Usage

To use Protein Runway for visualizing molecular movements, follow these steps:

1. Prepare Input Data:

   • Ensure you have trajectory (.trr) and topology (.top) files.

   • The github repository comes with a file in the input directory called 5vde_example that you can use to do a test run.

2. Run the Workflow:

   snakemake
   

3. Visualize Results:

   • Import the 03_output/ *.nmd_traj.pdb files to Blender via Add-on

   • Import the 03_output/ *.segmentation.tsv files to color functional domains

   • Choose segmentation method (Chainsaw, Merizo, GeoStaS) and number of clusters

Visualization Demo