DynGeoTest

Dynamic Geometry Test:

• Start Blender with Factory Settings (may need to save startup and restart)
• Delete everything from the Scene (a,a,x,Delete)
• Enable CellBlender and Capsule Test Addons
• Open CellBlender tab, Initialize CellBlender, Expand the panel
• Open the "Growing Capsule" Tab (beside CellBlender)
• Disable "Freeze Geometry" (defaulted to frozen to minimize interference)
• Check the "Use CellBlender Data" box to get iterations from CellBlender
• Drag the time line to watch the geometry change
• Zoom in on object and right click to select it (outlined in orange)
• When selected, set the Maximum Draw Type to "Wire" (easier to see molecules)
• You can change Geometry Settings here, but leave as is the first time
• Save the .blend file somewhere to start a new project (File / SaveAs)
• Begin building your CellBlender project with the Model Objects Panel
• With the capsule selected, click the "+" button to add it to the model objects
• Add volume and surface molecules to the model and release them in and on the capsule
  • Add molecules "v" (Volume 1e-5) and "s" (Surface 1e-4)
  • Release 1000 of each on Object/Region "capsule"
• Open the Preferences panel and "Set Path to MCell Binary" to dynamic geometry mcell
• Open the "Run" panel and expand the Output/Control Options subpanel
• Check the "Decouple Export and Run" button so you can export and run separately
• Set the time on the timeline to zero (0) so your geometry.mdl file will start there
• Click the Export CellBlender Project button to export all of your static MDL
• Open the Growing Capsule tab again
• Click on Generate Dynamic Geometry MDL and wait for the button to return
  • Note that this may take some time while it's generating the MDL for 1000 frames
• When the button returns, Click on the "Show MDL Geometry" button
• Drag the cursor in the timeline to see the Dynamic MDL changing (this is reading MDL)
• Click the "Update MDL Files" button to insert Dynamic Geometry commands in the static MDL
• Return to the CellBlender tab and the Run Simulation panel
• Click the "Run" button and wait while MCell runs the simulation for 1000 steps
• When done, click the "Reload Visualization Data" button
• Then drag the cursor through the time line and watch the dynamic geometry simulation
• Try changing the molecule size, shape, and color in the Molecule Display Options panel
• The procedure for changing the MCell simulation (not geometry) is:
  • Change the model (molecules, reactions, plots, etc)
  • Set the time to zero to export the original geometry file
  • "Export CellBlender Project" in the CellBlender Run Simulation Panel
  • "Update MDL Files" in the Growing Capsule tab
  • Run the simulation and reload the visualization data
• The procedure for changing the geometry is very similar:
  • Change values in the Growing Capsule panel and check with timeline
  • Set the time to zero to export the original geometry file
  • "Export CellBlender Project" in the CellBlender Run Simulation Panel
  • "Update MDL Files" in the Growing Capsule tab
  • Run the simulation and reload the visualization data