I am finishing to refine a structure using Phenix. A sulfate ion is located on a 2 fold axis. When I refine the structure with Refmac, the geometry of the ion is well conserved, while when I use Phenix the geometry is destroyed and the sulfate ion is like a cross!! Any idea to keep the good geometry of this ion in Phenix during the refinement?

Sorry, currently, phenix.refine doesn't support disorder around special positions. One possible workaround is to keep the sulfate fixed during refinement (atom selection such as "not resname SO4" in the refine scope) with occ 0.5 for the O and full occ for the S, another one to remove the O from the PDB file and only refine the S. Ralf