fold3Dplot_jupyter
Graphical viewer of the alphafold results in jupyter notebook.
This is a jupyter notebook that draws the same figure as ColabFold (https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb) from the result of AlphaFold (https://github.com/deepmind/alphafold) run on the local machine.
Requirements
- numpy
- pickle
- py3Dmol
- matplotlib.pyplot
- ipywidgets
- alphafold (only for save graphs (coverage_lDDT.png and PAE.png))
- jupyter-notebook
3D plot on jupyter notebook
put fold3Dplot.ipynb in the result directory of alphafold.
{mv,cp} fold3Dplot.ipynb alphafold_results_directory/
Start jupyter
jupyter-notebook
Open fold3Dplot.ipynb on jupyter and run. The display changes interactively when the parameters are changed.
Save graphs
If you want to save the plddt and pae graphs,
python3 save_foldplot.py alphafold_results_directory
saved coverage_lDDT.png and PAE.png