[phenixbb] Question about Adding Hydrogens

Jeff Headd jjheadd at lbl.gov
Mon Feb 28 12:37:03 PST 2011

Hi Louis,

Hydrogen atoms in Phenix are added using the Reduce program, and one
of the real strengths of Reduce is that it determines H-atom positions
by optimizing the local H-bond network. By only adding hydrogens to
one residue, this step would be lost.

Is there a reason that you'd like to add H atoms to just one residue?

You can find out more about Reduce here:



On Mon, Feb 28, 2011 at 8:45 AM, Louis Lazar <louisl at brandeis.edu> wrote:
> All,
> I was curious if there is a way to add hydrogens to an individual residue.
> For example, rather than running the command: phenix.ready_set model.pdb,
> run something like:
> phenix.ready_set model.pdb resid=X or
> phenix.ready_set=resid 10 model.pdb
> Any thoughts/recommendations on the subject are greatly appreciated. Thanks
> in advance.
> Louis
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