CIF to PDB: issue in pdb_fromcif for predicted structures

[venzera]

Hi!

When i use pdb_fromcif.py it gets:
Traceback (most recent call last): File "pdb_fromcif.py", line 261, in <module> main() File "pdb_fromcif.py", line 240, in main for lineno, line in enumerate(new_pdb): File "pdb_fromcif.py", line 179, in run charge = fields[labels.get('_atom_site.pdbx_formal_charge')] ~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ TypeError: list indices must be integers or slices, not NoneType

There is no charge fields in cif files from Chai-1 or AF3 predictions (maybe in all cif files in general, idk).
It can be solved by simply removing lines 179-184:

charge = fields[labels.get('_atom_site.pdbx_formal_charge')]
try:
    charge = charge
    except ValueError:
    charge = '  '

and changing line 187 into
atom_line = _a.format(record, serial, atname, altloc, resname, chainid, resnum, icode, x, y, z, occ, bfactor, segid, element)

I hope it will be useful, since most of the tools still require pdb format.
Sorry, if it is mentioned before.

[callum-b]

Hi,
I'm getting the same issue with an AF3 prediction. It could be nice to maybe try to get the charge from the CIF if it exists, but not fail if it isn't present, seeing as AF3 doesn't use it.
Best,
Cal

[camilogarciabotero]

Hi there, also having similar problem with the pdb_fromcif subcommand:

Traceback (most recent call last):
  File "~/.miniforge/envs/reseek/bin/pdb_fromcif", line 10, in <module>
    sys.exit(main())
             ~~~~^^
  File "~/.miniforge/envs/reseek/lib/python3.14/site-packages/pdbtools/pdb_fromcif.py", line 240, in main
    for lineno, line in enumerate(new_pdb):
                        ~~~~~~~~~^^^^^^^^^
  File "~/.miniforge/envs/reseek/lib/python3.14/site-packages/pdbtools/pdb_fromcif.py", line 179, in run
    charge = fields[labels.get('_atom_site.pdbx_formal_charge')]
             ~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: list indices must be integers or slices, not NoneType

Any change to know how to fix this?

Best.

[amjjbonvin]

The solution was posted before, but never implemented so far. Files from the PDB don't have this issue. It seems more AF3/Chai specific. Where does your file come from?

[amjjbonvin]

Can you share your problematic file?

[camilogarciabotero]

Yes those are AF3 predictions:

The file I am using is here https://www.meta-virome.org/Data/CIF/imgvr_pc_000001435.cif

[rvhonorato]

Thank you for reporting the issue and thanks @amjjbonvin for patching it.

Fix has been merged and is available in v2.6.1 -> pip install --upgrade pdb-tools

[camilogarciabotero]

Thanks!