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So I have the following image:enter image description here

I created three spheres, placed them in a cloner and applied the twist deformer. I then repeated this for the opposite side. Essentially the helix structure in the middle is made of two chains. The repeating unit in my cloner is the three spheres to the left of the helix.

The problem is when I apply the twist deformer it distorts my spheres to the point they are not spheres any more. How I can apply the twist deformer on my cloner but keep the shape of my spheres.

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One way to achieve your desired effect is to use a matrix object.

The matrix acts like a cloner but instead of containing cloned geometry, it only contains the positions, scales, and rotations (matrices) of the clones.

You can apply your twist to the matrix object, and then use the matrix to drive a cloner in object mode. The cloner will place the clones at the positions in the matrix object without deforming the geometry.

Here is a screenshot of one such setup: Matrix Cloner Setup

Note that I have placed 4 spheres in one clone and 2 in the other, just to simplify the example slightly.

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