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Hi Mohammad,<br>
<br>
could you please describe steps you have done and at what point this
happens? Apart from water (optionally), phenix.refine would not add
or remove atoms. <br>
<br>
Pavel<br>
<br>
<blockquote type="cite"
cite="mid:CAEkidzCKDvQzYk0USHhM-2DXbnh8OXA_cconB54+=qMXrW2t4w@mail.gmail.com">
<div dir="ltr"><span
style="font-size:12pt;font-family:Arial,sans-serif;color:rgb(34,34,34)"><span>
</span></span><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></span></span><span
style="font-size:12pt;font-family:Arial,sans-serif;color:rgb(34,34,34)"><span></span></span>
<p class="MsoNormal" style="margin:0in 0in
0.0001pt;color:rgb(34,34,34);font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif"><span
style="font-size:12pt;font-family:Arial,sans-serif;color:rgb(34,34,34)"><span> </span></span></p>
<p class="MsoNormal" style="margin:0in 0in
0.0001pt;color:rgb(34,34,34);font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif"><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></span></span></p>
<p class="MsoNormal" style="margin:0in 0in
0.0001pt;color:rgb(34,34,34);font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif"><span
style="font-size:12pt;font-family:Arial,sans-serif;color:rgb(34,34,34)"><br>
</span></p>
<p class="MsoNormal" style="margin:0in 0in
0.0001pt;color:rgb(34,34,34);font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif"><span
style="font-size:12pt;font-family:Arial,sans-serif;color:rgb(34,34,34)">
</span></p>
<div
style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial">HETATM
5535 CD CD F 1 156.533 -64.594 138.360 1.00 76.11
CD</div>
<div
style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial">HETATM
5536 CD CD F 2 119.954-111.545 105.562 1.00 35.85
CD</div>
<div
style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial">HETATM
5537 CD CD F 3 152.936 -93.077 102.747 1.00 28.68
CD</div>
<div
style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial">HETATM
5538 CD CD F 4 121.467 -96.375 128.574 1.00 72.24
CD</div>
<br>
<p class="MsoNormal" style="margin:0in 0in
0.0001pt;color:rgb(34,34,34);font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif"><span
style="font-size:12pt;font-family:Arial,sans-serif;color:rgb(34,34,34)"><span> </span></span></p>
<p class="MsoNormal" style="margin:0in 0in
0.0001pt;color:rgb(34,34,34);font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif"><span
style="font-size:12pt;font-family:Arial,sans-serif;color:rgb(34,34,34)">Can
someone suggest what may be wrong?</span><br>
</p>
</div>
</blockquote>
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