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<p>​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,<br>
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<p>Diana<br>
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<div class="PlainText">**************************************************<br>
Diana R. Tomchick<br>
Professor<br>
Departments of Biophysics and Biochemistry<br>
University of Texas Southwestern Medical Center<br>
5323 Harry Hines Blvd.<br>
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Dallas, TX 75390-8816<br>
Diana.Tomchick@UTSouthwestern.edu<br>
(214) 645-6383 (phone)<br>
(214) 645-6353 (fax)</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> phenixbb-bounces@phenix-online.org <phenixbb-bounces@phenix-online.org> on behalf of Mohammad Khan <mohdkhan0504@gmail.com><br>
<b>Sent:</b> Monday, February 26, 2018 6:17 PM<br>
<b>To:</b> phenixbb@phenix-online.org<br>
<b>Subject:</b> [phenixbb] Issues with refinement of cadmium</font>
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<span style="font-size:12pt; font-family:Arial,sans-serif; color:rgb(34,34,34)">Dear all,</span></p>
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<span style="font-size:12pt; font-family:Arial,sans-serif; color:rgb(34,34,34)"><span> </span></span></p>
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<span style="font-size:12pt; font-family:Arial,sans-serif; color:rgb(34,34,34); background:white">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 (</span><span style="font-size:12.5pt; font-family:Helvetica,sans-serif; color:black">2'-DEOXYCYTIDINE-5'-<wbr>MONOPHOSPHATE</span><span style="font-size:12pt; font-family:Arial,sans-serif; color:rgb(34,34,34); background:white">)
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.</span><span style="font-size:12pt; font-family:"Times New Roman",serif"></span></p>
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<span style="font-size:12pt; font-family:Arial,sans-serif; color:rgb(34,34,34)"><span> </span></span></p>
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<span style="font-size:12pt; font-family:Arial,sans-serif; color:rgb(34,34,34)">Cd is present in my crystallization condition and fits well into the density. Other metal atoms such as Zn and Cl have refined well.</span></p>
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HETATM 5535 CD CD F 1 156.533 -64.594 138.360 1.00 76.11 CD</div>
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HETATM 5536 CD CD F 2 119.954-111.545 105.562 1.00 35.85 CD</div>
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HETATM 5537 CD CD F 3 152.936 -93.077 102.747 1.00 28.68 CD</div>
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HETATM 5538 CD CD F 4 121.467 -96.375 128.574 1.00 72.24 CD</div>
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<span style="font-size:12pt; font-family:Arial,sans-serif; color:rgb(34,34,34)"><span> </span></span></p>
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<span style="font-size:12pt; font-family:Arial,sans-serif; color:rgb(34,34,34)">Can someone suggest what may be wrong?</span></p>
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Thanks in advance!</div>
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