real-space refinement resolution
Hi, When refining a model against a density-modified cryo-EM map, should one use the resolution of the original or modified map? Thanks
Hi Alexei,
When refining a model against a density-modified cryo-EM map, should one use the resolution of the original or modified map?
phenix.real_space_refine uses the resolution only to calculate and report map-model correlation coefficient. The resolution you specify does not affect refinement results in any way. It's best though to provide the resolution of the map that is used in refinement. Pavel
Hi, When refining a crystal structure in phenix.refine, presence of explicit hydrogens usually decreases the number of clashes. In the real-space refinement of a model against a cryo-EM map, however, explicit hydrogens did not improve the clashscore. Is this normal? Does it depend on resolution? Thanks
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
participants (2)
-
Alexei Gorelik -
Pavel Afonine