[phenixbb] ligands at a special position

Ralf Grosse-Kunstleve rwgrosse-kunstleve at lbl.gov
Mon Oct 17 12:50:26 PDT 2011

> So I left only half of that DPA ligand structure on PDB file and changed
> the occupancy of N1 and C4 to 1/2 while keeping the occupancy of all other
> atoms of the half ligand structure at 1.00.

Keep the occupancy of N1 and C4 as 1.00, then phenix.refine should
automatically detect those as special positions and keep them exactly on the
two-fold axis.
The bonds and other restraints to the atoms on special positions will not
work automatically. Currently, the only option is to define custom bonds
(see phenix.refine docs) with symmetry_operation=x,y,z. You can use Coot to
obtain the symmetry operation (turn on drawing of symmetry copies; when
clicking atom Coot will show the sym op). Emulate angle and dihedral
restraints with pseudo-bonds. Inspect the .geo file to verify that all
restraints are correct.

You can also keep all DPA atoms, with all occupancies set to 0.5. Then the
restraints will work as usual; probably you don't have to do anything
special. However, the N1 and C4 are allowed to float around the special
position. It may be OK though. I think I'd try this option first.

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