Thanks! Didn't realize it was so easy.
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.
Cheers! MM
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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-- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697