Can not load AlphaFold multimer checkpoint params_model_[1-5]_multimer.npz for inference

[bing-song]

Can not load multimer checkpoint in the main branch for both Docker container and ENV.

Here is command

Here is the error message

[bing-song]

This issue may be the same as issue #110

[bing-song]

More information

The inference works fine when I use AlphaFold models params_model_[1-5].npz (not multimer model).

[bing-song]

In main branch openfold:config.py, it does not have

elif "multimer" in name:
        c.globals.is_multimer = True
        for k,v in multimer_model_config_update.items():
            c.model[k] = v

However, this line is in multimer branch.

My question is that should we use multimer branch or main branch to load a multimer model?

[gahdritz]

For now, you should definitely use the hacky AlphaFold-Gap implementation on the main branch. The multimer branch is still experimental (I've had zero time to work on that recently), and while I'd say it's nearly done, there are still some huge blemishes like this.

[gieses]

@gahdritz can I ask, have you looked at what the gap trick does to the template and MSA feature retrieval / computation? Are they primarily from the longer sequence or anything like that? If I understand correctly, the pipeline with or without linker is the same in terms of MSA computation and template retrieval?