4. Add Simple Mesh Geometry¶
4.1. Tutorial Overview¶
In this tutorial, a sphere will be added to the simulation around the diffusing molecules.
4.2. Initial Configuration¶
4.2.1. Save the File with a New Name in Your Working Directory¶
- Select File > Save As...
- Change unimol_reactions.blend to add_meshgeom.blend
- Click Save As Blender File button
4.2.2. Add Sphere¶
- Click the Create tab
- Hit the Ico Sphere button
- The Add Ico Sphere options appear in the lower left corner
- Change Subdivisions to 3
- Change Size to 0.5
- Change each Location (X, Y, and Z) to 0.0 if it isn't set already.
4.2.3. Add Sphere to Model Objects¶
- Click the CellBlender tab
- Click the Model Objects button
- Click the "plus" sign (+) to the right of the Model Objects box
- Expand the Icosphere Display Options panel
- Select Wire from the drop-down menu.
4.2.4. Release Molecules inside Sphere¶
- Click the Molecule Placement button
- Select Release_Site
- Change Release Shape to Object/Region
- Type Icosphere in the Object/Region field
- Change Quantity to Release to 1000
4.2.5. Simulate the Model¶
- Click the Run Simulation button
- Click the Run button
- Wait for the simulation to complete
- Press the "Reload Visualization Data" button to load the results of the simulation.
4.2.6. View the Results¶
- Press the "Play" () button below the time line
4.2.7. Save Your File¶
- File > Save