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### FoldMason MSA (`foldmason-msa`) Aligns two or more PDB structures and returns the amino-acid and 3Di MSAs as FASTA strings together with the Newick guide tree, the alignment length, and the number of sequences aligned. The tool executes against the public Steinegger Lab web service in `remote` mode and against the bundled `foldmason easy-msa` program in `local` mode. #### API Reference

Source Structures to align (≥2). Accepts `Structure` objects, file paths, or raw PDB/CIF content strings per item; each is normalised to a `Structure`. Raw structure content in PDB or CIF format. Format of the content string (auto-detected if omitted). What the B-factor column represents. Optional source identifier (filepath or tool name). Associated metrics (e.g., pLDDT, pTM scores, per-chain lists, pairwise matrices). None values are stripped at construction. Optional IDs per structure (default: `'structure_0'`, `'structure_1'`, ...). Length must match `structures`. IDs become the FASTA record headers and Newick leaf labels in the output.

Source 'remote' (default) hits the public FoldMason server; 'local' runs the FoldMason CLI. Available options: `remote`, `local` Remote-only — delay between status polls. Remote-only — max wall-clock time. Local-only — gap open cost. Local-only — gap extension cost. Local-only — number of alignment-refinement iterations. 0 = no refinement. Local-only — pre-cluster structures before MSA construction. Recommended for large datasets (>1k structures). Local-only — Newick guide tree to use instead of computing one. Leaf labels must match `structure_ids`. Local-only — CPU threads. Verbosity level (0=quiet, 1=info, 2=debug, 3=raw subprocess stderr). `True` is coerced to `1` and `False` to `0`. Device to run the tool on. Maximum execution time in seconds. `None` waits indefinitely. Random seed. When set, tools run reproducibly up to small GPU float noise (see `BaseToolOutput.approx_equal`), and the seed participates in cache keys. When None, cacheable seed-sensitive tools skip cache until seeded.

Source Remote job ticket ID; empty in local mode. Amino-acid alphabet MSA in FASTA format. 3Di alphabet MSA in FASTA format. Newick guide tree. Number of sequences in the alignment. Number of MSA columns. Remote result-archive URL; empty in local mode.

#### Applications This tool is appropriate for aligning a fold family retrieved from a Foldseek search, for comparing designed scaffolds against their target backbone, or for assembling a multi-structure template ensemble for downstream template-based modelling. It also applies to AlphaFold predictions across an evolutionary set, where the alignment can identify residues that are structurally conserved as well as loops that vary in conformation. #### Usage Tips * **`foldmason-msa` supports both remote (`search_mode="remote"`, the default) and local (`search_mode="local"`) execution.** Remote mode targets the Steinegger Lab web service. Local mode runs the bundled FoldMason program and accepts the full set of alignment parameters. * **The Steinegger Lab web service does not accept alignment parameters.** The configuration fields `gap_open`, `gap_extend`, `refine_iters`, `precluster`, and `guide_tree_newick` therefore require `search_mode="local"`. * **`refine_iters` controls how many iterative LDDT-maximising refinement passes run after the initial progressive alignment.** Each pass adds runtime, and the default of `0` is appropriate for most workflows. Increase it only when an alignment shows poor quality in difficult regions. * **The remote service has no authentication and no published rate limit.** `search.foldseek.com/foldmason` is a free public academic resource. High-throughput or batch workloads should be performed in `local` mode to avoid overloading the shared service.

### FoldMason Score MSA (`foldmason-score-msa`) Accepts a precomputed amino-acid MSA in FASTA format together with the underlying PDB structures, and returns the average MSA-wide LDDT score, the per-column LDDT scores, the number of columns considered, and the total alignment length. #### API Reference

Source Structures (≥2). Accepts `Structure` objects, file paths, or raw PDB/CIF content strings per item; each is normalised to a `Structure`. Order must match the rows of `msa`. Raw structure content in PDB or CIF format. Format of the content string (auto-detected if omitted). What the B-factor column represents. Optional source identifier (filepath or tool name). Associated metrics (e.g., pLDDT, pTM scores, per-chain lists, pairwise matrices). None values are stripped at construction. Optional IDs per structure (default: `'structure_0'`, ...). Must match the FASTA record headers in `msa` so msa2lddt can resolve each row to its structure. Amino-acid MSA, typically from `foldmason-msa`. Accepts an `MSA` object or a raw FASTA string. Aligned sequences with `-` characters indicating gaps. All sequences must have the same length. Identifiers for each sequence. Auto-generated as `seq_0`, `seq_1`, ... if not provided.

Source Minimum fraction of pair sub-alignments with LDDT information required to score a column (0-1). 0.0 (default) keeps all columns. If True, normalise the average LDDT by the number of scoring columns rather than total alignment length. Newick guide tree to score against; leaf labels must match `structure_ids`. None lets foldmason recompute the tree internally. CPU threads. Verbosity level (0=quiet, 1=info, 2=debug, 3=raw subprocess stderr). `True` is coerced to `1` and `False` to `0`. Device to run the tool on. Maximum execution time in seconds. `None` waits indefinitely. Random seed. When set, tools run reproducibly up to small GPU float noise (see `BaseToolOutput.approx_equal`), and the seed participates in cache keys. When None, cacheable seed-sensitive tools skip cache until seeded.

Source Average MSA LDDT score (0-1) across all scored columns. Number of columns that had enough pairwise information to be scored. Total number of MSA columns. Per-column LDDT scores, length equal to `alignment_length`.

#### Applications This tool is appropriate for assigning a structural quality score to an MSA produced elsewhere, for identifying low-LDDT columns that should be masked or treated as variable loops before downstream analysis, or for comparing two candidate alignments of the same structures using a single summary score. #### Usage Tips * **FASTA record headers must match `structure_ids`.** `msa2lddt` resolves each MSA row to its corresponding structure by matching the header against the supplied identifiers. Headers that do not correspond to a supplied structure are not scored, which can produce a misleadingly high score derived from a partial alignment. * **`only_scoring_cols=True` normalises the average LDDT by the number of scored columns rather than by the total alignment length.** Use this option when comparing alignments with different gap content. Leaving it `False` (the default) includes gap columns in the denominator. * **This tool runs only in local mode.** The public web service does not provide an `msa2lddt` endpoint, so every `foldmason-score-msa` call requires the local FoldMason program.