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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="moz-txt-link-freetext" href="http://phenix-online.org/documentation/reference/refinement.html#definition-of-custom-bonds-and-angles">http://phenix-online.org/documentation/reference/refinement.html#definition-of-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<br>
<br>
<div class="moz-cite-prefix">On 2/22/18 05:13, Sebastiano Pasqualato
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:349A542C-E48E-4E19-A686-ABF3D15A1DEA@gmail.com">
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<div class=""><br class="">
</div>
Hi there,
<div class="">I have a pretty basic question.</div>
<div class="">I am refining a structure in which a drug has been
covalently linked to a Cys of the protein.</div>
<div class="">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 class="">Thanks a lot for the feedback and sorry for the
naive question,</div>
<div class="">ciao,</div>
<div class="">Sebastiano</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap:
break-word; -webkit-nbsp-mode: space; -webkit-line-break:
after-white-space;" class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;
word-wrap: break-word; -webkit-nbsp-mode: space;
-webkit-line-break: after-white-space;" class="">
<div class="">
<div class="" style="orphans: 2; text-align: -webkit-auto;
widows: 2; word-wrap: break-word; -webkit-nbsp-mode:
space; -webkit-line-break: after-white-space;">-- <br
class="">
<b class="">Sebastiano Pasqualato, PhD</b><br class="">
Crystallography Unit<br class="">
Department of Experimental Oncology<br class="">
European Institute of Oncology<br class="">
IFOM-IEO Campus<br class="">
via Adamello, 16<br class="">
20139 - Milano<br class="">
Italy<br class="">
<br class="">
tel +39 02 9437 5167<br class="">
fax +39 02 9437 5990</div>
<div class="" style="orphans: 2; text-align: -webkit-auto;
widows: 2; word-wrap: break-word; -webkit-nbsp-mode:
space; -webkit-line-break: after-white-space;">web <a
href="http://is.gd/IEOXtalUnit" class=""
moz-do-not-send="true">http://is.gd/IEOXtalUnit</a></div>
</div>
</div>
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<br class="">
<br>
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<br>
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