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AMI ePMV workshop 2013

Introduction to ePMV

Association of Medical Illustrators Annual Meeting 2013, 1/2 day workshop

Instructors: Graham Johnson, Fabian de Kok Mercado, Merry Shiyu Wang

This workshop teach basic and advanced principles of ePMV. Participants will learn and practice ePMV skills while assembling from scratch a complex animated molecular mechanism of action scene showing a ligand binding event.

Desktop systems running Cinema 4D and Maya will be provided, but we will also teach students who bring their own laptops with ePMV preinstalled or 3D Studio Max 2013 or 2014 or preinstalled for Blender. The instructors have limited experience in these last two packages, so we expect anyone using Max or Blender instead of C4D or Maya to be at least an intermediate level animator (more than 50 hours of hands on experience with the software.)

Novice-level 3D users, should plan to use our preinstalled versions of Cinema 4D to be able to follow the tutorials efficiently with its user-friendly interface.

8:30–10:30 ePMV basics

  1. 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.
  2. Loading, modeling (ribbons, atoms, sticks, ladders, surfaces, etc.), and chemically coloring dozens of molecular file types with single mouse clicks
  3. Building accurate DNA strands in several automated styles directly from any ATCG sequence in seconds
  4. Constructing massive, but efficient macromolecules like viruses and microtubules that won’t crash your software or computer
  5. Loading multi-state data like NMR structures and Molecular Dynamics trajectories
  6. Loading volumetric files like CT and 3D electron microscopy data
  7. Building lipid bilayers around transmembrane proteins

8:30–10:15 ePMV advanced

  1. Building simple lipid blilayers around transmemberane proteins
  2. Running molecular dynamics inside of the host software

Things to cover

  1. Molecular Dynamics
    1. ePMV hacks using host dynamics
    2. Online MD?
      1. e.g: Vallery Dagget for downloading
      2. iMD?
      3. Schulten?
    3. Modeller
  2. Morphing
    1. walk through online tutorials slowly and cleanly
      1. Online morphing with University of Phoenix server
      2. Rigged morphing with Modeller
  3. Selections
    1. text editing of PDB
    2. ePMV selections
    3. Mix representations =  chains, active site, ribbons with ball and stick active site
  4. Small molecule isolation from, e.g., "androgen" and "oxytocin"
    1. draw small molecule
    2. download direct from PDB
    3. pull from a PDB file
    4. See my notes to SciMed C4D list serve for this
  5. Biological Unit
    1. How to tell if something is part of a biounit?
      1. Online from pdb site
      2. in file
      3. with ePMV/object manager
    2. Does BioUnit monomer work (where assymetric unit is larger than biounit?
  6. Macromolecules
    1. Polio
    2. Microtubule
  7. Restarting a scene
    1. getting back to the same place
    2. edit old polygons (bring them back to life, etc.)
    3. project reopening
  8. Large molecule management (tricks for efficient viewing in the hosts)
    1. C4D instances
    2. Maya rebuilding with nCloth?  Read up on the contest winners descriptions
  9. Rigging
    1. Ribbon with IK
    2. Domains with IK
    3. Hinges
    4. Hack rigging (eyeballing and real