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

Nigel W Moriarty NWMoriarty at lbl.gov
Thu Mar 19 16:44:29 PDT 2009


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?


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: qunwan1 at gmail.com <mailto:qunwan1 at gmail.com>
> lab phone: 216-368-3337
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Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax   : 510-486-5909
Email : NWMoriarty at LBL.gov
Web   : CCI.LBL.gov

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