[phenixbb] riding model and deposition

Nathaniel Echols NEchols at lbl.gov
Thu Feb 18 11:32:02 PST 2010

On Feb 18, 2010, at 11:07 AM, Pavel Afonine wrote:
> PS: I was talking about command line version of phenix.refine. If you use the GUI then there is an option to add H.

Technically, the GUI just runs ready_set, then passes that file to phenix.refine.  The only program that generates and uses "implicit hydrogens" is Refmac, and even in that case the internal model has explicit hydrogens, they just aren't printed out at the end.  I considered adding an option to the GUI to strip out hydrogens at the end, but Pavel has convinced me that this is a bad idea - it is generally okay to do this during refinement (where different programs have very different attitudes towards hydrogens), but not for deposition.


Nathaniel Echols
Lawrence Berkeley Lab
NEchols at lbl.gov

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