ILE     8       1.994   5.890  14.941 
ATOM     98 1HG1 ILE     8       4.662   6.922  14.976 
ATOM     99 2HG1 ILE     8       4.104   6.126  13.743 
ATOM    100 1HG2 ILE     8       3.375   6.798  17.185 
ATOM    101 2HG2 ILE     8       2.307   7.638  16.404 
ATOM    102 3HG2 ILE     8       1.878   6.335  17.163 
ATOM    103 1HD1 ILE     8       2.439   7.789  13.425 
ATOM    104 2HD1 ILE     8       2.997   8.584  14.656 
ATOM    105 3HD1 ILE     8       3.861   8.446  13.355 
ATOM    106  N   GLN     9       1.568   3.015  16.550 
ATOM    107  CA  GLN     9       0.911   2.196  17.602 
ATOM    108  C   GLN     9       1.655   0.958  17.980 
ATOM    109  O   GLN     9       1.263   0.292  18.947 
ATOM    110  CB  GLN     9      -0.515   1.736  17.086 
ATOM    111  CG  GLN     9      -1.483   2.809  16.995 
ATOM    112  CD  GLN     9      -1.712   3.600  18.204 
ATOM    113  OE1 GLN     9      -1.704   3.103  19.341 
ATOM    114  NE2 GLN     9      -1.737   4.933  18.099 
ATOM    115  H   GLN     9       1.282   2.960  15.740 
ATOM    116  HA  GLN     9       0.793   2.749  18.402 
ATOM    117 1HB  GLN     9      -0.414   1.332  16.210 
ATOM    118 2HB  GLN     9      -0.859   1.056  17.685 
ATOM    119 1HG  GLN     9      -1.198   3.412  16.290 
ATOM    120 2HG  GLN     9      -2.331   2.426  16.721 
ATOM    121 1HE2 GLN     9      -1.747   5.420  18.808 
ATOM    122 2HE2 GLN     9      -1.744   5.303  17.323 
ATOM    149  N   GLU    12       3.089  -4.518  14.660 
ATOM    150  CA  GLU    12       3.774  -4.990  13.456 
ATOM    151  C   GLU    12       2.912  -5.712  12.482 
ATOM    152  O   GLU    12       3.083  -5.643  11.264 
ATOM    153  CB  GLU    12       5.001  -5.826  13.875 
ATOM    154  CG  GLU    12       5.800  -6.264  12.646 
ATOM    155  CD  GLU    12       7.105  -7.002  13.014 
ATOM    156  OE1 GLU    12       7.603  -7.032  14.115 
ATOM    157  OE2 GLU    12       7.612  -7.651  12.023 
ATOM    158  H   GLU    12       3.340  -4.793  15.435 
ATOM    159  HA  GLU    12       4.117  -4.196  12.996 
ATOM    160 1HB  GLU    12       5.568  -5.299  14.460 
ATOM    161 2HB  GLU    12       4.707  -6.609  14.366 
ATOM    162 1HG  GLU    12       5.249  -6.848  12.102 
ATOM    163 2HG  GLU    12       6.018  -5.482  12.115 
ATOM    164  N   SER    13       1.920  -6.484  13.028 
ATOM    165  CA  SER    13       1.076  -7.239  12.160 
ATOM    166  C   SER    13       0.324  -6.363  11.167 
ATOM    167  O   SER    13       0.007  -6.792  10.066 
ATOM    168  CB  SER    13       0.128  -8.087  12.980 
ATOM    169  OG  SER    13      -0.739  -7.320  13.698 
ATOM    170  H   SER    13       1.808  -6.514  13.880 
ATOM    171  HA  SER    13       1.647  -7.846  11.645 
ATOM    172 1HB  SER    13      -0.374  -8.670  12.388 
ATOM    173 2HB  SER    13       0.640  -8.646  13.585 
ATOM    174  HG  SER    13      -1.237  -7.805  14.133 
ATOM    175  N   ALA    14       0.024  -5.155  11.540 
ATOM    176  CA  ALA    14      -0.691  -4.208  10.662 
ATOM    177  C   ALA    14       0.172  -3.600   9.632 
ATOM    178  O   ALA    14      -0.368  -3.032   8.645 
ATOM    179  CB  ALA    14      -1.353  -3.146  11.567 
ATOM    180  H   ALA    14       0.249  -4.898  12.329 
