MDPath visualization

Currently, three options for 3D visualization are integrated into MDPath.

NGL Visualization

For visualization using NGLView, open the corresponding Jupyter notebook. Then, insert the path to your topology or first_frame.pdb, along with the path to your desired MDPath output, such as quick_precomputed_clusters_paths.json or precomputed_clusters_paths.json.

Afterward, simply execute the notebook and navigate through the visualization as you would in NGLView.

Pymol Visualization

To visualize the paths in PyMOL, start by launching PyMOL according to your installation method. Under the “File” menu, select the option “Run Script…” and navigate to the mdpath folder.

From there, select the vis_pymol.py script. Now, you can run the script from the command line using the following command:

Afterward, you can execute the visualization steps in PyMOL as you normally would.

Spline Visualization

The spline visualization is a more advanced option that requires slightly more manual labor to retrieve a final picture. However, the results are often more visually appealing than the other options.

To begin you will generate STL files of the paths as splines based on the using the “quick_precomputed_clusters_paths.json”. This can be done by running the following command:

mdpath_spline -json PATH/quick_precomputed_clusters_paths.json -top PATH/topology.pdb

This will generate multiple STL files corresponding to the clusters from the analysis.

Now you can load the STL files into your favorite 3D modeling software, such as Blender, to create a final image. Be carefull to generate the protein structure based on the coordinates of the first_frame.pdb, as this is what the splines are based on. This will allow you to generate images like the one below.