How to select specific lines from a file

Anonymous Monk has asked for the wisdom of the Perl Monks concerning the following question:

Dear Monks,
I am having some issues with

+  A ATOM     31  CA  HIS A  66 +  A ATOM     32  C   HIS A  66 +  A ATOM     33  O   HIS A  66 +  A ATOM     34  CB  HIS A  66 +  A ATOM     35  CG  HIS A  66 +  A ATOM     36  ND1 HIS A  66 +  A ATOM     37  CD2 HIS A  66 +  A ATOM     38  CE1 HIS A  66 +  A ATOM     39  NE2 HIS A  66 +  A ATOM     40  N   HIS A  67 +  A ATOM     41  CA  HIS A  67 +  A ATOM     42  C   HIS A  67 +  A ATOM     43  O   HIS A  67 +  A ATOM     44  CB  HIS A  67 +  A ATOM     45  CG  HIS A  67 +  A ATOM     46  ND1 HIS A  67 +  A ATOM     47  CD2 HIS A  67 +  A ATOM     48  CE1 HIS A  67 +  A ATOM     49  NE2 HIS A  67 +  A ATOM     50  N   PHE A  68 +  A ATOM     51  CA  PHE A  68 +  A ATOM     52  C   PHE A  68 +  A ATOM     53  O   PHE A  68 +  A ATOM     54  CB  PHE A  68 +  A ATOM     55  CG  PHE A  68 +  A ATOM     56  CD1 PHE A  68 +  A ATOM     57  CD2 PHE A  68 +  A ATOM     58  CE1 PHE A  68 +  A ATOM     59  CE2 PHE A  68 +  A ATOM     60  CZ  PHE A  68 +  A ATOM     61  N   SER A  69 +  A ATOM     62  CA  SER A  69 +  A ATOM     63  C   SER A  69 +  A ATOM     64  O   SER A  69 +  A ATOM     65  CB  SER A  69 +  A ATOM     66  OG  SER A  69 +  A ATOM     67  N   GLU A  70 +  A ATOM     68  CA  GLU A  70 +  A ATOM     69  C   GLU A  70 +  A ATOM     70  O   GLU A  70 +  A ATOM     71  CB  GLU A  70 +  A ATOM     72  CG  GLU A  70 +  A ATOM     73  CD  GLU A  70 +  A ATOM     74  OE1 GLU A  70 +  A ATOM     75  OE2 GLU A  70 +  A ATOM     76  N   PRO A  71 +  A ATOM     77  CA  PRO A  71 +  A ATOM     78  C   PRO A  71 +  A ATOM     79  O   PRO A  71 +  A ATOM     80  CB  PRO A  71 +  A ATOM     81  CG  PRO A  71 +  A ATOM     82  CD  PRO A  71 +  A ATOM     83  N   GLU A  72 +  A ATOM     84  CA  GLU A  72 +  A ATOM     85  C   GLU A  72 +  A ATOM     86  O   GLU A  72 +  A ATOM     87  CB  GLU A  72 +  A ATOM     88  CG  GLU A  72 +  A ATOM     89  CD  GLU A  72 +  A ATOM     90  OE1 GLU A  72 +  A ATOM     91  OE2 GLU A  72 +  A ATOM     92  N   ILE A  73 +  A ATOM     93  CA  ILE A  73 +  A ATOM     94  C   ILE A  73 +  A ATOM     95  O   ILE A  73 +  A ATOM     96  CB  ILE A  73 +  A ATOM     97  CG1 ILE A  73 +  A ATOM     98  CG2 ILE A  73 +  A ATOM     99  CD1 ILE A  73 +  A ATOM    100  N   THR A  74 +  A ATOM    101  CA  THR A  74 +  A ATOM    102  C   THR A  74 +  A ATOM    103  O   THR A  74 +  A ATOM    104  CB  THR A  74 +  A ATOM    105  OG1 THR A  74 +  A ATOM    106  CG2 THR A  74 +  A ATOM    107  N   LEU A  75 +  A ATOM    108  CA  LEU A  75 +  A ATOM    109  C   LEU A  75 +  A ATOM    110  O   LEU A  75 +  A ATOM    111  CB  LEU A  75 +  A ATOM    112  CG  LEU A  75 +  A ATOM    113  CD1 LEU A  75 +  A ATOM    114  CD2 LEU A  75 +  A ATOM    115  N   ILE A  76 +  A ATOM    116  CA  ILE A  76 +  A ATOM    117  C   ILE A  76 +  A ATOM    118  O   ILE A  76 +  A ATOM    119  CB  ILE A  76 +  A ATOM    120  CG1 ILE A  76 +  A ATOM    121  CG2 ILE A  76 +  A ATOM    122  CD1 ILE A  76 +  A ATOM    123  N   ILE A  77 +  A ATOM    124  CA  ILE A  77 +  A ATOM    125  C   ILE A  77 +  A ATOM    126  O   ILE A  77 +  A ATOM    127  CB  ILE A  77 +  A ATOM    128  CG1 ILE A  77 +  A ATOM    129  CG2 ILE A  77 +  A ATOM    130  CD1 ILE A  77 +  A ATOM    131  N   PHE A  78 +  A ATOM    132  CA  PHE A  78 +  A ATOM    133  C   PHE A  78 +  A ATOM    134  O   PHE A  78 +  A ATOM    135  CB  PHE A  78 +  A ATOM    136  CG  PHE A  78 +  A ATOM    137  CD1 PHE A  78 +  A ATOM    138  CD2 PHE A  78 +  A ATOM    139  CE1 PHE A  78 +  A ATOM    140  CE2 PHE A  78 +  A ATOM    141  CZ  PHE A  78 +  A ATOM    142  N   GLY A  79 +  A ATOM    143  CA  GLY A  79 +  A ATOM    144  C   GLY A  79 +  A ATOM    145  O   GLY A  79 +  A ATOM    146  N   VAL A  80 +  A ATOM    147  CA  VAL A  80 +  A ATOM    148  C   VAL A  80 +  A ATOM    149  O   VAL A  80 +  A ATOM    150  CB  VAL A  80 +  A ATOM    151  CG1 VAL A  80 +  A ATOM    152  CG2 VAL A  80 +  A ATOM    153  N   MET A  81 +  A ATOM    154  CA  MET A  81 +  A ATOM    155  C   MET A  81 +  A ATOM    156  O   MET A  81 +  A ATOM    157  CB  MET A  81 +  A ATOM    158  CG  MET A  81 +  A ATOM    159  SD  MET A  81 +  A ATOM    160  CE  MET A  81 +  A ATOM    161  N   ALA A  82 +  A ATOM    162  CA  ALA A  82 +  A ATOM    163  C   ALA A  82 +  A ATOM    164  O   ALA A  82 +  A ATOM    165  CB  ALA A  82 +  A ATOM    166  N   GLY A  83 +  A ATOM    167  CA  GLY A  83 +  A ATOM    168  C   GLY A  83 +  A ATOM    169  O   GLY A  83 +  A ATOM    170  N   VAL A  84 +  A ATOM    171  CA  VAL A  84 +  A ATOM    172  C   VAL A  84 +  A ATOM    173  O   VAL A  84 +  A ATOM    174  CB  VAL A  84 +  A ATOM    175  CG1 VAL A  84 +  A ATOM    176  CG2 VAL A  84 +  A ATOM    177  N   ILE A  85 +  A ATOM    178  CA  ILE A  85 +  A ATOM    179  C   ILE A  85 +  A ATOM    180  O   ILE A  85 +  A ATOM    181  CB  ILE A  85 +  A ATOM    182  CG1 ILE A  85 +  A ATOM    183  CG2 ILE A  85 +  A ATOM    184  CD1 ILE A  85 +  A ATOM    185  N   GLY A  86 +  A ATOM    186  CA  GLY A  86 +  A ATOM    187  C   GLY A  86 +  A ATOM    188  O   GLY A  86 +  A ATOM    189  N   THR A  87 +  A ATOM    190  CA  THR A  87 +  A ATOM    191  C   THR A  87 +  A ATOM    192  O   THR A  87 +  A ATOM    193  CB  THR A  87 +  A ATOM    194  OG1 THR A  87 +  A ATOM    195  CG2 THR A  87 +  A ATOM    196  N   ILE A  88 +  A ATOM    197  CA  ILE A  88 +  A ATOM    198  C   ILE A  88 +  A ATOM    199  O   ILE A  88 +  A ATOM    200  CB  ILE A  88 +  A ATOM    201  CG1 ILE A  88 +  A ATOM    202  CG2 ILE A  88 +  A ATOM    203  CD1 ILE A  88 +  A ATOM    204  N   LEU A  89 +  A ATOM    205  CA  LEU A  89 +  A ATOM    206  C   LEU A  89 +  A ATOM    207  O   LEU A  89 +  A ATOM    208  CB  LEU A  89 +  A ATOM    209  CG  LEU A  89 +  A ATOM    210  CD1 LEU A  89 +  A ATOM    211  CD2 LEU A  89 +  A ATOM    212  N   LEU A  90 +  A ATOM    213  CA  LEU A  90 +  A ATOM    214  C   LEU A  90 +  A ATOM    215  O   LEU A  90 +  A ATOM    