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
image

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

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. 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

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