[phenixbb] About Restrain Files for ligands

Paul Emsley pemsley at mrc-lmb.cam.ac.uk
Fri Jan 8 10:57:26 PST 2021

On 07/01/2021 18:20, Sharan Karade wrote:
>  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.

It is highly likely that you have restraints at this point.

> I generated the restrain files using Phenix.ReadySet to further 
> proceed for refinement.


> Unfortunately, after refinement the double bonds were converted to 
> single bonds.

refinement won't change the bond orders.

> I tried to generate new restrain files and refined the model,


> resulting in similar output.

Similar but different?

> 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.

Hmm... Probably the best way of interacting between Coot and ELBOW at 
the moment is, after you have drawn your ligand in Lidia, click on the 
red-lipped smiley icon to capture the SMILES string - and then feed that 

On 07/01/2021 20:03, Pavel Afonine wrote:
> 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.

Re Figure 3b: Oh yikes, that doesn't look right - the elements have been 
lost. Can you send me that dictionary so that I can try to reproduce the 


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