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

junfeng liu jliu at nimr.mrc.ac.uk
Fri Mar 20 03:47:29 PDT 2009

Hi Qun,
You can remove hydrogen atoms easily using coot if you want .
Anyway, hydrogen are in the structure even if  the resolution for them 
is not high enough. So someone suggest to add them when we check or 
refine structures. Just as Carsten said ,you can refine your structure  
with  hydrogen  and see what is there difference or not.
Schubert, Carsten [PRDUS] wrote:
> 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.
>     Carsten
>     -----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
>     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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