When Chimera reads a PDB file, it adheres to the implied conventions of the PDB — which is what is tripping you up here.  The two conventions that are getting you are: (1) consecutive residues in ATOM records with no intervening TER card are connected, and (2) jumps in the residue numbering of consecutive residues along with separation in 3D space imply missing intervening structure.  (1) will add extra bonds you didn’t explicitly put in your CONECT records.  (2) will change some inter-residue bonds into “missing structure” pseudobonds.

So if we fix your PDB file, Chimera will like it better. :-)  The changes are:

— Change ATOM records to HETATM records

— Put all the atoms into a single residue

— Change the residue name from GLY to UNK

— Give the atoms unique names (I used C0 through C69)

I have attached the edited version of your file.

—Eric