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<p><font face="Arial">You could add the link description to your
dictionary, import that in coot and it should work.</font></p>
<p><font face="Arial">The non phenix way would be to create the link
in jligand, write out the dictionary description and merge it
with your ligand dictionary. The link statement needs to be in
the pdb of course.</font></p>
<p><font face="Arial">There might be also a way in phenix to do
this, but I'm not aware of it at the moment. Maybe Pavel or
Nigel can help out here.</font></p>
<p><font face="Arial">Cheers</font></p>
<p><font face="Arial">Christian</font></p>
<br>
<div class="moz-cite-prefix">Am 26.02.2018 um 10:45 schrieb
Sebastiano Pasqualato:<br>
</div>
<blockquote type="cite"
cite="mid:CD1EBA21-A7AF-46CB-A93C-3970CFC9124E@gmail.com">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
Dear Nigel and Pavel,
<div class="">thank you very much for you feedback and precious
advice.</div>
<div class="">It is a compound with a C=C double bond that gets
attacked by the S of a Cys, hence I think it’s normal that the
program is not recognising automatically the bond.</div>
<div class="">I have changed the C=C bond to C-C and recreated the
CIF file for the compound, than provided phenix the bond
restrains (bond length and angles) for the C-S bond.</div>
<div class="">It all seems to work very nicely.</div>
<div class="">Thanks.</div>
<div class=""><br class="">
</div>
<div class="">Any idea on how to tell Coot the same things? ;-)</div>
<div class="">(I guess this one should go to the Coot_bb though
;-))</div>
<div class=""><br class="">
</div>
<div class="">Thanks again,</div>
<div class="">ciao,</div>
<div class="">S<br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On 22 Feb 2018, at 18:35, Nigel Moriarty <<a
href="mailto:nwmoriarty@lbl.gov" class=""
moz-do-not-send="true">nwmoriarty@lbl.gov</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">Sebastiano
<div class=""><br class="">
</div>
<div class="">As Pavel said, send me the inputs if you
are having issues.</div>
<div class=""><br class="">
</div>
</div>
<div class="gmail_extra"><br class="" clear="all">
<div class="">
<div class="gmail_signature"
data-smartmail="gmail_signature">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div dir="ltr" class="">Cheers
<div class=""><br class="">
</div>
<div class="">Nigel
<div class=""><br class="">
</div>
<div class="">---</div>
<div class="">Nigel W. Moriarty<br
class="">
Building 33R0349, Molecular Biophysics
and Integrated Bioimaging</div>
<div class="">Lawrence Berkeley National
Laboratory<br class="">
Berkeley, CA 94720-8235<br class="">
Phone : 510-486-5709 <a
href="mailto:NWMoriarty@LBL.gov"
class="" moz-do-not-send="true">Email
: NWMoriarty@LBL.gov</a><br class="">
Fax : 510-486-5909 Web : <a
href="http://cci.lbl.gov/"
target="_blank" class=""
moz-do-not-send="true">CCI.LBL.gov</a></div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br class="">
<div class="gmail_quote">On Thu, Feb 22, 2018 at 9:25
AM, Pavel Afonine <span dir="ltr" class=""><<a
href="mailto:pafonine@lbl.gov" target="_blank"
class="" moz-do-not-send="true">pafonine@lbl.gov</a>></span>
wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF" class=""> Hi
Sebastiano,<br class="">
<br class="">
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 class="">
<br class="">
<a
class="m_8786071025687345902moz-txt-link-freetext"
href="http://phenix-online.org/documentation/reference/refinement.html#definition-of-custom-bonds-and-angles"
target="_blank" moz-do-not-send="true">http://phenix-online.org/<wbr
class="">documentation/reference/<wbr class="">refinement.html#definition-of-<wbr
class="">custom-bonds-and-angles</a><br
class="">
<br class="">
Phenix does not recognize LINK records.<br
class="">
<br class="">
To verify the link, check .geo file that lists all
the restraints used in refinement.<br class="">
<br class="">
Let us know if you more questions or need help!<br
class="">
<br class="">
Pavel
<div class="">
<div class="h5"><br class="">
<br class="">
<div
class="m_8786071025687345902moz-cite-prefix">On
2/22/18 05:13, Sebastiano Pasqualato wrote:<br
class="">
</div>
</div>
</div>
<blockquote type="cite" class="">
<div class="">
<div class="h5">
<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="letter-spacing: normal;
text-align: start; text-indent: 0px;
text-transform: none; white-space:
normal; word-spacing: 0px; word-wrap:
break-word;" class="">
<div style="letter-spacing: normal;
text-align: start; text-indent: 0px;
text-transform: none; white-space:
normal; word-spacing: 0px; word-wrap:
break-word;" class="">
<div class="">
<div
style="text-align:-webkit-auto;word-wrap:break-word"
class="">-- <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 <a
href="tel:+39%2002%209437%205167"
value="+390294375167"
target="_blank" class=""
moz-do-not-send="true">+39 02
9437 5167</a><br class="">
fax <a
href="tel:+39%2002%209437%205990"
value="+390294375990"
target="_blank" class=""
moz-do-not-send="true">+39 02
9437 5990</a></div>
<div
style="text-align:-webkit-auto;word-wrap:break-word"
class="">web <a
href="http://is.gd/IEOXtalUnit"
target="_blank" class=""
moz-do-not-send="true">http://is.gd/IEOXtalUnit</a></div>
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