- I have a complicated secondary structure for a very large RNA (1kb) that I want to visualize.
- I need to be able to interactively/manually edit the visualization according to my liking.
- I also need to color certain residues.
- I also would like to save the visualization for later use.
Does anybody know of any RNA secondary structure visualization software which can do all of these?
For example, the following popular programs do not work:
VARNA is interactive and can color bases, but it only has the option to save structure files, NOT visualization coordinates. So if I interactively edit the visualization (move some helices around, etc.), I cannot save those changes. I'd have to start from scratch, from the raw .ct/.db/.bpseq file.
RNAfdl allows you to color positions, but the GUI for pushing around residues/helices is very slow and cumbersome.