[phenixbb] Elbow and smiles to make CO coordinates

Machius, Mischa Christian machius at med.unc.edu
Fri Jul 8 11:13:09 PDT 2011

For getting carbon monoxide coordinates: In coot, go to File > Get Monomer...
Type in "CMO" and click OK.

A carbon monoxide molecule will po up in the middle of the window (provided everything is set up correctly).

If you are trying to fit an electron density, place that density in the middle of the window before you retrieve the ligand.

Hope that helps.


On Jul 8, 2011, at 1:41 PM, Yarrow Madrona 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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> phenixbb at phenix-online.org
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