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Also, have a look at <br>
<br>
<a
href="https://journals.iucr.org/d/issues/2014/04/00/lv5059/lv5059.pdf">https://journals.iucr.org/d/issues/2014/04/00/lv5059/lv5059.pdf</a><br>
<br>
to know what to expect from "Place elemental ions" option. Briefly,
it won't place anything and it relies on meaningful inputs!<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 5/22/20 18:19, Nigel Moriarty wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CANkP=2fGous-sszD-MCxn+Cm-SqusKFOQtvxXLntrVoDS2pqpg@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<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 :
<a class="moz-txt-link-abbreviated" href="mailto:NWMoriarty@LBL.gov">NWMoriarty@LBL.gov</a><br>
Fax : 510-486-5909 Web : <a
href="http://CCI.LBL.gov" target="_blank"
moz-do-not-send="true">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"
moz-do-not-send="true">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"
moz-do-not-send="true">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"
moz-do-not-send="true">NWMoriarty@LBL.gov</a><br>
Fax : 510-486-5909 Web :
<a href="http://CCI.LBL.gov"
target="_blank"
moz-do-not-send="true">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"
moz-do-not-send="true">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>
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<div><span
style="font-family:Helvetica;font-size:medium">------------------------------------------------------</span></div>
<span
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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
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of Biochemistry</span><br
style="font-family:Helvetica;font-size:medium">
<span
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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
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<br
style="font-family:Helvetica;font-size:medium">
<span
style="font-family:Helvetica;font-size:medium">Phone: </span><a
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<span
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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
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target="_blank" moz-do-not-send="true">mbk@ualberta.ca</a><br>
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