216  CB  LEU A  90 +  A ATOM    217  CG  LEU A  90 +  A ATOM    218  CD1 LEU A  90 +  A ATOM    219  CD2 LEU A  90 +  A ATOM    220  N   ILE A  91 +  A ATOM    221  CA  ILE A  91 +  A ATOM    222  C   ILE A  91 +  A ATOM    223  O   ILE A  91 +  A ATOM    224  CB  ILE A  91 +  A ATOM    225  CG1 ILE A  91 +  A ATOM    226  CG2 ILE A  91 +  A ATOM    227  CD1 ILE A  91 +  A ATOM    228  N   SER A  92 +  A ATOM    229  CA  SER A  92 +  A ATOM    230  C   SER A  92 +  A ATOM    231  O   SER A  92 +  A ATOM    232  CB  SER A  92 +  A ATOM    233  OG  SER A  92 +  A ATOM    234  N   TYR A  93 +  A ATOM    235  CA  TYR A  93 +  A ATOM    236  C   TYR A  93 +  A ATOM    237  O   TYR A  93 +  A ATOM    238  CB  TYR A  93 +  A ATOM    239  CG  TYR A  93 +  A ATOM    240  CD1 TYR A  93 +  A ATOM    241  CD2 TYR A  93 +  A ATOM    242  CE1 TYR A  93 +  A ATOM    243  CE2 TYR A  93 +  A ATOM    244  CZ  TYR A  93 +  A ATOM    245  OH  TYR A  93 +  A ATOM    246  N   GLY A  94 +  A ATOM    247  CA  GLY A  94 +  A ATOM    248  C   GLY A  94 +  A ATOM    249  O   GLY A  94 +  A ATOM    250  N   ILE A  95 +  A ATOM    251  CA  ILE A  95 +  A ATOM    252  C   ILE A  95 +  A ATOM    253  O   ILE A  95 +  A ATOM    254  CB  ILE A  95 +  A ATOM    255  CG1 ILE A  95 +  A ATOM    256  CG2 ILE A  95 +  A ATOM    257  CD1 ILE A  95 +  A ATOM    258  N   ARG A  96 +  A ATOM    259  CA  ARG A  96 +  A ATOM    260  C   ARG A  96 +  A ATOM    261  O   ARG A  96 +  A ATOM    262  CB  ARG A  96 +  A ATOM    263  CG  ARG A  96 +  A ATOM    264  CD  ARG A  96 +  A ATOM    265  NE  ARG A  96 +  A ATOM    266  CZ  ARG A  96 +  A ATOM    267  NH1 ARG A  96 +  A ATOM    268  NH2 ARG A  96 +  A ATOM    269  N   ARG A  97 +  A ATOM    270  CA  ARG A  97 +  A ATOM    271  C   ARG A  97 +  A ATOM    272  O   ARG A  97 +  A ATOM    273  CB  ARG A  97 +  A ATOM    274  CG  ARG A  97 +  A ATOM    275  CD  ARG A  97 +  A ATOM    276  NE  ARG A  97 +  A ATOM    277  CZ  ARG A  97 +  A ATOM    278  NH1 ARG A  97 +  A ATOM    279  NH2 ARG A  97 +  A ATOM    280  N   LEU A  98 +  A ATOM    281  CA  LEU A  98 +  A ATOM    282  C   LEU A  98 +  A ATOM    283  O   LEU A  98 +  A ATOM    284  CB  LEU A  98 +  A ATOM    285  CG  LEU A  98 +  A ATOM    286  CD1 LEU A  98 +  A ATOM    287  CD2 LEU A  98 +  A ATOM    288  N   ILE A  99 +  A ATOM    289  CA  ILE A  99 +  A ATOM    290  C   ILE A  99 +  A ATOM    291  O   ILE A  99 +  A ATOM    292  CB  ILE A  99 +  A ATOM    293  CG1 ILE A  99 +  A ATOM    294  CG2 ILE A  99 +  A ATOM    295  CD1 ILE A  99 +  A ATOM    296  N   LYS A 100 +  A ATOM    297  CA  LYS A 100 +  A ATOM    298  C   LYS A 100 +  A ATOM    299  O   LYS A 100 +  A ATOM    300  CB  LYS A 100 +  A ATOM    301  CG  LYS A 100 +  A ATOM    302  CD  LYS A 100 +  A ATOM    303  CE  LYS A 100 +  A ATOM    304  NZ  LYS A 100 +  A ATOM    305  N   LYS A 101 +  A ATOM    306  CA  LYS A 101 +  A ATOM    307  C   LYS A 101 +  A ATOM    308  O   LYS A 101 +  A ATOM    309  CB  LYS A 101 +  A ATOM    310  CG  LYS A 101 +  A ATOM    311  CD  LYS A 101 +  A ATOM    312  CE  LYS A 101 +  A ATOM    313  NZ  LYS A 101 +  A ATOM    314  OXT LYS A 101 +  A ATOM    345  N   HIS B  66 +  B ATOM    346  CA  HIS B  66 +  B ATOM    347  C   HIS B  66 +  B ATOM    348  O   HIS B  66 +  B ATOM    349  CB  HIS B  66 +  B ATOM    350  CG  HIS B  66 +  B ATOM    351  ND1 HIS B  66 +  B ATOM    352  CD2 HIS B  66 +  B ATOM    353  CE1 HIS B  66 +  B ATOM    354  NE2 HIS B  66 +  B ATOM    355  N   HIS B  67 +  B ATOM    356  CA  HIS B  67 +  B ATOM    357  C   HIS B  67 +  B ATOM    358  O   HIS B  67 +  B ATOM    359  CB  HIS B  67 +  B ATOM    360  CG  HIS B  67 +  B ATOM    361  ND1 HIS B  67 +  B ATOM    362  CD2 HIS B  67 +  B ATOM    363  CE1 HIS B  67 +  B ATOM    364  NE2 HIS B  67 +  B ATOM    365  N   PHE B  68 +  B ATOM    366  CA  PHE B  68 +  B ATOM    367  C   PHE B  68 +  B ATOM    368  O   PHE B  68 +  B ATOM    369  CB  PHE B  68 +  B ATOM    370  CG  PHE B  68 +  B ATOM    371  CD1 PHE B  68 +  B ATOM    372  CD2 PHE B  68 +  B ATOM    373  CE1 PHE B  68 +  B ATOM    374  CE2 PHE B  68 +  B ATOM    375  CZ  PHE B  68 +  B ATOM    376  N   SER B  69 +  B ATOM    377  CA  SER B  69 +  B ATOM    378  C   SER B  69 +  B ATOM    379  O   SER B  69 +  B ATOM    380  CB  SER B  69 +  B ATOM    381  OG  SER B  69 +  B ATOM    382  N   GLU B  70 +  B ATOM    383  CA  GLU B  70 +  B ATOM    384  C   GLU B  70 +  B ATOM    385  O   GLU B  70 +  B ATOM    386  CB  GLU B  70 +  B ATOM    387  CG  GLU B  70 +  B ATOM    388  CD  GLU B  70 +  B ATOM    389  OE1 GLU B  70 +  B ATOM    390  OE2 GLU B  70 +  B ATOM    391  N   PRO B  71 +  B ATOM    392  CA  PRO B  71 +  B ATOM    393  C   PRO B  71 +  B ATOM    394  O   PRO B  71 +  B ATOM    395  CB  PRO B  71 +  B ATOM    396  CG  PRO B  71 +  B ATOM    397  CD  PRO B  71 +  B ATOM    398  N   GLU B  72 +  B ATOM    399  CA  GLU B  72 +  B ATOM    400  C   GLU B  72 +  B ATOM    401  O   GLU B  72 +  B ATOM    402  CB  GLU B  72 +  B ATOM    403  CG  GLU B  72 +  B ATOM    404  CD  GLU B  72 +  B ATOM    405  OE1 GLU B  72 +  B ATOM    406  OE2 GLU B  72 +  B ATOM    407  N   ILE B  73 +  B ATOM    408  CA  ILE B  73 +  B ATOM    409  C   ILE B  73 +  B ATOM    410  O   ILE B  73 +  B ATOM    411  CB  ILE B  73 +  B ATOM    412  CG1 ILE B  73 +  B ATOM    413  CG2 ILE B  73 +  B ATOM    414  CD1 ILE B  73 +  B ATOM    415  N   THR B  74 +  B ATOM    416  CA  THR B  74 +  B ATOM    417  C   THR B  74 +  B ATOM    418  O   THR B  74 +  B ATOM    419  CB  THR B  74 +  B ATOM    420  OG1 THR B  74 +  B ATOM    421  CG2 THR B  74 +  B ATOM    422  N   LEU B  75 +  B ATOM    423  CA  LEU B  75 +  B ATOM    424  C   LEU B  75 +  B ATOM    425  O   LEU B  75 +  B ATOM    426  CB  LEU B  75 +  B ATOM    427  CG  LEU B  75 +  B ATOM    428  CD1 LEU B  75 +  B ATOM    429  CD2 LEU B  75 +  B ATOM    430  N   ILE B  76 +  B ATOM    431  CA  ILE B  76 +  B ATOM    432  C   ILE B  76 +  B ATOM    433  O   ILE B  76 +  B ATOM    434  CB  ILE B  76 +  B ATOM    435  CG1 ILE B  76 +  B ATOM    436  CG2 ILE B  76 +  B ATOM    