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How to manipulate an RNA secondary structure?

You have: an RNA secondary structure.
You want: play with it!!

In this tutorial, you will learn how to:

• select secondary interactions and helices
• select single-strands and junctions
• select tertiary interactions
• select contiguous residues
• select non-contiguous residues

Once a secondary structure loaded (for more details, see the tutorial "how to load data into Assemble2?"), it is displayed in the main panel. A secondary structure is made with helices linked and oriented by single-strands and junctions (apical loops, inner loops, 3-way junctions,...). In Assemble2, the helices can be moved to modify the layout of the secondary structure.

Using the mouse, you can:

• zoom in/out the whole secondary structure with the mouse wheel,
• translate the whole secondary structure by keeping the right-mouse pressed on this panel and by dragging the mouse,
• select parts of the secondary structure,
• edit the secondary structure (add/remove helices and/or tertiary interactions) if it is unlocked. (for more details, see the tutorial "how to edit an RNA secondary structure?")

If you have selected some residues, you can double left-click anywhere on the main panel to clear the selection.

Selection of secondary interactions and helices

Choose a residue inside the helix you want to select, and left-click on it. By accumulating the mouse clicks on this residue, you will iterate over the selection process:

• one click will select the residue.,
• two consecutive clicks will select its secondary interaction,
• three consecutive clicks will select its helix.

Once an helix selected, you can rotate it:
or translate it:

Selection of single-strands and junctions

Choose a residue inside the junction or the single-strand you want to select, and left-click on it. By accumulating the mouse clicks on this residue, you will iterate over the selection process:

• one click will select the residue.,
• two consecutive clicks will select its single-strand and pop-up the lateral panel named "3D folds",
• three consecutive clicks will select its junction and pop-up the lateral panel named "3D folds".

The lateral panel named "3D folds" lists you all the single-strands/junctions with the same length and topology (apical loop, inner loop, 3-way junction,...) extracted from solved tertiary structures and stored in our database. You can select an entry and use the 3D toolbar to export its 3D fold in Chimera.

Selection of tertiary interactions

Choose one of the two residues establishing the tertiary interaction, and left-click on it. [Ctrl or Alt] + left-click on the second residue to select the tertiary interaction.

Selection of contiguous residues

Selection of non-contiguous residues