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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_tidy` does not correct `MODEL` records #118

Closed rvhonorato closed 2 years ago

rvhonorato commented 2 years ago

Describe the bug When running pdb_tidy on a PDB in which the MODEL record is incorrectly formatted (wrong position of the model identifier) it is not corrected. We identified this on https://github.com/haddocking/haddock3/issues/221

To Reproduce Using this PDB

$ less incorrect_model.pdb
MODEL 1
ATOM      1  N   ASP     1      -0.610  -1.825  -0.630  1.00 15.00      B
ATOM      2  HN  ASP     1      -0.690  -2.310  -1.478  1.00 15.00      B
ATOM      3  CA  ASP     1      -0.051  -0.476  -0.630  1.00 15.00      B
ATOM      4  CB  ASP     1      -0.586   0.337   0.582  1.00 15.00      B
ATOM      5  CG  ASP     1      -0.126   1.802   0.652  1.00 15.00      B
ATOM      6  OD1 ASP     1      -0.007   2.453  -0.406  1.00 15.00      B
ATOM      7  OD2 ASP     1       0.165   2.283   1.767  1.00 15.00      B
ATOM      8  C   ASP     1       1.360  -0.472  -0.590  1.00 15.00      B
ATOM      9  O   ASP     1       2.096  -1.275  -1.374  1.00 15.00      B
$ pdb_tidy incorrect_model.pdb 
MODEL 1                                                                         
ATOM      1  N   ASP     1      -0.610  -1.825  -0.630  1.00 15.00      B       
ATOM      2  HN  ASP     1      -0.690  -2.310  -1.478  1.00 15.00      B       
ATOM      3  CA  ASP     1      -0.051  -0.476  -0.630  1.00 15.00      B       
ATOM      4  CB  ASP     1      -0.586   0.337   0.582  1.00 15.00      B       
ATOM      5  CG  ASP     1      -0.126   1.802   0.652  1.00 15.00      B       
ATOM      6  OD1 ASP     1      -0.007   2.453  -0.406  1.00 15.00      B       
ATOM      7  OD2 ASP     1       0.165   2.283   1.767  1.00 15.00      B       
ATOM      8  C   ASP     1       1.360  -0.472  -0.590  1.00 15.00      B       
ATOM      9  O   ASP     1       2.096  -1.275  -1.374  1.00 15.00      B

Expected behavior

MODEL 1

be changed to

MODEL        1

Desktop (please complete the following information):

$ pip show pdb-tools
Name: pdb-tools
Version: 2.4.1
(...)
joaomcteixeira commented 2 years ago

Thanks Rodrigo. I am going to address that now.