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Structural View of HIV/AIDS:

A Video Challenge for High School Students

Tutorial 1

Protein Visualization with UCSF Chimera, Video Editing with Blender, and Sound Editing with Audacity

There are several different programs and resources that can be used to create videos for this challenge.

This tutorial describes one possible combination - UCSF Chimera to visualize proteins, and then Blender and Audacity to edit video together.

Some understanding of PDB data and protein structure is recommended before starting these tutorials. A list of helpful resources and materials is available, in particular, the introduction to Understanding the PDB Data and the video What is a Protein?.

The video you submit for the challenge can use the molecule highlighted in this example. Alternatively, you may decide to use different molecules and different resources to create your video.


Final video

Example video created following the steps shown below.

Part 1

Getting Started with UCSF Chimera and the PDB Archive

Video Guide

00:00 Challenge Introduction

00:40 Downloading and Installing UCSF Chimera

02:35 Finding HIV-related molecules on the rcsb.org

04:16 Opening a structure in Chimera

04:28 Manipulating 3d model in the Chimera window

04:50 Analyzing the reverse transcriptase structure using .pdb file

06:56 Selecting and deleting chains

07:30 Analyzing the key frames in the final video

08:27 Saving the position of the structure

09:34 Sizing the Chimera window to HDTV 720 setting

10:25 Saving Chimera session


Part 2

Visualizing a protein stucture in UCSF Chimera

Video Guide

00:04 Restoring the Chimera session

00:40 Changing the color of a chain

01:28 Adding a scene in the Animation interface

02:20 Hiding a chain

03:28 Showing molecular surface

03:55 Changing the transparency of the surface

04:30 Setting up a turn using command line

04:57 Adding scenes to the timeline

09:50 Saving the animation


Part 3

Creating text labels and more vizualization options

Video Guide

00:00 Previewing the animation

00:29 Creating 2d labels

03:22 More depiction options


Part 4

Video Editing in Blender

00:00 Downloading Blender

00:37 Setting up the video editing interface

01:04 Adjusting the video settings

02:47 Adding an image strip to the video

03:22 Manipulating a strip in the video sequence editor

04:35 Offsetting the footage

06:05 Adding transitions

06:48 Changing the blending mode of a strip

08:06 Adding key frames


Part 5

Adding Audio and Rendering

Video Guide

00:00 Downloading Audacity

00:31 Adjusting the length of a soundtrack

01:00 Adding effects to the soundtrack

01:40 Exporting the soundtrack from Audacity

02:46 Adding the sound to the movie in Blender

03:16 Rendering the movie