How can I connect two seams on a mesh? They come apart while posing but not while modeling I am learning how to rig properly using this simple molecule character.  I joined all the spheres and created seams by using ctrl-F and self-intersect.  I then deleted the internal faces.  The molecule now comes apart when I am testing the armature.  



However, when I am modeling, there is no break in the seam; it is connected:



What can i do to make the seams remain connected while i am posing the character?

Here is the .Blend file:



Thank you!
Idle Chit-chat

Ok, I switched to answer to give a more detailed, well, answer! It appears that your mesh is not actually one piece, despite appearances.

Problem

I am not familiar with the self-intersect tool you described (or Ctrl + F if those are one and the same), but the spheres are separate. I proved this by selecting a single verticy of one of the spheres and keying L. If the mesh were a whole, like rigging requires, everything would select. Everything, obviously, did not.

Solution

Luckily, there is a simple solution! Select the entire mesh with A, key W, and select Remove Doubles:



This will join all the seemingly joined edge loops. Now you can continue on and rig!