Error reading file

[AlessioDelConte]

Hello,

I am testing the alphafill software installed locally and I have some issue running it on a cif file. I've tried to run it on a mmCIF file downloaded from the PDB and it works just fine. Then I wanted to isolate a chain from the structure using PyMOL and then re-exporting the structure in another cif. At this point when I run alphafill process on the newly exported structure it outputs this error:

alphafill process --verbose --config=/etc/alphafill.conf /home/alessio/3vn3_A.cif /home/alessio/test_A.cif
Error reading file /home/alessio/3vn3_A.cif
 >> map::at

without any detailed info about why the error happens. I think it could be related to the fact that when exporting the structure in the cif file I only have a very short header and the atom_site table (see attached figure). Are there some mandatory tables for alphafill to work maybe?

Thank you, Alessio

[drlemmus]

I think PyMOL has brutalised your mmCIF file to the point that AlphaFill won't use it. If you want to just work on chain, A you can delete all _atom_site records that refer to other chains with a text editor. I did just that and here is the result: https://alphafill.eu/model?id=CS-24925dcf59965334e32907be5183b35f2502f6c8&identity=25