<div dir="ltr">Smith<div><br></div><div>If you have the Mg in the PDB model with MG as the atom name, residue name and element you don't need to do anything more.</div><div><br></div><div>For ligands, eLBOW takes a wide variety of inputs and PDB is the least useful. I recommend SMILES, Mol3D and/or SDF. If it's known ligand from Ligand Expo, then you can use eLBOW thus</div><div><br></div><div>phenix.elbow --chemical-component=XYZ</div><div><br></div><div>to get a restraints file and a PDB file.</div><div><br></div><div>You'll need a set of restraints for each ligand but they can be combined into one file using </div><div><br></div><div>
<p class=""><span class="">elbow.join_cif_files </span></p>
<p class=""><span class=""></span><br></p>
<p class=""><span class=""> usage:</span></p>
<p class=""><span class=""> elbow.join_cif_files merge1 merge2 ... target</span></p>
<p class=""><span class=""></span><br></p></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---</div><div>Nigel W. Moriarty<br>Building 33R0349, Physical Biosciences Division<br>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>
<br><div class="gmail_quote">On Wed, Sep 30, 2015 at 8:31 AM, Smith Liu <span dir="ltr"><<a href="mailto:smith_liu123@163.com" target="_blank">smith_liu123@163.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial"><div>Dear All,</div><div><br></div><div>If my protein contains a metal ion (Mg2+ for example, do I need a cif for the metal for phenix.refine? If my protein contains another ligand, which server can produce the ligand PDB suitable for the eLBOW? If my protein contains 2 ligands, then do I need 2 cif files for the phenix.refine or the phenix.real_space_refine?</div><div><br></div><div>I am looking forward to getting your reply.</div><div><br></div><div>Best regards.</div><span class="HOEnZb"><font color="#888888"><div><br></div><div><br></div><div>Smith</div></font></span></div><br><br><span title="neteasefooter"><p> </p></span><br>_______________________________________________<br>
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