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Maya Basics Tutorial

cellPack: OVERVIEW TUTORIALS November 2012                         iGEM Workshop

Presented by Merry Wang

Prepared by Merry Wang & Graham Johnson

Made possible by Graham Johnson, Ludovic Autin, David Goodsell, Michel Sanner & Arthur Olson  Download free | Install | Tutorials | Gallery | Forum | Contests

autoPack positions 3D geometries into, onto, and around volumes with minimal to zero overlap. autoPack mixes several packing approaches and procedural growth algorithms. autoPack can thus place objects with forces and constraints to allow a high degree of control ranging from completely random distributions to highly ordered structures. 

cellPack is a specialization of autoPack that generates probabilistic 3D models of large sections of cells that can contain dozens to trillions+ of molecules. It can position these molecules to recapitulate observed data where available and can further optimize the molecular interactions on a local level as each molecule is placed into a mesoscale model.

If you have experience with 3D software, especially with Maya, this tutorial should take about 2 hours and it will turn you into an beginner level autoPack user. If you are new to 3D software, the tutorial could take you anywhere between 3 and 12 hours. It introduces you slowly and methodically to the Maya interface as you learn how to generate and work with molecules in the cellPack GUI.

Quickstart Activities

  1. Basics 1: Install Maya 2013 Student edition here
  2. Basics 2: Install autoPack here
  3. Basics 3: Learn the principles of autoPack with some simple Test Scenes:
    1. Start Maya
    2. Open autoPack GUI
      1. Maya's Shelf Tabs: {uPy} tab > Click autoPack icon
    3. View an existing recipe scene using the autoPack GUI
      1. Click and drag on <Synaptic Vesicle> to select <HIV_0.0.1>
        1. The autoPack GUI {Viewer} tab should now read Load an auto/cellPack recipe for: HIV_0.0.1
      2. Click [Construct]
        1. If this is your first time building this scene into this version of Maya on your computer, autoPack will take a few seconds to download the needed geometries from the web to your autoPack cache folder.
        2. After a few moments your scene should have a large HIV particle (half sphere shape) filled with surface proteins, a nucleocapsid, and "cytoplasmic" proteins in the space in between
      3. Use Maya Viewport 2.0 to enhance the scene
        1. If necessary Click in the upper right of the HIV_x_x Viewer GUI palette to float it.  Do the same for the autoFill GUI to make your viewport larger.
        2. In the Viewport menu and toolbar:
          1. Click ViewportMenu>View>FrameAll
          2. Click to turn on the High Quality and Textured icons at the top of the viewport
        3. In the HIV_x_x Viewer GUI
          1. Uncheck [ ] Display HistoVolume HIV_x_x
          2. Uncheck [ ] Display Capside Geom
          3. Uncheck [ ] Display Nucleus Geom
        4. In the Viewport, hold option and drag to rotate until you can see the nucleocapsid of the HIV inside of the cut open sphere of the capsid surface proteins
        5. ViewPort Menu: Renderer> check [√]ViewPort2.0
        6. ViewPort Menu: Renderer> ViewPort2.0 [] 
          1. click the box to the right of "ViewPort2.0" to open Hardwar Renderer 2.0 Setting
          2. Unfold >ScreenSpace Ambient Occlusion
            1. Check [√] Enable
            2. Set Amount to ~2 and adjust the radius to something nice like ~56.
        7. Merry, take it from here- help them rotate, zoom in, pick ideal viewport render settings that the average 2 year old computer can handle, show them how to turn things on and off.  Give them some specific task, like animate a camera move to zoom in on one of the spike proteins, etc.
        8. Tomorrow we'll work on something fun and short for the "Filler" Tab like the gradient Spheres
        9. Then we'll hook it with ePMV and/or mMaya to let people change the default molecular geometries
Style format for Merry:
Actions for the user as verbs in bold
Supporting action text in regular font
Descriptions of results or background information in
middle grey
[Buttons have brackets]
{Tabs have curly braces}
<Pulldown menus>
[√] Checked CheckBoxes √=optionV on a mac
[ ] Unchecked CheckBoxes
Menu items>Submenu>SubSubMenu: FinallyTheMenuItemToClickOrSelect
I can show you how to format the HTML if you want the nicer numbering instead of Google's nasty <ol style=default>
Build the Outline in regular font first- just hitting return, tab, shift tab to indent the outline or deIndent, then afterwards, format the Bold and grey text... otherwise the HTML gets ugly in Google's crumby builder.