<div dir="ltr"><div>Hi,<br>one solution would be to create a custom link/angle... using a .param file with the restrains as in below example.<br><br></div>on the phenix website:<br><h2><a class="gmail-toc-backref" href="http://www.phenix-online.org/documentation/reference/refinement.html#id49">Definition of custom bonds and angles</a></h2>
<p>Most geometry restraints (bonds, angles, etc.) are generated
automatically based on the CCP4 monomer library. Additional custom
bond and angle restraints, e.g. between protein and a ligand or ion,
can be specified in this way:</p>
<pre class="gmail-literal-block">refinement.geometry_restraints.edits {
zn_selection = chain X and resname ZN and resid 200 and name ZN
his117_selection = chain X and resname HIS and resid 117 and name NE2
asp130_selection = chain X and resname ASP and resid 130 and name OD1
bond {
action = *add
atom_selection_1 = $zn_selection
atom_selection_2 = $his117_selection
symmetry_operation = None
distance_ideal = 2.1
sigma = 0.02
slack = None
}
bond {
action = *add
atom_selection_1 = $zn_selection
atom_selection_2 = $asp130_selection
symmetry_operation = None
distance_ideal = 2.1
sigma = 0.02
slack = None
}
angle {
action = *add
atom_selection_1 = $his117_selection
atom_selection_2 = $zn_selection
atom_selection_3 = $asp130_selection
angle_ideal = 109.47
sigma = 5
}
}
<br><br></pre><pre class="gmail-literal-block">cheers<br></pre><pre class="gmail-literal-block">Maxime<br></pre><br><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div><div>Dr. Maxime Cuypers<br></div></div></div><div><div><div><span><span>Post-Doctoral Research Associate, </span>Structural Biology</span><br></div><div></div><div>St Jude Children s Research Hospital,<br></div><div><span>262 Danny Thomas Place<br></span><span>Memphis, TN 38105-3678, USA</span><br></div><div><br></div><div>or<br><br></div><div>3000 Eagle Dr.<br></div><div>Memphis, TN 38115, USA<br></div><div><br><div>Mobile phone: <br></div><div>USA: 001 901 491 4649<br></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">2018-02-26 12:41 GMT-06:00 Christian Roth <span dir="ltr"><<a href="mailto:christianroth034@gmail.com" target="_blank">christianroth034@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<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><span class="HOEnZb"><font color="#888888">
<p><font face="Arial">Christian</font></p></font></span><div><div class="h5">
<br>
<div class="m_-3890634613180972512moz-cite-prefix">Am 26.02.2018 um 10:45 schrieb
Sebastiano Pasqualato:<br>
</div>
<blockquote type="cite">
Dear Nigel and Pavel,
<div>thank you very much for you feedback and precious
advice.</div>
<div>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>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>It all seems to work very nicely.</div>
<div>Thanks.</div>
<div><br>
</div>
<div>Any idea on how to tell Coot the same things? ;-)</div>
<div>(I guess this one should go to the Coot_bb though
;-))</div>
<div><br>
</div>
<div>Thanks again,</div>
<div>ciao,</div>
<div>S<br>
<div><br>
<blockquote type="cite">
<div>On 22 Feb 2018, at 18:35, Nigel Moriarty <<a href="mailto:nwmoriarty@lbl.gov" target="_blank">nwmoriarty@lbl.gov</a>> wrote:</div>
<br class="m_-3890634613180972512Apple-interchange-newline">
<div>
<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="m_-3890634613180972512gmail_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 <a href="mailto:NWMoriarty@LBL.gov" target="_blank">Email
: NWMoriarty@LBL.gov</a><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_-3890634613180972512m_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/docum<wbr>entation/reference/refinement.<wbr>html#definition-of-custom-<wbr>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="m_-3890634613180972512h5"><br>
<br>
<div class="m_-3890634613180972512m_8786071025687345902moz-cite-prefix">On
2/22/18 05:13, Sebastiano Pasqualato wrote:<br>
</div>
</div>
</div>
<blockquote type="cite">
<div>
<div class="m_-3890634613180972512h5">
<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>
<div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">
<div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">
<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>
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<br>
<br>
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