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30 Jun
2020
30 Jun
'20
1:28 a.m.
Hi Alexei,
When refining a crystal structure in phenix.refine, presence of explicit hydrogens usually decreases the number of clashes.
that's a desirable outcome. But that depends on many factors and varies case by case.
In the real-space refinement of a model against a cryo-EM map, however, explicit hydrogens did not improve the clashscore. Is this normal?
May be this is a case where they don't. And they may do in some other case.
Does it depend on resolution?
Generally, yes. At higher resolution the map should have more impact. Pavel