AMI ePMV & Scripting Workshop 2015

Project result previews for the tutorials covered our 2015 workshop will be posted here by May 20th.

ePMV & Scripting in Advanced Molecular Techniques for Cinema 4D

Push your modeling and animation skills to the next level! Our half-day workshop will incorporate ePMV (the embedded Python Molecular Viewer) into advanced molecular-animation techniques taught in Cinema 4D (C4D). Learn how to increase productivity while simultaneously generating more natural-looking and accurate molecular and cellular visualizations. Sick of editing keyframes? The project-based lessons will teach you how to apply wise rigging, efficient cloning, physics, and simple scripting to replace unwieldy keyframe approaches with controlled simulation. Automation and semi-automation techniques that are broadly applicable beyond C4D and molecular subjects will be taught through the sequential buildup of the following projects: ligands binding to a shape-shifting protein, a massive collection of agent-based molecular interactions (a signaling cascade of protein phosphorylations simulated using random Brownian walks with distant-dependent actions), efficient actin filament construction followed by dynamic filament assembly, and motor proteins walking on a microtubule that you will construct by coupling electron microscopy protein structure data with C4D’s powerful character motion systems.

Participants must have completed the ePMV Basics Tutorial (epmv.scripps.edu/documentation/tutorials) prior to the workshop. We strongly recommend having at least 50 hours of previous C4D experience, but no programming experience is required. Project output previews will post by May 20th at mesoscope.org/workshops/ami-epmv-scripting-workshop-2015.

Syllabus

Transmembrane Ligand Binding Animation/Simulation

Objective: Create a semi-scripted, simplified ligand-receptor binding animation taking place in a scene of multiple receptors on a membrane. Leverage Cinema4D’s Xpresso and Dynamics systems to minimize manual keyframing and simulate random motion.

Ligand Binding with Atomistic Conformational Changes and Dynamics

Objective: Animate a realistic yet informative depiction of a ligand binding to a transmembrane protein called a G-protein coupled receptor (GPCR) using minimal keyframes. Use ePMV to import a protein with atomistic conformational changes and control its conformation based on ligand-binding using Xpresso. Leverage Cinema4D’s Dynamics system to create a refined binding event animation.

Dynamic Actin Filament Assembly Demo

Objective: Learn an efficient approach to actin filament construction and simulation of actin filament assembly.

Walking Motor Proteins using Character Rigging Demo

Objective: Learn an approach to animating a kinesin walking on a microtubule using electron microscopy data and Cinema4D’s character rigging system.

Preliminary versions in development (polished versions will post on May 20, 2015):

Ligands binding to a shape-shifting protein version 0.0.1

Phase 1 version 1 of Project 1: Ligand Binding. Here we use only 4 keyframes to easily control the timing of when a ligand will bind, then use a combination of physics, dynamics, various effectors and a small amount of scripting to program the binding and related color changes, etc. This provides a rough starting point.

Phase 2 version 1 of Project 1: Here, we use UCSF Chimera to morph between two conformations of the Muscarinic Acetylcholine Receptor M2, program a random walk from one conformation to the next with a preference towards the inactive conformation when the ligand is unbound and towards the active conformation when the ligand binds. We add random walks to the atoms to simulate some intramolecular atomic Brownian motion. This version just pushes the ligand inside with two position keyframes, but in Phase 3, it will simply wander inside semi-randomly.

Here it is in context of the bilayer.

And here is a diferent protein with a more dramatic change to show the generality of this approach and to emphasize the utility of morphing.

Phase 3 version 1 of Project 1: Now we bring it all together to show a relatively realistic protein with relatively realistic motion binding a ligand that does a controlled but otherwise random walk before binding and inducing a conformational change (atomically accuratish) and a corresponding color change.)
A massive collection of agent-based molecular interactions (a signaling cascade of protein phosphorylations simulated using random Brownian walks with distant-dependent actions)
Efficient actin filament construction followed by dynamic filament assembly version 0.1.0
Motor proteins walking on a microtubule that you will construct by coupling electron microscopy protein structure data with C4D’s powerful character motion systems.

Workshop Files

ePMV AMI 2015 Workshop Resources

Quick XPresso Reference

1. Transmembrane Ligand Binding
AMI workshop 2015: 1. Transmembrane Ligand Binding

2. Ligand Binding with Atomistic Conformational Changes and Dynamics for AMI 2015
ePMV Advanced Molecular T...and Dynamics for AMI 2015