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

crystallogrphy qunwan1 at gmail.com
Thu Mar 19 16:21:50 PDT 2009

I am using phenix.elbow to generate pdb and cif files with the tripos format

   phenix.elbow --initial_geometry egcg.mol2 --opt --output="LIG"

The input pdb file contains hydrogen atoms and the output pdb file also
contains hydrogen atom. 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
lab phone: 216-368-3337
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