Hi, One way of dealing with this is to place a (symmetry) unique copy of the ligand , which may be its part. Alternatively it's possible to disable nonbonded repulsion forces for selected atoms. Send me model and data files if still need help with this. Pavel On 5/20/20 01:01, Tom Vanmarcke wrote:
Dear,
We are trying to solve a protein structure that contains a ligand (polyoxometalate). We found the ligand in the electron density but through the middle of the ligand goes a 2 fold axis. For this reason, we placed the occupendency of the ligand on 0.50. When we try to refine the structure using phenix.refine, the ligand breaks down even when adding a cif restrain file.
The cif restrain file contains information about atoms, angles and bond lengths.
Is there a way to fix this problem?
Greetings