Two mMaya tutorials

By | Molecular, Process | No Comments

Through the molecular visualization work that we have been doing, a number of processes have been explored that may be worthwhile sharing with the broader science visualization community. Here are two tutorials that explore the use of Molecular Maya to help visualize macromolecules.

Molecular Visual Storytelling Workshop – AMI 2016

By | Event, Molecular | No Comments

Jodie, Gaël, and Stuart will be presenting a workshop at the AMI meeting in Atlanta, Georgia.
Principle 9 - Crowded molecular environment

The workshop is titled “Visual Storytelling in Molecular Animation: Accuracy and Design” and covers the unique challenges of creating visual narratives in the molecular world. For one thing, you’d be too small to hold a pencil. Oh, I mean creating narratives about the molecular world.

We’ll cover molecular-scale phenomena and narrative design that takes these into account. There will be an exercise that puts the discussed ideas into practice. The exercise resource booklet can be downloaded here, along with a standalone storyboard template used in the workshop.

AMI 2016 Reference Materials Booklet

AMI 2016 Digital Storyboard Template

 

Generating geometry for ball and stick molecules

By | Molecular, Process | 2 Comments

For an upcoming Molecular Visualization Principle, I decided to include a small molecule, which is something new for the series.

Small molecules typically use CPK space-filling or ball and stick representations, because surface meshes aren’t very informative. It’s more interesting to see structures like benzene rings when present. In order to bring the associated small molecule in with the protein structure I was importing using Molecular Maya, it was necessary to ensure that the HETATMs option was checked in the import options.

For the protein component, I kept the established simplified surface mesh used in the series so far. I decided on a modified ball and stick representation with pinched bonds, which Molecular Maya is capable of generating. The requirements of the animation and rendering process were such that I really needed regular geometry for the atoms and bonds, respectively balls and sticks. However, in the version of the software I was using, these structures were built with spherical particles and geometry instanced to particles. Maya unfortunately doesn’t have a particle instance to regular geometry conversion tool, so I was left to find my own workaround for this task. I’m confident that in the future, either or both of Autodesk Maya and Molecular Maya will have the capability of automatically performing the following, but at the time, this process was not implemented in the software.

First, I needed access to the underlying nodes in the mMaya hierarchy. I did this by selecting the mMaya node prefixed with pdbMolStruc_ and running the below code.

Note: this webpage has likely converted the regular quote marks to “smart quotes”, which will need to be replaced in your script editor with “straight quotes”.

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Upcoming VizBi Molecular Visualization Workshop

By | Misc, Molecular | No Comments

A series of image slices showing various colorful molecules, including DNA, a ribosome, and an actin filament

Gaël McGill, Stuart Jantzen, & Jodie Jenkinson will be giving a workshop at the upcoming VizBi (Visualizing Biological Data) meeting in Heidelberg, Germany on March 8, 2016. The workshop is titled “Best practices for visual storytelling in science” and will be composed of three parts.

In the first section, an introduction to design principles for visual communication will be discussed, with specific examples tied to biological visualization. The second section will explore a number of visualization guidelines that relate to molecular behaviours and cellular environments. These guidelines are exemplified by the paired visualization examples that we have been developing. The final section will involve a group discussion and collaborative iteration on a storyboard treatment that we will provide. Combining the design principles and guidelines introduced in the first and second parts of the workshop, attendees will explore solutions to the storytelling challenges inherent in the accurate depiction of molecular scale phenomena.

Registration for the conference and workshops can be found through this link. We hope to see you there!

 

Simulating molecular water

By | Molecular, Process | No Comments

As part of one of the Molecular Visualization Principles, I am attempting to design a simulation of molecular water with correct scale, density, and an approximation of brownian motion.

I began by creating a very simple water molecule model, ensuring that the dimensions were accurate. Okay, the bond angles might be very slightly out, but who would ever be able to tell? I knew there were going to be a huge number of copies, so keeping the poly count low was a must.

When making the simulation, I decided to ignore hydrogen bonding interactions, but I did use the bonding radius for the collision radius, which created a natural looking separation between the molecules.

In order to determine how the simulation would look once rendered, I made a small cube’s worth of molecules at the size, speed, and resolution I would be using for the final animation. This is the reason it takes up only a small part of the frame. If the result was a fuzzy blurry mess, I would know that changes were required.

A used a hand animated sphere as a collider and included noisy turbulence to induce brownian motion. The final animation will include a lateral wipe to show and hide the water, so I made sure to include a simple test of that. The result is below, and I think it is successful enough to move on to the full scale simulation.

Measured bond length: 0.9584 Angstroms

Measured bond angle: 107.9 degrees

Making DNA

By | Molecular, Process | No Comments

One of the Molecular Visualization Principles I am currently developing is “avoiding snake motion”. This refers to the depiction of long polymer motion, typically mRNA and DNA. To illustrate this principle, we decided to use a short linear strand of DNA.

I wanted to maintain consistency of style with the other principles, so I was aiming for a specific representation that was an interesting challenge to achieve.

I generated a mesh using Molecular Maya, and then decided to retopologize it by hand in order to create clean topology that was based on the atomic structure. Each nucleotide was made from two face loops. Edge loops were continuous along the long axis & backbone as well.

DNA modeling process retopologizing model on atoms
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Faces of U of T Medicine profiles Vijay Shahani

By | Molecular, Research | No Comments

“Vijay Shahani knows just how confusing chemistry can be. To help budding scientific minds better understand complicated concepts, he has developed Chemversity, a computer program meant to help students and educators alike. “

Faces of U of T Medicine is a series that profiles Faculty of Medicine students with unique stories to tell. Their profile of Vijay Shahani’s Masters Research Project, is featured at: http://medicine.utoronto.ca/…/faces-u-t-medicine-vijay-shah…