[phenixbb] About Restrain Files for ligands
pafonine at lbl.gov
Thu Jan 7 12:03:02 PST 2021
I'm guessing your are over-relying on graphic representations of your
molecules which is discussed here to some extent:
What really matters is that the ligand fits the map and its geometry
matches what's expected.
On 1/7/21 10:20, Sharan Karade wrote:
> Hello all,
> I hope everybody is doing well. Happy New Year 2021!!!
> I am stuck with some unusual behavior of restrain files generated by
> Phenix.ReadySet. I crystallized the protein with ligands which have
> double bonds between the atoms. As I see clear electron density for
> the ligand, I drew a ligand molecule in Coot (Ligand builder) and
> fitted in electron density very nicely. Until here, I can see the
> double bonds in the modelled ligand. I generated the restrain files
> using Phenix.ReadySet to further proceed for refinement.
> Unfortunately, after refinement the double bonds were converted to
> single bonds. I tried to generate new restrain files and refined the
> model, resulting in similar output. But, fortunately in one case, the
> double bonds were retained after refinement also. I tried to repeat
> with other ligands, where I was unsuccessful to retain the double bonds.
> please help me. Thank you so much.
> Sharan Karade
> IBBR-UMD, 9600 Gudelsky Dr,
> Maryland 20850
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> phenixbb at phenix-online.org
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