437  CD1 ILE B  76 +  B ATOM    438  N   ILE B  77 +  B ATOM    439  CA  ILE B  77 +  B ATOM    440  C   ILE B  77 +  B ATOM    441  O   ILE B  77 +  B ATOM    442  CB  ILE B  77 +  B ATOM    443  CG1 ILE B  77 +  B ATOM    444  CG2 ILE B  77 +  B ATOM    445  CD1 ILE B  77 +  B ATOM    446  N   PHE B  78 +  B ATOM    447  CA  PHE B  78 +  B ATOM    448  C   PHE B  78 +  B ATOM    449  O   PHE B  78 +  B ATOM    450  CB  PHE B  78 +  B ATOM    451  CG  PHE B  78 +  B ATOM    452  CD1 PHE B  78 +  B ATOM    453  CD2 PHE B  78 +  B ATOM    454  CE1 PHE B  78 +  B ATOM    455  CE2 PHE B  78 +  B ATOM    456  CZ  PHE B  78 +  B ATOM    457  N   GLY B  79 +  B ATOM    458  CA  GLY B  79 +  B ATOM    459  C   GLY B  79 +  B ATOM    460  O   GLY B  79 +  B ATOM    461  N   VAL B  80 +  B ATOM    462  CA  VAL B  80 +  B ATOM    463  C   VAL B  80 +  B ATOM    464  O   VAL B  80 +  B ATOM    465  CB  VAL B  80 +  B ATOM    466  CG1 VAL B  80 +  B ATOM    467  CG2 VAL B  80 +  B ATOM    468  N   MET B  81 +  B ATOM    469  CA  MET B  81 +  B ATOM    470  C   MET B  81 +  B ATOM    471  O   MET B  81 +  B ATOM    472  CB  MET B  81 +  B ATOM    473  CG  MET B  81 +  B ATOM    474  SD  MET B  81 +  B ATOM    475  CE  MET B  81 +  B ATOM    476  N   ALA B  82 +  B ATOM    477  CA  ALA B  82 +  B ATOM    478  C   ALA B  82 +  B ATOM    479  O   ALA B  82 +  B ATOM    480  CB  ALA B  82 +  B ATOM    481  N   GLY B  83 +  B ATOM    482  CA  GLY B  83 +  B ATOM    483  C   GLY B  83 +  B ATOM    484  O   GLY B  83 +  B ATOM    485  N   VAL B  84 +  B ATOM    486  CA  VAL B  84 +  B ATOM    487  C   VAL B  84 +  B ATOM    488  O   VAL B  84 +  B ATOM    489  CB  VAL B  84 +  B ATOM    490  CG1 VAL B  84 +  B ATOM    491  CG2 VAL B  84 +  B ATOM    492  N   ILE B  85 +  B ATOM    493  CA  ILE B  85 +  B ATOM    494  C   ILE B  85 +  B ATOM    495  O   ILE B  85 +  B ATOM    496  CB  ILE B  85 +  B ATOM    497  CG1 ILE B  85 +  B ATOM    498  CG2 ILE B  85 +  B ATOM    499  CD1 ILE B  85 +  B ATOM    500  N   GLY B  86 +  B ATOM    501  CA  GLY B  86 +  B ATOM    502  C   GLY B  86 +  B ATOM    503  O   GLY B  86 +  B ATOM    504  N   THR B  87 +  B ATOM    505  CA  THR B  87 +  B ATOM    506  C   THR B  87 +  B ATOM    507  O   THR B  87 +  B ATOM    508  CB  THR B  87 +  B ATOM    509  OG1 THR B  87 +  B ATOM    510  CG2 THR B  87 +  B ATOM    511  N   ILE B  88 +  B ATOM    512  CA  ILE B  88 +  B ATOM    513  C   ILE B  88 +  B ATOM    514  O   ILE B  88 +  B ATOM    515  CB  ILE B  88 +  B ATOM    516  CG1 ILE B  88 +  B ATOM    517  CG2 ILE B  88 +  B ATOM    518  CD1 ILE B  88 +  B ATOM    519  N   LEU B  89 +  B ATOM    520  CA  LEU B  89 +  B ATOM    521  C   LEU B  89 +  B ATOM    522  O   LEU B  89 +  B ATOM    523  CB  LEU B  89 +  B ATOM    524  CG  LEU B  89 +  B ATOM    525  CD1 LEU B  89 +  B ATOM    526  CD2 LEU B  89 +  B ATOM    527  N   LEU B  90 +  B ATOM    528  CA  LEU B  90 +  B ATOM    529  C   LEU B  90 +  B ATOM    530  O   LEU B  90 +  B ATOM    531  CB  LEU B  90 +  B ATOM    532  CG  LEU B  90 +  B ATOM    533  CD1 LEU B  90 +  B ATOM    534  CD2 LEU B  90 +  B ATOM    535  N   ILE B  91 +  B ATOM    536  CA  ILE B  91 +  B ATOM    537  C   ILE B  91 +  B ATOM    538  O   ILE B  91 +  B ATOM    539  CB  ILE B  91 +  B ATOM    540  CG1 ILE B  91 +  B ATOM    541  CG2 ILE B  91 +  B ATOM    542  CD1 ILE B  91 +  B ATOM    543  N   SER B  92 +  B ATOM    544  CA  SER B  92 +  B ATOM    545  C   SER B  92 +  B ATOM    546  O   SER B  92 +  B ATOM    547  CB  SER B  92 +  B ATOM    548  OG  SER B  92 +  B ATOM    549  N   TYR B  93 +  B ATOM    550  CA  TYR B  93 +  B ATOM    551  C   TYR B  93 +  B ATOM    552  O   TYR B  93 +  B ATOM    553  CB  TYR B  93 +  B ATOM    554  CG  TYR B  93 +  B ATOM    555  CD1 TYR B  93 +  B ATOM    556  CD2 TYR B  93 +  B ATOM    557  CE1 TYR B  93 +  B ATOM    558  CE2 TYR B  93 +  B ATOM    559  CZ  TYR B  93 +  B ATOM    560  OH  TYR B  93 +  B ATOM    561  N   GLY B  94 +  B ATOM    562  CA  GLY B  94 +  B ATOM    563  C   GLY B  94 +  B ATOM    564  O   GLY B  94 +  B ATOM    565  N   ILE B  95 +  B ATOM    566  CA  ILE B  95 +  B ATOM    567  C   ILE B  95 +  B ATOM    568  O   ILE B  95 +  B ATOM    569  CB  ILE B  95 +  B ATOM    570  CG1 ILE B  95 +  B ATOM    571  CG2 ILE B  95 +  B ATOM    572  CD1 ILE B  95 +  B ATOM    573  N   ARG B  96 +  B ATOM    574  CA  ARG B  96 +  B ATOM    575  C   ARG B  96 +  B ATOM    576  O   ARG B  96 +  B ATOM    577  CB  ARG B  96 +  B ATOM    578  CG  ARG B  96 +  B ATOM    579  CD  ARG B  96 +  B ATOM    580  NE  ARG B  96 +  B ATOM    581  CZ  ARG B  96 +  B ATOM    582  NH1 ARG B  96 +  B ATOM    583  NH2 ARG B  96 +  B ATOM    584  N   ARG B  97 +  B ATOM    585  CA  ARG B  97 +  B ATOM    586  C   ARG B  97 +  B ATOM    587  O   ARG B  97 +  B ATOM    588  CB  ARG B  97 +  B ATOM    589  CG  ARG B  97 +  B ATOM    590  CD  ARG B  97 +  B ATOM    591  NE  ARG B  97 +  B ATOM    592  CZ  ARG B  97 +  B ATOM    593  NH1 ARG B  97 +  B ATOM    594  NH2 ARG B  97 +  B ATOM    595  N   LEU B  98 +  B ATOM    596  CA  LEU B  98 +  B ATOM    597  C   LEU B  98 +  B ATOM    598  O   LEU B  98 +  B ATOM    599  CB  LEU B  98 +  B ATOM    600  CG  LEU B  98 +  B ATOM    601  CD1 LEU B  98 +  B ATOM    602  CD2 LEU B  98 +  B ATOM    603  N   ILE B  99 +  B ATOM    604  CA  ILE B  99 +  B ATOM    605  C   ILE B  99 +  B ATOM    606  O   ILE B  99 +  B ATOM    607  CB  ILE B  99 +  B ATOM    608  CG1 ILE B  99 +  B ATOM    609  CG2 ILE B  99 +  B ATOM    610  CD1 ILE B  99 +  B ATOM    611  N   LYS B 100 +  B ATOM    612  CA  LYS B 100 +  B ATOM    613  C   LYS B 100 +  B ATOM    614  O   LYS B 100 +  B ATOM    615  CB  LYS B 100 +  B ATOM    616  CG  LYS B 100 +  B ATOM    617  CD  LYS B 100 +  B ATOM    618  CE  LYS B 100 +  B ATOM    619  NZ  LYS B 100 +  B ATOM    620  N   LYS B 101 +  B ATOM    621  CA  LYS B 101 +  B ATOM    622  C   LYS B 101 +  B ATOM    623  O   LYS B 101 +  B ATOM    624  CB  LYS B 101 +  B ATOM    625  CG  LYS B 101 +  B ATOM    626  CD  LYS B 101 +  B ATOM    627  CE  LYS B 101 +  B ATOM    628  NZ  LYS B 101 +  B ATOM    629  OXT LYS B 101 +  B 


