[phenixbb] About Restrain Files for ligands

[Maxime Cuypers]

Hello,
Naively, Perhaps the issue is that the molecule  used to generate the .cif
restraints does not have the hydrogens in the right place/ right
hybridization?
My suggestion would be to check it i.e. with Avogadro or any other chemical
structure editor.

Cheers
Maxime

Le jeu. 7 janv. 2021 à 14:04, Pavel Afonine <pafonine at lbl.gov> a écrit :

> 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 listphenixbb at phenix-online.orghttp://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org
>
>
> _______________________________________________
> 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/20210108/433adcf9/attachment.htm>