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flipping side chain orientations #79

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alejandrovr opened this issue Oct 8, 2021 · 4 comments
Open

flipping side chain orientations #79

alejandrovr opened this issue Oct 8, 2021 · 4 comments

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@alejandrovr
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@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
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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
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proteinPrepare automatically does flips to optimize hydrogen networking

@MaciejMajew
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Does it take into account the ligand?

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

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@stefdoerr @alejandrovr @MaciejMajew