issues using AlphaFold 2.3.2

[gabrieliacc]

Dear AF_analysis developers,

Thank you for such helpful tool!

I have successfully tested for AlphaFold3 server and Boltz-2. However, I struggle with AlphaFold2.

I received the next error:

########

AssertionError Traceback (most recent call last)
Cell In[46], line 5
3 directory='~/AF2/teste/'
4 # Run analysis on the specified folder
----> 5 results = af_analysis.Data(directory, format='default')

File ~/.local/lib/python3.10/site-packages/af_analysis/data.py:115, in Data.init(self, directory, data_dict, csv, verbose, format)
112 """ """
114 if directory is not None:
--> 115 self.read_directory(directory, verbose=verbose, format=format)
116 elif csv is not None:
117 self.format = "csv"

File ~/.local/lib/python3.10/site-packages/af_analysis/data.py:193, in Data.read_directory(self, directory, keep_recycles, verbose, format)
191 else:
192 self.format = "default"
--> 193 self.df = default.read_dir(directory)
194 self.df["format"] = "default"
195 self.add_json(verbose=verbose)

File ~/.local/lib/python3.10/site-packages/af_analysis/format/default.py:76, in read_dir(directory)
74 rank = int(token[start_index + 2])
75 weight = "_".join(token[start_index + 3 : -4])
---> 76 assert weight in weigths
77 model = int(token[-3])
78 seed = int(token[-1][:-4])

AssertionError:

#######

• Looking the AF2 outputs:

#######
features.pkl
ranked_1.pdb
ranked_4.pdb
relax_metrics.json
result_model_3_ptm_pred_0.pkl
timings.json
unrelaxed_model_3_ptm_pred_0.pdb
msas
ranked_2.pdb
ranking_debug.json
result_model_1_ptm_pred_0.pkl
result_model_4_ptm_pred_0.pkl
unrelaxed_model_1_ptm_pred_0.pdb
unrelaxed_model_4_ptm_pred_0.pdb
ranked_0.pdb
ranked_3.pdb
relaxed_model_2_ptm_pred_0.pdb
result_model_2_ptm_pred_0.pkl
result_model_5_ptm_pred_0.pkl
unrelaxed_model_2_ptm_pred_0.pdb
unrelaxed_model_5_ptm_pred_0.pdb
#########

I think that the outputs are not parsed for the af2_analysis, however they are the raw output from AlphaFold 2.3.2 (monomer_ptm in this case).

In addition, the ptm are in a pkl file format, not in a json file format.

How can I overcome this issue?

Thank you in advance

Gabriel

[samuelmurail]

Dear Gabriel,

I think I have fix part of the issue with vanilla alphafold data. Install the last version of af_analysis.

From my experience I can load the data, however I still have issue to read the .pkl files.
From what I understand you might need to use the same jax version to read the file as the version you use to compute it.

Let me know if it help.

Cheers,
Samuel