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Hi, <br>
<br>
I can have a closer look into this issue if : a) you send me all
relevant input files, and b) describe what you did (step-by-step) so
that I try to reproduce your steps up to the crash and then see how
we can address this.<br>
<br>
If you choose to send files, please make sure to send them to my
email address, not the entire mailing list!<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 1/22/18 21:20, Mian-Chee Gor wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAJOxWfyi-+UMCfOvg1PnKtm3zwmAJ1SRHgBu9f79CbpGUxwB9A@mail.gmail.com">
<div dir="ltr">Hello all,
<div><br>
</div>
<div>I run into this problem when I tried to refine my protein
structure after adding ligand.</div>
<div><br>
</div>
<div>The ligand that I am adding is a malonate, and the 3-letter
chemical code is MLI. I add the ligand using Coot and it fit
perfectly into the electron density map.</div>
<div><br>
</div>
<div>I then tried to run phenix.refine by giving the protein
structure pdb file, the original mtz file and the protein
sequence fasta file. However, there was an error message
saying missing restraints for the ligand. So I generate the
CIF file for the ligand using the Ready Set icon in the
toolbar. The ligand CIF file and a updated protein structure
pdb file was generated and automatically added to the
refinement windows. However, when I run the refinement, I saw
this error message: Number of nonbonded interaction distances
<0.001:2. Please inspect the output above (or in the log
window) and correct the input model file.</div>
<div><br>
</div>
<div>When I inspect the log window, the error is due to the
oxygen atoms in the ligand being too close to each other. Why
is there an error if the ligand was generated automatically in
Phenix? Has anyone encounter this problem before? How do you
solve that?</div>
<div><br>
</div>
<div>Many thanks in advance!</div>
<div><br>
</div>
<div>
<div><br>
</div>
-- <br>
<div class="gmail_signature" data-smartmail="gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">Dr Mian-Chee Gor
<div>Research Fellow</div>
<div>Griffith Institute for Drug Discovery (GRIDD)</div>
<div>Don Young Road, Nathan, QLD 4111</div>
<div>Mobile: +61 4 2084 7785</div>
<div>Email: <a href="mailto:m.gor@griffith.edu.au"
target="_blank" moz-do-not-send="true">m.gor@griffith.edu.au</a></div>
</div>
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