Qun Two things. I think you will find a large group of people who will disagree with your assertion that your refinement should not contain hydrogens. Secondly, can you tell me which version your are using? Is it 1.4-3? Nigel On 3/19/09 4:21 PM, crystallogrphy wrote:
Hi, I am using phenix.elbow to generate pdb and cif files with the tripos format file:
phenix.elbow --initial_geometry egcg.mol2 --opt --output="LIG" --pdb-ligand
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: [email protected] mailto:[email protected] lab phone: 216-368-3337 ------------------------------------------------------------------------
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