[phenixbb] Issues with refinement of cadmium

Diana Tomchick Diana.Tomchick at utsouthwestern.edu
Mon Feb 26 16:57:31 PST 2018

?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,


Diana R. Tomchick
Departments of Biophysics and Biochemistry
University of Texas Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
Diana.Tomchick at UTSouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)
From: phenixbb-bounces at phenix-online.org <phenixbb-bounces at phenix-online.org> on behalf of Mohammad Khan <mohdkhan0504 at gmail.com>
Sent: Monday, February 26, 2018 6:17 PM
To: phenixbb at 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!


UT Southwestern

Medical Center

The future of medicine, today.

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