Hi David Briggs,
Thank you for the suggestion of AceDrg. I gave it a try, using the Coot way
and the Jligand way for AceDrg. For some reason the Coot method didn't make a
cif, only jligand did. But the cif didn't have any effect on refinement. What
did work for Phenix was to define the planarity in a phil file:
planarity {
action = *add
atom_selection = \
chain A and resname LIG and resid 3 and name C1 or \
chain A and resname LIG and resid 3 and name C2 or \
chain A and resname IGL and resid 6 and name C3 or \
chain A and resname IGL and resid 6 and name C4
sigma = 0.02
}
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