Re: [phenixbb] real-space refinement hydrogens

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