ATOM    181  HA  ALA    14      -1.404  -4.701  10.205 
ATOM    182 1HB  ALA    14      -1.901  -3.582  12.223 
ATOM    183 2HB  ALA    14      -0.672  -2.633  12.008 
ATOM    184 3HB  ALA    14      -1.897  -2.564  11.031 
ATOM    185  N   CYS    15       1.477  -3.696   9.725 
ATOM    186  CA  CYS    15       2.308  -3.191   8.605 
ATOM    187  C   CYS    15       1.975  -3.899   7.294 
ATOM    188  O   CYS    15       2.030  -3.304   6.232 
ATOM    189  CB  CYS    15       3.808  -3.398   8.859 
ATOM    190  SG  CYS    15       4.517  -2.546  10.292 
ATOM    191  H   CYS    15       1.843  -4.044  10.421 
ATOM    192  HA  CYS    15       2.138  -2.232   8.496 
ATOM    193 1HB  CYS    15       3.968  -4.349   8.965 
ATOM    194 2HB  CYS    15       4.291  -3.110   8.069 
ATOM    195  N   GLU    16       1.667  -5.187   7.314 
ATOM    196  CA  GLU    16       1.430  -5.931   6.110 
ATOM    197  C   GLU    16       0.156  -5.451   5.422 
ATOM    198  O   GLU    16       0.100  -5.353   4.192 
ATOM    199  CB  GLU    16       1.428  -7.442   6.289 
ATOM    200  CG  GLU    16       1.044  -8.157   4.985 
ATOM    201  CD  GLU    16       1.407  -9.599   4.948 
ATOM    202  OE1 GLU    16       1.736 -10.214   5.969 
ATOM    203  OE2 GLU    16       1.368 -10.134   3.797 
ATOM    204  H   GLU    16       1.607  -5.590   8.071 
ATOM    205  HA  GLU    16       2.171  -5.723   5.503 
ATOM    206 1HB  GLU    16       2.310  -7.734   6.568 
ATOM    207 2HB  GLU    16       0.798  -7.683   6.986 
ATOM    208 1HG  GLU    16       0.086  -8.075   4.856 
ATOM    209 2HG  GLU    16       1.480  -7.708   4.244 
ATOM    210  N   SER    17      -0.869  -5.247   6.225 
ATOM    211  CA  SER    17      -2.172  -4.980   5.581 
ATOM    212  C   SER    17      -2.344  -3.505   5.280 
ATOM    213  O   SER    17      -3.155  -3.183   4.446 
ATOM    214  CB  SER    17      -3.275  -5.410   6.507 
ATOM    215  OG  SER    17      -3.218  -4.787   7.747 
ATOM    216  H   SER    17      -0.783  -5.269   7.080 
ATOM    217  HA  SER    17      -2.232  -5.490   4.747 
ATOM    218 1HB  SER    17      -4.129  -5.211   6.094 
ATOM    219 2HB  SER    17      -3.224  -6.370   6.634 
ATOM    220  HG  SER    17      -3.829  -5.063   8.220 
ATOM    221  N   LEU    18      -1.632  -2.581   5.945 
ATOM    222  CA  LEU    18      -1.851  -1.181   5.784 
ATOM    223  C   LEU    18      -0.765  -0.443   5.006 
ATOM    224  O   LEU    18      -0.917   0.722   4.696 
ATOM    225  CB  LEU    18      -2.125  -0.476   7.077 
ATOM    226  CG  LEU    18      -3.325  -1.012   7.842 
ATOM    227  CD1 LEU    18      -3.376  -0.270   9.218 
ATOM    228  CD2 LEU    18      -4.628  -0.783   7.166 
ATOM    229  H   LEU    18      -1.020  -2.844   6.490 
ATOM    230  HA  LEU    18      -2.670  -1.096   5.252 
ATOM    231 1HB  LEU    18      -1.339  -0.547   7.642 
ATOM    232 2HB  LEU    18      -2.269   0.465   6.892 
ATOM    233  HG  LEU    18      -3.206  -1.972   7.997 
ATOM    234 1HD1 LEU    18      -2.544  -0.397   9.681 
ATOM    235 2HD1 LEU    18      -3.520   0.668   9.070 
ATOM    236 3HD1 LEU    18      -4.094  -0.625   9.746 
ATOM    237 1HD2 LEU    18      -4.623  -1.212   6.307 
ATOM    238 2HD2 LEU    18      -5.335  -1.148   7.702 
ATOM    239 3HD2 LEU    18      -4.767   0.160   7.051 
