[phenixbb] About Restrain Files for ligands

Pavel Afonine pafonine at lbl.gov
Fri Jan 8 10:16:08 PST 2021

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.


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 at lbl.gov 
> <mailto: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
>     <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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