Stockholm format to dot-brackets format?
If what you want is to find a consensus structure for a group of alignments in stockholm format then you might try with 
RNAalifold
 and for single sequence folding check RNAfold. Both have online servers and can also be run offline.

After you get the consensus structure update the stockholm file by adding  a structure consensus line as: #=GC SS_cons followed by the dot bracket notation.

A nice RNA structure editor that will make your life easier is EMACS when complemented with RALEE. It allows you to view and manipulate RNA structures, predict structure folding and color the alignments based on basepairs relationships. It will be worth it to invest time into mastering RALEE.