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Yale Workshop 2014

Introduction to uPy, ePMV, and autoPACK

Instructors: Graham Johnson & Anna Kuo

This workshop will overview and teach four related software projects via a collection of hands-on tutorials. Participants will:

1.   create a collection of professional quality scientific visualizations

2.   learn how to use, write, and modify scripts and GUI development code that will automatically function inside of a growing number of 3D animation software hosts that currently include: Autodesk’s Maya and 3D Studio Max, Maxon’s Cinema 4DBlender, and the molecular graphics viewer DejaVu.

Two of the projects covered, uPy and autoPACK, have broad scientific and artistic applications. We will also explore two highly developed plugins, written in uPy (ePMV and cellPACK), to learn these tools of molecular modeling and animation while exploring the potential of the uPy programming API from a user’s perspective.


Participants must bring their own laptop with at least one of the following uPy supported hosts preloaded: Maya, Cinema4D, or Blender. We encourage students experienced with 3D animation software to use their favorite package (you may also use 3DS Max, but uPy support is currently limited so you'll need an additional host like Maya to complete some of the more advanced tutorials).

New and intermediate-level 3D users, should preinstall and use Cinema 4D in the class (free demo version is fine) to be able to follow the tutorials efficiently with its user-friendly interface.


9:30–10:15 Programming in uPy

An overview of the ubiquitous Python API (uPy) will include basic tutorials aimed at first-time programmers, but with extensibility paths highlighted for experienced programmers. Participants will learn how they can write a single file that functions in every host to efficiently extend their potential user base.


10:15-11:45 ePMV to model, animate, simulate and render molecules

The embedded Python Molecular Viewer (ePMV) runs molecular-modeling software directly in the host GUIs. A series of short tutorials will introduce participants to Molecular Biology visualization via ePMV basics (low learning curves) that include, for example, loading and animating molecules like proteins, DNA, RNA, lipids and macromolecules (e.g., microtubules and viruses) directly from multiple data types as well as modeling volumetric file types e.g., CT or 3D electron microscopy data. The workshop will then transition smoothly to cover advanced ePMV techniques, for example, running molecular dynamics simulations and rigging molecules for animation, enabling participants to easily create accurate and sophisticated molecular interactions and molecular machines for numerous applications.

Open-source and free– more information at


11:45–1:00 Introduction to autoPACK and cellPACK

Participants will explore the basic functionalities of the autoPACK software running as a plugin inside of the hosts, and in PMV and Chimera. Participants will:

  • •load and tame massive molecular models like HIV floating in Human Blood Serum (with atomic detail) using the basic “Viewer” functions

  • •construct both artistic and biological worlds from scratch using the “Filler” functions including filling a blood vessel with blood cells at proper concentrations

  • •add accurate background/contextual details to existing pedagogic scenes, e.g., build lipid bilayers around transmembrane proteins

Open-source and free– more information at