[Chimera-users] What happened to my model?

So, in my line of work we are focusing on the protein Dihydrofolate Reductase. Using Jmol, I was able to remove all chains except for chain A, and also increased the diameter of the backbone so that it may be printed. When I opened it in Chimera to export it from VRML file to an STL file, it still looked fine. However, when it was opened in my 3d printing program, parts of the protein were missing. All I see is floating fragments. Is there any way I can fix this using chimera? I have included images of the protein.