Tethering a Transcription Factor to Dynamic DNA

Using Molecular Maya (mMaya) and the dsDNA kit, this short tutorial explains how to convert an imported co-crystal structure of a protein bound to DNA (in this case a PDB of Myc:Max:DNA) into a dynamic animation where the protein dimer is tethered to an extended strand of simulated DNA.

Introduction to Molecular Maya Modeling Kit

Molecular Maya’s (mMaya) Modeling kit facilitates many of the challenges in the modeling of high-quality full-length protein models. Incomplete structural data often require us to create structural fragments based on primary sequence and then pose and connect these peptide fragments to existing structures. This course will provide an introduction to the Modeling kit’s basic functionalities to address these common tasks. We’ll begin by synthesizing dynamic modeling peptides, applying secondary structure folds, creating poses, connecting with other structures and exporting custom PDBs. Because all newly synthesized peptides in the kit are pre-rigged, we’ll learn how to control their dynamics with various tools like handles, elastic networks and colliders. Finally we will also look at the kit’s built-in Domain Library which offers a convenient collection of 3D domain models ready-to-go for various modeling tasks. We will end with various ‘PDB surgery’ operations like extracting, splitting and merging PDB fragments. This course will let you to take full advantage of mMaya’s Modeling kit and reveal its unique advantages in production.

Learning Objectives:

  • Gain an overview of the functionalities of the mMaya Modeling Kit
  • Understanding common molecular modeling challenges that the kit can help with
  • Learn how to synthesize, control, and export full-length protein models


Introduction to Molecular Maya Rigging Kit

Molecular Maya’s (mMaya) Rigging kit automates the modeling, rigging, simulation and visualization of macromolecules. A rig is a virtual skeleton that controls the range of dynamic motion of a 3D model. In the case of macromolecules like proteins, this can be an incredibly challenging task. This course will provide an introduction to the Rigging kit’s basic functionalities and we’ll begin with our single-click rig creation process as well as the different levels of detail you can create in a molecular rig – from all-atom to more coarse-grained rigs. We will create custom selections to define subdomains of your model and use those to create handles that help steer the simulation. We will look at elastic networks as a means to control the secondary structure of your protein, as well as several options for creating complex molecular morphs. Finally we will also look at the ability to save conformational poses of your molecule as well as how to cache your simulation for smoother playback and in preparation for rendering. This course will let you to take full advantage of mMaya’s Rigging kit and reveal its unique advantages in production.

Learning Objectives:

  • Gain an overview of the functionalities of the mMaya Rigging Kit
  • Learn how to change molecular representations of your rigged models
  • Create sub-domain selections to drive the creation of rig handles that help steer your molecular simulation
  • Apply elastic networks to control how your model maintains secondary structure
  • Use different targeting methods to morph your protein
  • Gain an understanding for the production challenges that the kit can help with


Introduction to iBooks Author

Creating engaging interactive books can be a challenging task that necessitates not only command of text and graphics production, but also specialized authoring environments for video, animation and sound, as well as programming experience for more advanced interactivity. Apple’s iBooks Author software streamlines the production of interactive books that combine text with a great variety of multimedia types. These digital books can then be distributed and read on both iPad and desktop platforms through the iBooks application. Leveraging my experience as the lead designer for E.O. Wilson’s Life on Earth digital biology textbook created in close partnership with Apple, I will share with you not only the basics of the iBooks Author workflow, but also the design strategies we used to select different widget types depending on content goals and target audience. We will review numerous examples selected from the 500+ widgets we created for this seven volume book. By the end of the course you will not only be able to create your own interactive book, but also understand how multimedia widgets are effectively woven into the reading experience.

Learning Objectives:

  • Strong understanding of what an iBook is and how it is different from an eBook
  • Familiarity with iBA’s capabilities to assess whether it is the right tool for your project
  • Proficiency with basic iBA production workflow
  • Introduction to how content and audience drive design decisions and multimedia production in iBooks Author.
  • Preview work on iPad and in the iBooks desktop application


  • none

Introduction to Molecular Maya dsDNA Kit

Molecular Maya’s (mMaya) double-stranded DNA (dsDNA) kit automates the modeling, animation and visualization of structurally-accurate dsDNA. This course serves as an introduction to the kit and all its basic functionalities. We’ll begin with de novo modeling of dsDNA starting from a base-pair count, a DNA sequence or a custom- and/or PDB-derived curve. Molecular representation defaults as well as custom representations and color controls will also be introduced. The models are pre-rigged and animation/simulation-ready, so we will review the myriad ways in which one can control the strands, including shape holds, pose-to-pose morphing, controlling motion with turbulence and basic cloning operations like cleaving and ligating dsDNA strands. We will look at features to control the binding and/or sliding of proteins along the dynamic dsDNA model, such as strand mounts and meta-mounts. Finally we apply a combination of all these tools in a short final project that shows cyclic AMP Receptor protein (CRP) binding and bending a dynamic dsDNA strand based on an imported PDB co-crystal structure. This course will let you to take full advantage of mMaya’s dsDNA kit and reveal its unique advantages in production.

Learning Objectives:

  • Gain an overview of the functionalities of the mMaya dsDNA Kit
  • Learn how to quickly model and edit the representation and color of your dsDNA
  • Understand how to control the animation/simulation of dsDNA and interaction with binding proteins
  • Gain an understanding for the production challenges that the kit can help with, as well as those it is not well suited for.


Creating Web-Based Interactive Molecular Visualizations

3D animation software empowers scientific illustrators and animators to create stunning visualizations of the molecular world. While animations can be an efficient and eye-catching way of communicating scientific findings, they do not let the audience interact and explore the data. Interactive media can provide an immersive way of communicating a story, and allows the audience to explore data at their own pace, order and desired level of detail. In this tutorial, you will learn how to create a 3D visualization tool that allows anyone with access to the internet (and a modern web browser) to explore a biomolecule interactively. The goal is not to program software for data analysis, but instead to craft a flexible, fully customizable and powerful data presentation tool. You will use the protein hemoglobin as an example structure, but are welcome to use your favorite protein structure instead. After preparing and exporting the structure in UCSF Chimera, you will use a combination of HTML, CSS, Javascript, THREE.js and Tween.js to create the web-based tool. All software packages and libraries used in this tutorial are available online free of charge.

Learning Objectives:

  • Understand the pros and cons of different technologies and methods of creating web-based 3D-visualizations
  • Build a simple website with the basic framework necessary for browser-based 3D-visualization, using HTML, CSS, and JavaScript
  • Create a setup for a 3D-viewer for biomolecular structures using the WebGL library THREE.js
  • Prepare biomolecular structures in USCF Chimera for upload to a browser
  • Import biomolecular structures into a browser
  • Connect your 3D-model with other elements of a website to make it interactive
  • Smoothly animate interactively triggered motion using the tweening library Tween.js

Software Links:

MODO for Scientific Visualization: Hardsurface Modeling

This tutorial introduces The Foundry’s MODO as a tool for hard-surface modeling. We assume some basic knowledge of 3D modeling, but no
experience with MODO. This tutorial provides a broad overview of MODO’s
modeling interface, then uses a few fundamental tools to box-model a
realistic laboratory device. We then examine the model for potential
render artifacts and use a variety of methods to clean them up. By the
end of the tutorial, you should have a sense of the direct, responsive
modeling workflow possible with MODO. While this tutorial is recorded in
version 9xx, the techniques covered apply to version 10.x as well.

Learning Objectives:

  • Learn the general layout of the MODO interface
  • Learn where to find inline help, tutorials, and online resources for
    learning MODO
  • Understand common MODO concepts including Action Centers, Falloffs,
    Symmetry, and Component Modes
  • Learn to use reference geometry to guide the creation of freeform
    shapes with known dimensions
  • Use box, bevel, thicken, and transform tools to build a basic shape
  • Use viewport shading to identify potential render artifacts
  • Use polygon splitting techniques to control rendertime tesselation

MODO for Scientific Visualization: Photorealistic Rendering

This tutorial introduces the render engine in The Foundry’s MODO as a tool for photoreal rendering. This tutorial assumes some basic
familiarity with rendering concepts, and builds on the general
introduction to MODO provided in “MODO for Scientific Visualization:
Hardsurface Modeling.” This tutorial provides an introduction to the
MODO render workspace and introduces MODO-specific shading and rendering
concepts. We then build a naturalistic benchtop scene around the device
model from the Hardsurface Modeling tutorial. We cover framing, lighting
with Area Lights and HDRI, global illumination, camera settings,
material settings and presets, and progressive render controls. By the
end of the tutorial, you should be able to navigate the MODO workspace
and take advantage of the “out-of-the-box realism” provided by render
defaults and material presets; you should also have a sense of the range
of control available, and the advantages of quick feedback for tweaking
a final look. While this tutorial is recorded in version 9xx, the
techniques covered apply to MODO 10.x as well.

