Hi TW, My only guess is that these parts are originally in two different models and you are using the Join Models panel in Build Structure to form "C-N peptide bond." In that case, make sure you are setting the "Move atoms on [...] side" option so that it moves the linker part, not the Fc part. You said the linker is the part with "N" selected, so try: Move atoms on [selected N atom] side See the help: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Aug 15, 2021, at 4:47 PM, tiger wang via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Dear Ms/Mr helper: I encounted an issue when I try to fuse one (G4S)x linker to one of the Fc "C" terminal using "join bond". Once selected the "C" atom on Fc C terminal and "N" atom on (G4S)x N terminal and hit "apply" button, the Fc dimer fall apart but the (G4S)x linker was connected to the C terminal of Fc. How to avoid the Fc dimer from falling apart? Thanks very much for your help Sincerely TW