sokrypton
AF2 Using MMseqs ColabFold 1.5.4 crash with ValueError: unknown model_type af2_multimer_v3
When I ran an open ColabFold1.5.3 on my browser this morning for a multimer_v3 job, it crashed at the "Run Prediction" stage right after collecting the MSAs and drawing the sequence coverage plot, with an error message signaling ValueError: Unknown model_type alphafold2_multimer_v3. This error recurred when choosing 'multimer_v3' or 'auto' settings. When I restarted a clean AF2, it upgraded to ColabFold1.5.4––a happy surprise!––& I guessed that that ValueError occurred because I was trying to run an outdated ColabFold. So I tried again, first sampling the new "DeepFold v1" choice (how does this compare with Multimer_v3?), and this ran well....but when I tried to purposefully run model_type = auto (or multimer_v3), the program crashed with that same ValueError message, see below. Thanks very much in advance for tracking down the bug, & looking forward to using the new ColabFold version!
2023-12-28 17:52:48,081 Setting max_seq=508, max_extra_seq=2048
ValueError Traceback (most recent call last)
2 frames /content/colabfold/alphafold/models.py in get_model_haiku_params(data_dir, model_type, model_number, use_fuse, to_jnp) 35 is_deepfold = True 36 else: ---> 37 raise ValueError(f"Unknown model_type {model_type}") 38 39 path = os.path.join(data_dir, "params", file)
ValueError: Unknown model_type alphafold2_multimer_v3
Could you please reload the notebook and try again? The issue should be gone now.
The patch seems to work––multimer_v3 option runs just fine! However, one problem remains: the final PAE plots for the top 5 models do not show, and one only gets the sequence coverage & lDDT plots. I noticed that the (initially working) DeepFold_v1 models also did not show their PAE plots, but wasn't sure they'd be implemented yet.
Indeed, DeepFold_v1 doesn't divulge PAE (yet;), while AF2's multimer_3 still does...but reveals them only in a .png file that's part of the zipped download. In short, it fails to show PAE plots as part of the 3 types of viewable plots (PAE, seq coverage, lDDT) for the models at the end of the prediction run.
I am confused, I do see the PAE plots in colab. Which notebook does not show the PAE plots for multimer?
After reloading the new ColabFold, have not experienced the missing PAE plot on my end, chalk it up to weird browser behavior. Thx for your patience, again...& HNY!