<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Sergio,<div class=""><br class=""></div><div class="">This is how I proceed for modified residues.</div><div class=""><br class=""></div><div class="">1. Generate (draw) the desired modified residue in a program such as Chemdraw or MarvinSketch, then copy it as a SMILES string.</div><div class=""><br class=""></div><div class="">2. Generate a cif file with phenix eLBOW, from the SMILES string. Name it as you want with 3 letter code.</div><div class=""><br class=""></div><div class="">4. Modify the cif file, especially the definition as a L-peptide and not as Ligand. Change the corresponding atoms to atom names such as C, N, CA, O and OXT (CB, …) as in common residues (additional atom names can remain as they are).</div><div class=""><br class=""></div><div class="">5. In Coot, import the new cif and the new residue. Remove the OXT atom, then change the residue number to the one to replace. It should make the binding with residues -1 and +1 automatically. </div><div class=""><br class=""></div><div class="">For better refinement you can fix the atom occupancy of the residue (CYS in your case) to 1 and modify the occupancy of the « bound » atoms (as a group).</div><div class=""><br class=""></div><div class="">Hope this way will help you.</div><div class=""><br class=""></div><div class="">Take care.</div><div class=""><br class=""></div><div class="">Xavier<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">Le 22 janv. 2022 à 20:12, Sergio A. Sampieri <<a href="mailto:sampieridae@gmail.com" class="">sampieridae@gmail.com</a>> a écrit :</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hi all, hope this message finds you well.
</div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">As in a previous topic from 2018, I’m
having problems refining a covalent-bounded ligand.</div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">The link shall be made between a carbon
atom that is double bonded to an oxigen </div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">“SMILES <span style="font-size:10.5pt;font-family:"Segoe UI",sans-serif;color:rgb(33,33,33);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial" class="">C1=CC=C(C=C1)C=O”
and the SG group of a Cys residue. </span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size:10.5pt;font-family:"Segoe UI",sans-serif;color:rgb(33,33,33);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial" class="">I generated a CIF dictionary through AceDRG in
COOT and CCP4i2. But after trying different approaches during refinement,
(Automatic Linking parameters, Atom selection, acceptor & donnor,
ligand bond cut off and so) the result keeps being a non bounded enzyme-ligand
complex (“Not linked: pdbres="LIG A 401”).</span></div><p class="MsoNormal" style="margin:0cm;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:10.5pt;font-family:"Segoe UI",sans-serif;color:rgb(33,33,33);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial" class=""> </span></p><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size:10.5pt;font-family:"Segoe UI",sans-serif;color:rgb(33,33,33);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial" class="">I readed in the phenixbb that this was solved
by changing the nature of the ligand (<a href="http://www.phenix-online.org/pipermail/phenixbb/2018-February/023718.html" style="color:rgb(5,99,193)" class="">http://www.phenix-online.org/pipermail/phenixbb/2018-February/023718.html</a>),
but is not the way I would like to follow.</span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size:10.5pt;font-family:"Segoe UI",sans-serif;color:rgb(33,33,33);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial" class="">Any suggestions or ideas would be greatly
appreciated, thanks a lot for your time. Stay safe. </span></div><div class=""><br class=""></div>-- <br class=""><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><font color="#999999" class="">“I’ve learned to think like a virus; no neurons, a lot of sex, and a lot of errors.”<br class="">John J. Holland<br class=""><br class=""><br class="">Biól. Sergio Aguirre Sampieri<br class=""><br class=""></font></div></div>
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