[phenixbb] About Restrain Files for ligands

Maxime Cuypers maximecuypers at gmail.com
Fri Jan 8 08:02:18 PST 2021

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


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
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