I’ve been predicting structures recently using the AlphaFold tool through ChimeraX (which directs to the alphafold21_predict_colab.ipynb notebook), but I’ve noticed I get often quite different results when I run the same prediction through the
AlphaFold.ipynb notebook directly in Colab. I was wondering if anybody could point me to the major differences between these two implementations? Are they searching different libraries to generate a multiple sequence alignment? Are they using different numbers
of iterations or energy minimization strategies?