Execution against the local Alphafold2 output

[xvtyzn]

Hi,

First of all, I would like to thank the author for creating a great tool.
The problem I am having is very simple. Currently, DPAM uses json to read predicted aligned errors (for AF2 database and Colabfold). But Alphafold2 running locally contains these information in the pkl file.

Below is an example output from Alphafold2 (ver. 2.2.4) running on local.

features.pkl        relaxed_model_1_pred_0.pdb  result_model_4_pred_0.pkl
msas                relaxed_model_2_pred_0.pdb  result_model_5_pred_0.pkl
ranked_0.pdb        relaxed_model_3_pred_0.pdb  timings.json
ranked_1.pdb        relaxed_model_4_pred_0.pdb  unrelaxed_model_1_pred_0.pdb
ranked_2.pdb        relaxed_model_5_pred_0.pdb  unrelaxed_model_2_pred_0.pdb
ranked_3.pdb        result_model_1_pred_0.pkl   unrelaxed_model_3_pred_0.pdb
ranked_4.pdb        result_model_2_pred_0.pkl   unrelaxed_model_4_pred_0.pdb
ranking_debug.json  result_model_3_pred_0.pkl   unrelaxed_model_5_pred_0.pdb

Do you have any plans to support pkl files in the future?

Best,

Keigo

[CongLabCode]

In fact, we find that even without PAE, the quality of domain parsing is only slightly affected. And we will have this new version very soon.

[xvtyzn]

That is wonderful news!
Being able to parse a domain from structure only will streamline a lot of things.
Looking forward to the new version :)

Best,