Hello, I searched for a similar issue but could not find it.
I would like to use pdbfixer on a pdbx/mmcif file. But when I try to read it i get this error message:
Traceback (most recent call last):
File "path/to/my/executable.py", line 119, in <module>
fixer = pdbfixer.PDBFixer(pdbxfile= f)
File "path/to/my/conda/env/lib/python3.6/site-packages/pdbfixer/pdbfixer.py", line 254, in __init__
self._initializeFromPDBx(pdbxfile)
File "path/to/my/conda/env/lib/python3.6/site-packages/pdbfixer/pdbfixer.py", line 335, in _initializeFromPDBx
asymIdCol = modData.getAttributeIndex('label_asym_id')
AttributeError: 'NoneType' object has no attribute 'getAttributeIndex'
The code I wrote is incredibly simple (1fkb.cif is in my working dir, downloaded from the wwPDB database):
import pdbfixer
with open('1fkb.cif', 'r') as f:
fixer = pdbfixer.PDBFixer(pdbxfile= f)
I am using pdbfixer version 1.6 and openmm version 7.4.0 both installed through conda
Any tips on what I got wrong or on how to avoid the problem?
Hello, I searched for a similar issue but could not find it. I would like to use pdbfixer on a pdbx/mmcif file. But when I try to read it i get this error message:
The code I wrote is incredibly simple (1fkb.cif is in my working dir, downloaded from the wwPDB database):
I am using pdbfixer version 1.6 and openmm version 7.4.0 both installed through conda
Any tips on what I got wrong or on how to avoid the problem?