Secondary Structure Plugin Reference

For task-oriented guidance, start with Which Analysis Should I Run? and then enable secondary_structure in comparison.yaml.

Settings

Top-level plugin key: plugins.secondary_structure.

Field	Type	Default	Description
`chain_id`	`str`	`"A"`	Protein chain letter passed to DSSP. Chain A is the PolyzyMD protein convention.
`selection`	`str \| null`	`null`	Explicit MDAnalysis selection for the protein residues. When set, this overrides `chain_id`.

The plugin computes simplified DSSP classes with MDTraj, aggregates helix, strand, and coil persistence across replicates, and uses default scalar comparison on helix_fraction.

By default, PolyzyMD selects protein and chainid A. This matches the PDB and PolyzyMD chain convention where chain A is the protein. GROMACS .gro topologies may not preserve chain IDs, so chainid selections can fail in MDAnalysis. For .gro inputs, set selection explicitly, for example:

plugins:
  secondary_structure:
    selection: "protein"

Use MDAnalysis residue syntax to restrict the protein region:

plugins:
  secondary_structure:
    selection: "protein and resid 1:269"

or zero-based residue indices:

plugins:
  secondary_structure:
    selection: "protein and resindex 0:268"

DSSP requires complete, backbone-compatible protein residues. Do not use CA-only selections such as protein and name CA for this plugin.

Output files

Per-replicate results are written under analysis/<condition>/secondary_structure/run_<replicate>/. Aggregated results are written under analysis/<condition>/secondary_structure/aggregated/, and cross-condition statistics are written to comparison/secondary_structure/result.json.

Plot outputs

Plot output	Description
`ss_timeline_<condition>.png`	Residue-by-time secondary-structure heatmap for one condition
`ss_content_bars.png`	Condition-level helix, strand, and coil fractions
`ss_helix_bars.png`, `ss_strand_bars.png`, `ss_coil_bars.png`	One bar chart per secondary-structure class
`ss_persistence_diff_heatmap.png`	Difference in helix persistence relative to the control condition

Time-axis plots assume uniformly saved frames. PolyzyMD maps frame index to time as frame_index * dt; variable-timestep concatenated trajectories are not supported.