Hi Stephen,
(1) Is it possible to add RNA base-pair restraints into Phenix Real-space-refinement of a lowish resolution cryoEM structure?
If so how?
They are turned on by default, so you don't have to do anything. They are controlled by "Use secondary structure restraints" flag in GUI or secondary_structure.enabled=True in command-line - the same as for protein secondary structure. Best regards, Oleg Sobolev.
(2) We are also lucky enough to have some impressively high resolution cryoEM maps (2.4 A average) which show among other things hundreds of water molecules.
I was wondering whether Phenix Real-space-refinement was really adapted to high resolution, e.g. it uses grouped B-factor refinement and has no water handling options
(putting them in manually is a pain and you always miss some). How have other people dealt with these issues ?
thanks for any help
Stephen Cusack
--
********************************************************************** Dr. Stephen Cusack, FRS Head of EMBL Grenoble Group leader in the structural biology of protein-RNA complexes and viral proteins **********************************************************************
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