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

Hi Jeremy, The "magic wand" button calls the RNAplot algorithm from the RNA Vienna package. Assemble recovers the helices coordinates to produce the new drawing. The single-strands are recalculated by Assemble since they're the flexible parts of the 2D drawing allowing you to edit it. To resolve your problem you can perhaps select one or several helices and translate/rotate/flip them yourself. Does it help? Fabrice