Error during parsing PDB using Biopython.

Question

[Manvitha Reddy]

parser.get_structure() doesn't return any structure for some self-generated PDB files. It does work for some file but not all of them. I have checked several websites for the solution but couldn't find any.

def getModel(pdb_filename):
    pdb_code = "pdb"
    print(pdb_code,pdb_filename)
    parser=PDBParser(QUIET=True)
    structure = parser.get_structure(pdb_code, pdb_filename)
    model = structure[0]
    return model

This is my code. Please help.

[Joe]

Can you provide an example of a file that works and one that doesn’t?

[Manvitha Reddy]

ATOM      1  N   MET     1       4.672   7.838  34.130  1.00  0.00      PROA
ATOM      2  CA  MET     1       5.235   9.161  34.540  1.00  0.00      PROA
ATOM      3  CB  MET     1       6.146   8.997  35.790  1.00  1.00      PROA
ATOM      4  CG  MET     1       7.248   7.908  35.710  1.00  1.00      PROA
ATOM      5  SD  MET     1       6.681   6.195  35.973  1.00  1.00      PROA
ATOM      6  CE  MET     1       7.885   5.379  34.886  1.00  1.00      PROA
ATOM      7  C   MET     1       5.952   9.846  33.388  1.00  0.00      PROA
ATOM      8  O   MET     1       6.014   9.289  32.299  1.00  0.00      PROA

These are the coordinates for the first AA in the file that is working.

ATOM 359965  N   MET     1       4.376   7.836  34.434  1.00  0.00      PROA
ATOM 359966  CA  MET     1       5.020   9.146  34.745  1.00  0.00      PROA
ATOM 359967  CB  MET     1       6.070   9.001  35.890  1.00  1.00      PROA
ATOM 359968  CG  MET     1       7.219   7.989  35.650  1.00  1.00      PROA
ATOM 359969  SD  MET     1       6.799   6.260  36.039  1.00  1.00      PROA
ATOM 359970  CE  MET     1       8.096   5.498  35.022  1.00  1.00      PROA
ATOM 359971  C   MET     1       5.663   9.802  33.542  1.00  0.00      PROA
ATOM 359972  O   MET     1       5.648   9.247  32.441  1.00  0.00      PROA

These are the coordinates for the second conformation of the same amino acid in the same protein

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.