<div dir="ltr">It's place_ions at the CLI or "Place elemental ions" in the GUI on the "Refinement settings" tab. As Pavel said, UNX is an unknown ion so you can't really refine it. You could make it HOH to see what happens but you should know something about what it may be.<div><br clear="all"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><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 : NWMoriarty@LBL.gov<br>Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, May 22, 2020 at 6:13 PM Muhammad Bashir Khan <<a href="mailto:mbk@ualberta.ca">mbk@ualberta.ca</a>> 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"><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 <<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>> 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">
<div>
Hi,<br>
<br>
please define "refinement still not working". 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>
<div><br clear="all">
<div>
<div dir="ltr">
<div dir="ltr">
<div>
<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>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Fri, May 22, 2020 at 1:27
PM Muhammad Bashir Khan <<a href="mailto:mbk@ualberta.ca" target="_blank">mbk@ualberta.ca</a>> 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">
<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>
<div dir="ltr">
<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>
</div>
</div>
_______________________________________________<br>
phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" rel="noreferrer" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.org</a></blockquote>
</div>
<br>
<fieldset></fieldset>
<pre>_______________________________________________
phenixbb mailing list
<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a>
Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.org</a></pre>
</blockquote>
<br>
</div>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr"><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>
</blockquote></div>