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Issue when residue numbers > 999 #18

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danielguion opened this issue Sep 30, 2024 · 1 comment
Open

Issue when residue numbers > 999 #18

danielguion opened this issue Sep 30, 2024 · 1 comment

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@danielguion
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I see this error when processing pdb files with residue numbers into the thousands, which shifts over column placement starting at the residue number:

Input:

ATOM  16105 N    GLN D 998      43.421 -12.294 -52.399  1.00  0.00      PROT N 0
ATOM  16106 H    GLN D 998      42.753 -12.039 -51.685  1.00  0.00      PROT H 0
ATOM  16107 CA   GLN D 998      43.531 -13.687 -52.800  1.00  0.00      PROT C 0
ATOM  16108 HA   GLN D 998      44.572 -13.996 -52.704  1.00  0.00      PROT H 0
ATOM  16109 CB   GLN D 998      42.668 -14.596 -51.921  1.00  0.00      PROT C 0
ATOM  16110 HB2  GLN D 998      42.994 -14.478 -50.888  1.00  0.00      PROT H 0
ATOM  16111 HB3  GLN D 998      41.631 -14.269 -51.997  1.00  0.00      PROT H 0
ATOM  16112 CG   GLN D 998      42.738 -16.107 -52.280  1.00  0.00      PROT C 0
ATOM  16113 HG2  GLN D 998      42.017 -16.645 -51.665  1.00  0.00      PROT H 0
ATOM  16114 HG3  GLN D 998      42.470 -16.233 -53.329  1.00  0.00      PROT H 0
ATOM  16115 CD   GLN D 998      44.120 -16.708 -52.047  1.00  0.00      PROT C 0
ATOM  16116 OE1  GLN D 998      44.916 -16.216 -51.221  1.00  0.00      PROT O 0
ATOM  16117 NE2  GLN D 998      44.433 -17.744 -52.793  1.00  0.00      PROT N 0
ATOM  16118 HE21 GLN D 998      43.767 -18.105 -53.461  1.00  0.00      PROT H 0
ATOM  16119 HE22 GLN D 998      45.340 -18.179 -52.698  1.00  0.00      PROT H 0
ATOM  16120 C    GLN D 998      43.114 -13.820 -54.271  1.00  0.00      PROT C 0
ATOM  16121 O    GLN D 998      43.733 -14.588 -54.959  1.00  0.00      PROT O 0
ATOM  16122 N    CYS D 999      42.055 -13.130 -54.739  1.00  0.00      PROT N 0
ATOM  16123 H    CYS D 999      41.485 -12.589 -54.104  1.00  0.00      PROT H 0
ATOM  16124 CA   CYS D 999      41.725 -13.164 -56.189  1.00  0.00      PROT C 0
ATOM  16125 HA   CYS D 999      41.494 -14.195 -56.458  1.00  0.00      PROT H 0
ATOM  16126 CB   CYS D 999      40.490 -12.316 -56.469  1.00  0.00      PROT C 0
ATOM  16127 HB2  CYS D 999      40.592 -11.362 -55.952  1.00  0.00      PROT H 0
ATOM  16128 HB3  CYS D 999      40.417 -12.135 -57.541  1.00  0.00      PROT H 0
ATOM  16129 SG   CYS D 999      38.962 -13.138 -55.897  1.00  0.00      PROT S 0
ATOM  16130 HG   CYS D 999      38.881 -13.052 -54.566  1.00  0.00      PROT H 0
ATOM  16131 C    CYS D 999      42.893 -12.688 -57.084  1.00  0.00      PROT C 0
ATOM  16132 O    CYS D 999      43.214 -13.299 -58.083  1.00  0.00      PROT O 0
ATOM  16133 N    ILE D1000      43.525 -11.581 -56.717  1.00  0.00      PROT N 0
ATOM  16134 H    ILE D1000      43.197 -11.085 -55.900  1.00  0.00      PROT H 0
ATOM  16135 CA   ILE D1000      44.675 -11.048 -57.443  1.00  0.00      PROT C 0
