Using MASH & Python to export dsDNA geometry from mMaya

Molecular Maya’s dsDNA kit facilitates the modeling and simulation of double-stranded DNA. However it is sometimes useful to export these dsDNA models as mesh geometry for use in other 3D programs and game engines. This tutorial explains how to use Maya’s MASH instancing system and Python to export geometry from mMaya’s dsDNA kit.

Using MASH & Python to export atomic geometry from mMaya

Although Molecular Maya (mMaya) facilitates the import and modeling of molecular models, it is sometimes useful to export these models as geometry for use in other 3D programs and game engines. This tutorial explains how to use Maya’s MASH instancing system and Python to export mMaya ball-and-stick atomic geometry.

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

Prerequisites:

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

Prerequisites:

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.

Prerequisites:

Controlling & Simulating 3D Fluids: Maya Fluids & Bifrost

In this tutorial, Controlling & Simulating 3D Fluids: Maya Fluids and Bifrost, we will introduce you to Maya’s two main fluid simulation techniques.  Maya’s Fluid Effects beautifully simulates gaseous effects. We will demonstrate this tool by creating a venom ejection simulation. You’ll also learn about Maya’s new Bifrost liquid simulator and how it is useful for creating 3D liquid splash and pour simulations.

We encourage you to also explore the related tutorial, Controlling & Simulating 3D Fluids: Maya nParticles, to fully understand the strengths of these different approaches to fluid simulation.  We developed these two tutorials to help you determine which method is most appropriate for your production needs.  

Learning Objectives:

  • Learn how to use Maya’s Fluid Effects to create a gaseous simulation.
  • Learn how to use Bifrost, Maya’s new 3D liquid simulation engine.
  • Compare the two techniques to help determine which simulation method is most appropriate.  

Controlling & Simulating 3D Fluids: Maya nParticles

In this tutorial, Controlling & Simulating 3D Fluids: Maya nParticles, we will demonstrate how Maya’s powerful nParticle dynamics can be used to create flowing liquids and apply this technique in a 3D liquid splash simulation. Although nParticles have many applications in Maya, we will customize settings that are effective for a gel loading animation.

We encourage you to also explore the related tutorial, Controlling & Simulating 3D Fluids: Maya Fluids & Bifrost, to fully understand the strengths of these different approaches to fluid simulation.  We developed these two tutorials to help you determine which method is most appropriate for your production needs.  

Learning Objectives:

  • Learn how to use nParticles to create liquid splash effects.
  • Learn strategies for customizing settings for nParticles
  • Learn strategies for efficiently rendering and compositing fluids

Advanced iBook Widget Design with Maya nDynamics

This behind-the-scenes look at how we created the Herbivore Carnivore Dentition Widget for the iBook, E. O. Wilson’s Life on Earth, will demonstrate the principles of creating dynamic simulations using Maya nDynamics. You’ll learn how to apply nParticle fluid dynamics and nConstraints through a gelatin-like meat simulation, as well as the utility of nCloth and nRigid colliders, through a leaf-clipping simulation. You’ll understand how food mastication can be simulated using keyframed animation, nParticles and instancing. Alongside these technical step-by-step explanations, we explain the motivation behind the design of these simplified models that represent food and teeth, as well as how these animations can be further improved. Finally, we explain how all of these assets can be combined using Keynote and iBooks Author to create an interactive widget for an iBook.

LEARNING OBJECTIVES

  • Understand the use of simplified models to represent more complex objects.
  • Learn how to use a combination of nDynamics techniques (nParticle fluid simulations, constraints, nCloth, nRigid colliders, and nParticle instancing) to create simulations of dynamic objects.
  • Learn how to use Keynote and iBooks Author to create an interactive widget for an iBook.

Bringing Corals to Life: Building Dynamic Rigs for Animation in Maya

Creating animations for scientific visualization often requires the use of custom rigs in order to manipulate the complex models we often encounter in our work. Standard entertainment industry tools and techniques that are often appropriate for characters and creatures are usually insufficient for visualization which means that we are required to build our own rigs. Building custom rigs demands a deep understanding of the Maya rigging and animation toolkit. This tutorial takes you through my process for creating a rig to animate a coral polyp that blends direct keyframe control with organic Maya Nucleus dynamic motion. The chapters in this tutorial go step by step through the process from building the virtual skeleton, to skinning geometry to the joints, to creating custom controls and attributes, and incorporating nDynamic hair curves into the rig. Along the way I demonstrate best practices for keeping the complex rig neat, orderly, and easy to use. The tutorial also covers using Maya shelf buttons and a limited amount of MEL scripting as a way to increase the speed of rig set up and reduce the tedium. The emphasis of the tutorial is on helping you understand Maya rigging technology so that you can design custom rigs for your own projects that will facilitate your ability to create compelling scientific visualizations using Maya.

LEARNING OBJECTIVES

  • Understand the need for creating custom animation rigs
  • Learn the how to create a skeleton for a multi tentacle organism using joints
  • Understand the various options for skinning geometry to a joint skeleton
  • Learn how to skin geometry to the skeleton and the benefits of different skinning methods
  • Understand skin weighting, influence objects, and blend shape deformers
  • Learn how to to use Forward and Inverse Kinematics
  • Learn techniques for creating ergonomic animation controls
  • Incorporate nDynamic hairs into Inverse Kinematic controls
  • Learn how to create custom Maya shelf buttons from snippets of MEL scripts

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.

LEARNING OBJECTIVES

  • 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

The Making of Apoptosome

A behind-the-scenes look at how we created our 2013 Apoptosome Assembly animation for Cell Signaling Technologies, with step-by-step tutorials that cover key concepts including research and pre-production, construction of complete protein models from available 3D structural data as well as missing data, and compositing techniques used to avoid split-attention issues.

LEARNING OBJECTIVES

  • Finding structural data in the Protein Data Bank and using the data to
    reconstruct complex 3D models in Maya & Molecular Maya.
  • Finding structural data in the Protein Data Bank and using the data to reconstruct complex 3D models in Maya & Molecular Maya.
  • Dealing with incomplete or controversial scientific information
  • Learning how to rig and animate multi-domain protein models
  • Using compositing techniques to increase clarity and viewer’s learning  experience

Generating ZBrush Texture & Displacement Maps for Rendering in Maya: Brain Coral

One of the biggest challenges in creating compelling animations for scientific visualization is rendering highly organic detailed structures. This requires an understanding displacement texture map generation and application. In this tutorial you will learn the processes involved in incorporating Pixologic’s ZBrush and Autodesk’s Maya into a scientific animation workflow. The demonstration uses the example of a highly detailed brain coral model. You will learn how to create UV texture coordinates for a model, and how to use ZBrush to generate texture, displacement, and normal maps. You’ll learn how to edit the texture maps in Adobe Photoshop and how to incorporate the maps in an Autodesk Maya 2015 shader network and how to render the model using the mental ray plug in for Maya. The tutorial finishes with discussions on troubleshooting displacement maps and a brief overview of using vector displacement maps.

LEARNING OBJECTIVES

  • Understand what displacement maps are and how they are useful for rendering detail in Maya
  • Generate UV texture coordinates for ZBrush models
  • Learn how to create and export texture maps using ZBrush plugins
  • Learn how to export models from ZBrush and import them into Maya
  • Learn how to build shader networks in Maya using displacement maps
  • Learn how to render a brain coral model using mental ray for Maya
  • Compare different types of displacement maps including vector displacement maps.