pythonbiopythonprotein-database

How to separately get the X, Y or Z coordinates from a pdb file


I have a PDB file '1abz' (https://files.rcsb.org/view/1ABZ.pdb), which is containing the coordinates of a protein structure. Please ignore the lines of the header remarks, the interesting information starts at line 276 which says 'MODEL 1'.

I would like to separately get the X, Y or Z coordinates from a pdb file.

This link explains the column numbers of a pdb file: http://cupnet.net/pdb-format/

This is the code that I have but I got an error message.

from Bio import PDB

parser = PDB.PDBParser()
io = PDB.PDBIO()
struct = parser.get_structure('1abz','1abz.pdb')

for model in struct:
    for chain in model:
        for residue in chain:
            for atom in residue:
                XYZ = atom.get_coord()
                for line in XYZ:
                    x_coord = float(line[30:38].strip())
                    y_coord = float(line[38:46].strip())
                    z_coord = float(line[46:54].strip())
                    print x_coord
                    print y_coord
                    print z_coord

Solution

  • >>> Bio.__version__
    '1.69'
    

    from Bio import PDB
    
    parser = PDB.PDBParser()
    io = PDB.PDBIO()
    struct = parser.get_structure('1ABZ','1ABZ.pdb')
    
    for model in struct:
        for chain in model:
            for residue in chain:
                for atom in residue:
                    x,y,z = atom.get_coord()
                    print(x,y,z)
    

    Result:

    15.254 -0.607 3.211
    16.429 -0.874 3.019
    14.337 -1.034 2.53
    14.908 0.287 4.404
    13.772 1.237 4.018
    12.591 1.037 4.971
    11.729 0.213 4.737
    15.778 0.862 4.685
    14.596 -0.326 5.237
    13.458 1.028 3.007
    14.118 2.259 4.084
    ...