[phenixbb] question about generating cif and pdb file using elbow
Pavel Afonine
PAfonine at lbl.gov
Thu Mar 19 21:14:37 PDT 2009
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: qunwan1 at gmail.com <mailto:qunwan1 at gmail.com>
> lab phone: 216-368-3337
> ------------------------------------------------------------------------
>
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