<div dir="ltr">Gents<div><br></div><div>You can link a ligand be placing it in the model and using link_ligands=True.</div></div><div class="gmail_extra"><br clear="all"><div><div 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 : 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></div>
<br><div class="gmail_quote">On Mon, Jul 4, 2016 at 10:53 PM, Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<p>Hello Lu,<br>
</p><span class="">
<blockquote type="cite">
<div style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial">
<div>However, as this structure had been solved and the cif file
is then created by ReadySet. My question is that how to use
ReadySet or eLBOW to generate a cif file to describe the
ligand that is covalently link to my protein. </div>
</div>
</blockquote>
<br></span>
Custom restraints is what you are looking for. Phenix provides with
a possibility to define bonds, angles etc restraints between any
atoms, as many as you like. For instance, you can define a bond
between any pair of atoms, any number of pairs. Same with angle.
This is described in the documentation. Please get back to me if you
have any questions or have any problems with this.<span class=""><br>
<br>
<blockquote type="cite">
<div style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial">
<div>I can load the ligand in REEL. I guess the next step is to
add the atom (or the whole residue?) to the ligand and then
run optimization. I did what I thought but the program output
some errors and I have sent them to the developer. Is there
any tutorial?<br>
</div>
</div>
</blockquote>
<br></span>
No idea. I'm interested too. Hope some one explains this.<br>
<br>
I guess we can solve this issue using simple command
line/nasty-file-editing practices. However, let's see if other
developers suggest a solution. If not.. get back to me and we will
solve this one way or another.<span class="HOEnZb"><font color="#888888"><br>
<br>
Pavel<br>
<br>
</font></span></div>
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