TBA
TBA
Dynophores can be easily visualized in Jupyter Notebooks with the dynophores
Python package.
Install the dynophores
package as described here.
You have different options what to do next:
Take a look at a demo notebook showing the dynophore from an MD simulation for ligand-bound kinase CDK2 (PDB ID: 1KE7):
dynoviz demo path/to/some/folder
Explore your own dynophore data in a new notebook:
dynoviz create --dyno path/to/dyno/folder --pdb path/to/pdb/file --dcd path/to/dcd/file --workspace path/to/workspace/folder
If you already have set up your dynophore notebook (i.e. if you want to revisit a notebook created with option b), run:
dynoviz open path/to/your/dyno/notebook
Note: This command is equivalent to:
jupyter lab path/to/your/dyno/notebook