<div dir="ltr">Hi,<div><br></div><div>Update to a newer Phenix version, 1.14 is pretty old.</div><div><br></div><div>Does the atom that leaves the density have otherwise correct geometry, i.e. are bond lengths and angles according to your restraints file (you can see it in .geo file)? Does this atom have correct ideal values (check cif restraints file or use Reel)? </div><div><br></div><div>I don't know what could be the issue with coot. Does the terminal window give some message when you load the cif file?</div><div><br></div><div>Dorothee</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, May 4, 2020 at 12:49 PM Schulz, Eike-Christian <<a href="mailto:eike.schulz@mpsd.mpg.de">eike.schulz@mpsd.mpg.de</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
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<p class="MsoNormal"><span lang="EN-US">Dear all, <u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">I am refining a structure with a simple ligand in phenix 1.14. The ligand is present in 2 conformations at approx. equal occupancy. Refinement of the 2 conformations runs smoothly, but 2 problems occur<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
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<li class="gmail-m_55557523776877098MsoListParagraph" style="margin-left:0cm"><span lang="EN-US">One of the ligand atoms is placed out of the electron density after refinement. The geometry file (via elbow) is present during refinement. The atom is not in an
extreme position or clashes with anything else. </span><u></u><u></u></li><li class="gmail-m_55557523776877098MsoListParagraph" style="margin-left:0cm"><span lang="EN-US">After refinement the ligand conformation cannot be changed in coot, although I import the cif dictionary.
</span><u></u><u></u></li></ol>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><span lang="DE">Any advise ? <u></u><u></u></span></p>
<p class="MsoNormal"><span lang="DE"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="DE">Best, <u></u><u></u></span></p>
<p class="MsoNormal"><span lang="DE"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="DE">Eike<u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
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Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.org</a></blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div>Project Scientist, Molecular Biophysics and Integrated Bioimaging<br></div><div>Lawrence Berkeley National Laboratory</div><div>1 Cyclotron Road, M/S 33R0345</div><div>Berkeley, CA 94720</div><div>Tel: (510) 486-5709</div><div>Fax: (510) 486-5909</div><div>Web: <a href="https://phenix-online.org/" style="color:rgb(17,85,204)" target="_blank">https://phenix-online.org</a></div></div></div>