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jaredsagendorf / pnabind

A python package and collection of scripts for computing protein surface meshes, chemical, electrostatic, geometric features, and building/training graph neural network models of protein-nucleic acid binding
GNU General Public License v3.0
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Issue Generating Mesh Data #5

Open kvhuynh opened 1 month ago

kvhuynh commented 1 month ago

I'm attempting to run the example generate_protein_meshdata.py listed here using a fresh install of your repository on an M1 MacBook Air but have also reproduced this issue on a Windows machine with an NVIDIA GPU but I'm encountering the following error:

File "/Users/kevinhuynh/pnabind/pnabind/structure/get_atom_charge_radius.py", line 100, in getAtomChargeRadius
    atom.xtra["radius"] = max(data.AMBER[resn][atmn]["radius"], min_radius)
KeyError: 'U'

I've attempted some debugging but believe my biological knowledge may be lacking to resolve this. Any insights or suggestions would be greatly appreciated.

Thanks!

timkartar commented 2 weeks ago

Hi There, I am not the primary author of this, but i think you got the error because you have Uracil (U) in your structure, which is not a protein amino acid. Hope this is helpful.