ATOM    295  N   GLU    23       9.333  -0.276   0.185 
ATOM    296  CA  GLU    23       9.826   0.653   1.171 
ATOM    297  C   GLU    23       8.840   0.959   2.297 
ATOM    298  O   GLU    23       9.259   1.093   3.424 
ATOM    299  CB  GLU    23      10.325   1.921   0.540 
ATOM    300  CG  GLU    23      10.916   2.847   1.683 
ATOM    301  CD  GLU    23      12.317   3.194   1.151 
ATOM    302  OE1 GLU    23      12.312   3.576  -0.032 
ATOM    303  OE2 GLU    23      13.279   2.843   1.795 
ATOM    304  H   GLU    23       9.278  -0.029  -0.637 
ATOM    305  HA  GLU    23      10.602   0.227   1.590 
ATOM    306 1HB  GLU    23      11.013   1.719  -0.113 
ATOM    307 2HB  GLU    23       9.597   2.376   0.087 
ATOM    308 1HG  GLU    23      10.378   3.645   1.801 
ATOM    309 2HG  GLU    23      10.969   2.371   2.526 
ATOM    310  N   ASP    24       7.545   1.080   2.021 
ATOM    311  CA  ASP    24       6.578   1.456   2.996 
ATOM    312  C   ASP    24       6.494   0.434   4.133 
ATOM    313  O   ASP    24       6.495   0.773   5.304 
ATOM    314  CB AASP    24       5.191   1.484   2.253 
ATOM    315  CB BASP    24       5.265   1.879   2.478 
ATOM    316  CG AASP    24       4.141   2.327   2.967 
ATOM    317  CG BASP    24       5.248   3.162   1.679 
ATOM    318  OD1AASP    24       4.571   3.306   3.637 
ATOM    319  OD1BASP    24       6.269   3.566   1.111 
ATOM    320  OD2AASP    24       2.942   2.035   2.732 
ATOM    321  OD2BASP    24       4.151   3.739   1.602 
ATOM    322  H   ASP    24       7.279   0.924   1.218 
ATOM    323  HA  ASP    24       6.788   2.344   3.354 
ATOM    324 1HB AASP    24       5.321   1.835   1.358 
ATOM    325 1HB BASP    24       4.915   1.168   1.920 
ATOM    326 2HB AASP    24       4.861   0.576   2.169 
ATOM    327 2HB BASP    24       4.660   1.981   3.230 
ATOM    328  N   ARG    25       6.468  -0.850   3.785 
ATOM    329  CA  ARG    25       6.481  -1.917   4.730 
ATOM    330  C   ARG    25       7.768  -1.982   5.503 
ATOM    331  O   ARG    25       7.746  -2.193   6.697 
ATOM    332  CB  ARG    25       6.233  -3.282   4.080 
ATOM    333  CG  ARG    25       4.939  -3.786   4.243 
ATOM    334  CD  ARG    25       4.593  -5.053   3.521 
ATOM    335  NE  ARG    25       3.283  -4.845   2.866 
ATOM    336  CZ  ARG    25       2.745  -5.680   2.027 
ATOM    337  NH1 ARG    25       3.329  -6.802   1.738 
ATOM    338  NH2 ARG    25       1.606  -5.294   1.451 
ATOM    339  H   ARG    25       6.442  -1.046   2.948 
ATOM    340  HA  ARG    25       5.757  -1.757   5.370 
ATOM    341 1HB  ARG    25       6.419  -3.209   3.131 
ATOM    342 2HB  ARG    25       6.862  -3.919   4.453 
ATOM    343 1HG  ARG    25       4.793  -3.933   5.191 
ATOM    344 2HG  ARG    25       4.314  -3.101   3.959 
ATOM    345 1HD  ARG    25       5.271  -5.258   2.858 
ATOM    346 2HD  ARG    25       4.541  -5.793   4.146 
ATOM    347  HE  ARG    25       2.850  -4.125   3.052 
ATOM    348 1HH1 ARG    25       4.082  -7.002   2.104 
ATOM    349 2HH1 ARG    25       2.964  -7.346   1.182 
ATOM    350 1HH2 ARG    25       1.266  -4.528   1.643 
ATOM    351 2HH2 ARG    25       1.212  -5.811   0.889 
ATOM    352  N   THR    26       8.905  -1.802   4.817 
