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:
However, the program failed. Does anyone know why?
phenix.elbow --initial_geometry --write-hydrogens=False egcg.mol2 --opt --output="LIG" --pdb-ligand
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]
lab phone: 216-368-3337
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