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

Schubert, Carsten [PRDUS] CSCHUBER at prdus.jnj.com
Thu Dec 6 10:34:58 PST 2007


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 

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