(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
--
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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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Email: cusack@embl.fr, stephen.cusack@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
Postal address: EMBL Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 71 Avenue des Martyrs, 38000 Grenoble, France
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