[phenixbb] Base-pair restraints and high resolution cryoEM maps

[Oleg Sobolev]

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
> **********************************************************************
>
> Email:  cusack at embl.fr, stephen.cusack at embl.org
> Website: http://www.embl.fr
> Tel:    (33) 4 76 20 7238    Secretary (33) 4 76 20 7123
>
> Fax:    (33) 4 76 20 7199
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