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° | OptHyd<Obj|All> | - | Optimize hydrogen bonding network |
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| Command | | Argument | | Datatype | | Default | | Min |
| Max | |
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| Format: | | OptHyd<Obj|All> | Object selection | | SELECTION | |
- | | - | | - | | |
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| Python: | | OptHyd<Obj|All>(selection1) | | ||||||||||
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| Menu: | | Edit > Add > hydrogens to: object & optimize | | ||||||||||
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| Related: | | AddHyd , DelHyd, Experiment , Clean | | ||||||||||
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| Required: | |  |
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The OptHyd
command first adds hydrogens to the selected objects
, and then invokes WHAT IF's OPTHYD option to optimize the hydrogen bonding network. Side-chains of Asn,
Gln and His residues will be flipped if that improves the network.
WHAT IF normally restricts the analysis to standard amino acid and DNA bases.
Ambiguous, pH dependent cases like protonation of Asp and Glu residues are handled via pKa prediction by
'Experiment Neutralize'.
If the OptHyd command takes a lot of time
, this is caused by the presence of water molecules, which cause a lot of ambiguity. Deleting less important waters on the protein surfaces results in an enormous speedup.
It is usually helpful to clean a structure before optimizing the network
, since this removes alternate atoms.
Example:
OptHydObj 1crn
Optimize hydrogen bonding network of object 1crn.