[phenixbb] ligands at a special position

Subhani Bandara ramssb17 at gmail.com
Mon Oct 17 11:42:33 PDT 2011


I am trying to solve a structure of a protein that is cocrystallized with a
chelator complex using phenix (GUI). The complex is Tb(DPA)3 and DPA stands
for dipicolinic acid.  In the structure (C222) there are few Tb complexes on
the two fold axis with symmetry coordinates 1/4X, 1/4Y, Z. In those, Tb and
the center C (C4) and N (N1) of  one DPA are sitting directly on the 2 fold

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.

Then I refined it while keeping above  occupancies and xyz coordinated of
the ligand fixed. After doing  this the other half of the ligand could be
built by symmetry, but it left a space between two halves(so it was not as
one ligand).

Can you please let me know what I can do to fix this structure. Also is
there a way to keep only x and y coordinates fixed while varying z during

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