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

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Qun Wan
Department of Pharmacology, Case Western Reserve University
10900 Euclid Avenue, Cleveland, OH 44106
email: [email protected]
lab phone: 216-368-3337
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Nigel W. Moriarty
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