This might be something that can't be fixed, but I am dealing with a pretty large RNA (401 nt). I was wondering if there is another way of making the 2D model more readable besides the "magic wand" button (Reorganize helices). I have tried to use this button, but I am still seeing some clashes of helices (only one instance after clicking the button) or letters crunching really close together in the single stranded regions. Is this a algorithm problem or can it be changed in the Assemble program? Thanks for the help! Jeremy