<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="">2 solutions that I use<div class=""><br class=""></div><div class="">A first one consists in designing your residue linked to your ligand (under ChemDraw / MarvinSketch) then prepare the restraints under eLBOW (from smiles for examples). You will have to modify some atom names into the generated cif file (C, O, CA, N, CB, etc… depending of the modified residue) and above all change the nature of this molecule to L-peptide. Then you can use it in coot as a modified residue and use the modified cif file in Phenix. You can adjust the modification by tuning the occupancy of the atoms corresponding to the ligand and keep the occupancy to 1 for the atoms of the residue. Here you will have a nice covalent bond.</div><div class=""><br class=""></div><div class="">The second solution would be to restrain the distance between the atom of your residue and the atom of the ligand to a covalent bond (C-C distance or whatever it is). Certainly, angles should be restraint too.</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">Le 15 avr. 2020 à 00:59, Muhammad Bashir Khan <<a href="mailto:mbk@ualberta.ca" class="">mbk@ualberta.ca</a>> a écrit :</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi All;<div class=""><br class=""></div><div class="">I have a protein molecule and a ligand structure. I want to make a covalent bond between the ligand and protein molecule, could somebody explain to me how I can do that using phenix.</div><div class=""> I used the </div><div class=""><br class=""></div><div class="">" <i style="" class="">phenix.ligand_linking pdb_file_name" commond</i><div class=""><br class=""></div><div class="">It creates </div><div class="">apply_link.def<br class=""></div><div class="">and </div><div class="">data_link.cif<br class=""></div><div class=""><br class=""></div><div class="">I did refine the structure again giving the above file as well but did not see any covalent bond created between the protein and ligand.</div><div class=""><br class=""></div><div class="">Thanks for your help</div><div class=""><br class=""></div><div class="">Bashir</div>-- <br class=""><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><span style="font-family: Helvetica; font-size: inherit;" class="">------------------------------------------------------</span></div><span style="font-family: Helvetica; font-size: inherit;" class="">Muhammad Bashir Khan, Ph.D.</span><br style="font-family: Helvetica; font-size: inherit;" class=""><span style="font-family: Helvetica; font-size: inherit;" class="">Research Associate</span><br style="font-family: Helvetica; font-size: inherit;" class=""><span style="font-family: Helvetica; font-size: inherit;" class="">Department of Biochemistry</span><br style="font-family: Helvetica; font-size: inherit;" class=""><span style="font-family: Helvetica; font-size: inherit;" class="">Medical Science Bldg.</span><br style="font-family: Helvetica; font-size: inherit;" class=""><span style="font-family: Helvetica; font-size: inherit;" class="">Lab 3-27</span><br style="font-family: Helvetica; font-size: inherit;" class=""><span style="font-family: Helvetica; font-size: inherit;" class="">University of Alberta</span><br style="font-family: Helvetica; font-size: inherit;" class=""><span style="font-family: Helvetica; font-size: inherit;" class="">Edmonton AB, T6G 2H7</span><br style="font-family: Helvetica; font-size: inherit;" class=""><br style="font-family: Helvetica; font-size: inherit;" class=""><span style="font-family: Helvetica; font-size: inherit;" class="">Phone: </span><a value="+17804923465" style="color: rgb(17, 85, 204); font-family: Helvetica; font-size: inherit;" class="">780-492-4577-</a><br style="font-family: Helvetica; font-size: inherit;" class=""><span style="font-family: Helvetica; font-size: inherit;" class="">e-mail: </span><a href="mailto:cbrooks1@ualberta.ca" style="color: rgb(17, 85, 204); font-family: Helvetica; font-size: inherit;" target="_blank" class="">mbk@ualberta.ca</a><br class=""></div></div></div></div></div></div>
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