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

Schubert, Carsten [PRDUS] CSCHUBER at its.jnj.com
Thu Mar 19 17:16:32 PDT 2009

As far as I recall the write-hydrogens options is an expert option, depending on the version of elbow. Check out the elbow documentation on how to become an expert. 
As far as hydrogens are concerned, I would second Nigel's concern. Adding hydrogens in riding mode has the very real potential of improving the geometry of your structure due to the imposed anti-bumping restraints. You could try refinement with and without and see where it takes you. 
As a note of caution, elbow writes (Nigel correct me if I am wrong) PDB V3 compatible hydrogen names, which may cause some graphics programs to choke. Newer versions of coot (0.5.2 or later) seem to work fine. 

-----Original Message-----
From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org]On Behalf Of crystallogrphy
Sent: Thursday, March 19, 2009 7:22 PM
To: phenixbb at phenix-online.org
Subject: [phenixbb] question about generating cif and pdb file using elbow

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
lab phone: 216-368-3337

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