Region highlight figures

FastMDXplora can add user-defined residue-region highlights to report outputs. This is intended for loops, helices, active-site neighborhoods, or other regions you already know and want to call out visually.

Use RMSF for this view. RMSD is a frame/time metric that summarizes global deviation across a trajectory. RMSF is residue- or atom-indexed, so it is the right metric for highlighting residue intervals.

YAML example

include: [analysis, report]

analysis:
  include: [rmsf]
  trajectory: simulation/production.dcd
  topology: simulation/topology.pdb

report:
  title: "Trp-cage RMSF region highlights"
  region_highlights:
    - label: "example region 1"
      start: 3
      end: 7
      color: "#4E79A7"
    - label: "example region 2"
      start: 12
      end: 16
      color: "#F28E2B"

The labels are user-provided annotations. FastMDXplora does not infer that a range is biologically a loop, helix, catalytic motif, or binding site.

Outputs

When report.region_highlights is configured and RMSF analysis output exists, the report phase writes:

  • analysis/rmsf/rmsf_region_highlights.png

  • report/structure_region_highlights.png when PyMOL rendering succeeds

  • report/structure_region_highlights.pml when PyMOL rendering succeeds

  • report/region_highlight_summary.png

  • report/region_highlight_manifest.json

If PyMOL and a topology/PDB file are available, the summary includes a PyMOL-rendered cartoon/ribbon structure panel with the same regions highlighted. If PyMOL is unavailable, FastMDXplora still writes the RMSF highlight plot and records the skipped structure-rendering reason in report/region_highlight_manifest.json.

Install PyMOL into the environment that runs FastMDXplora when you want the cartoon structure panel:

conda install -c conda-forge pymol-open-source

With micromamba:

micromamba install -c conda-forge pymol-open-source

Run examples

Bash:

fastmdx explore --config region_highlights.yml

Windows PowerShell fallback when fastmdx is not on PATH:

python -m fastmdxplora.cli.main explore --config region_highlights.yml

For an analysis-only/report-only workflow, provide existing trajectory and topology paths in the analysis: block and set include: [analysis, report]. Setup and simulation will not be run.