[phenixbb] About Restrain Files for ligands

Sharan Karade sharankarade at gmail.com
Thu Jan 7 10:20:42 PST 2021

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

please help me. Thank you so much.


Sharan Karade
IBBR-UMD, 9600 Gudelsky Dr,
Maryland 20850
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