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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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Error when processing 2ONG for nohd >> max-ligand-to-polymer-atom-distance: unknown option #39

Closed eporetsky closed 10 months ago

eporetsky commented 10 months ago

I get the following error after running a structure I predicted with the alphafold2 colabfold notebook: Error when processing 2ONG for nohd >> max-ligand-to-polymer-atom-distance: unknown option JobID: https://alphafill.eu/model?id=CS-39a097880b28c8d35ce46ad6d78e42d18429a69b

Below is the uploaded PDB file (renamed to.txt so I can upload it) 2ONG_colabfod_af2.txt

The protein sequence I used to generate the predicted structures is the same as the 2ONG experimental structure that seems to be in the error message. I tried running the experimental PDB and a AF2 colabfold-predicted PDB of the example sequence and both ran successfully so I wonder if this might be an issue (uncommon) on the AlphaFill side?

Let me know if there is any additional information I can provide. Thank you for the help!

mhekkel commented 10 months ago

This should now be fixed. Finally.