ATOM    353  CA  THR    26      10.154  -1.810   5.523 
ATOM    354  C   THR    26      10.210  -0.678   6.527 
ATOM    355  O   THR    26      10.682  -0.883   7.638 
ATOM    356  CB  THR    26      11.365  -1.691   4.530 
ATOM    357  OG1 THR    26      11.250  -2.794   3.577 
ATOM    358  CG2 THR    26      12.671  -1.765   5.262 
ATOM    359  H   THR    26       8.887  -1.684   3.966 
ATOM    360  HA  THR    26      10.232  -2.658   6.007 
ATOM    361  HB  THR    26      11.309  -0.839   4.049 
ATOM    362  HG1 THR    26      10.524  -2.754   3.199 
ATOM    363 1HG2 THR    26      12.728  -2.600   5.732 
ATOM    364 2HG2 THR    26      13.394  -1.701   4.634 
ATOM    365 3HG2 THR    26      12.727  -1.040   5.889 
ATOM    366  N   GLY    27       9.745   0.504   6.136 
ATOM    367  CA  GLY    27       9.780   1.635   7.013 
ATOM    368  C   GLY    27       8.911   1.477   8.245 
ATOM    369  O   GLY    27       9.232   2.015   9.304 
ATOM    370  H   GLY    27       9.419   0.591   5.345 
ATOM    371 1HA  GLY    27      10.696   1.786   7.294 
ATOM    372 2HA  GLY    27       9.489   2.421   6.524 
ATOM    373  N   CYS    28       7.821   0.743   8.138 
ATOM    374  CA  CYS    28       6.903   0.489   9.277 
ATOM    375  C   CYS    28       7.656  -0.419  10.284 
ATOM    376  O   CYS    28       7.686  -0.110  11.456 
ATOM    377  CB  CYS    28       5.665  -0.223   8.696 
ATOM    378  SG  CYS    28       4.315  -0.568   9.820 
ATOM    379  H   CYS    28       7.634   0.396   7.374 
ATOM    380  HA  CYS    28       6.644   1.333   9.703 
ATOM    381 1HB  CYS    28       5.320   0.321   7.971 
ATOM    382 2HB  CYS    28       5.957  -1.064   8.311 
ATOM    383  N   TYR    29       8.295  -1.482   9.790 
ATOM    384  CA  TYR    29       9.088  -2.358  10.716 
ATOM    385  C   TYR    29      10.247  -1.595  11.290 
ATOM    386  O   TYR    29      10.548  -1.718  12.474 
ATOM    387  CB  TYR    29       9.614  -3.574   9.912 
ATOM    388  CG  TYR    29      10.520  -4.518  10.686 
ATOM    389  CD1 TYR    29      10.093  -5.166  11.837 
ATOM    390  CD2 TYR    29      11.796  -4.811  10.254 
ATOM    391  CE1 TYR    29      10.877  -6.030  12.516 
ATOM    392  CE2 TYR    29      12.587  -5.705  10.948 
ATOM    393  CZ  TYR    29      12.135  -6.301  12.099 
ATOM    394  OH  TYR    29      12.930  -7.218  12.733 
ATOM    395  H   TYR    29       8.253  -1.663   8.950 
ATOM    396  HA  TYR    29       8.510  -2.672  11.443 
ATOM    397 1HB  TYR    29       8.853  -4.078   9.584 
ATOM    398 2HB  TYR    29      10.101  -3.245   9.141 
ATOM    399  HD1 TYR    29       9.234  -4.998  12.152 
ATOM    400  HD2 TYR    29      12.127  -4.402   9.487 
ATOM    401  HE1 TYR    29      10.548  -6.443  13.281 
ATOM    402  HE2 TYR    29      13.438  -5.906  10.631 
ATOM    403  HH  TYR    29      12.530  -7.527  13.378 
ATOM    404  N   MET    30      10.949  -0.787  10.499 
ATOM    405  CA  MET    30      12.097  -0.042  11.035 
ATOM    406  C   MET    30      11.669   0.919  12.090 
ATOM    407  O   MET    30      12.377   1.090  13.089 
ATOM    408  CB AMET    30      12.832   0.699   9.921 
ATOM    409  CB BMET    30      12.811   0.650   9.888 
ATOM    410  CG AMET    30      13.669  -0.195   9.045 
