[phenixbb] About Restrain Files for ligands

Pavel Afonine pafonine at lbl.gov
Thu Jan 7 12:03:02 PST 2021

Hi Sharan,

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.
> Regards
> Sharan
> -- 
> Sharan Karade
> Postdoc-fellow
> IBBR-UMD, 9600 Gudelsky Dr,
> Rockville
> Maryland 20850
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