If not already installed, you will need the Quicktime plugin to watch these screencasts. If you experienced some problems, use the link below each video to download it at high resolution and to watch it locally with your favorite movie player.
Load and save RNA data
With this tutorial, you will learn:
- how to load a RNA molecule described in a FASTA file
- how to load a RNA secondary structure described in a CT/BPSEQ/FASTA file
- how to load a RNA tertiary structure described in a PDB file
- the basic manipulation of the 2D scene
- the synchronization between the 2D and 3D scenes
- how to export some building blocks into the 3D scene
- how to save your data
Manipulate the 2D and 3D scenes
With this tutorial, you will learn:
- how to export some building blocks into the 3D scene
- how to translate and rotate the 2D and 3D scenes
- how to translate and rotate a selection in the 2D and 3D scenes
- how to redefine the center of rotation for the 3D scene
- how to redefine the center of rotation for the selection in the 3D scene
- how to zoom the 2D and 3D scenes
The manipulation and edition of a RNA secondary structure
With this tutorial, you will learn:
- how to translate/zoom the 2D structure
- how to translate and rotate helices
- how to delete/create helices and base-base interactions
- how to change the type of a base-base interaction
- how to replot the 2D scene automatically
The alteration of the torsion angles
With this tutorial, you will learn:
- how to alter the torsion angles of a residue
- how to cut and link the molecular chains in the 3D scene
- how to use the "Chains" selection mode
The extraction of RNA motifs (a.k.a. RNA modules)
With this tutorial, you will learn:
- how to load a 3D structure from the MyPDB library
- the synchronization between the 2D and 3D scenes
- how extract a RNA motif
- how to recover this motif from the MyMotifs library
A concrete example of RNA 3D modelling
With this tutorial, you will learn:
- how to export the building blocks into the 3D scene
- how to thread a selection of the 3D model into a RNA motif
- how Assemble is creating named selections once a RNA motif applied
- how the Model Explorer panel allows you to easily center the 2D and 3D scenes on a given RNA element
- how to move automatically a selection of residues close to a residue defined as an anchor
- how to refine a 3D model
- how to display the backbone between residues not linked with a phosphodiester bond
The MyPDB embedded library
With this tutorial, you will learn:
- how to load the annotated 3D structures packaged with Assemble
- how to add new 3D structures to this library
- how to search for RNA modules in this library
How to infer a 3D model from S2S?
With this tutorial, you will learn:
- how to infer a 3D model from a structural alignment constructed with S2S
- how to load this 3D model with Assemble
- how to make the communication between S2S and Assemble
