Good Afternoon, 

I'm currently a master's student using chimera but I have a problem and I was wondering if you guys have a solution for it. When the original PDB file is loaded onto chimera, I can see different alpha and beta chains however, when I run optimization using gaussian program and load the fchk file or pdb file converted from chk file, the chains are gone and I'm left with just atoms. When I convert the chk file to pdb file in gaussian, it does the same and I was wondering if you guys know a solution or tips to bypass this. If you could help me out, it would be great!

Thank you