Running clustered msa on Local ColabFold

[jimfeng9705]

The predication by AF takes a long time, for a longer sequence. And the run can be disconnected. How can we run our local colabfold using the clustered msa?

[KhondamirRustamov]

You need to download ColabFold on your local machine (see LocalColabFold here)

Simply download the clusters from Colab (or generate them locally), and run something like this in your folder containing clustered MSAs:

import glob
import os

for cluster in glob.glob("*.a3m"):
    os.system(f"colabfold_batch {cluster} pdb/")