AlphaFold2_advanced notebook

Hi sokrypton,

First, many thanks for the notebooks...

I was using intensively the AlphaFold2_advanced notebook, and I am very sad that it is not working anymore.
What is missing for me on the new main notebook is :

• the homooligomer "1:2" --> because it is more user friendly that copy/paste sequences, especially to quickly check is the sequence length is >1.400 for example.
• Trim sequence --> really useful (use the full length sequence for the MSA but not to generate the model) and convenient with the graphic representation before and after trim !
• The extra output, especially the distogram plot, to see coevolution between proteins: If I am correct, the coevolution is a very useful information by itself, and because the AlphaFOLD model could be wrong, but not the coevolution, it is a robust result. So sometime I used the AlphaFold2_advanced notebook just to have the coevolution information rather than structural models.

So, my question is: it is doable to simply update the AlphaFold2_advanced notebook to use it again? Or to integrate in the AlphaFold2_mmseqs2 notebook the functions mentioned above?

Best,

Kevin

Start by comparing the AlphaFold2_advanced notebook with the AlphaFold2_mmseqs2 notebook, focusing on homooligomer input, sequence trimming, and extra outputs such as the distogram plot. Confirm which requested capabilities are still present and define completion as restoring or integrating the requested functions in a usable notebook.