Why is the effect after superposition not as good as before superposition

[tang2552]

Why is the effect after superposition not as good as before superposition

[ppillot]

This code looks strange to me: you are referring to this link https://github.com/nglviewer/ngl/blob/master/examples/scripts/test/superposition.js but none of the code pasted is looking alike, in particular stage.alignView() which is not a method existing on the stage object (it exists on the ViewerControls class, but that's not how superposition are done in the examples; all examples are using NGL.superpose(...) for performing superpositions). To me, this looks like code that has been hallucinated by an AI.

Regarding the issue you are reporting, I have no experience with using the superposition method, but my recommandation would be to use the code from the following example, https://github.com/nglviewer/ngl/blob/master/examples/scripts/test/alignment2.js where the chains to be aligned are specified (:A). In the case of the 2 structures you want to superpose, I suppose that getting good results would require to specify the correct pair of chains for the alignment, otherwise the combinatorial is too random.