[phenixbb] Special positions

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Wed Apr 11 10:55:28 PDT 2007

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

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:


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.


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