SEC_STRUCTURE problem

[LarrySMelidis]

Is there a way to stop the rna on the .svg image collapsing on itself during minimisation (on the 2d image).

[sreisser]

I'm afraid the algorithm has a limit to what it can reasonably fold. Possibly it helps to chop the molecule into different parts, make the svg image, and manually combine them in inkscape. You can also post your input file and I can have a look myself.