<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">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>
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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>