yseif
commented
6 years ago from Bio.PDB import *
parser = MMCIFParser()
structure = parser.get_structure('test','4C13.cif')
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
<ipython-input-162-a4d420356111> in <module>()
1 from Bio.PDB import *
2 parser = MMCIFParser()
----> 3 structure = parser.get_structure('test','4C13.cif')
/usr/local/lib/python2.7/dist-packages/Bio/PDB/MMCIFParser.pyc in get_structure(self, structure_id, filename)
62 warnings.filterwarnings("ignore", category=PDBConstructionWarning)
63 self._mmcif_dict = MMCIF2Dict(filename)
---> 64 self._build_structure(structure_id)
65
66 return self._structure_builder.get_structure()
/usr/local/lib/python2.7/dist-packages/Bio/PDB/MMCIFParser.pyc in _build_structure(self, structure_id)
184 element = element_list[i] if element_list else None
185 structure_builder.init_atom(name, coord, tempfactor, occupancy, altloc,
--> 186 name, element=element)
187 if aniso_flag == 1:
188 u = (aniso_u11[i], aniso_u12[i], aniso_u13[i],
/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.pyc in init_atom(self, name, coord, b_factor, occupancy, altloc, fullname, serial_number, element)
202 PDBConstructionWarning)
203 self.atom = Atom(name, coord, b_factor, occupancy, altloc,
--> 204 fullname, serial_number, element)
205 if altloc != " ":
206 # The atom is disordered
/usr/local/lib/python2.7/dist-packages/Bio/PDB/Atom.pyc in __init__(self, name, coord, bfactor, occupancy, altloc, fullname, serial_number, element)
68 self.xtra = {}
69 assert not element or element == element.upper(), element
---> 70 self.element = self._assign_element(element)
71 self.mass = self._assign_atom_mass()
72
/usr/local/lib/python2.7/dist-packages/Bio/PDB/Atom.pyc in _assign_element(self, element)
84 # Hs may have digit in [0]
85 if self.name[0].isdigit():
---> 86 putative_element = self.name[1]
87 else:
88 putative_element = self.name[0]
IndexError: string index out of range
This issue will be left open for all PDBs that have strange errors...
ID: 5nc5 Problem: Biopython loading of mmcif file fails, says duplicated atom name