ATOM  16136 HA   ILE D1000      44.372 -10.902 -58.480  1.00  0.00      PROT H 0
ATOM  16137 CB   ILE D1000      45.031  -9.669 -56.863  1.00  0.00      PROT C 0
ATOM  16138 HB   ILE D1000      45.126  -9.776 -55.782  1.00  0.00      PROT H 0
ATOM  16139 CG2  ILE D1000      46.381  -9.195 -57.407  1.00  0.00      PROT C 0
ATOM  16140 HG21 ILE D1000      46.619  -8.218 -56.988  1.00  0.00      PROT H 0
ATOM  16141 HG22 ILE D1000      46.329  -9.121 -58.493  1.00  0.00      PROT H 0
ATOM  16142 HG23 ILE D1000      47.156  -9.909 -57.128  1.00  0.00      PROT H 0
ATOM  16143 CG1  ILE D1000      43.878  -8.670 -57.141  1.00  0.00      PROT C 0
ATOM  16144 HG12 ILE D1000      43.932  -8.369 -58.187  1.00  0.00      PROT H 0
ATOM  16145 HG13 ILE D1000      42.929  -9.178 -56.973  1.00  0.00      PROT H 0
ATOM  16146 CD1  ILE D1000      43.915  -7.427 -56.291  1.00  0.00      PROT C 0
ATOM  16147 HD11 ILE D1000      43.074  -6.784 -56.550  1.00  0.00      PROT H 0
ATOM  16148 HD12 ILE D1000      44.849  -6.893 -56.469  1.00  0.00      PROT H 0
ATOM  16149 HD13 ILE D1000      43.850  -7.704 -55.239  1.00  0.00      PROT H 0
ATOM  16150 C    ILE D1000      45.845 -12.055 -57.436  1.00  0.00      PROT C 0
ATOM  16151 O    ILE D1000      46.413 -12.398 -58.501  1.00  0.00      PROT O 0
ATOM  16152 N    LYS D1001      46.113 -12.622 -56.269  1.00  0.00      PROT N 0
ATOM  16153 H    LYS D1001      45.602 -12.352 -55.440  1.00  0.00      PROT H 0
ATOM  16154 CA   LYS D1001      47.138 -13.624 -56.197  1.00  0.00      PROT C 0
ATOM  16155 HA   LYS D1001      48.096 -13.172 -56.454  1.00  0.00      PROT H 0
ATOM  16156 CB   LYS D1001      47.197 -14.127 -54.786  1.00  0.00      PROT C 0
ATOM  16157 HB2  LYS D1001      46.312 -14.737 -54.605  1.00  0.00      PROT H 0
ATOM  16158 HB3  LYS D1001      47.173 -13.272 -54.111  1.00  0.00      PROT H 0
ATOM  16159 CG   LYS D1001      48.417 -14.960 -54.465  1.00  0.00      PROT C 0
ATOM  16160 HG2  LYS D1001      48.629 -15.647 -55.284  1.00  0.00      PROT H 0
ATOM  16161 HG3  LYS D1001      49.276 -14.311 -54.294  1.00  0.00      PROT H 0
ATOM  16162 CD   LYS D1001      48.094 -15.740 -53.196  1.00  0.00      PROT C 0
ATOM  16163 HD2  LYS D1001      47.247 -15.262 -52.703  1.00  0.00      PROT H 0
ATOM  16164 HD3  LYS D1001      47.813 -16.757 -53.471  1.00  0.00      PROT H 0
ATOM  16165 CE   LYS D1001      49.220 -15.799 -52.239  1.00  0.00      PROT C 0
ATOM  16166 HE2  LYS D1001      48.845 -16.077 -51.254  1.00  0.00      PROT H 0
ATOM  16167 HE3  LYS D1001      49.700 -14.822 -52.182  1.00  0.00      PROT H 0
ATOM  16168 NZ   LYS D1001      50.201 -16.804 -52.694  1.00  0.00      PROT N 0
ATOM  16169 HZ1  LYS D1001      51.133 -16.497 -52.454  1.00  0.00      PROT H 0
ATOM  16170 HZ2  LYS D1001      50.011 -17.688 -52.244  1.00  0.00      PROT H 0
ATOM  16171 HZ3  LYS D1001      50.131 -16.914 -53.695  1.00  0.00      PROT H 0
ATOM  16172 C    LYS D1001      46.869 -14.798 -57.141  1.00  0.00      PROT C 0
ATOM  16173 O    LYS D1001      47.773 -15.266 -57.875  1.00  0.00      PROT O 0

output:

