Hi Oarabile, The pdb residue name of cacodylate is CAC. In Coot, position the density peak at the center of the screen then go to File -> Get Monomer..., type in CAC, OK, then do a real-space fit to see if the atoms still fly apart. Since cacodylate ion is in the standard CCP4 monomer library ($CCP4/lib/data/monomers/c/CAC.cif), there's no need to generate a restraints file, as long as your pdb residue name is CAC. Otherwise, use eLBow to generate restraints for the non-standard ligand for Phenix Refine to work properly. Cheers! Jason On Oct 25, 2014, at 1:50 PM, Kgosisejo, Oarabile wrote: Hello all, I am trying to fit cacodylate ion in my model using Coot but it does not stay where I put it. The molecule breaks apart and some of its components attach to the peptide residues. Due to this, phenix.refine would not accept this as the input for refinement. Is there a way I can make cacodylate ion stay in its electron density and refine my structure with cacodylate ion? I appreciate your help! Best Regards, Oarabile M. Kgosisejo [email protected]mailto:[email protected] _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb