msa-nim 0.2.0

CLI tool to generate A3M MSA alignments via NVIDIA NIM MSA-Search

msa-nim

Generate A3M alignments for AlphaFold — no GPUs, no database downloads

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Install

pip install msa-nim

Get an API key

Grab a free key from NVIDIA, then:

export NIM_API_KEY="nvapi-..."

Or save it permanently:

msa-nim init   # creates .msa-nim.env — paste your key there

Usage

From a FASTA file

msa-nim run

Finds all .fasta / .fa / .faa files in the current directory and outputs .a3m files to msa_results/.

>my_protein
MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGTQDNLSGAEK...

Multiple > records in one file each get their own MSA.

From a PDB ID

msa-nim pdb 7DKF              # all chains
msa-nim pdb 7DKF --chain A    # specific chain
msa-nim pdb 7DKF 6HBB 1ABC    # multiple IDs

Common options

msa-nim run /path/to/fastas       # custom input directory
msa-nim run -o my_output          # custom output directory
msa-nim run --resume               # skip already-completed sequences
msa-nim run --db Uniref30_2302 --db PDB70_220313   # override databases

Databases

Defaults match ColabFold (UniRef30 + ColabFold env DB). Add PDB70_220313 with --db for structural templates.

Database	Name	Purpose
UniRef30	Uniref30_2302	MSA profile (default)
ColabFoldDB	colabfold_envdb_202108	Metagenomic search (default)
PDB70	PDB70_220313	Structural templates (opt-in)

Troubleshooting

Problem	Fix
NIM_API_KEY is required	Set the env var or run msa-nim init
No .fasta files found	Use .fasta, .fa, or .faa extensions
422: Database not available	Check spelling/casing (see table above)
Interrupted run	Re-run with --resume

License

MIT — see LICENSE.

Acknowledgements

• MMseqs2-GPU — GPU-accelerated homology search
• ColabFold — MSA + structure prediction pipeline
• NVIDIA NIM — Cloud inference microservices