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Write PDB with mmCIF resseq and without icode #4335

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EdwardTran121 opened this issue Jun 19, 2023 · 1 comment · May be fixed by #4390
Open

Write PDB with mmCIF resseq and without icode #4335

EdwardTran121 opened this issue Jun 19, 2023 · 1 comment · May be fixed by #4390

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@EdwardTran121
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Hello, I am trying to write PDB file with new resseq (not author resseq) from mmcif file. Because of the new resseq, icode is not needed for me. I used FastMMCIFParser(auth_residues = False, QUIET = True) to get structure, and tried to write pdb with PDBIO(). However, the icode is still inserted into the resseq in the file. Can this be removed during the reading or writing?
I am using biopython version 1.81.
This is my code:

parser = FastMMCIFParser(auth_residues = False, QUIET = True)
structure = parser.get_structure('1adq','1adq.cif')
io = PDBIO()
io.set_structure(structure)
io.save('test.pdb')

This is the result at the end of chain H:

ATOM   3302  N   VAL H 223      20.852  57.112  63.569  1.00 68.80           N  
ATOM   3303  CA  VAL H 223      21.846  57.383  62.539  1.00 68.80           C  
ATOM   3304  C   VAL H 223      22.286  58.838  62.735  1.00 68.80           C  
ATOM   3305  O   VAL H 223      21.502  59.664  63.217  1.00 68.80           O  
ATOM   3306  CB  VAL H 223      21.228  57.215  61.122  0.00 68.80           C  
ATOM   3307  CG1 VAL H 223      22.314  57.097  60.070  0.00 68.80           C  
ATOM   3308  CG2 VAL H 223      20.322  55.995  61.077  0.00 68.80           C  
ATOM   3309  N   PRO H 224A     23.563  59.157  62.446  1.00 68.80           N  
ATOM   3310  CA  PRO H 224A     24.043  60.536  62.608  1.00 68.80           C  
ATOM   3311  C   PRO H 224A     23.350  61.529  61.661  1.00 68.80           C  
ATOM   3312  O   PRO H 224A     22.268  61.242  61.132  1.00 68.80           O  
ATOM   3313  CB  PRO H 224A     25.539  60.410  62.314  0.00 68.80           C  
ATOM   3314  CG  PRO H 224A     25.601  59.251  61.375  0.00 68.80           C  
ATOM   3315  CD  PRO H 224A     24.664  58.275  62.029  0.00 68.80           C  
ATOM   3316  N   LEU H 225B     23.962  62.697  61.469  1.00 68.80           N  
ATOM   3317  CA  LEU H 225B     23.395  63.728  60.602  1.00 68.80           C  
ATOM   3318  C   LEU H 225B     24.182  63.864  59.302  1.00 68.80           C  
ATOM   3319  O   LEU H 225B     23.722  64.623  58.423  1.00 68.80           O  
ATOM   3320  CB  LEU H 225B     23.339  65.080  61.329  0.00 68.80           C  
ATOM   3321  CG  LEU H 225B     24.642  65.784  61.725  0.00 68.80           C  
ATOM   3322  CD1 LEU H 225B     24.357  67.244  62.032  0.00 68.80           C  
ATOM   3323  CD2 LEU H 225B     25.291  65.101  62.919  0.00 68.80           C  
ATOM   3324  OXT LEU H 225B     25.245  63.217  59.178  0.00 68.80           O  
TER    3325      LEU H 225B                                                      
END

Thank you
@speleo3
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speleo3 commented Jul 27, 2023

Seems reasonable. The docstring of MMCIFParser actually says:

auth_residues [...] If false, use the mmCIF "label" residue numbering, which has no insertion codes, and strictly increments residue numbers.

So I would also expect that auth_residues=False implies no insertion codes.

speleo3 added a commit to speleo3/biopython that referenced this issue Jul 27, 2023
@speleo3
No insertion codes with auth_residues=False
f0758f2 
Closes biopython#4335
speleo3 added a commit to speleo3/biopython that referenced this issue Jul 27, 2023
@speleo3
No insertion codes with auth_residues=False
d267edd 
Closes biopython#4335
@speleo3 speleo3 linked a pull request Jul 27, 2023 that will close this issue
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No insertion codes with auth_residues=False speleo3/biopython
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@speleo3 @EdwardTran121