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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
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Warning: Missing atom for atom ID #41

Closed DamienWaits closed 7 months ago

DamienWaits commented 8 months ago

I am receiving warnings like the following during some of my Alphafold runs on Omegafold output:

3ZW9 Missing atom for atom ID OAP

The offending lines from my cif look like:

HETATM 5006 O OAP B COA BV 3 . ? 7.041 15.430 9.293 0.30 154.79 ? 1 COA BV OAP 1

Alphafill is completing successfully but some inputs throw warnings like this for multiple atoms and I'm curious if the output will likely be affected.

Pdb-repo downloaded with 'rsync -av rsync://rsync.pdb-redo.eu/db/ pdb-redo/'

drlemmus commented 8 months ago

Sometimes an atom is missing in the experimental model that can trigger such a warning. If there are more experimental models with the same compound the most complete one is taken. In your case the COA seems to have been transplanted from a different model. The occupancy is 0.30 which none of the parent molecules in 3zw9 have.