ATOM  16105  N   GLN D 998      43.421 -12.294 -52.399 -0.126  1.550
ATOM  16106  H   GLN D 998      42.753 -12.039 -51.685  0.081  1.200
ATOM  16107  CA  GLN D 998      43.531 -13.687 -52.800  0.016  1.700
ATOM  16108  HA  GLN D 998      44.572 -13.996 -52.704  0.073  1.200
ATOM  16109  CB  GLN D 998      42.668 -14.596 -51.921  0.006  1.700
ATOM  16110  HB2 GLN D 998      42.994 -14.478 -50.888  0.070  1.200
ATOM  16111  HB3 GLN D 998      41.631 -14.269 -51.997  0.069  1.200
ATOM  16112  CG  GLN D 998      42.738 -16.107 -52.280  0.005  1.700
ATOM  16113  HG2 GLN D 998      42.017 -16.645 -51.665  0.067  1.200
ATOM  16114  HG3 GLN D 998      42.470 -16.233 -53.329  0.068  1.200
ATOM  16115  CD  GLN D 998      44.120 -16.708 -52.047  0.023  1.700
ATOM  16116  OE1 GLN D 998      44.916 -16.216 -51.221 -0.254  1.520
ATOM  16117  NE2 GLN D 998      44.433 -17.744 -52.793 -0.134  1.550
ATOM  16118 HE21 GLN D 998      43.767 -18.105 -53.461  0.073  1.200
ATOM  16119 HE22 GLN D 998      45.340 -18.179 -52.698  0.074  1.200
ATOM  16120  C   GLN D 998      43.114 -13.820 -54.271  0.029  1.700
ATOM  16121  O   GLN D 998      43.733 -14.588 -54.959 -0.254  1.520
ATOM  16122  N   CYS D 999      42.055 -13.130 -54.739 -0.128  1.550
ATOM  16123  H   CYS D 999      41.485 -12.589 -54.104  0.080  1.200
ATOM  16124  CA  CYS D 999      41.725 -13.164 -56.189  0.011  1.700
ATOM  16125  HA  CYS D 999      41.494 -14.195 -56.458  0.068  1.200
ATOM  16126  CB  CYS D 999      40.490 -12.316 -56.469  0.000  1.700
ATOM  16127  HB2 CYS D 999      40.592 -11.362 -55.952  0.064  1.200
ATOM  16128  HB3 CYS D 999      40.417 -12.135 -57.541  0.059  1.200
ATOM  16129  SG  CYS D 999      38.962 -13.138 -55.897 -0.182  1.800
ATOM  16130  HG  CYS D 999      38.881 -13.052 -54.566  0.073  1.200
ATOM  16131  C   CYS D 999      42.893 -12.688 -57.084  0.022  1.700
ATOM  16132  O   CYS D 999      43.214 -13.299 -58.083 -0.259  1.520
ATOM  16133  N   ILE D 1000      43.525 -11.581 -56.717 -0.134  1.550
ATOM  16134  H   ILE D 1000      43.197 -11.085 -55.900  0.073  1.200
ATOM  16135  CA  ILE D 1000      44.675 -11.048 -57.443  0.004  1.700
ATOM  16136  HA  ILE D 1000      44.372 -10.902 -58.480  0.061  1.200
ATOM  16137  CB  ILE D 1000      45.031  -9.669 -56.863 -0.008  1.700
ATOM  16138  HB  ILE D 1000      45.126  -9.776 -55.782  0.063  1.200
ATOM  16139  CG2 ILE D 1000      46.381  -9.195 -57.407 -0.014  1.700
ATOM  16140 HG21 ILE D 1000      46.619  -8.218 -56.988  0.055  1.200
ATOM  16141 HG22 ILE D 1000      46.329  -9.121 -58.493  0.054  1.200
ATOM  16142 HG23 ILE D 1000      47.156  -9.909 -57.128  0.060  1.200
