How to open AlphaFold .pkl files

Question

[fvasquez]

Hello.

I am struggling to open the .pkl files produced by AlphaFold. I installed jax, which is required by pickle to open .pkl files, and then tried opening the file as:

data = pickle.load(open(filepath, 'rb'))

It throws the error:

No module named jax.src_.device_array

Apparently device arrays exist for jax versions 0.3.25 or older. When I try one of those versions, I get an error saying that the jax version is not compatible with jaxlib, which is also required. Thus suggesting me to update jax, which will bring me back to No module named jax.src_.device_array .

How are people opening these files?

Thanks in advance.

Answer 1

[Mensur Dlakic]

Generally speaking, for these kinds of problems it is best to create a fresh conda environment that has the required jax and jaxlib versions. That way you will not alter the other environment that contains newer versions.

This might be of interest:

https://github.com/mattarnoldbio/alphapickle