flipping side chain orientations

[alejandrovr]

@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]

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]

proteinPrepare automatically does flips to optimize hydrogen networking

[MaciejMajew]

Does it take into account the ligand?

[stefdoerr]

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