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