[phenixbb] ligand fitting

Nathaniel Echols nechols at lbl.gov
Mon Oct 13 09:35:53 PDT 2014

On Mon, Oct 13, 2014 at 9:31 AM, Sneha Rangarajan <rsneha at umd.edu> wrote:

>  One more question- When does one use “add hydrogens” in refinement? Does
> it help in the final stages of refinement?

In theory, yes.  Early in refinement hydrogen atoms tend to just make
phenix.refine much slower.  Later in refinement, they can help with
geometry and R-factors.  Personally I've never seen much benefit from using
hydrogens at moderate resolution, but it's worth trying them and seeing
what happens.  It's more important to pick optimal restraint weights (use
the automatic weight optimization for this) and a good refinement strategy
(add TLS, turn off real-space), and deal with any notable difference
density peaks.

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