For this section, we need at least two external pieces of software—PyMOL and MUSCLE—a 3D structure-rendering program and a sequence aligner.

MUSCLE can be installed with conda as follows:

conda install -c bioconda muscle 

A version of MUSCLE is installed with the msa package, and bio3d can be referred to that installation instead. We'll use the msa version in this recipe.

PyMOL is absolutely necessary for visualization and can be installed with conda as follows:

conda install -c schrodinger pymol

To find the install path for this software, use which pymol.

Beyond these, you'll need two files containing structures of human and fruit fly thioredoxins to work with: datasets/ch3/1xwc.pdb and datasets/ch3/3trx.pdb.