[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:
http://phenix-online.org/newsletter/CCN_2016_01.pdf#page=10
What really matters is that the ligand fits the map and its geometry
matches what's expected.
Pavel
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
>
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20210107/f85a928c/attachment.htm>
More information about the phenixbb
mailing list