Dear ccp4-ers,
I have a data set at 2.8 A. There is clear *continuous*  density for a
ligand + residue. I used the LINK record to connect the S-gamma-atom
from Cys to C1-atom of ligand OCA. My biochemistry collaborator says
that CB-SG-C1-O1 should be approximately planar. However, during
refinement with REFMAC5, the connecting region does lose planarity.
The ligand and residue does indeed stay properly inside the density. I
assume this is due to the low(er) resolution. Should I fix the
planarity or should I leave it to the refinement?
Thank you all,
Markus