PDBarrows

Use this notebook to generate a file in chimera that draws arrows between two PDB models.

1. Prereqs
2. Instructions
3. License

Prereqs

• Set up a fresh conda environment with Python >= 3.7: conda create -n arrows python=3.7

• Activate the environment: conda activate arrows.

• Install jupyter, biopandas, and biopython: pip install notebook biopandas Bio.

• Start jupyter notebook: jupyter notebook.

• Open the notebook PDBArrows.ipynb.

Instructions

• Open the notebook to see the instructions. Briefly, the PDB files are parsed and a fasta-format output is generated for you to run a sequence alignment. This is then input to the second part of the notebook to generate a chimera bild file.

• There should only be one chain in each PDB file.

License

This project is licensed under the MIT License - see the LICENSE.txt file for details.