[phenixbb] weights optimization, add hydrogens

Christian Roth christian.roth at bbz.uni-leipzig.de
Tue Feb 23 14:26:17 PST 2010

Dear Ursula,

I usually remove the hydrogens and add them again in the next refinement cycle. 
Something strange happens If you simply try to update the hydrogens. 
I use phenix.pdbtools to remove the hydrogens. 
Also Coot cannot handle the hydrogens properly in real space refinement. At 
least in my version the Hydroges from the refined residue got to everywhers in 
any density. 

Best regards 


Am Dienstag 23 Februar 2010 19:33:03 schrieb Nathaniel Echols:
> On Feb 23, 2010, at 10:19 AM, Ursula Schulze-Gahmen wrote:
> > The other question is about adding hydrogens to the model. I did add them
> > in a previous refinement cycle. After rebuilding the model in coot, most
> > of the model still has the hydrogens in the input file for the next
> > refinement cycle, but some residues and waters don't have hydrogens. When
> > I tried to add hydrogens again to the model, I got an error message about
> > atoms being to close. Does Phenix know where to add hydrogens if the
> > input model has already hydroegns on many residues?
> In theory it should, but the underlying problem is almost certainly
>  incompatible names for hydrogen atoms, which will appear invisible to
>  Reduce (the program that adds them).  This usually results from switching
>  between programs that have different conventions for hydrogen naming (e.g.
>  Coot and Phenix), depending on which version of the PDB format they use. 
>  (Phenix uses PDB v3.2, which is very new.)
> Would you mind sending me (not the list!) the PDB file so I can
>  double-check this?  Unfortunately I don't have any suggestions for how to
>  fix this other than wiping out the old hydrogen atoms (I like PyMOL for
>  this: "remove elem h").  Since this keeps coming up, we'll add an option
>  to the GUI to erase old hydrogen atoms before running the automatic
>  addition.
> thanks,
> Nat
> -------------------
> Nathaniel Echols
> Lawrence Berkeley Lab
> 510-486-5136
> NEchols at lbl.gov
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> phenixbb at phenix-online.org
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Christian Roth
Institut für Bioanalytische Chemie
Biotechnologisch-Biomedizinisches Zentrum
Fakultät für Chemie und Mineralogie
Universität Leipzig
Deutscher Platz 5
04103 Leipzig
Telefon: +49 (0)341 97 31316
Fax: +49 (0)341 97 31319

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