<div dir="ltr">Sebastiano<div><br></div><div>As Pavel said, send me the inputs if you are having issues.</div><div><br></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 Thu, Feb 22, 2018 at 9:25 AM, 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 text="#000000" bgcolor="#FFFFFF">
Hi Sebastiano,<br>
<br>
if the ligand in PDB file is placed correctly and distance between
atoms that are supposed to have a bond is within reasonable then it
should be linked automatically. Otherwise you can use custom bonds
as described here (available in GUI and command line):<br>
<br>
<a class="m_8786071025687345902moz-txt-link-freetext" href="http://phenix-online.org/documentation/reference/refinement.html#definition-of-custom-bonds-and-angles" target="_blank">http://phenix-online.org/<wbr>documentation/reference/<wbr>refinement.html#definition-of-<wbr>custom-bonds-and-angles</a><br>
<br>
Phenix does not recognize LINK records.<br>
<br>
To verify the link, check .geo file that lists all the restraints
used in refinement.<br>
<br>
Let us know if you more questions or need help!<br>
<br>
Pavel<div><div class="h5"><br>
<br>
<div class="m_8786071025687345902moz-cite-prefix">On 2/22/18 05:13, Sebastiano Pasqualato
wrote:<br>
</div>
</div></div><blockquote type="cite"><div><div class="h5">
<div><br>
</div>
Hi there,
<div>I have a pretty basic question.</div>
<div>I am refining a structure in which a drug has been
covalently linked to a Cys of the protein.</div>
<div>I have generated the .cif fie for the ligand, but I
don’t know how to tell the program that carbon C04 has to be
covalently linked to the SG of the Cys. Is that sufficient to
insert a LINK record in the pdb file? What is the correct syntax
for that?</div>
<div>Thanks a lot for the feedback and sorry for the
naive question,</div>
<div>ciao,</div>
<div>Sebastiano</div>
<div><br>
</div>
<div><br>
</div>
<div>
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<div>
<div style="text-align:-webkit-auto;word-wrap:break-word">-- <br>
<b>Sebastiano Pasqualato, PhD</b><br>
Crystallography Unit<br>
Department of Experimental Oncology<br>
European Institute of Oncology<br>
IFOM-IEO Campus<br>
via Adamello, 16<br>
20139 - Milano<br>
Italy<br>
<br>
tel <a href="tel:+39%2002%209437%205167" value="+390294375167" target="_blank">+39 02 9437 5167</a><br>
fax <a href="tel:+39%2002%209437%205990" value="+390294375990" target="_blank">+39 02 9437 5990</a></div>
<div style="text-align:-webkit-auto;word-wrap:break-word">web <a href="http://is.gd/IEOXtalUnit" target="_blank">http://is.gd/IEOXtalUnit</a></div>
</div>
</div>
</div>
</div>
<br>
<br>
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