Colabfold Batch¶
Runs batch protein structure prediction using ColabFold from precomputed MSA inputs in A3M format. It aggregates ranked folding results per input sequence and returns predicted structures as PDB content. Note: This node is currently disabled and will raise an error if executed.
Usage¶
Use this node after obtaining multiple sequence alignments (MSAs) with an A3M-based search step (e.g., Colabfold Search or another MSA provider). Provide a dictionary mapping sequence IDs to their A3M content. The node is intended to execute ColabFold predictions in batch and return ranked PDB structures keyed by sequence ID and rank.
Inputs¶
| Field | Required | Type | Description | Example |
|---|---|---|---|---|
| a3m | True | A3M | MSA results in A3M format for one or more sequences. Expected as a dictionary mapping sequence IDs to their corresponding A3M content. | {'seq_A': '>seq_A/1-100\nACDEFGHIK...\n>ref1/1-100\nACDEYGHIK...\n', 'seq_B': '>seq_B/1-95\nMKTLLV...\n>ref2/1-95\nMKTLIV...\n'} |
Outputs¶
| Field | Type | Description | Example |
|---|---|---|---|
| folding.pdb | PDB | Predicted ranked structures as a dictionary mapping composite IDs (e.g., seqID_ranked_0.pdb) to PDB file content. | {'seq_A_ranked_0.pdb': 'MODEL 1\nATOM ...\nENDMDL\n', 'seq_A_ranked_1.pdb': 'MODEL 1\nATOM ...\nENDMDL\n'} |
Important Notes¶
- This node is currently disabled and will raise an error indicating the feature is not available.
- Input must be valid A3M content; invalid or empty A3M entries will cause failures when the feature is enabled.
- Output keys include the original sequence ID combined with a rank suffix (e.g., seqID_ranked_0.pdb).
- Designed for batch processing: provide one or more A3M entries in a single run.
Troubleshooting¶
- Error: 'Colabfold Batch is currently disabled' — The feature is not available at this time. Contact support to request access or enablement.
- Unexpected output structure when enabled — Verify that each A3M entry corresponds to a single sequence ID and that the A3M format is valid.
- Missing outputs for some sequences when enabled — Ensure all input A3M entries are non-empty and properly formatted.