PDB files (for those that are into Bioinformatics that is...). This file has the format: class='codetext'>ATOM     30  N   HIS A  66       7.514  15.296  11.222  1.00 12.98     N 7.318  14.688  12.568  1.00 12.48     C 8.676  14.309  13.156  1.00 11.62     C 9.708  14.518  12.545  1.00 11.76     O 6.450  13.434  12.442  1.00 12.81     C 5.000  13.829  12.378  1.00 13.36     C 4.332  14.002  11.175  1.00 13.57     N 4.073  14.085  13.360  1.00 13.93     C 3.063  14.347  11.461  1.00 14.23     C 2.851  14.410  12.778  1.00 14.47     N 8.695  13.753  14.336  1.00 10.90     N 9.995  13.365  14.954  1.00 10.21     C 9.781  12.968  16.417  1.00  9.43     C 10.182  11.906  16.847  1.00  9.32     O 10.961  14.553  14.889  1.00 10.37     C 12.242  14.124  14.232  1.00 10.53     C 13.309  13.614  14.955  1.00 10.58     N 12.644  14.121  12.918  1.00 10.88     C 14.291  13.330  14.081  1.00 10.97     C 13.939  13.620  12.826  1.00 11.15     N 9.157  13.817  17.187  1.00  9.11     N 8.928  13.491  18.622  1.00  8.55     C 7.941  12.326  18.743  1.00  7.46     C 7.041  12.176  17.939  1.00  7.39     O 8.356  14.718  19.338  1.00  8.98     C 9.474  15.476  20.012  1.00  9.76     C 10.320  16.294  19.252  1.00 10.29     C 9.668  15.358  21.393  1.00 10.19     C 11.359  16.997  19.877  1.00 11.19     C 10.706  16.060  22.017  1.00 11.10     C 11.552  16.880  21.258  1.00 11.57     C 8.099  11.502  19.744  1.00  6.86     N 7.169  10.349  19.925  1.00  6.01     C 7.060   9.557  18.620  1.00  5.07     C 7.602   9.936  17.600  1.00  5.28     O 5.787  10.870  20.316  1.00  6.54     C 5.072  11.237  19.142  1.00  7.08     O 6.360   8.457  18.648  1.00  4.41     N 6.205   7.633  17.416  1.00  3.84     C 4.716   7.484  17.092  1.00  2.84     C 4.056   6.606  17.612  1.00  3.00     O 6.813   6.249  17.649  1.00  4.55     C 8.251   6.398  18.150  1.00  5.41     C 9.076   5.193  17.695  1.00  6.00     C 9.596   5.236  16.592  1.00  6.49     O 9.175   4.246  18.458  1.00  6.28     O 4.226   8.354  16.244  1.00  2.18     N 2.810   8.341  15.838  1.00  1.51     C 2.457   7.010  15.165  1.00  1.23     C 2.811   6.762  14.027  1.00  1.13     O 2.675   9.502  14.842  1.00  1.87     C 4.070  10.160  14.696  1.00  2.49     C 5.041   9.412  15.622  1.00  2.65     C 1.757   6.154  15.858  1.00  1.29     N 1.380   4.847  15.257  1.00  1.13     C 0.686   5.089  13.917  1.00  1.00     C 0.892   4.370  12.960  1.00  0.97     O 0.425   4.107  16.200  1.00  1.32     C 1.202   3.588  17.411  1.00  1.94     C 1.030   4.556  18.583  1.00  2.47     C 0.067   4.403  19.316  1.00  2.89     O 1.864   5.436  18.726  1.00  3.01     O -0.133   6.101  13.839  1.00  0.99     N -0.837   6.398  12.569  1.00  0.91     C 0.178   6.773  11.488  1.00  0.80     C 0.103   6.312  10.369  1.00  0.74     O -1.797   7.563  12.793  1.00  1.03     C -2.739   7.663  11.602  1.00  1.05     C -1.005   8.866  12.931  1.00  1.28     C -3.854   6.627  11.754  1.00  1.48     C 1.127   7.609  11.812  1.00  0.81     N 2.137   8.010  10.793  1.00  0.76     C 2.836   6.763  10.246  1.00  0.68     C 2.992   6.606   9.050  1.00  0.62     O 3.174   8.941  11.427  1.00  0.86     C 3.745   8.312  12.563  1.00  1.35     O 2.495  10.247  11.847  1.00  1.19     C 3.258   5.873  11.102  1.00  0.72     N 3.946   4.644  10.604  1.00  0.69     C 2.948   3.778   9.834  1.00  0.58     C 3.230   3.323   8.746  1.00  0.50     O 4.511   3.843  11.781  1.00  0.82     C 5.693   2.991  11.307  1.00  0.88     C 6.011   1.928  12.360  1.00  0.87     C 5.338   2.302   9.986  1.00  1.02     C 1.782   3.545  10.378  1.00  0.62     N 0.798   2.715   9.636  1.00  0.57     C 0.546   3.368   8.277  1.00  0.45     C 0.597   2.726   7.247  1.00  0.38     O -0.512   2.633  10.426  1.00  0.69     C -0.268   1.887  11.738  1.00  0.91     C -1.558   1.881   9.599  1.00  0.76     C -1.449   2.116  12.685  1.00  1.10     C 0.311   4.652   8.270  1.00  0.44     N 0.097   5.363   6.982  1.00  0.36     C 1.322   5.151   6.095  1.00  0.28     C 1.215   4.831   4.927  1.00  0.25     O -0.094   6.859   7.243  1.00  0.39     C -1.441   7.088   7.931  1.00  1.21     C -0.063   7.615   5.915  1.00  1.18     C -1.571   8.564   8.316  1.00  1.58     C 2.490   5.338   6.650  1.00  0.31     N 3.737   5.156   5.858  1.00  0.32     C 3.768   3.744   5.274  1.00  0.30     C 4.042   3.555   4.109  1.00  0.30     O 4.961   5.360   6.756  1.00  0.41     C 5.322   6.825   6.795  1.00  0.80     C 4.315   7.795   6.880  1.00  1.52     C 6.664   7.215   6.742  1.00  1.66     C 4.651   9.153   6.913  1.00  1.97     C 7.003   8.573   6.775  1.00  2.09     C 5.996   9.542   6.861  1.00  1.95     C 3.488   2.749   6.072  1.00  0.31     N 3.506   1.359   5.538  1.00  0.32     C 2.538   1.265   4.358  1.00  0.26     C 2.873   0.754   3.307  1.00  0.26     O 1.343   1.772   4.510  1.00  0.23     N 0.372   1.725   3.383  1.00  0.22     C 0.988   2.429   2.174  1.00  0.21     C 0.984   1.921   1.070  1.00  0.22     O -0.920   2.435   3.795  1.00  0.24     C -1.923   2.384   2.642  1.00  0.28     C -1.513   1.725   5.015  1.00  0.28     C 1.537   3.594   2.387  1.00  0.22     N 2.178   4.339   1.269  1.00  0.25     C 3.276   3.473   0.648  1.00  0.27     C 3.375   3.345  -0.557  1.00  0.28     O 2.785   5.636   1.805  1.00  0.29     C 1.665   6.623   2.136  1.00  0.36     C 2.273   8.316   1.947  1.00  1.07     S 0.687   9.081   1.529  1.00  1.70     C 4.108   2.887   1.464  1.00  0.28     N 5.207   2.039   0.933  1.00  0.32     C 4.624   0.923   0.059  1.00  0.30     C 5.097   0.679  -1.033  1.00  0.30     O 6.022   1.442   2.092  1.00  0.37     C 3.597   0.244   0.508  1.00  0.28     N 3.013  -0.836  -0.336  1.00  0.27     C 2.602  -0.239  -1.680  1.00  0.23     C 2.911  -0.768  -2.730  1.00  0.23     O 1.916   0.872  -1.654  1.00  0.21     N 1.501   1.512  -2.933  1.00  0.19     C 2.739   1.795  -3.786  1.00  0.20     C 2.772   1.502  -4.966  1.00  0.19     O 0.774   2.826  -2.636  1.00  0.22     C 0.564   3.598  -3.941  1.00  0.28     C -0.587   2.526  -2.000  1.00  0.27     