Hi Morton,

I have a symmetrical ligand, malonate -OOCCCOO-, that binds right on the crystallographic axis of a C2 structure. Is the correct approach to set the occupancy to 0.5 and then refine or is there a better way to handle is in Phenix?

The 0.5 trick currently doesn't work in phenix.refine since we don't provide a way to turn off nonbonded interactions between symmetry copies. However, we fully support handling of atoms on special positions and bonds involving symmetry operations. For this to work, you have to give only an asymmetric unit worth of atoms, i.e. in your case half of your molecule. Is the C in the middle exactly on the two-fold axis? If so, delete these atoms from the PDB file: -OOCCCOO- ^^^ Then use the custom bond and angle feature (for the angles you'll need the 2007_04_06 CCI Apps) to define the required bonds and angles, including the bonds to the protein. I hope it is straightforward. If not, could you send me the fragments from you pdb file with the malonate and the piece of protein it is linked to? Then I could work out the bond and angle definitions for you. Ralf