[phenixbb] Weird Hydorgen refinement

Jeff Headd jjheadd at lbl.gov
Mon Aug 22 18:23:36 PDT 2011

Hi Yuri,

You can remove hydrogens by running:

phenix.reduce --trim model_H.pdb > model_noH.pdb

Keep in mind that the calculated R factors will change slightly when
you remove the hydrogens from your model.


On Mon, Aug 22, 2011 at 6:08 PM, Yuri <yuri.pompeu at ufl.edu> wrote:
> Hi Pavel,
> The pdb did have anisou records for H's. I believe that is because in some
> previous runs I had only selected chain 'A' - I left out "and not elemnt H"
> - which I believe caused the H's to get refined anisotropically.
> I am trying to get rid of the ANISOU records and Ill run refinement again.
> ps. I am getting ready to deposit the coordinates and I dont want to keep
> hydrogens in the model, how can I get rid of them? I ve been using pyMol to
> remove them, but pymol gets rid of all the info -including symmetry -that
> phenix adds...
> Thanks
> --
> Yuri Pompeu
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