<div dir="ltr">Hi All;<div><br></div><div>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> I used the </div><div><br></div><div>&quot;  <i style="color:rgb(0,0,0)">phenix.ligand_linking pdb_file_name&quot;   commond</i><div><br></div><div>It creates </div><div>apply_link.def<br></div><div>and </div><div>data_link.cif<br></div><div><br></div><div>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><br></div><div>Thanks for your help</div><div><br></div><div>Bashir</div>-- <br><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><span style="font-family:Helvetica;font-size:medium">------------------------------------------------------</span></div><span style="font-family:Helvetica;font-size:medium">Muhammad Bashir Khan, Ph.D.</span><br style="font-family:Helvetica;font-size:medium"><span style="font-family:Helvetica;font-size:medium">Research Associate</span><br style="font-family:Helvetica;font-size:medium"><span style="font-family:Helvetica;font-size:medium">Department of Biochemistry</span><br style="font-family:Helvetica;font-size:medium"><span style="font-family:Helvetica;font-size:medium">Medical Science Bldg.</span><br style="font-family:Helvetica;font-size:medium"><span style="font-family:Helvetica;font-size:medium">Lab 3-27</span><br style="font-family:Helvetica;font-size:medium"><span style="font-family:Helvetica;font-size:medium">University of Alberta</span><br style="font-family:Helvetica;font-size:medium"><span style="font-family:Helvetica;font-size:medium">Edmonton AB, T6G 2H7</span><br style="font-family:Helvetica;font-size:medium"><br style="font-family:Helvetica;font-size:medium"><span style="font-family:Helvetica;font-size:medium">Phone: </span><a value="+17804923465" style="color:rgb(17,85,204);font-family:Helvetica;font-size:medium">780-492-4577-</a><br style="font-family:Helvetica;font-size:medium"><span style="font-family:Helvetica;font-size:medium">e-mail: </span><a href="mailto:cbrooks1@ualberta.ca" style="color:rgb(17,85,204);font-family:Helvetica;font-size:medium" target="_blank">mbk@ualberta.ca</a><br></div></div></div></div></div></div>