To add to this: best way to generate restraints file within Phenix framework is to use eLBOW with a SMILES string (using GUI or CL), then quickly inspect the restraints file (aka 'ligand CIF file') to make sure it reflects what you know about the ligand.

Pavel

On 1/8/21 08:02, Maxime Cuypers wrote:

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@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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