If you run ReadySet on your coordinates prior to refinement, does it properly identify these as metal ions and yield the proper *.cif and *.metal.edits files? If so, try using these restraint files in your refinement runs,

From: phenixbb-bounces@phenix-online.org <phenixbb-bounces@phenix-online.org> on behalf of Mohammad Khan <mohdkhan0504@gmail.com>
Sent: Monday, February 26, 2018 6:17 PM
To: phenixbb@phenix-online.org
Subject: [phenixbb] Issues with refinement of cadmium

Dear all,

I am trying to fit Cd ion in a protein structure using Phenix. However, the refinement transposes CD to DC and returns me a result with DC (2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE) in the validation report and gives me the missing atoms accordingly. When I open the same structure in Coot, it shows me the ion Cd. Also, the .pdb file contains Cd.

Cd is present in my crystallization condition and fits well into the density. Other metal atoms such as Zn and Cl have refined well.

HETATM 5535 CD CD F 1 156.533 -64.594 138.360 1.00 76.11 CD

HETATM 5536 CD CD F 2 119.954-111.545 105.562 1.00 35.85 CD

HETATM 5537 CD CD F 3 152.936 -93.077 102.747 1.00 28.68 CD

HETATM 5538 CD CD F 4 121.467 -96.375 128.574 1.00 72.24 CD

Can someone suggest what may be wrong?

Thanks in advance!