How to edit an RNA secondary structure?

You have: a secondary structure.
You want: to change this secondary structure.

In this tutorial, you will learn how to:

Having the right secondary structure allows you to more easily understand and construct your RNA. A secondary structure is made with helices linked and oriented by single-strands and junctions (apical loops, inner loops, 3-way junctions,...). As described in the tutorial "How to construct a 3D model from scratch?", helices, single-strands and junctions can be selected and their 3D fold can be easily exported in Chimera.

All the modifications done on the secondary structure are automatically synchronized with the hierarchical view displayed in the lateral panel "Secondary Structure" and with the bracket notation of the reference structure in the lateral panel "Structural Alignment".

By clicking on lock icon, you lock and unlock your secondary structure. If unlocked, you will discover new buttons.

Modify base-base interactions

Orange circles allows you to change the edge of interaction for each residue
Each click allows you to iterate over the different edges: Watson-Crick (circle), Hoogsteen (squarre) and Sugar (triangle)
The pink circle changes the orientation of the interaction: color filled (cis orientation) or not (trans orientation)

Create tertiary interactions

If secondary interactions can only be created with new helices, tertiary interactions can be created directly.

By selecting two residues, a blue circle is displayed.
By clicking on it, you create a new tertiary interaction.
As described previously, the pink and orange circles allows you to change the type of interaction.

Delete tertiary interactions

If secondary interactions can only be deleted by removing their enclosing helix, tertiary interactions can be deleted directly.

A fourth red circle allows you to delete the tertiary interaction
Once deleted, you can easily recreate a new one by clicking on the blue circle.

Delete helices

If unlocked, the selection of an helix display a red circle in its center.
Click on it to delete it, and click on it one more time to quickly recreate it.

Create helices

  • step 1: select a first residue,
  • step 2: select a second one,
  • step 3: when you select a third one, Assemble2 select the last one automatically to have two strands with the same length,
  • step 4: once the red circle clicked, a new helix is created. Ok, i know, the initial layout is not so great. I should improve it. For the time being, rotate your helix with the mouse and/or flip it with flip icon in the 2D toolbar

Fabrice Jossinet, PhD | University of Strasbourg, ARN | UPR 9002 of CNRS | f[dot]jossinet[at]ibmc-cnrs[dot]unistra[dot]fr