<div dir="ltr">Hi Nigel;<div>I tried to find that option, but I can not find it. Could you please give some more hints where is that option is hidden.</div><div><br></div><div>Thanks</div><div><br></div><div>Bashir</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, May 22, 2020 at 4:11 PM Pavel Afonine &lt;<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>&gt; wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
  
    
  
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    Hi,<br>
    <br>
    please define &quot;refinement still not working&quot;. I think phenix.refine
    wont accept UNX because it has undefined scattering type.<br>
    <br>
    Pavel<br>
    <br>
    <div>On 5/22/20 13:41, Nigel Moriarty wrote:<br>
    </div>
    <blockquote type="cite">
      
      <div dir="ltr">Muhammad
        <div><br>
        </div>
        <div>There is an option in refinement that will determine the
          ion that best fits a density blob. You should try that after
          removing the UNX. </div>
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                  <div dir="ltr">
                    <div dir="ltr">Cheers
                      <div><br>
                      </div>
                      <div>Nigel
                        <div><br>
                        </div>
                        <div>---</div>
                        <div>Nigel W. Moriarty<br>
                          Building 33R0349, Molecular Biophysics and
                          Integrated Bioimaging</div>
                        <div>Lawrence Berkeley National Laboratory<br>
                          Berkeley, CA 94720-8235<br>
                          Phone : 510-486-5709     Email :
                          <a href="mailto:NWMoriarty@LBL.gov" target="_blank">NWMoriarty@LBL.gov</a><br>
                          Fax   : 510-486-5909       Web  : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div>
                      </div>
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          </div>
          <br>
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      <br>
      <div class="gmail_quote">
        <div dir="ltr" class="gmail_attr">On Fri, May 22, 2020 at 1:27
          PM Muhammad Bashir Khan &lt;<a href="mailto:mbk@ualberta.ca" target="_blank">mbk@ualberta.ca</a>&gt; wrote:<br>
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        <blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
          <div dir="ltr">Hi there;
            <div><br>
            </div>
            <div>I find some unknown density in my map, where I put SO4
              and in some UNX. I merged and save all in one PDB. I run
              ReadySet to make cif. file, but refinement still not
              working. Can anybody explain what else I should provide?</div>
            <div><br>
            </div>
            <div>Thanks in advance</div>
            <div><br>
            </div>
            <div>Bashir</div>
            <div>
              <div><br>
              </div>
              -- <br>
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                      <div><span style="font-family:Helvetica;font-size:medium">------------------------------------------------------</span></div>
                      <span style="font-family:Helvetica;font-size:medium">Muhammad
                        Bashir Khan, Ph.D.</span><br style="font-family:Helvetica;font-size:medium">
                      <span style="font-family:Helvetica;font-size:medium">Research
                        Associate</span><br style="font-family:Helvetica;font-size:medium">
                      <span style="font-family:Helvetica;font-size:medium">Department
                        of Biochemistry</span><br style="font-family:Helvetica;font-size:medium">
                      <span style="font-family:Helvetica;font-size:medium">Medical
                        Science Bldg.</span><br style="font-family:Helvetica;font-size:medium">
                      <span style="font-family:Helvetica;font-size:medium">Lab
                        3-27</span><br style="font-family:Helvetica;font-size:medium">
                      <span style="font-family:Helvetica;font-size:medium">University
                        of Alberta</span><br style="font-family:Helvetica;font-size:medium">
                      <span style="font-family:Helvetica;font-size:medium">Edmonton
                        AB, T6G 2H7</span><br style="font-family:Helvetica;font-size:medium">
                      <br style="font-family:Helvetica;font-size:medium">
                      <span style="font-family:Helvetica;font-size:medium">Phone: </span><a value="+17804923465" style="color:rgb(17,85,204);font-family:Helvetica;font-size:medium">780-492-4577-</a><br style="font-family:Helvetica;font-size:medium">
                      <span style="font-family:Helvetica;font-size:medium">e-mail:
                      </span><a href="mailto:cbrooks1@ualberta.ca" style="color:rgb(17,85,204);font-family:Helvetica;font-size:medium" target="_blank">mbk@ualberta.ca</a><br>
                    </div>
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</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><span style="font-family:Helvetica;font-size:medium">------------------------------------------------------</span></div><span style="font-family:Helvetica;font-size:medium">Muhammad Bashir Khan, Ph.D.</span><br style="font-family:Helvetica;font-size:medium"><span style="font-family:Helvetica;font-size:medium">Research Associate</span><br style="font-family:Helvetica;font-size:medium"><span style="font-family:Helvetica;font-size:medium">Department of Biochemistry</span><br style="font-family:Helvetica;font-size:medium"><span style="font-family:Helvetica;font-size:medium">Medical Science Bldg.</span><br style="font-family:Helvetica;font-size:medium"><span style="font-family:Helvetica;font-size:medium">Lab 3-27</span><br style="font-family:Helvetica;font-size:medium"><span style="font-family:Helvetica;font-size:medium">University of Alberta</span><br style="font-family:Helvetica;font-size:medium"><span style="font-family:Helvetica;font-size:medium">Edmonton AB, T6G 2H7</span><br style="font-family:Helvetica;font-size:medium"><br style="font-family:Helvetica;font-size:medium"><span style="font-family:Helvetica;font-size:medium">Phone: </span><a value="+17804923465" style="color:rgb(17,85,204);font-family:Helvetica;font-size:medium">780-492-4577-</a><br style="font-family:Helvetica;font-size:medium"><span style="font-family:Helvetica;font-size:medium">e-mail: </span><a href="mailto:cbrooks1@ualberta.ca" style="color:rgb(17,85,204);font-family:Helvetica;font-size:medium" target="_blank">mbk@ualberta.ca</a><br></div></div></div></div>