Hi Qun Wan, check out this: http://www.phenix-online.org/documentation/refinement.htm#anch28 and slide #37 here: http://www.phenix-online.org/presentations/neutron_japan_2009/ -> Structure refinement and PHENIX (morning session) (PDF) this says some things about hydrogens in refinement. Pavel.
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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