> ## Documentation Index > Fetch the complete documentation index at: https://proto.evodesign.org/docs/llms.txt > Use this file to discover all available pages before exploring further. # Structure Ensemble RMSD > Generate a conformational ensemble and compute RMSD against a target structure via PyMOL.
Structure Ensemble RMSD
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evo-design/proto-language/proto\_language/constraint/protein\_structure/structure\_ensemble\_similarity\_constraint.py
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Generate conformational ensembles and compute RMSD against an experimental. target structure. This constraint: 1. Prepares the target structure (extracting chain/residue range if specified). 2. For each proposal sequence, generate a conformational ensemble. 3. Computes PyMOL-aligned RMSD between each ensemble frame and the target. 4. Summarizes the RMSDs using the specified aggregation method. 5. Converts the summarized RMSD to a 0-1 score using a sigmoid function. ## API Reference
ConfigStructureEnsembleSimilarityConfig Source
Configuration for structure ensemble similarity constraints. This constraint generates a conformational ensemble for a proposal protein sequence and computes the RMSD between ensemble members and an experimental target structure using PyMOL alignment. Target structure: a Structure object, file path (.pdb/.cif), or raw PDB/CIF content string. Chain ID to extract from the target structure (e.g., 'A'). Residue range (start, end) to extract from target (1-indexed, inclusive). Residue range (start, end) of the proposal sequence to use. Dictionary of configuration parameters passed to the ensemble prediction tool. How to summarize ensemble RMSD values: min (best match), p10, mean, or median. Options: `min`, `p10`, `mean`, `median` PyMOL alignment routine for ensemble RMSD calculation. Options: `cealign`, `align` RMSD in Ångströms where the sigmoid score equals 0.5; values below 3 Å are generally a good match. Steepness of the penalty curve. Whether to print progress messages.
ReturnsConstraintOutput
Per-proposal score in `[0, 1]` (0 is a perfect match) with ensemble RMSD summary/distribution metadata.
## Usage ```python python icon="python" theme={null} from proto_language.core import Constraint from proto_language.constraint import structure_ensemble_rmsd_constraint, StructureEnsembleSimilarityConfig constraint = Constraint( inputs=[segment], function=structure_ensemble_rmsd_constraint, function_config=StructureEnsembleSimilarityConfig( # Configure parameters here ), ) scores = constraint.evaluate() ``` ## Metadata | Property | Value | | --------------- | ------------------------------------ | | Key | `structure-ensemble-rmsd` | | Function | `structure_ensemble_rmsd_constraint` | | Category | `protein_structure` | | Mode | `discrete` | | Uses GPU | `True` | | Supported Types | `protein` |