ATOM  16143  CG1 ILE D 1000      43.878  -8.670 -57.141 -0.017  1.700
ATOM  16144 HG12 ILE D 1000      43.932  -8.369 -58.187  0.049  1.200
ATOM  16145 HG13 ILE D 1000      42.929  -9.178 -56.973  0.055  1.200
ATOM  16146  CD1 ILE D 1000      43.915  -7.427 -56.291 -0.021  1.700
ATOM  16147 HD11 ILE D 1000      43.074  -6.784 -56.550  0.048  1.200
ATOM  16148 HD12 ILE D 1000      44.849  -6.893 -56.469  0.051  1.200
ATOM  16149 HD13 ILE D 1000      43.850  -7.704 -55.239  0.056  1.200
ATOM  16150  C   ILE D 1000      45.845 -12.055 -57.436  0.023  1.700
ATOM  16151  O   ILE D 1000      46.413 -12.398 -58.501 -0.257  1.520
ATOM  16152  N   LYS D 1001      46.113 -12.622 -56.269 -0.130  1.550
ATOM  16153  H   LYS D 1001      45.602 -12.352 -55.440  0.078  1.200
ATOM  16154  CA  LYS D 1001      47.138 -13.624 -56.197  0.012  1.700
ATOM  16155  HA  LYS D 1001      48.096 -13.172 -56.454  0.069  1.200
ATOM  16156  CB  LYS D 1001      47.197 -14.127 -54.786  0.001  1.700
ATOM  16157  HB2 LYS D 1001      46.312 -14.737 -54.605  0.067  1.200
ATOM  16158  HB3 LYS D 1001      47.173 -13.272 -54.111  0.066  1.200
ATOM  16159  CG  LYS D 1001      48.417 -14.960 -54.465 -0.001  1.700
ATOM  16160  HG2 LYS D 1001      48.629 -15.647 -55.284  0.068  1.200
ATOM  16161  HG3 LYS D 1001      49.276 -14.311 -54.294  0.065  1.200
ATOM  16162  CD  LYS D 1001      48.094 -15.740 -53.196 -0.002  1.700
ATOM  16163  HD2 LYS D 1001      47.247 -15.262 -52.703  0.064  1.200
ATOM  16164  HD3 LYS D 1001      47.813 -16.757 -53.471  0.065  1.200
ATOM  16165  CE  LYS D 1001      49.220 -15.799 -52.239  0.001  1.700
ATOM  16166  HE2 LYS D 1001      48.845 -16.077 -51.254  0.065  1.200
ATOM  16167  HE3 LYS D 1001      49.700 -14.822 -52.182  0.064  1.200
ATOM  16168  NZ  LYS D 1001      50.201 -16.804 -52.694 -0.140  1.550
ATOM  16169  HZ1 LYS D 1001      51.133 -16.497 -52.454  0.073  1.200
ATOM  16170  HZ2 LYS D 1001      50.011 -17.688 -52.244  0.072  1.200
ATOM  16171  HZ3 LYS D 1001      50.131 -16.914 -53.695  0.074  1.200
ATOM  16172  C   LYS D 1001      46.869 -14.798 -57.141  0.028  1.700
ATOM  16173  O   LYS D 1001      47.773 -15.266 -57.875 -0.253  1.520
@krab1k
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krab1k commented Oct 3, 2024

The output is not in PDB format but in PQR, which, to my knowledge, has no exact definition. The exact format ChargeFW2 uses conforms to specifications, which are whitespace-delimited:
https://docs.mdanalysis.org/1.0.0/documentation_pages/coordinates/PQR.html
https://apbs.readthedocs.io/en/latest/formats/pqr.html

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