[phenixbb] Question about adding hydrogrens with reduce -- parameters for phenix.refine

Pavel Afonine PAfonine at lbl.gov
Thu Dec 6 11:06:53 PST 2007

Hi Carsten,

there was a bug in phenix.reduce that is fixed already (I'm not sure if 
this fix is in the latest PHENIX rc6). Meanwhile you can still use the 
online version of Reduce to add H atoms:

Adding all hydrogens is a good idea.


On 12/6/2007 10:34 AM, Schubert, Carsten [PRDUS] wrote:
> Hi
> I am trying to generate a model with all hydrogens placed using 
> reduce. To my surprise it only applies hydrogens to a selected few 
> residues. How do I coax reduce to add ALL hydrogens to my model, 
> according to the Richardson Lab paper this should be possible? The 
> help from reduce was not helpful in that regard. Or is adding all 
> hydrogens a bad idea?
> Along those lines. If I would use another tool to generate the 
> hydrogens, like CNS(X) or Maeastro, how compatible are the parameter 
> files?
> Thanks for any input
>         Carsten
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