Open tang2552 opened 3 months ago
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.
before superposition
after superposition
![after](https://github.com/nglviewer/ngl/assets/87934317/a800e2e2-163b-431a-9788-b8d5976450d8)
Previous code `const pdbFile1 = “./data/7KMB.pdb”; const pdbFile2 = ”./data/7KMS.pdb“;
function initNGL() { // Create a stage const stage = new NGL.Stage("viewport");
}`
The following code refers to the following URL https://github.com/nglviewer/ngl/blob/master/examples/scripts/test/superposition.js
Obviously, the effect after superpose is not as good as before.
I'd appreciate it if someone could solve my problem. Thanks!