[phenixbb] Elbow and smiles to make CO coordinates

Ralf Grosse-Kunstleve rwgrosse-kunstleve at lbl.gov
Fri Jul 8 10:48:48 PDT 2011


Hi Yarrow,

Try:

phenix.elbow --smiles '[C-]#[O+]'

(The smiles string is from the wikipedia page on carbon monoxide.)

Ralf

On Fri, Jul 8, 2011 at 10:41 AM, Yarrow Madrona <amadrona at uci.edu> wrote:

>
> Hi,
>
> I am trying to use Elbow and smiles to generate carbon monoxide
> coordinates. I thought it would be easy enough. I made two waters in coot
> and changed the the oxygens to C and O and set the distance around 1.13
> angstrom.  Saved these coordinates as a PDB. I then used this in Elbow but
> it gives me a methyl group.  Not sure what is going on. Any help would be
> appreciated. Thank you!
>
> -Yarrow
>
> --
> Yarrow Madrona
>
> Graduate Student
> Molecular Biology and Biochemistry Dept.
> University of California, Irvine
> Natural Sciences I, Rm 2403
> Irvine, CA 92697
>
>
>
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>
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