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I've been trying to model molecular structures on blender using coordinates I've gotten off scientific papers.

The only problem i've been struggling to form bonds between them consistently. When I use a cylinder mesh and set the faces to the centre of the spheres it cylinder itself has been distorting, as shown here.

enter image description here

Moving cylinders manually into place is very inconsistent. I would like some help figuring out how I can achieve something looking like this.

enter image description here

Like is there a way to snap each cylinder face to the centre of each sphere without affecting the cylinder shape? Or is there something else entirely I should be doing?

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Poly Curves and Bevel Object

You could try to take advantage of curves instead of meshes.

enter image description here

This way you'll just have to control the cylinder main axis with two control points for each connection, you don't have to worry about the deformation because the cylinder is being built automatically and it's much easier to change the section size/shape.

enter image description here

To set up the curve like in the shown image sequence, choose a "Poly" Spline type once in edit mode and fill the Bevel Object field with the wanted section shape (in my case the little black bezier circle you can see near the origin).

enter image description here

Note: it's not your case, but if needed the cylinder ends can be capped by enabling the Fill Caps option in the Geometry panel of the Curve tab.

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    $\begingroup$ Using this setup you can also assign hooks to the control points of the curves. $\endgroup$ – cegaton May 2 '16 at 2:42

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