Getting started

Generate dynophores

Download

TBA

Usage

TBA

Visualize dynophores

Dynophores can be easily visualized in Jupyter Notebooks with the dynophores Python package.

Installation

Install the dynophores package as described here.

Usage

You have different options what to do next:

1. 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
   

2. 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
   

3. 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