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Molecular Viewers

The molecular viewers PMV and Chimera can now interoperate with autoPACK

Overview
What can you do with molecular viewers?

You'll find the molecular viewers fast and fairly friendly... Experienced users can crank out entries with less than one or two hours of work. 
Fast realtime viewports. Molecular viewers are optimized to look at tons of biological objects in realtime. 
Checkout these four videos made of PMV and Chimera in action on the HIV 1.4 model: 
PMV exploring HIV 1.1 with realtime Screenspace Ambient Occlusion
Chimera exploring HIV 1.4 with shadows and outlines in realtime
Tom Goddard a developer of Chimera has posted an example of a research-talk style movie made with Chimera
PMV has autoPACK plugged in with uPy and offers the full autoPACK GUI including a Viewer and Filler tab. More about PMV. 
Chimera has a clean and easy autoPACK result file (.apr) reader that allows you to drag and drop or otherwise open an .apr or multiple .apr files into the same scene and use the standard tools of Chimera to analyze the model or alter the representations. More about Chimera . 
Both molecular viewers have relatively new animation capabilities that enable users to create movies with simple GUI widgets.

Install an autoPACK enabled Molecular Viewer

  1. To use autoPACK with either viewer, you must first install a special version of either software package.
  2. Follow the installation instructions for the molecular viewer of choice
    1. PMV (Python Molecular Viewer) Install PMV
    2. Chimera 1.8 with autoPACK reader Install Chimera
  3. Enter the autoPACK Visualization Challenge Molecular Viewer Only Category before March 18, 2013
    1. The challenge has special category for animations created with molecular viewers only 
      1. Video only
      2. No post-processing other than to add labels or credits or to change the format of the movie.
      3. Video Entry using Molecular Viewer Only, no post-effects 
    2. Prizes:
      1. Molecular Graphics Lab @ Scripps: 3D ZCorp print of the HIV in Blood Serum Model 
      2. Autodesk: $250 Cash 
      3. AMD FirePro™ V4900 professional graphics card 
      4. CGSociety - 12 months CGS CONNECT membership

Complete basic tutorials for autoPACK PMV and/or Chimera

  1. This alpha version of autoPACK will improve several times each week and the tutorials will expand
    1. Follow the video tutorials to learn how to select and modify properties like colors and transparency or how to set lights and depth cuing properties for any model type.
    2. Molecules from the .stl folder are "dead" meshes that you can only change basic properties
    3. Molecules from the .pdb folder can change representations and perform analysis like distance measurements using all of the standard tools in chimera
    4. Follow the tutorials for a basic overview and check back frequently for new tutorials
    5. We are making frequent and major additions and adjustments to this software, so please check back here frequently to get the latest performance, stability and functionality enhancements!
  2. Here is an overview of autoPACK for Chimera. This 17 minute video shows you how to:
    1. load and autoPACK result file (.apr which in this demo is HIV 1.0)
    2. add a complementary file to the same scene (in this case the "low" resolution lipid bilayer shell)
    3. set up nice lights with shadows
    4. customize colors, transparency and effects like outlines
    5. keyframe and render an animation to a quicktime movie
    6. the fast viewports of the molecular viewers, optimized to capably visualize hundreds of thousands of objects at a time enable users to create effective and attractive animations with minimal effort
    7. The instructional ChimeraautoPACK video:
      1. How to load cellPACK HIV in Chimera


    8. and the simple movie produced during this instructional video:
      1. Chimera autoPACK HIV 1.0

    9. More detailed instructions for making movies in Chimera:
      1. Official Movie making tutorial and examples web pages:
        1. http://www.cgl.ucsf.edu/chimera/data/nih-oct2012/movies.html
        2. http://www.cgl.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.html
      2. HIV autoPACK movie made by Tom Goddard of the Chimera development team
        1. this movie: http://www.cgl.ucsf.edu/home/goddard/temp/hiv_autopack.mp4
        2. generated by this script: http://www.cgl.ucsf.edu/home/goddard/temp/hiv_autopack.py
    10. Another movie testing a white background:
      1. YouTube Video


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