View structures with pseudoknots

[VonBoss]

Is there a way to export secondary figures with the pseudoknots visible?
The MD file makes it sound like removing the pseudoknots is optional?

[davidhoksza]

Funny you ask because I started working on enabling this feature in Traveler (the program responsible for laying out the structures within the R2DT pipeline) today :) I started developing this feature about three years ago, but it never got into production. Should be ready in a week or so. Once ready, we can make it available via R2DT.

[VonBoss]

Brilliant! I would definitely appreciate that! Thank you.

[VonBoss]

I'm curious if you were able to implement your new feature.

[davidhoksza]

Just yesterday, I pushed it to Traveler. See the corresponding section of README. However, it might take some time before it gets into R2DT. Currently, @AntonPetrov is testing it. But if you have a concrete template, you could try using Traveler directly. Or if you are interested in a single (or a few) structure only, I could run it for you...

[AntonPetrov]

@davidhoksza is right, I am working on integrating pseudoknot visualisation into R2DT right now.

@VonBoss - if you are willing to send me your sequence(s) at contact @ antonpetrov .com, I can test them and send you back the images (as long as the R2DT template for that RNA has pseudoknots of course).