google-deepmind / google-deepmind/alphafold

`template_domain_names` missing in features.pkl on multimer mode.

Open
#625 0 comments 0 reactions 0 assignees View on GitHub
Dominant language
Python
Stars
14.9k
Forks
2.9k
PR merge metrics
No merged PRs in 30d

Description

I tried to check out `features.pkl` generated by running AlphaFold to find which templates are used.

When `--model_preset=monomer` is used I could find `template_domain_names` as a key name of the dictionary unpickled, but not upon `--model_preset=multimer`.

```python
import pickle

with open("../features.pkl", "rb") as f:
features = pickle.load(f)
print('template_domain_name' in features) # => False

```

```python
features.keys()

# => `template_domain_names` not found
# dict_keys(['aatype', 'residue_index', 'seq_length', 'msa', 'num_alignments', 'template_aatype', 'template_all_atom_mask', 'template_all_atom_positions', 'asym_id', 'sym_id', 'entity_id', 'deletion_matrix', 'deletion_mean', 'all_atom_mask', 'all_atom_positions', 'assembly_num_chains', 'entity_mask', 'num_templates', 'cluster_bias_mask', 'bert_mask', 'seq_mask', 'msa_mask'])

```

When running with multimer mode, templates are not used for prediction models? (I could see things like template names in docker log file, though.)

Otherwise, running on multimer mode generates no data related to templates used for prediction while it makes use of templates' information?

Contributor guide

Open the contributing guide

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.