How does phenix handle deuterium atoms in neutron diffraction data?
Hello, I'm performing a joint neutron-xray refinement with phenix, for a dataset collected from a crystal exchanged with deuterated water, ie, all exchangeable H atoms are replaced by D. I was wondering whether phenix has libraries of .cif dictionaries (or equivalent) in order to handle the name "D" of some "H" atoms in the .pdb files? I would like to use those dictionaries to input into Coot, so that it can handle deuterated molecules during geometry regularization, real space refinement, etc. Any help will be greatly appreciated. Thanks, Javier -- Javier M. Gonzalez Protein Crystallography Station Bioscience Division Los Alamos National Laboratory TA-3, Building 4200, Room 202 Mailstop T001 work: (505) 667-9376 (temporary)
Hi Javier,
I'm performing a joint neutron-xray refinement with phenix, for a dataset collected from a crystal exchanged with deuterated water, ie, all exchangeable H atoms are replaced by D. I was wondering whether phenix has libraries of .cif dictionaries (or equivalent) in order to handle the name "D" of some "H" atoms in the .pdb files?
you can have HOH or DOD or any mixture. Are you having any problem with this? You don't need them, as phenix.refine will recognize DOD/HOH (water) automatically. Pavel
participants (2)
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Javier Gonzalez
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Pavel Afonine