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haddocking / pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.
https://haddocking.github.io/pdb-tools/
Apache License 2.0
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pdb_delinsertion #62

Closed joaomcteixeira closed 4 years ago

joaomcteixeira commented 4 years ago

Describe the bug I found an example where pdb_delinsert fails to renumber residues properly.

To Reproduce

pdb_fetch.py 1FIW > 1FIW.pdb
pdb_delinsertion 1FIW.pdb > 1FIWdi.pdb

Now if you look for this particular region of the PDB results side by side (parsed|original):

   4 ATOM    192  N   ASN A  42      27.347  48.999  55.631  1.00 48.07  | 804 ATOM    192  N   ASN A  37E     27.347  48.999  55.631  1.00 48.07
   5 ATOM    193  CA  ASN A  42      27.379  47.849  56.520  1.00 47.93  | 805 ATOM    193  CA  ASN A  37E     27.379  47.849  56.520  1.00 47.93
   6 ATOM    194  C   ASN A  42      28.507  47.861  57.542  1.00 47.95  | 806 ATOM    194  C   ASN A  37E     28.507  47.861  57.542  1.00 47.95
   7 ATOM    195  O   ASN A  42      28.776  46.838  58.158  1.00 47.97  | 807 ATOM    195  O   ASN A  37E     28.776  46.838  58.158  1.00 47.97
   8 ATOM    196  CB  ASN A  42      27.457  46.565  55.699  1.00 48.23  | 808 ATOM    196  CB  ASN A  37E     27.457  46.565  55.699  1.00 48.23
   9 ATOM    197  CG  ASN A  42      28.679  46.532  54.799  1.00 49.30  | 809 ATOM    197  CG  ASN A  37E     28.679  46.532  54.799  1.00 49.30
  10 ATOM    198  OD1 ASN A  42      28.735  45.785  53.819  1.00 49.23  | 810 ATOM    198  OD1 ASN A  37E     28.735  45.785  53.819  1.00 49.23
  11 ATOM    199  ND2 ASN A  42      29.652  47.383  55.105  1.00 46.68  | 811 ATOM    199  ND2 ASN A  37E     29.652  47.383  55.105  1.00 46.68
  12 ATOM    200  N   ASN A  42      29.131  49.027  57.731  1.00 47.02  | 812 ATOM    200  N   ASN A  37F     29.131  49.027  57.731  1.00 47.02
  13 ATOM    201  CA  ASN A  42      30.270  49.222  58.620  1.00 45.87  | 813 ATOM    201  CA  ASN A  37F     30.270  49.222  58.620  1.00 45.87
  14 ATOM    202  C   ASN A  42      31.421  48.278  58.483  1.00 42.93  | 814 ATOM    202  C   ASN A  37F     31.421  48.278  58.483  1.00 42.93
  15 ATOM    203  O   ASN A  42      32.113  48.092  59.431  1.00 40.20  | 815 ATOM    203  O   ASN A  37F     32.113  48.092  59.431  1.00 40.20
  16 ATOM    204  CB  ASN A  42      29.920  49.170  60.087  1.00 48.11  | 816 ATOM    204  CB  ASN A  37F     29.920  49.170  60.087  1.00 48.11
  17 ATOM    205  CG  ASN A  42      28.801  50.098  60.452  1.00 52.88  | 817 ATOM    205  CG  ASN A  37F     28.801  50.098  60.452  1.00 52.88
  18 ATOM    206  OD1 ASN A  42      28.709  51.223  59.955  1.00 55.93  | 818 ATOM    206  OD1 ASN A  37F     28.709  51.223  59.955  1.00 55.93
  19 ATOM    207  ND2 ASN A  42      27.927  49.637  61.337  1.00 57.46  | 819 ATOM    207  ND2 ASN A  37F     27.927  49.637  61.337  1.00 57.46

You will see that it fails to separate those two asparagines. I haven't scan the whole 1FIW but other residues seem working.

Desktop (please complete the following information):

joaomcteixeira commented 4 years ago

I haven't inspected much yet, but it seems pdb_delinsertion does not like two consecutive residues of the same type.