Getting error with PDB 1A6W

[mc-robinson]

For some reason, I am getting an error with PDB 1A6W (unmodified from file downloaded from PDB). This could be on my end, but other proteins seem to working fine.

Thanks,
Matt

The relevant error message is included below:

File "/Users/matthewrobinson/bin/propka31", line 11, in
load_entry_point('PROPKA==3.1', 'console_scripts', 'propka31')()
File "/Users/matthewrobinson/.local/lib/python3.6/site-packages/PROPKA-3.1-py3.6.egg/propka/run.py", line 13, in main
File "/Users/matthewrobinson/.local/lib/python3.6/site-packages/PROPKA-3.1-py3.6.egg/propka/molecular_container.py", line 55, in init
File "/Users/matthewrobinson/.local/lib/python3.6/site-packages/PROPKA-3.1-py3.6.egg/propka/molecular_container.py", line 110, in extract_groups
File "/Users/matthewrobinson/.local/lib/python3.6/site-packages/PROPKA-3.1-py3.6.egg/propka/conformation_container.py", line 41, in extract_groups
File "/Users/matthewrobinson/.local/lib/python3.6/site-packages/PROPKA-3.1-py3.6.egg/propka/conformation_container.py", line 146, in setup_and_add_group
File "/Users/matthewrobinson/.local/lib/python3.6/site-packages/PROPKA-3.1-py3.6.egg/propka/conformation_container.py", line 155, in init_group
File "/Users/matthewrobinson/.local/lib/python3.6/site-packages/PROPKA-3.1-py3.6.egg/propka/group.py", line 356, in setup
File "/Users/matthewrobinson/.local/lib/python3.6/site-packages/PROPKA-3.1-py3.6.egg/propka/group.py", line 739, in setup_atoms
IndexError: list index out of range

[amashaly]

Any solution to this error yet?

[dspencer12]

My testing indicates that this issue occurs when atoms are missing in the PDB file (i.e. not resolved by the crystallography experiment). Currently I am working around this issue by using Modeller to fill the missing atom positions.

[FloLangenfeld]

Had the same issue with pdb 1zgl (chains P, R, T and V). Using Modeller solved the issue, indeed. In my case, only OXT atoms at the C-ter residues were missing (which is a quite common feature in X-ray structures).

IMO, the end-user should not be forced to use Modeller, but just be informed that the input structure has something wrong. And it would avoid to add a dependency to propka. A message to the stdout / log should be enough to warn the user that atoms may be missing in the input structure.