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While wrestling with the creation of animated molecule models, I came across this older YouTube tutorial and indeed succeeded using Blender v2.59, exactly following the video description. In pose mode, the smaller sphere can be moved around, and the cylinder, representing the bond between atoms, will follow adapting its length and axis direction accordingly.

The simple atom/bond model in Blender v2.59

However, when I tried to rig up the same in Blender v3.6.4 or v4.2.1, the cylinder behaves differently: it still follows the small sphere as before, but its cross-section is distorted (flattened) while moving. Furthermore, the two bones don't point towards each other as with the old Blender version, but haphazardly point somewhere when moving the small sphere.

The only obvious difference I could find, is the now missing checkbox named "Target" in the inverse kinematics bone constraint panel, which was unchecked in the tutorial. Instead, there is a "Weight Position" checkbox in the same place of the "new" IK constraint panel, but it doesn't seem to have the same meaning. If this would solve the problem: where has the "Target" checkbox gone in the newer versions?

"Old" IK panel "New" IK panel

The v4.2 manual still insinuates the existance of the "Target" checkbox, but this doesn't match the accompanying picture.

I tried all possible combinations of checking/unchecking the checkboxes available in the IK constraint panel, but could not get the result as expected.

BTW, my goal is to create animated molecule models showing the movements of atoms within a molecule during a chemical reaction, such as bond stretching or breaking, changing angles between bonds, torsions, etc..

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  • $\begingroup$ If your goal is to have pure non deforming objects in a more "mechanical" type of rig it is generally best to just parent objects to bones directly without armature modifiers, you may even forego the armature entirely if you don't need to replace objects or reuse the animations. $\endgroup$
    – Duarte Farrajota Ramos ♦
    Commented Sep 9 at 10:29
  • $\begingroup$ See a few examples blender.stackexchange.com/questions/86804/… blender.stackexchange.com/questions/102990/… blender.stackexchange.com/questions/204814/… blender.stackexchange.com/questions/78170/… $\endgroup$
    – Duarte Farrajota Ramos ♦
    Commented Sep 9 at 10:29
  • $\begingroup$ I see your point. My example from the tutorial is very basic and mechanical indeed. For me, just to learn the principle. From the YT tutorial I assumed the armature modifiers were necessary. But would your suggestions still work, when I proceed to much more complicated structures (molecules), having lots of spheres and cylinders, with all movements depending on and constraining each other in some way? $\endgroup$
    – Dirk_63
    Commented Sep 9 at 10:49
  • $\begingroup$ From my limited rigging experience, you can pretty much do almost any non deforming animation you would do with an armature by applying the same constraints to objects directly, save for Inverse Kinematics, which does require an armature. The armature does afford you a degree of safety and reusability by safeguarding all your constraints and animations in a dedicated object, so you can replace the visible objects at will without breaking the animation and relationships. For your particular case maybe you could keep the armature, but just parent objects directly to bones for simple motion only. $\endgroup$
    – Duarte Farrajota Ramos ♦
    Commented Sep 9 at 11:01
  • $\begingroup$ Well, I'll work myself through the linked examples and see, how far I can get. Unfortunately, my Blender experience is very basic, and I still learn from detailed tutorials rather than by struggling through manuals ;-). I don't know your background in chemistry, but I'm afraid I will have to replace objects some time, too. In chemistry, atom positions and movements are calculated by highly sophisticated programs using force fields, defined by elaborate parameter sets. Unfortunately, they just produce lots of exact coordinates, but no nice animations... $\endgroup$
    – Dirk_63
    Commented Sep 9 at 11:38

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