ATOM    411  CG BMET    30      14.005   1.475  10.250 
ATOM    412  SD AMET    30      14.471   0.753   7.727 
ATOM    413  SD BMET    30      14.944   1.947   8.787 
ATOM    414  CE AMET    30      14.905   2.248   8.635 
ATOM    415  CE BMET    30      15.397   0.346   8.138 
ATOM    416  H   MET    30      10.730  -0.700   9.672 
ATOM    417  HA  MET    30      12.717  -0.684  11.439 
ATOM    418 1HB AMET    30      12.181   1.158   9.368 
ATOM    419 1HB BMET    30      13.093  -0.028   9.253 
ATOM    420 2HB AMET    30      13.406   1.372  10.319 
ATOM    421 2HB BMET    30      12.173   1.223   9.435 
ATOM    422 1HG AMET    30      14.346  -0.634   9.584 
ATOM    423 1HG BMET    30      13.715   2.273  10.718 
ATOM    424 2HG AMET    30      13.106  -0.881   8.652 
ATOM    425 2HG BMET    30      14.576   0.968  10.849 
ATOM    426 1HE AMET    30      14.110   2.647   8.993 
ATOM    427 1HE BMET    30      14.603  -0.156   7.942 
ATOM    428 2HE AMET    30      15.503   2.024   9.352 
ATOM    429 2HE BMET    30      15.910   0.460   7.334 
ATOM    430 3HE AMET    30      15.336   2.869   8.042 
ATOM    431 3HE BMET    30      15.923  -0.126   8.788 
ATOM    432  N   TYR    31      10.526   1.565  11.956 
ATOM    433  CA  TYR    31      10.065   2.484  13.000 
ATOM    434  C   TYR    31       9.814   1.710  14.299 
ATOM    435  O   TYR    31      10.250   2.118  15.373 
ATOM    436  CB  TYR    31       8.756   3.200  12.579 
ATOM    437  CG  TYR    31       8.267   3.992  13.773 
ATOM    438  CD1 TYR    31       8.851   5.234  14.116 
ATOM    439  CD2 TYR    31       7.329   3.440  14.678 
ATOM    440  CE1 TYR    31       8.499   5.910  15.275 
ATOM    441  CE2 TYR    31       6.981   4.150  15.769 
ATOM    442  CZ  TYR    31       7.538   5.382  16.044 
ATOM    443  OH  TYR    31       7.191   6.079  17.208 
ATOM    444  H   TYR    31      10.048   1.445  11.251 
ATOM    445  HA  TYR    31      10.759   3.158  13.160 
ATOM    446 1HB  TYR    31       8.923   3.792  11.829 
ATOM    447 2HB  TYR    31       8.088   2.548  12.313 
ATOM    448  HD1 TYR    31       9.488   5.607  13.550 
ATOM    449  HD2 TYR    31       6.958   2.602  14.522 
ATOM    450  HE1 TYR    31       8.918   6.706  15.512 
ATOM    451  HE2 TYR    31       6.349   3.799  16.353 
ATOM    452  HH  TYR    31       6.601   5.671  17.606 
ATOM    453  N   ILE    32       9.123   0.578  14.183 
ATOM    454  CA  ILE    32       8.789  -0.212  15.347 
ATOM    455  C   ILE    32      10.053  -0.625  16.093 
ATOM    456  O   ILE    32      10.184  -0.529  17.301 
ATOM    457  CB  ILE    32       7.879  -1.387  14.953 
ATOM    458  CG1 ILE    32       6.521  -0.859  14.500 
ATOM    459  CG2 ILE    32       7.713  -2.356  16.108 
ATOM    460  CD1 ILE    32       5.561  -1.922  13.957 
ATOM    461  H   ILE    32       8.871   0.313  13.405 
ATOM    462  HA  ILE    32       8.273   0.364  15.949 
ATOM    463  HB  ILE    32       8.293  -1.864  14.203 
ATOM    464 1HG1 ILE    32       6.097  -0.416  15.252 
ATOM    465 2HG1 ILE    32       6.664  -0.191  13.811 
ATOM    466 1HG2 ILE    32       8.573  -2.695  16.368 
ATOM    467 2HG2 ILE    32       7.311  -1.901  16.852 
ATOM    468 3HG2 ILE    32       7.151  -3.085  15.837 
