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Visualization Guide

Visualizing the results of CABS-flex and CABS-dock simulations is essential for interpreting the conformational ensembles and binding poses.

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PyMOL

PyMOL is the standard tool for high-quality rendering and movie generation.

  • Ensemble Visualization: Load the 10 models from output_pdbs/ as states in a single object.
  • Flexibility Mapping: Color the structure by B-factor to visualize the RMSF data (B-factors in the output models correspond to local fluctuations).

Mol* (Molstar)

A web-based viewer suitable for quick inspection without installation.

  • Drag and drop output_pdbs/model_1.pdb or the trajectory replica_1.pdb.

UCSF Chimera / ChimeraX

Useful for handling trajectories and performing detailed structural analysis.

Visualization Scripts

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The CABSflex package provides three main flags to automate the preparation of visualization files and analysis reports:

--generate-pymol-visualizations

Generates a set of PyMOL script files (.pml) in the working directory to automate common visualization tasks:

  • load_models.pml: Loads all generated models and aligns them to the first one.
  • color_by_ss.pml: Colors the structure by secondary structure (using CABS-assigned values).
  • color_by_rmsf.pml: Colors the structure by B-factors (representing local fluctuations/RMSF).
  • animate_models.pml: Loads models into a single object as states for easy animation.
  • load_restraints.pml: Visualizes the distance restraints used during the simulation.

--generate-chimera-visualizations

Generates ChimeraX command scripts (.cxc) for high-quality analysis:

  • color_rmsf.cxc: Maps RMSF data onto the structure using a color gradient. Example visualization generated by the script is shown below:

ChimeraX color_rmsf

  • rmsf_worm.cxc: Displays the protein as a "worm" where the thickness corresponds to flexibility. Example visualization generated by the script is shown below:

ChimeraX color_worm

  • record_movie.cxc: A template script to automate recording a spinning animation of the ensemble. Example spin movies generated by the script can be found on the Examples page.

  • make_movies.py (CABSdock only): A standalone Python script generated in the working directory after a CABS-dock run with --generate-chimera-visualizations.

Prerequisites: chimerax and ffmpeg must be available in PATH.

Run with python make_movies.py from the working directory to produce movies and snapshots in the movies/ subdirectory:

  • Top_10_Models.mp4 — 360° rotation of the top 10 clustered docking models overlaid on the receptor.
  • Trajectory_N.mp4 — full trajectory animation for the best-scoring replica.
  • Total_Energy_vs_RMSD.mp4 / Interaction_Energy_vs_RMSD.mp4 — animated energy-vs-RMSD scatter plots.
  • Combined_Trajectory_N_Total_Energy_vs_RMSD.mp4 / Combined_Trajectory_N_Interaction_Energy_vs_RMSD.mp4 — side-by-side trajectory and energy plot.

  • snapshots/top10_snapshot_1–10.png — 10 snapshots of the top models at 36° intervals.

  • load_restraints.cxc: Visualizes restraints as distance monitors in ChimeraX. Example visualization generated by the script is shown below:

ChimeraX load_restraints

--generate-notebook

Generates a comprehensive Jupyter Notebook (report.ipynb) and an HTML report (report.html) in the working directory. The report includes:

  • Interactive 3D View: A Mol* (Molstar) viewer integrated into the notebook, showing the structure colored by flexibility with a "putty" representation.
  • RMSF Plots: Dynamic, interactive plots (using Plotly) showing fluctuations per residue for all chains.
  • Contact Maps: An interactive heatmap of residue-residue contact frequencies.

More information can be found on the Generating Report page.

Tips for Better Visualization

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  • Smoothing: Use PyMOL's smooth command for trajectories to reduce coarse-grained artifacts.
  • Coloring: Use the spectrum command in PyMOL to highlight flexible vs. rigid regions.
  • Surface representation: Showing the receptor surface with a transparent style can help visualize the peptide binding pocket in docking results.

For practical examples, see the Examples page.

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