Learning Objectives:

  • Learn the layout of the MODO render workspace
  • Learn basic concepts behind the MODO Shader Tree
  • Review principles of setting up a non-studio shot, including open framing, realistic camera settings, and using reflections to highlight form while preserving the impression of “found lighting.”
  • Learn to work with MODO’s material system, starting from scratch or using presets
  • Learn to adjust MODO’s progressive renderer for quick feedback or final quality

MODO for Scientific Visualization: Rigging & Animation

In this tutorial, we will explore the power of Modo’s rigging and animation tools by building and animating a tetrapod rig. You’ll not only become familiar with the basics of the UI, joints, rigs, animation channels and poses, but also understand how these compare to similar tools and methods in programs like Maya. In the end, we will develop custom controls to create a looping tetrapod walk cycle. We also encourage you to explore the related Modo tutorials, Hardsurface Modeling and Photorealistic Rendering, to get a broader overview and understanding of Modo’s unique strengths and how these can be leveraged for scientific visualization.

Learning Objectives:

  • Become familiar with Modo’s user interface
  • Understand the basics of keyframe animation in Modo
  • Learn about joints, inverse kinematics, and how to rig a skeleton
  • Optimize animation workflow with custom controls and poses
  • Create a looping walk cycle

Design Principles for Data Presentation

This tutorial is for scientists looking to improve their data figures and visualizations.  In our approach, we’ve broken down the design process into a series of practical and functional units. By doing so, we hope to help you make sense of visual design process and to show you how you can apply these principles to solve common visual problems and challenges in data presentation. By the end of the tutorial, you’ll have the tools and strategies that will allow you to design clear and strong figures that will better communicate your data.

Learning Objectives:

  • Understand cognitive design as an intersection of visual design and cognitive science.
  • Learn the three variables of cognitive design.
  • Understand how these variables can change the scope of your design.
  • Learn to focus your designs by identifying your communication objectives.
  • Learn the five key elements of design.
  • Understand how the elements can change the aesthetic nature and legibility of your designs.
  • Learn the five key principles of design.
  • Understand how the principles can affect the interpretation and communication of your designs.
  • Learn common design software used in creating data figures and visualizations.
  • Learn different formatting requirements for print versus digital media.

Illustrator for Scientific Visualization I – Drawing Scientific Figures

This tutorial demonstrates beginner-level tools in Adobe Illustrator that support data visualization.  We’ll walk through the creation of a poster and the placement of customized data plots, charts, and graphics.  The tutorial is parsed so that each chapter tackles a specific tool or function, making it easier to find the topic most relevant to your work.  With an emphasis on creating data figures for scientific publication, the topics covered here will give viewers a fundamental understanding of Illustrator and how the program may be used to create and manipulate vector graphics.

Learning Objectives:

  • Learn to set-up a new document
  • Learn to edit document settings to fit your purpose
  • Understand the difference between CMYK and RGB
  • Learn to create basic shapes
  • Understand how to handle raster and imported images
  • Understand the difference between the Selection Tool and Direct Selection Tool
  • Manipulate and transform shapes with the Transform Tool and via control points
  • Learn to create custom shapes with the Pen Tool
  • Learn to use and understand the difference between guides, grids, and rulers
  • Learn to use the Text Tool and to manipulate Text Boxes
  • Learn and understand the Graph Tools provided in Illustrator
  • Learn how to export a file in different formats


Photoshop for Scientific Visualization

This tutorial series explores beginner and intermediate-level Photoshop tools. For our beginner-level Photoshoppers, the chapters take you step-by-step through three mini-projects. We start with basic document creation, and move onwards to more and more advanced tools as we progress through the projects. We’ve also kept the course modular for our intermediate-level Photoshoppers. Chapters cover a single function, tool, or aspect of a tool, making it easier to jump in and out of the topics you need to explore. In this course, we will cover a wide variety of common, as well as not-so-common, tools and features that will help improve and expedite your storyboarding, illustration, and design needs.