ATOM    469 1HD1 ILE    32       5.390  -2.577  14.638 
ATOM    470 2HD1 ILE    32       4.735  -1.506  13.698 
ATOM    471 3HD1 ILE    32       5.956  -2.350  13.194 
ATOM    472  N   TYR    33      11.046  -1.139  15.317 
ATOM    473  CA  TYR    33      12.292  -1.565  15.897 
ATOM    474  C   TYR    33      13.029  -0.407  16.556 
ATOM    475  O   TYR    33      13.826  -0.566  17.499 
ATOM    476  CB  TYR    33      13.154  -2.243  14.790 
ATOM    477  CG  TYR    33      14.066  -3.275  15.385 
ATOM    478  CD1 TYR    33      15.158  -2.997  16.140 
ATOM    479  CD2 TYR    33      13.705  -4.619  15.244 
ATOM    480  CE1 TYR    33      15.930  -4.045  16.679 
ATOM    481  CE2 TYR    33      14.414  -5.660  15.777 
ATOM    482  CZ  TYR    33      15.554  -5.350  16.468 
ATOM    483  OH  TYR    33      16.237  -6.383  17.086 
ATOM    484  H   TYR    33      10.927  -1.209  14.468 
ATOM    485  HA  TYR    33      12.096  -2.235  16.585 
ATOM    486 1HB  TYR    33      12.572  -2.662  14.138 
ATOM    487 2HB  TYR    33      13.682  -1.569  14.334 
ATOM    488  HD1 TYR    33      15.398  -2.113  16.302 
ATOM    489  HD2 TYR    33      12.937  -4.817  14.758 
ATOM    490  HE1 TYR    33      16.692  -3.854  17.177 
ATOM    491  HE2 TYR    33      14.134  -6.541  15.674 
ATOM    492  HH  TYR    33      16.848  -6.075  17.537 
ATOM    493  N   SER    34      12.844   0.772  16.083 
ATOM    494  CA  SER    34      13.557   1.963  16.575 
ATOM    495  C   SER    34      12.950   2.566  17.788 
ATOM    496  O   SER    34      13.608   3.309  18.555 
ATOM    497  CB ASER    34      13.553   3.076  15.438 
ATOM    498  CB BSER    34      13.638   2.928  15.354 
ATOM    499  OG ASER    34      12.413   3.945  15.615 
ATOM    500  OG BSER    34      14.493   2.380  14.346 
ATOM    501  H   SER    34      12.274   0.871  15.446 
ATOM    502  HA  SER    34      14.485   1.717  16.774 
ATOM    503 1HB ASER    34      14.372   3.595  15.484 
ATOM    504 1HB BSER    34      12.751   3.066  14.989 
ATOM    505 2HB ASER    34      13.511   2.653  14.566 
ATOM    506 2HB BSER    34      13.984   3.788  15.641 
ATOM    507  HG ASER    34      11.724   3.501  15.592 
ATOM    508  HG BSER    34      15.247   2.278  14.652 
ATOM    509  N   ASN    35      11.615   2.428  18.062 
ATOM    510  CA  ASN    35      10.925   3.271  18.975 
ATOM    511  C   ASN    35       9.854   2.614  19.812 
ATOM    512  O   ASN    35       9.237   3.328  20.640 
ATOM    513  CB  ASN    35      10.506   4.597  18.417 
ATOM    514  CG  ASN    35      10.539   5.778  19.332 
ATOM    515  OD1 ASN    35      11.373   5.994  20.212 
ATOM    516  ND2 ASN    35       9.625   6.723  19.078 
ATOM    517  H   ASN    35      11.175   1.804  17.664 
ATOM    518  HA  ASN    35      11.613   3.507  19.631 
ATOM    519 1HB  ASN    35      11.075   4.794  17.657 
ATOM    520 2HB  ASN    35       9.601   4.507  18.081 
ATOM    521 1HD2 ASN    35       9.631   7.458  19.526 
ATOM    522 2HD2 ASN    35       9.033   6.596  18.468 
##########
--
View this message in context: http://www.nabble.com/convert-xyz-coordinates-to-distance-t1325102.html#a3535971
Sent from the Perl - Bioperl-L forum at Nabble.com.



More information about the Bioperl-l mailing list