Globally dupli works on the convention that normals (vertex normals) correspond to the Y axis of the dupli.
To orient the protein:
- First apply rotation and scale CtrlA so that we start with something we can work with
- Then rotate it to the Y axis
- And apply rotation again
If you want to do that (I had a look at some images on google):
- Enter edit mode in the protein object
- Select all vertices
- Rotate and grab them so that the wanted inner part meets the origin of the object (still oriented along Y) as the dupli start at each vertex of its parent from this origin
The expected setting for the sphere, concerning instancing is the following:
Corrected blend file:
To do it from a particle system, you can use this setting for the particle system created for the sphere:
The orientation to Y is the same but can be perturbed if you activate physics, so it is disabled here.
- Set to 'emitter'
- Start and end frames set to one (if not particles will appear during animation)
- Emit from vertices
- Physics 'none'
- Render as object
- Scale: tune as you need
- Use the protein as instance object
- Don't use the orientation as you want to emit along normals