flipping side chain orientations

Acellera / moleculekit

MoleculeKit: Your favorite molecule manipulation kit

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flipping side chain orientations #79

Open alejandrovr opened 2 years ago

alejandrovr commented 2 years ago

@Acellera/maciej mentioned that it would be nice to be able to flip a residue's sidechain at will to improve hydrogen networking when there are ligands involved, which proteinPrepare does not consider, afaik.

MaciejMajew commented 2 years ago

It matters most for Asn and Gln where O and N of the amid group have the same electron density and can sometimes be misinterpreted. also His but to a lesser degree.

stefdoerr commented 2 years ago

proteinPrepare automatically does flips to optimize hydrogen networking

MaciejMajew commented 2 years ago

Does it take into account the ligand?

stefdoerr commented 2 years ago

Not yet. I somehow have never managed to pass a ligand correctly to pdb2pqr...