sokrypton / sokrypton/ColabFold
Unpaired single sequence MSA mode does not work (with Multimer v2)
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Description
Expected Behavior
Colabfold returns a structure
Current Behavior
TypeError: 'NoneType' object is not subscriptable
Steps to Reproduce (for bugs)
Seq: ENQALEQKNAQLKQEIAALEQEIAQLEY:KNAQLKEENAALEEKIQQLKEKIQALKY:ENQALEQEIAQLEQEIAALEQKNAQLKY:KNAQLKEKIAALKEKIQQLKEENQALEY
Name: P9P10P11P12_unpaired
MSA_Mode: single
pair_mode: unpaired

ColabFold Output (for bugs)
Downloading alphafold2 weights to .: 100%|██████████| 3.82G/3.82G [00:32<00:00, 127MB/s]
2022-03-18 09:09:25,521 Running colabfold 1.2.0 (62584e29d593eb57518607df92edc1af09f0fdd8)
2022-03-18 09:09:25,524 Found 2 citations for tools or databases
2022-03-18 09:09:31,490 Query 1/1: P9P10P11P12_unpaired_a961f (length 112)
2022-03-18 09:09:31,492 Could not generate input features P9P10P11P12_unpaired_a961f: 'NoneType' object is not subscriptable
Traceback (most recent call last):
File "/usr/local/lib/python3.7/dist-packages/colabfold/batch.py", line 1141, in run
model_type,
File "/usr/local/lib/python3.7/dist-packages/colabfold/batch.py", line 839, in generate_input_feature
paired_msa[sequence_index]
TypeError: 'NoneType' object is not subscriptable
2022-03-18 09:09:31,493 Done
PS: the paired mode also seems to be paired+unpaired
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start in colabfold/batch.py at generate_input_feature, especially the reported line 839 where paired_msa is indexed. Reproduce the issue with the supplied sequence using MSA_Mode single and pair_mode unpaired, then verify that the run returns a structure without the NoneType error.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 42/100