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### PyMOL RMSD Alignment (`pymol-rmsd-alignment`) Aligns two `Structure` inputs with Open-Source PyMOL and returns the post-alignment RMSD together with method-specific alignment statistics. The `method` configuration field selects between the CE-based `cealign` and the sequence-aware `align` routine. It also returns a `superposition` transform (rotation + translation) that superposes the mobile structure onto the target, so the two structures can be overlaid. Set the `include_superimposed_pdb` config option to also return a multi-model PDB of the overlay for download. #### API Reference

Source Target/reference 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. Mobile/query structure to align against the target. 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.

Source PyMOL alignment routine to use. Available options: `cealign`, `align` PyMOL selection for the target/reference structure. PyMOL selection for the mobile/query structure. RMSD returned when PyMOL cannot align the structures. When true, also return a multi-model PDB overlaying the aligned structures (off by default to keep results small). 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 PyMOL alignment method used. RMSD alignment metrics. Name of the metric that best summarizes the result overall (e.g. `"avg_plddt"` for AlphaFold2). Used by downstream UI and reporting to pick a headline value. Concrete Metrics subclass tag; enables typed reconstruction after a serialization round-trip. Rigid-body transform that superposes the mobile structure onto the target. `None` if PyMOL didn't return an object matrix. Multi-model PDB overlaying the aligned structures (MODEL 1 = transformed mobile, MODEL 2 = target). Present only when `config.include_superimposed_pdb` is set and a transform was found. **Metrics** | Metric | Type | Range | Availability | | ------------------------------ | ----- | --------- | ------------ | | `rmsd` | float | ≥ 0.0 | always | | `aligned_length` | int | ≥ 0.0 | cealign only | | `aligned_atoms` | int | ≥ 0.0 | align only | | `alignment_cycles` | int | ≥ 0.0 | align only | | `alignment_score` | float | unbounded | align only | | `pre_refinement_rmsd` | float | ≥ 0.0 | align only | | `pre_refinement_aligned_atoms` | int | ≥ 0.0 | align only | | `aligned_residues` | int | ≥ 0.0 | align only |

#### Applications This tool is appropriate for any analysis that needs a pairwise structural superposition of two proteins. Representative applications include scoring designed structures against a reference template, quantifying conformational drift across molecular dynamics snapshots, comparing predicted poses against experimental structures, and evaluating backbone or side-chain changes introduced by mutation. #### Usage Tips * **`method` selects the alignment routine and should match the expected sequence relationship between the two inputs.** The default `cealign` runs the Combinatorial Extension algorithm and is appropriate for proteins with low sequence similarity. `align` performs a sequence alignment followed by structural superposition and iterative outlier rejection, and is more appropriate when the two inputs share substantial sequence identity. * **`cealign` and `align` populate different metric fields.** A `cealign` call returns `rmsd` and `aligned_length` (the length of the CE alignment in CA atoms, equivalent to aligned residues since `cealign` operates only on CA atoms). An `align` call returns `rmsd` (after refinement), `aligned_atoms`, `alignment_cycles`, `alignment_score`, `pre_refinement_rmsd`, `pre_refinement_aligned_atoms`, and `aligned_residues`. Metric fields that do not apply to the selected method are returned as `None`. * **`target_selection` and `mobile_selection` accept arbitrary PyMOL selection strings.** The defaults select the full target and mobile objects. Pass a refined selection such as `"target and name CA"` or `"target and chain A"` to restrict the alignment to a specific residue subset, chain, or atom set. Selection syntax follows the standard PyMOL grammar documented on the [PyMOL Wiki](https://pymolwiki.org/index.php/Selection_Algebra). * **A failed alignment returns `failure_rmsd` rather than raising an exception.** When PyMOL cannot align the two structures (for example, when the structures are too dissimilar for CE to converge), the call returns the configured `failure_rmsd` value (default `999.0`) and attaches the underlying error message to the result metadata as `alignment_error`. This sentinel-value approach lets calling code distinguish a failed alignment from a near-zero RMSD between two essentially identical structures.