Must add that I had also tried "Join Models" at no avail. Restraing concerned dihedrals, through tmsd-colvars applied to the CA atom, so that the side chains could move. With "Join Models" I was therefore unable to get the continuous alpha helix shape: formation of the new peptide bond resulted in a kinked alpha helix, no matter how I dealt with the "Join Models" entries. What I need is that the new peptide bond is formed without altering the dihedrals based on the CA atoms. francesco pietra ---------- Forwarded message ---------- From: Francesco Pietra <chiendarret@gmail.com> Date: Mon, Aug 26, 2013 at 8:02 PM Subject: Make bonds in a large polypeptide To: chimera <chimera-users@cgl.ucsf.edu> Hello; Is there a limit in the number of atoms when using the function "make a bond"? I was trying that in a polypeptide of 450 standard residues (I made it a single model) and it did not work. Just to not be cryptic, that need arises from having modeled by special techniques the initial portion of the polypeptide. Now I would like to replace that portion with the modeled one. I had restrained with rmsd-colvars the dihedrals of a short stretch of alpha helix, so that I could align the modeled portion with the polypeptide. thanks francesco pietra