search

PDB-REDO / alphafill

AlphaFill is an algorithm based on sequence and structure similarity that “transplants” missing compounds to the AlphaFold models. By adding the molecular context to the protein structures, the models can be more easily appreciated in terms of function and structure integrity.
https://alphafill.eu
BSD 2-Clause "Simplified" License
90 stars 18 forks source link

Error reading file #43

Closed AlessioDelConte closed 6 months ago

AlessioDelConte commented 7 months ago

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?

image

Thank you, Alessio

drlemmus commented 7 months ago

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