[BioPython] BioPDB problem

Hua Wong wong at ebgm.jussieu.fr
Fri Jun 18 06:01:23 EDT 2004


I have a PDB file that count 3145 atoms [1...3145], and using BioPDB I try to get all the coordinate.

So I use the example:
parser=PDBParser()
structure=parser.get_structure('0b','0b.pdb')

liste=[]
for model in structure.get_iterator():
	for chain in model.get_iterator():
		for residue in chain.get_iterator():
			for atom in residue.get_iterator():
				a=atom.get_coord()
				liste.append(a)
To obtain a list of array representing the x y and z

But I can't have all the atoms. The liste[] list is 3144 which seems ok [0...3144]
But when I want to display the 3144th atom I obtain:
>>> len(liste)
3144
>>> liste[3144]
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
IndexError: list index out of range

The lastest atoms he accepts to display is 3143th.
Am I doing something wrong?

Thanks.


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