C 3.760   2.367  -3.200  1.00  0.23     N 4.996   2.672  -3.975  1.00  0.27     C 5.547   1.392  -4.608  1.00  0.27     C 5.886   1.365  -5.775  1.00  0.28     O 6.050   3.266  -3.039  1.00  0.33     C 5.504   4.550  -2.407  1.00  0.67     C 7.316   3.588  -3.834  1.00  0.75     C 5.459   5.661  -3.459  1.00  1.20     C 5.647   0.329  -3.855  1.00  0.29     N 6.184  -0.934  -4.435  1.00  0.33     C 5.336  -1.337  -5.640  1.00  0.30     C 5.849  -1.653  -6.693  1.00  0.33     O 4.038  -1.315  -5.496  1.00  0.25     N 3.164  -1.685  -6.644  1.00  0.25     C 3.479  -0.771  -7.827  1.00  0.26     C 3.649  -1.218  -8.945  1.00  0.32     O 1.695  -1.518  -6.246  1.00  0.24     C 1.410  -2.352  -5.132  1.00  0.34     O 0.803  -1.908  -7.425  1.00  0.31     C 3.561   0.510  -7.586  1.00  0.24     N 3.868   1.463  -8.687  1.00  0.33     C 5.195   1.075  -9.340  1.00  0.39     C 5.308   1.014 -10.549  1.00  0.47     O 3.970   2.879  -8.119  1.00  0.37     C 2.594   3.324  -7.619  1.00  0.39     C 4.450   3.836  -9.211  1.00  0.47     C 2.658   4.786  -7.171  1.00  0.49     C 6.201   0.811  -8.552  1.00  0.39     N 7.517   0.428  -9.127  1.00  0.49     C 7.322  -0.806 -10.021  1.00  0.53     C 7.795  -0.855 -11.139  1.00  0.62     O 8.509   0.152  -7.973  1.00  0.53     C 9.175  -1.221  -8.117  1.00  0.59     C 10.168  -1.191  -9.284  1.00  0.68     C 9.925  -1.557  -6.825  1.00  0.65     C 6.621  -1.798  -9.542  1.00  0.49     N 6.397  -3.013 -10.380  1.00  0.57     C 5.728  -2.598 -11.689  1.00  0.60     C 6.134  -2.995 -12.762  1.00  0.71     O 5.489  -3.997  -9.632  1.00  0.56     C 5.469  -5.334 -10.375  1.00  1.24     C 6.764  -6.096 -10.086  1.00  1.76     C 4.272  -6.164  -9.904  1.00  1.92     C 4.708  -1.788 -11.608  1.00  0.55     N 4.013  -1.329 -12.843  1.00  0.65     C 5.014  -0.643 -13.770  1.00  0.75     C 5.058  -0.907 -14.955  1.00  0.87     O 2.900  -0.347 -12.475  1.00  0.63     C 1.883  -1.050 -11.574  1.00  0.58     C 2.202   0.135 -13.748  1.00  0.75     C 0.969  -0.007 -10.928  1.00  0.66     C 5.821   0.240 -13.247  1.00  0.73     N 6.804   0.931 -14.123  1.00  0.87     C 7.674  -0.119 -14.812  1.00  0.94     C 7.877  -0.079 -16.008  1.00  1.07     O 7.686   1.851 -13.279  1.00  0.86     C 6.867   2.795 -12.602  1.00  1.29     O 8.182  -1.070 -14.075  1.00  0.89     N 9.018  -2.119 -14.719  1.00  1.00     C 8.202  -2.810 -15.817  1.00  1.05     C 8.661  -2.983 -16.930  1.00  1.18     O 9.448  -3.150 -13.672  1.00  0.96     C 10.382  -4.150 -14.306  1.00  1.27     C 10.075  -4.697 -15.558  1.00  1.62     C 11.557  -4.529 -13.646  1.00  2.13     C 10.942  -5.626 -16.149  1.00  1.95     C 12.424  -5.455 -14.237  1.00  2.53     C 12.117  -6.003 -15.487  1.00  2.15     C 12.973  -6.917 -16.071  1.00  2.64     O 6.988  -3.200 -15.516  1.00  0.97     N 6.140  -3.866 -16.542  1.00  1.05     C 5.987  -2.949 -17.753  1.00  1.16     C 6.148  -3.362 -18.886  1.00  1.29     O 5.676  -1.701 -17.524  1.00  1.14     N 5.510  -0.752 -18.665  1.00  1.29     C 6.801  -0.728 -19.492  1.00  1.41     C 6.775  -0.812 -20.703  1.00  1.55     O 5.151   0.656 -18.138  1.00  1.28     C 3.779   0.599 -17.461  1.00  1.74     C 5.104   1.681 -19.280  1.00  1.77     C 3.444   1.971 -16.868  1.00  2.19     C 7.931  -0.618 -18.843  1.00  1.37     N 9.221  -0.591 -19.590  1.00  1.51     C 9.332  -1.851 -20.445  1.00  1.58     C 9.672  -1.801 -21.608  1.00  1.73     O 10.388  -0.536 -18.598  1.00  1.46     C 11.710  -0.519 -19.367  1.00  1.73     C 11.774   0.732 -20.250  1.00  2.03     C 13.061   0.742 -21.007  1.00  2.00     N 13.335   1.731 -21.813  1.00  2.45     C 12.469   2.694 -21.983  1.00  3.14     N 14.475   1.757 -22.448  1.00  2.76     N 9.046  -2.988 -19.886  1.00  1.50     N 9.132  -4.234 -20.687  1.00  1.59     C 8.225  -4.110 -21.911  1.00  1.69     C 8.616  -4.419 -23.020  1.00  1.84     O 8.698  -5.431 -19.837  1.00  1.50     C 8.729  -6.702 -20.687  1.00  1.77     C 10.167  -6.987 -21.129  1.00  2.23     C 10.193  -8.174 -22.031  1.00  2.70     N 11.320  -8.587 -22.543  1.00  3.07     C 12.427  -7.943 -22.289  1.00  3.56     N 11.340  -9.641 -23.308  1.00  3.58     N 7.015  -3.660 -21.722  1.00  1.64     N 6.083  -3.519 -22.878  1.00  1.75     C 6.715  -2.612 -23.938  1.00  1.91     C 6.719  -2.926 -25.113  1.00  2.05     O 4.766  -2.900 -22.400  1.00  1.69     C 4.063  -3.870 -21.447  1.00  2.11     C 3.102  -3.090 -20.546  1.00  2.66     C 3.279  -4.903 -22.258  1.00  2.38     C 7.251  -1.492 -23.536  1.00  1.90     N 7.882  -0.574 -24.525  1.00  2.06     C 9.313  -1.053 -24.814  1.00  2.14     C 9.510  -2.109 -25.383  1.00  2.20     O 7.898   0.849 -23.959  1.00  2.05     C 6.467   1.290 -23.641  1.00  1.98     C 8.504   1.805 -24.990  1.00  2.03     C 6.471   2.199 -22.415  1.00  2.00     C 10.311  -0.303 -24.427  1.00  2.35     N 11.711  -0.743 -24.687  1.00  2.45     C 11.846  -1.196 -26.141  1.00  2.85     C 10.926  -1.082 -26.925  1.00  3.21     O 12.059  -1.904 -23.752  1.00  2.30     C 13.539  -2.258 -23.905  1.00  2.60     C 13.875  -3.454 -23.008  1.00  2.94     C 15.321  -3.880 -23.246  1.00  3.56     C 15.659  -5.016 -22.342  1.00  3.91     N 12.989  -1.712 -26.508  1.00  3.09     N 13.180  -2.173 -27.913  1.00  3.63     C 13.147  -0.966 -28.856  1.00  4.10     C 13.338  -1.165 -30.044  1.00  4.56     O 12.060  -3.142 -28.288  1.00  3.99     C 12.512  -4.017 -29.459  1.00  4.58     C 11.355  -4.192 -30.443  1.00  5.25     C 11.905  -4.596 -31.812  1.00  6.09     C 12.682  -5.862 -31.679  1.00  6.53     N 12.929   0.132 -28.372  1.00  4.44     O -10.725   2.701  13.152  1.00 13.65     N -10.036   1.822  14.141  1.00 12.91     C -10.950   0.653  14.519  1.00 12.30     C -11.988   0.833  15.123  1.00 12.38     O -9.699   2.628  15.397  1.00 12.96     C -8.323   2.255  15.881  1.00 13.34     C -7.174   2.829  15.357  1.00 13.54     N -7.895   1.370  16.840  1.00 13.74     C -6.123   2.289  15.998  1.00 14.03     C -6.506   1.393  16.912  1.00 14.18     N -10.570  -0.544  14.166  1.00 11.87     N -11.414  -1.726  14.502  1.00 11.46     C -10.910  -2.949  13.737  1.00 10.55     C -11.682  -3.768  13.278  1.00 10.53     O -12.866  -1.445  14.116  1.00 11.84     C -13.682  -1.212  15.358  1.00 12.35     C -14.413  -0.052  15.554  1.00 12.68     N -13.889  -1.980  16.476  1.00 12.80     C -15.022  -0.153  16.749  1.00 13.29     C -14.736  -1.310  17.354  1.00 13.39     N -9.619  -3.082  13.594  1.00 10.00     N -9.068  -4.253  12.856  1.00  9.29     C -7.788  -4.733  13.542  1.00  8.27     C -7.818  -5.593  14.400  1.00  8.29     O -8.753  -3.843  11.415  1.00  9.52     C -9.856  -4.323  10.503  1.00 10.43     C -11.115  -3.716  10.547  1.00 10.86     C -9.616  -5.377   9.613  1.00 11.07     C -12.137  -4.162   9.699  1.00 11.86     C -10.639  -5.822   8.764  1.00 12.06     C -11.899  -5.215   8.808  1.00 12.43     C -6.664  -4.184  13.172  1.00  7.61     N -5.383  -4.610  13.805  1.00  6.80     C -5.132  -3.775  15.062  1.00  5.60     C -4.777  -2.614  14.987  1.00  5.39     O -4.235  -4.409  12.818  1.00  7.36     C -4.382  -5.316  11.733  1.00  8.12     O -5.314  -4.354  16.216  1.00  5.12     N -5.088  -3.595  17.478  1.00  4.22     C -3.595  -3.285  17.641  1.00  3.04     C -3.220  -2.141  17.803  1.00  3.18     O -5.572  -4.425  18.669  1.00  4.88     C -6.895  -3.853  19.183  1.00  5.77     C -8.063  -4.588  18.523  1.00  6.71     C -8.099  -5.803  18.613  1.00  7.29     O -8.903  -3.920  17.940  1.00  7.09     O -2.782  -4.314  17.600  1.00  2.28     N -1.322  -4.162  17.747  1.00  1.48     C -0.761  -3.262  16.642  1.00  1.33     C -1.346  -3.116  15.587  1.00  1.29     O -0.763  -5.587  17.622  1.00  2.00     C -1.963  -6.549  17.434  1.00  2.71     C -3.245  -5.700  17.403  1.00  2.87     C 0.373  -2.658  16.879  1.00  1.30     N 0.975  -1.766  15.848  1.00  1.19     C 1.393  -2.593  14.630  1.00  1.06     C 0.765  -2.543  13.592  1.00  1.01     O 2.206  -1.071  16.431  1.00  1.29     C 1.789  -0.202  17.619  1.00  1.90     C 2.684  -0.519  18.819  1.00  2.25     C 2.687  -1.662  19.245  1.00  2.89     O 3.349   0.387  19.290  1.00  2.52     O 2.456  -3.346  14.748  1.00  1.07     N 2.930  -4.169  13.602  1.00  0.98     C 1.736  -4.780  12.861  1.00  0.89     C 1.702  -4.819  11.647  1.00  0.82     O 3.841  -5.282  14.129  1.00  1.09     C 4.696  -5.806  12.981  1.00  1.29     C 3.002  -6.427  14.707  1.00  1.27     C 6.170  -5.541  13.287  1.00  2.11     C 0.758  -5.256  13.580  1.00  0.92     N -0.431  -5.858  12.915  1.00  0.87     C -1.122  -4.800  12.051  1.00  0.77     C -1.476  -5.048  10.913  1.00  0.69     O -1.407  -6.386  13.973  1.00  0.99     C -1.442  -5.497  15.083  1.00  1.57     O -0.954  -7.769  14.440  1.00  1.43     C -1.329  -3.624  12.577  1.00  0.81     N -2.004  -2.571  11.765  1.00  0.74     C -1.042  -2.027  10.710  1.00  0.62     C -1.398  -1.895   9.558  1.00  0.52     O -2.460  -1.423  12.674  1.00  0.87     C -3.786  -0.854  12.164  1.00  1.11     C -4.041   0.507  12.817  1.00  1.02     C -3.730  -0.680  10.643  1.00  1.63     C 0.168  -1.698  11.078  1.00  0.66     N 1.105  -1.157  10.056  1.00  0.59     C 1.261  -2.172   8.919  1.00  0.48     C 1.135  -1.833   7.757  1.00  0.39     O 2.472  -0.899  10.696  1.00  0.70     C 2.311   0.070  11.868  1.00  0.89     C 3.414  -0.292   9.655  1.00  0.73     C 3.576   0.042  12.728  1.00  1.02     C 1.501  -3.417   9.237  1.00  0.51     N 1.623  -4.439   8.159  1.00  0.45     C 0.328  -4.451   7.349  1.00  0.35     C 0.336  -4.430   6.133  1.00  0.30     O 1.892  -5.820   8.767  1.00  0.52     C 2.302  -6.791   7.659  1.00  1.19     C 0.637  -6.345   9.462  1.00  1.41     C 3.696  -7.344   7.957  1.00  1.86     C -0.789  -4.477   8.027  1.00  0.37     N -2.103  -4.487   7.318  1.00  0.34     C -2.201  -3.263   6.413  1.00  0.29     C -2.590  -3.358   5.265  1.00  0.27     O -3.253  -4.460   8.333  1.00  0.44     C -3.822  -5.850   8.479  1.00  1.05     C -3.093  -6.837   9.156  1.00  1.80     C -5.076  -6.155   7.938  1.00  1.97     C -3.621  -8.128   9.291  1.00  2.57     C -5.604  -7.446   8.075  1.00  2.71     C -4.875  -8.432   8.751  1.00  2.81     C -1.859  -2.109   6.915  1.00  0.30     N -1.943  -0.879   6.079  1.00  0.28     C -1.104  -1.070   4.817  1.00  0.22     C -1.550  -0.792   3.722  1.00  0.23     O 0.104  -1.550   4.950  1.00  0.22     N 0.942  -1.755   3.736  1.00  0.23     C 0.195  -2.684   2.776  1.00  0.22     C 0.059  -2.403   1.600  1.00  0.23     O 2.271  -2.387   4.145  1.00  0.27     C 3.116  -2.654   2.896  1.00  0.33     C 3.021  -1.426   5.071  1.00  0.30     C -0.323  -3.775   3.276  1.00  0.22     N -1.093  -4.701   2.401  1.00  0.23     C -2.254  -3.927   1.772  1.00  0.24     C -2.497  -3.993   0.583  1.00  0.25     O -1.641  -5.858   3.238  1.00  0.26     C -0.477  -6.620   3.877  1.00  0.32     C -1.054  -8.242   4.435  1.00  1.15     S -2.279  -7.655   5.630  1.00  1.83     C -2.967  -3.188   2.581  1.00  0.25     N -4.115  -2.392   2.068  1.00  0.27     C -3.638  -1.442   0.963  1.00  0.26     C -4.262  -1.330  -0.073  1.00  0.27     O -4.760  -1.600   3.215  1.00  0.31     C -2.546  -0.745   1.170  1.00  0.25     N -2.072   0.195   0.118  1.00  0.26     C -1.867  -0.572  -1.186  1.00  0.24     C -2.310  -0.150  -2.235  1.00  0.24     O -1.212  -1.699  -1.139  1.00  0.22     N -1.009  -2.475  -2.397  1.00  0.21     C -2.378  -2.782  -3.017  1.00  0.21     C -2.595  -2.581  -4.197  1.00  0.21     O -0.285  -3.784  -2.087  1.00  0.23     C -0.067  -4.566  -3.383  1.00  0.28     C 1.070  -3.476  -1.444  1.00  0.31     C -3.305  -3.257  -2.227  1.00  0.23     N -4.662  -3.568  -2.763  1.00  0.25     C -5.271  -2.314  -3.399  1.00  0.26     C -5.802  -2.358  -4.489  1.00  0.26     O -5.560  -4.052  -1.623  1.00  0.30     C -5.065  -5.411  -1.127  1.00  0.32     C -6.997  -4.185  -2.129  1.00  0.40     C -5.532  -5.633   0.312  1.00  1.06     C -5.206  -1.200  -2.719  1.00  0.27     N -5.791   0.051  -3.281  1.00  0.30     C -5.162   0.349  -4.642  1.00  0.27     C -5.849   0.643  -5.600  1.00  0.29     O -3.862   0.275  -4.741  1.00  0.24     N -3.207   0.554  -6.047  1.00  0.24     C -3.780  -0.390  -7.108  1.00  0.24     C -4.145   0.027  -8.191  1.00  0.28     O -1.697   0.331  -5.925  1.00  0.25     C -1.204   1.051  -4.804  1.00  0.32     O -1.006   0.823  -7.198  1.00  0.28     C -3.871  -1.656  -6.801  1.00  0.23     N -4.433  -2.617  -7.791  1.00  0.29     C -5.841  -2.166  -8.188  1.00  0.33     C -6.184  -2.117  -9.352  1.00  0.40     O -4.499  -4.013  -7.167  1.00  0.33     C -3.082  -4.578  -7.038  1.00  0.34     C -5.333  -4.932  -8.059  1.00  0.40     C -3.100  -5.798  -6.114  1.00  0.41     C -6.654  -1.829  -7.225  1.00  0.33     N -8.037  -1.372  -7.533  1.00  0.41     C -7.963  -0.162  -8.476  1.00  0.44     C -8.667  -0.089  -9.464  1.00  0.51     O -8.757  -1.028  -6.210  1.00  0.44     C -9.339   0.392  -6.232  1.00  0.76     C -10.556   0.436  -7.156  1.00  1.14     C -9.761   0.789  -4.816  1.00  1.06     C -7.122   0.789  -8.172  1.00  0.40     N -7.009   1.991  -9.048  1.00  0.47     C -6.666   1.556 -10.473  1.00  0.51     C -7.269   2.002 -11.430  1.00  0.60     O -5.906   2.911  -8.516  1.00  0.47     C -5.953   4.248  -9.259  1.00  1.14     C -7.336   4.880  -9.094  1.00  2.02     C -4.897   5.191  -8.680  1.00  1.67     C -5.705   0.686 -10.630  1.00  0.47     N -5.337   0.226 -11.998  1.00  0.57     C -6.564  -0.365 -12.684  1.00  0.65     C -6.864  -0.046 -13.815  1.00  0.77     O -4.238  -0.832 -11.905  1.00  0.55     C -2.979  -0.209 -11.300  1.00  0.51     C -3.921  -1.366 -13.302  1.00  0.66     C -2.013  -1.317 -10.874  1.00  0.54     C -7.285  -1.221 -12.011  1.00  0.63     N -8.491  -1.807 -12.649  1.00  0.76     C -9.415  -0.668 -13.068  1.00  0.83     C -9.898  -0.620 -14.182  1.00  0.95     O -9.216  -2.714 -11.651  1.00  0.74     C -8.356  -2.977 -10.548  1.00  1.53     O -9.649   0.266 -12.187  1.00  0.77     N -10.522   1.415 -12.538  1.00  0.87     C -9.949   2.130 -13.766  1.00  0.94     C -10.659   2.424 -14.708  1.00  1.07     O -10.581   2.390 -11.359  1.00  0.83     C -11.419   3.587 -11.739  1.00  1.09     C -12.800   3.446 -11.923  1.00  1.68     C -10.813   4.838 -11.903  1.00  1.74     C -13.574   4.559 -12.271  1.00  2.03     C -11.588   5.950 -12.253  1.00  1.99     C -12.969   5.811 -12.436  1.00  1.84     C -13.735   6.907 -12.781  1.00  2.25     O -8.671   2.404 -13.767  1.00  0.88     N -8.058   3.094 -14.938  1.00  0.98     C -8.314   2.268 -16.198  1.00  1.10     C -8.734   2.784 -17.215  1.00  1.24     O -8.074   0.988 -16.135  1.00  1.07     N -8.317   0.133 -17.332  1.00  1.22     C -9.781   0.282 -17.758  1.00  1.34     C -10.082   0.472 -18.918  1.00  1.50     O -8.008  -1.334 -16.994  1.00  1.20     C -6.498  -1.567 -17.098  1.00  1.37     C -8.725  -2.266 -17.976  1.00  1.50     C -5.865  -1.466 -15.711  1.00  1.81     C -10.690   0.197 -16.825  1.00  1.29     N -12.136   0.338 -17.174  1.00  1.42     C -12.369   1.681 -17.865  1.00  1.52     C -13.026   1.753 -18.885  1.00  1.68     O -12.990   0.259 -15.904  1.00  1.36     C -14.464   0.431 -16.269  1.00  1.61     C -14.889  -0.683 -17.229  1.00  1.77     C -16.316  -0.490 -17.614  1.00  1.70     N -16.886  -1.329 -18.436  1.00  2.10     C -16.274  -2.432 -18.774  1.00  2.69     N -18.070  -1.069 -18.916  1.00  2.54     N -11.840   2.749 -17.329  1.00  1.43     N -12.046   4.068 -17.986  1.00  1.55     C -11.542   3.958 -19.420  1.00  1.67     C -12.217   4.327 -20.360  1.00  1.83     O -11.257   5.147 -17.238  1.00  1.45     C -11.506   6.507 -17.891  1.00  1.62     C -12.997   6.846 -17.817  1.00  1.72     C -13.258   8.124 -18.536  1.00  2.17     N -14.471   8.607 -18.599  1.00  2.50     C -14.697   9.727 -19.230  1.00  3.17     N -15.457   7.968 -18.031  1.00  2.89     N -10.372   3.410 -19.596  1.00  1.62     N -9.838   3.224 -20.968  1.00  1.76     C -10.847   2.387 -21.754  1.00  1.92     C -11.183   2.698 -22.876  1.00  2.09     O -8.499   2.488 -20.904  1.00  1.69     C -7.456   3.378 -20.230  1.00  1.72     C -6.300   2.514 -19.721  1.00  1.72     C -6.927   4.396 -21.241  1.00  2.01     C -11.311   1.322 -21.144  1.00  1.89     N -12.301   0.398 -21.779  1.00  2.07     C -11.559  -0.755 -22.449  1.00  2.17     C -10.995  -0.619 -23.516  1.00  2.50     O -13.168   1.136 -22.798  1.00  2.14     C -13.786   2.363 -22.124  1.00  2.13     C -14.281   0.207 -23.281  1.00  2.25     C -13.583   3.596 -23.005  1.00  2.38     C -11.549  -1.894 -21.809  1.00  2.25     N -10.840  -3.073 -22.378  1.00  2.60     C -11.762  -3.804 -23.357  1.00  2.97     C -12.864  -4.185 -23.020  1.00  3.27     O -10.447  -4.019 -21.240  1.00  2.80     C -9.148  -4.742 -21.599  1.00  3.38     C -8.868  -5.835 -20.564  1.00  3.94     C -8.754  -7.188 -21.269  1.00  4.56     C -8.755  -8.278 -20.251  1.00  5.22     N -11.317  -3.996 -24.571  1.00  3.27     N -12.165  -4.699 -25.578  1.00  3.83     C -13.408  -3.856 -25.871  1.00  4.00     C -14.436  -4.441 -26.180  1.00  4.36     O -12.597  -6.069 -25.037  1.00  4.43     C -11.369  -6.952 -24.794  1.00  5.03     C -10.711  -7.301 -26.132  1.00  5.77     C -9.211  -7.515 -25.929  1.00  6.68     C -8.981  -8.833 -25.272  1.00  7.38     N -13.313  -2.643 -25.782  1.00  4.28     O href="?node_id=1084358;abspart=1;part=1;displaytype=displaycode">[download]

Let me tell you now the important info for my case, taking the last line as example: The important characters in those lines for me are the A/B character (the chains), the number next to them (66) and the 3rd number after that (16.840).
I can get this info through pattern matching, with the following code:

    while($_=~/ATOM\s+\d+\s+.*?\s+.*?\s+(\w{1})\s+(\d+)\s+[\d\.\-]+\s+
+[\d\.\-]+\s+([\d\.\-]+)\s+.*/mg)
    {
        $chain=$1;
        $position=$2;
        $Zcoordinate=$3;
}
[download]

BUT, what I would need is somehow to be able to keep the info for each chain separately (in this example A and B, but it can be more letters) and also, for each chain only the $Zcoordinate for the smallest position (in this example 66). I was thinking that the idea would be to somehow create an array of $Zcoordinates for each chain and then get the smallest of the positions, but I don't know how to do that (since I can't know beforehand which are the chain numbers...)

