Comments (10)
there is also no 'ptm' and 'iptm' scores, the way it was:
dict_keys(['distogram', 'experimentally_resolved', 'masked_msa', 'predicted_aligned_error', 'predicted_lddt', 'structure_module', 'plddt', 'aligned_confidence_probs', 'max_predicted_aligned_error', 'ptm', 'iptm', 'ranking_confidence'])
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there is also no 'ptm' and 'iptm' scores, the way it was: dict_keys(['distogram', 'experimentally_resolved', 'masked_msa', 'predicted_aligned_error', 'predicted_lddt', 'structure_module', 'plddt', 'aligned_confidence_probs', 'max_predicted_aligned_error', 'ptm', 'iptm', 'ranking_confidence'])
I see. It seems 'seqs' was never here anymore. I think create_notebook.py still has to be updated.
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Actually, I rerun it again and 'seqs' is among the keys
['distogram', 'experimentally_resolved', 'masked_msa', 'predicted_aligned_error', 'predicted_lddt', 'structure_module', 'plddt', 'seqs', 'unrelaxed_protein', 'aligned_confidence_probs', 'max_predicted_aligned_error', 'ranking_confidence']
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Actually, I rerun it again and 'seqs' is among the keys ['distogram', 'experimentally_resolved', 'masked_msa', 'predicted_aligned_error', 'predicted_lddt', 'structure_module', 'plddt', 'seqs', 'unrelaxed_protein', 'aligned_confidence_probs', 'max_predicted_aligned_error', 'ranking_confidence']
hmm I just checked a random pkl from the prediction made today using this branch and there is no 'seqs', must be some recent fix?..
['distogram', 'experimentally_resolved', 'masked_msa', 'num_recycles', 'predicted_aligned_error', 'predicted_lddt', 'structure_module', 'plddt']
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but I didn't update alphafold submodule, so if you introduced some changes there this could be the reason
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Interesting. Perhaps it's better to update create_notebook.py so that it parses sequences from PDB files directly anyway
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Yes, you can do this, but we need to have ptm and iptm (as well as the rest of the missing keys) in the result.pkl anyways
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ah I found where it came from. It's not from the recalculations of metrics but rather here:
AlphaPulldown/alphapulldown/folding_backend/alphafold_backend.py
Lines 397 to 403 in b791e1b
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Plus the calculation of iptm iptm+ptm etc were moved to post processing after your restructuring
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Good catch!
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Related Issues (20)
- Add dropout
- Running calculate_mpdockq.py with only PDB HOT 1
- run_multimer_jobs issue HOT 5
- Replace this with non-cctbx solution HOT 7
- singularity error HOT 20
- jackhammer error running test HOT 3
- Multiple feature directories HOT 2
- Improve resume predictions HOT 1
- GPU seems not working when run_multimer_jobs.py HOT 5
- Runtime of each prediction HOT 1
- Use DEFINE_list for model_names flag HOT 3
- Clean duplicating functions/ redundant code
- create_indvidual_features.py HOT 2
- Merging individual monomer MSAs for multimer prediction HOT 2
- Problem with MSA for Q6DI86 HOT 2
- rename_colab_search_a3m.py does something unintended HOT 4
- output jupyter notebook is empty HOT 2
- Computing MSA takes long time
- jax error when create_notebook.py is run HOT 4
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