[phenixbb] question about generating cif and pdb file using elbow

Pavel Afonine PAfonine at lbl.gov
Thu Mar 19 21:14:37 PDT 2009

Hi Qun Wan,

check out this:


and slide #37 here:

   -> Structure refinement and PHENIX (morning session) (PDF)

this says some things about hydrogens in refinement.


> My crystal data only difftracted to 2.4A, so hydrogen atoms cannot be 
> seen. In the refinement, my ligand should not contain hydrogen atoms. 
> So I add one more option not to add hydrogen following the online 
> phenix documentation:
>       phenix.elbow --initial_geometry --write-hydrogens=False
>       egcg.mol2 --opt --output="LIG" --pdb-ligand
> *However, the program failed. Does anyone know why?*
> Usage: phenix.elbow [options]
> *phenix.elbow: error: no such option: --write-hydrogens*
> -- 
> Qun Wan
> Department of Pharmacology, Case Western Reserve University
> 10900 Euclid Avenue, Cleveland, OH 44106
> email: qunwan1 at gmail.com <mailto:qunwan1 at gmail.com>
> lab phone: 216-368-3337
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