  • Learn to set-up new documents
  • Learn to edit document settings
  • Understand the difference between CMYK and RGB
  • Learn to create text, painted layers, and vector shapes
  • Learn to create different brushes to create lines, textures, and color
  • Learn to manipulate and save paths and vector shapes
  • Learn how to manipulate visibility and editability of layers and objects
  • Learn different color and image adjustment tools
  • Understand difference between different color blending modes
  • Learn to use actions and layer comps
  • Understand how content and file types affect file size

From Structural Data to 3D Animation Software: Introduction to Chimera, Pymol, and VMD for Preproduction

An introductory look at the molecular visualization software to 3D animation software workflow, with step-by-step tutorials to acquaint the user to three of the popular molecular viewing softwares Chimera, Pymol and VMD. Pre-production tasks done in molecular viewing software to prepare PDB files for import into Maya (via the Molecular Maya plugin) will be discussed, including splitting macromolecules into multiple pieces and rebuilding large macromolecular complexes from separate PDB files.


  • Discussing pros and cons of the molecular viewing software Chimera, Pymol and VMD
  • Reviewing the Chimera, Pymol and VMD interfaces
  • Performing pre-production tasks on PDB files to prepare structural data for import into Maya

Introduction to ZBrush for Scientific Visualization

This tutorial introduces the absolute beginner to using Pixologic’s ZBrush for digital sculpting. You will learn how to navigate the ZBrush interface and how to start a ZBrush sculpting process. The tutorial shows the step by step process for creating a model of a bacterium and a 3D cross section of a human skull. You’ll learn how to import reference imagery to use as a sculpting guide, how to use and edit sculpting brushes, how to use ZSpheres, Dynamesh, and ZRemesher. At the end of the tutorial you should feel confident in your ability to sculpt a model suitable for scientific visualization.


  • ­ Learn how to navigate and customize the ZBrush interface
  • ­ Understand how to sculpt a polygon mesh
  • ­ Learn how to create high resolution details
  • ­ Learn how to create the flagella of a bacterium starting with ZSpheres
  • ­ Understand how to create and import reference imagery
  • ­ Learn how to use Dynamesh to sculpt the forms a human skull
  • ­ Learn how to split a model into separate parts
  • ­ Learn how to create fine details with custom brushes
  • ­ Create a cross section using clipping brushes

Storyboarding for Scientific Animation

This tutorial series will get you going with your first storyboard for scientific animation. We will cover the basics including: film and story structure, the function of shot types, the role of the camera, and the dynamics of lighting. Along the way, we will apply these topics to the storyboard. We’ll show you how to turn blank canvases into fully drawn panels that will communicate the production needs of your scientific stories.


  • Understand basic animated story structure
  • Draw and compose basic shot types
  • Draw character action and movement
  • Understand how cameras affect composition and framing
  • Draw camera action and movement
  • Apply colors and use them as visual cues
  • Understand basic lighting
  • Apply basic shading to colors
  • Understand the purpose of supporting graphics
  • Export images and create final documentation

Integrating ZBrush in the Scientific Visualization Pipeline

Learn what digital sculpting with Pixologic’s ZBrush can bring to the art of scientific illustration and visualization. This course provides a broad view of the powerful tools that are part of the ZBrush toolkit. Examples of the many unique ZBrush technologies such as dynamic subdivisions, 2.5 dimensional illustration, ZSpheres, Dynamesh, and ZRemesher are clearly explained and demonstrated to give you a sense of their place in the visualization workflow. Examples of ZBrush models used in illustration, animation, and 3D printing are presented. ZBrush is compared with other competing digital sculpting software packages.


  • Understand what ZBrush does and how it can be used in illustration, animation, and 3D Printing
  • Learn the many technologies that make up the ZBrush toolkit
  • Learn ZBrush terminology
  • Understand 2.5 Dimensional Illustration
  • Learn about the many available digital sculpting software packages