Load A3M MSA¶

Loads an A3M-formatted multiple sequence alignment (MSA) string and assigns it a user-defined ID. Produces an A3M object that can be routed to downstream protein modeling or analysis nodes. The node is designed for manual paste/upload of an A3M text block and simple identification via a unique label.

Usage¶

Use this node when you already have an A3M MSA (e.g., generated externally) and want to inject it into a workflow for structure prediction or MSA-based analysis. Provide the full A3M text and a unique identifier. Connect its output to nodes that consume MSAs for folding, scoring, or visualization.

Inputs¶

Field	Required	Type	Description	Example
a3m_string	True	STRING	Full A3M MSA content as plain text. Should follow A3M format conventions (aligned sequences, possible lowercase insertions, and header lines beginning with '>').	>query MSEQNNTEMTFQIQRIYTKDIS... >homolog_1 MSEQNN-E-TFQIQRIYTKDI... >homolog_2 MSEqnnteMTFQI-...
a3m_id	True	STRING	Identifier assigned to this A3M. Must be unique within the workflow. If paired with a specific protein sequence elsewhere in the workflow, use the matching sequence ID.	msa

Outputs¶

Field	Type	Description	Example
msa.a3m	A3M	A3M object containing the provided MSA, keyed by the given a3m_id. Intended for downstream nodes that accept MSAs.	{'msa': 'A3M text content here...'}

Important Notes¶

IDs should be unique across the workflow to avoid collisions.
If you provide a corresponding protein sequence elsewhere in the workflow, ensure the IDs match for correct alignment pairing.
The node does not modify or validate the biological correctness of the A3M content; ensure the format is valid.

Troubleshooting¶

A3M not recognized downstream: Verify the text follows A3M format (headers starting with '>' and aligned sequences).
Downstream node reports missing or mismatched ID: Ensure a3m_id matches the expected sequence or workflow ID and is unique.
Unexpected behavior with multiple MSAs: Confirm each Load A3M node uses a distinct a3m_id.