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.

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 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.