Class to view Alphafold models
alpha_viewer is based on the alphafold2 colab notebook visualization. It automatically chooses the best available prediction. alpha_viewer includes functions to plot PAE (plot_pae) and pLDDT (plot_pLDDT). It also allows for coloring of the py3Dmol view based on pLDDT with show_confidence. alpha_viewer contains .obs, a pandas data-frame, that can be used for custom annotations based on aa postion within the chain(s). You can use a key of .obs to color the py3Dmol view of your protein(s) based that annotation with show_annotation. This can also be used to inspect substructures with show_substructures.
alpha-viewer has been tested to work with monomer, monomer_ptm and multimer models.
So far it's sadly not possible to save the py3Dmol view for exporting.
If you use alpha_viewer in your publication please cite:
you can install this repository from pypi with:
pip install alpha-viewer
It's recommended to use alpha_viewer within jupyterlab. Please enable jupyterlab extensions and install jupyter-widgets/jupyterlab-manager and jupyterlab_3dmol
A tutorial notebook can be found in https://github.com/Intron7/alpha_viewer/tree/main/tutorials