Comment on How to select specific lines from a file Select or Download Code

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Re: How to select specific lines from a file by davido (Cardinal) on Apr 29, 2014 at 17:29 UTC
I love it. "Taking the last line..." (which is line 570 of the sample input): 66 occurs in the 6th column of the first row and the 293rd row, 16.840 occurs in the 9th column of line 293 from the sample input, and 'B' occurs on the last row and the 293rd, but not on the first. But a little searching through the sample input resolved any ambiguity. Anyway, this is fixed-width stuff, so you should probably be thinking in terms of unpack or substr rather than regular expressions: `use strict; use warnings; while ( <DATA> ) { next unless /^ATOM\b/; my $chain = substr $_, 21, 1; my $position = 0 + substr $_, 23, 3; my $Zcoordinate = 0 + substr $_, 47, 7; print "$chain, $position, $Zcoordinate\n"; } __DATA__ ATOM 30 N HIS A 66 7.514 15.296 11.222 1.00 12.98 + A N ATOM 31 CA HIS A 66 7.318 14.688 12.568 1.00 12.48 + A C ATOM 32 C HIS A 66 8.676 14.309 13.156 1.00 11.62 + A C ATOM 33 O HIS A 66 9.708 14.518 12.545 1.00 11.76 + A O` [download] Update: Using unpack is a more computationally efficient alternative, though from a programmer standpoint it always takes me longer to work out the template, which is why I posted the substr solution first. Now that I've had time to work out the template for the unpack solution, here it is: while ( <DATA> ) { next unless /^ATOM\b/; my( $chain, $position, $Zcoordinate ) = unpack( 'x21a1xA3x21A7',$_); print "$chain, $position, $Zcoordinate\n"; } __DATA__ ATOM 30 N HIS A 66 7.514 15.296 11.222 1.00 12.98 + A N ATOM 31 CA HIS A 66 7.318 14.688 12.568 1.00 12.48 + A C ATOM 32 C HIS A 66 8.676 14.309 13.156 1.00 11.62 + A C ATOM 33 O HIS A 66 9.708 14.518 12.545 1.00 11.76 + A O ATOM 34 CB HIS A 66 6.450 13.434 12.442 1.00 12.81 + A C ATOM 35 CG HIS A 66 5.000 13.829 12.378 1.00 13.36 + A C ATOM 36 ND1 HIS A 66 4.332 14.002 11.175 1.00 13.57 + A N ATOM 37 CD2 HIS A 66 4.073 14.085 13.360 1.00 13.93 + A C ATOM 38 CE1 HIS A 66 3.063 14.347 11.461 1.00 14.23 + A C ATOM 39 NE2 HIS A 66 2.851 14.410 12.778 1.00 14.47 + A N [download] Whether you use substr, or unpack, you'll then be able to feed the input into a data structure as described by Choroba. Dave	[reply] [d/l] [select]
Re^2: How to select specific lines from a file by Laurent_R (Canon) on Apr 29, 2014 at 21:05 UTC
I love it. "Taking the last line..." (which is line 570 of the sample input): 66 occurs in the 6th column of the first row and the 293rd row, 16.840 occurs in the 9th column of line 293 from the sample input, and 'B' occurs on the last row and the 293rd, but not on the first. You love it? So do I. I also spent a quite bit of time trying to figure out which line the OP was really talking about. Anyway, this is fixed-width stuff, so you should probably be thinking in terms of unpack or substr rather than regular expressions. I definitely agree that unpack or substr are the most efficient solutions in terms of computing resources (especially unpack, most probably). But, picking on your remark about the programmer standpoint, and assuming that the file is just a few hundreds or thousands of lines, I might as well consider a regular expression, but not a regex similar to what the OP posted, but a very simple one in a call to the split function. Sometimes, with data looking similar to the OP's data, I find it easier to use something like: `my ($key, $value, $predicate) = (split /\s+/, $line)[0,3,7];` [download] rather than having to compute the exact position of each piece of data (and testing to make sure that I don't have an off-by-one error). But I am doing that only insofar I am reading a relatively small parameter or reference data file before having to process very large or sometimes huge data sets. (Typically, my reference data files have a few hundred or thousand lines, while the real data files to be analyzed have at least dozens of millions of lines, sometimes hundreds of millions lines. In such cases, I really don't care spending a split second more reading the reference data, if I know that processing the main data will take 20 minutes anyway. In other words, I would most probably use the substr or unpack function for the main data, if appropriate, but I don't mind using a slightly slower process for small reference data if it saves me some development time and make the code easier to understand at first glance when I have to maintain it). But this was just a side note about slightly specific situations, I agree otherwise fully with just about everything that you said.	[reply] [d/l]
Re^3: How to select specific lines from a file by davido (Cardinal) on Apr 29, 2014 at 22:14 UTC
I like your comment, and intend to upvote it. In this specific case it appears that the data set is tame enough that the distinction between fixed-width and space-delimited is moot. However, one general principle that I try to adhere to as much as possible is placing the fewest possible demands on a data set as possible. This concept can be generalized from some lessons I learned by reading Effective STL, where Steve Meyers makes some strong cases for why a template container class should place as few requirements on the objects it contains as possible. I'd love to go into the details, but it's a big enough concept that I probably wouldn't do it justice in a simple PerlMonks node. Let's take it as a given, then, that the generalized practice of placing as few demands on an entity that we don't control as possible is "a good thing". In particular, doing so helps to simplify our parser, allows us to unambiguously reject data that is broken, and probably even makes it easier to generate valid data. So what is the simplest, least demanding set of requirements that we can place on our OP's data? As we look it over, it becomes pretty obvious that it is of fixed-width, and that it is space delimited. ...or is it? What if one of those numeric fields (66, for example) extends to four digits? We already see in his data set places where it extends to three digits. A fourth would cause it to run up against our "`[AB]`" field. So there's one requirement we have to place on the data set; no column can become filled to the point that it touches the one next to it. 1000 is illegal for the 6th field. Maybe this is reasonable, but I don't know. I do know that as 66 grows to 100, the field widths haven't shifted, so that field size must always be four or less. But I don't know if four digits is a possible in-range value. What about blank fields? The user's data set example has no blank fields (that I can detect, though there are some big gaps). `\s+` delimited data requires that every field contain something. There's another demand placed on our data set, or if not placed on the data set, another ambiguity that our parser must deal with. Next, by looking at his data it seems obvious that there cannot be embedded spaces. However, that is not just an observation, it's a requirement placed on the data. If a field ever changes such that it allows embedded spaces, our parser breaks. And if that ever happens, we run into all sorts of additional demands for our data; embedded spaces must be escaped or quoted, quotes must be balanced if used, embedded quotes must be escaped, and so on. This will probably never happen with the user's data set; it may never morph into something more complex. Splitting on space may forever be fine. ...it will have to be fine because the parser now demands it. It can never be permitted to morph into something that includes, for example, a notes field (unless it's in the last position, which is another requirement placed on the data and another rule for the parser), completely full fields, or blank fields. So here are the choices for how we can parse fixed-width data: As fixed width: Must be fixed width. As space delimited: No full fields, no blank fields, no embedded spaces. The first rule seems to be the most likely for this data set. If we treat it as If it's fixed width, we impose only one requirement. And probably that requirement is already part of the implementation of the producer. If we treat fixed width data as space delimited, we impose three additional restrictions on the data. Treat fixed width as fixed width for the most robust solution. Dave	[reply] [d/l] [select]
Re^4: How to select specific lines from a file by Laurent_R (Canon) on Apr 30, 2014 at 06:39 UTC
Re^3: How to select specific lines from a file by monkey_boy (Priest) on Apr 29, 2014 at 21:29 UTC
Although in the example shown here split would be fine, the fields in these types of file (PDB) are not always defined (e.g. sometimes the chain is blank) so substr or unpack is preferable. See the PDB documentation for more info http://www.wwpdb.org/documentation/format33/sect9.html#ATOM This is not a Signature...	[reply]
Re: How to select specific lines from a file by choroba (Cardinal) on Apr 29, 2014 at 17:26 UTC
I'd use a hash of arrays (see perldsc - Perl Data Structures Cookbook). The chain will be the key, there will be two values in each array: the Z-coordinate and the position. Then just iterate the input and test whether the new line should go to the hash or not: `my %hash; while (<>) { my ($chain, $pos, $zcoor) = (split)[4, 5, 8]; $hash{$chain} = [$pos, $zcoor] if not exists $hash{$chain} or $pos < $hash{$chain}[0]; }` [download] لսႽ� ᥲᥒ⚪⟊Ⴙᘓᖇ Ꮅᘓᖇ⎱ Ⴙᥲ𝇋ƙᘓᖇ	[reply] [d/l]
Re^2: How to select specific lines from a file by Anonymous Monk on Apr 29, 2014 at 17:41 UTC
Great, it seems to do the trick... Is it correct that I get all positions in the HoA that you create? `while(<>) %HoA=(); next unless /^ATOM\b/; @split_atom_line=split(/\s+/, $_); $chain=$split_atom_line[4]; $position=$split_atom_line[5]; $Zcoordinate=$split_atom_line[8]; if (not exists $HoA{$chain} or $position < $HoA{$chain}[0]) { $HoA{$chain} = [$position, $Zcoordinate]; } for $key ( keys %HoA ) { print "$key: $HoA{$key}[0]\n"; } }` [download]	[reply] [d/l]
Re^3: How to select specific lines from a file by Anonymous Monk on Apr 29, 2014 at 17:54 UTC
I mean, it keeps adding data although the position and the chain have already been inserted... Shouldn't the HoA contain only two lines in this example, i.e. chains A and B and 1 position for each (the smallest)?	[reply]
Re^4: How to select specific lines from a file by Anonymous Monk on Apr 29, 2014 at 17:59 UTC
Re: How to select specific lines from a file by pvaldes (Chaplain) on Apr 30, 2014 at 00:13 UTC
If you need to parse, write, change and manipulate PDB files you should probably make an effort and consider bioperl. This code is untested and positively wrong, (the docs of BIO::Structure are starting to bite me like a goliath tiger fish), but you can start playing with this.. use strict; use warnings; use Bio::Structure::IO; #use Data::Dumper; my $in = Bio::Structure::IO->new(-file => "myfile.pdb", -format => 'PDB'); while ( my $struc = $in->next_structure() ){ print "Structure: ", $struc->id; for my $model ($struc->get_models){ print "model: ", $model->id; for my $chain ($struc->get_chains) { if($chain->id eq "A"){ print "we have an A!"; foreach my $res ($struc->get_residues($chain)){ print "Yeah, Honestly, I don't know what I'm doing here"; foreach my $atom ($struc->get_atoms($res)){ print "This is the ATOM ",$atom->id;} } } last; } last; }} [download] mmmh, or maybe use Chemistry::File::PDB?	[reply] [d/l]

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