Protein-Modeling-2025

Centralized repository for Washington iGEM 2025 Protein Modeling

Initial Directory Setup

At this point, you should already have RFdiffusion setup and working. If not, follow these instructions.

Vague Directory Structure

.
└── iGEM/
    ├── RFdiffusion/
    │   ├── env
    │   ├── examples
    │   ├── scripts
    │   ├── setup.py
    │   ├── rfdiffusion
    │   └── 6iok
    └── Protein-Modeling-2025*/
        ├── aliases.sh
        └── Diffusion/
            ├── designs
            ├── inputs/
            │   ├── 6iok_ultra_remod.pdb
            │   └── 6iok_ultra_remod_with_strand.pdb
            ├── scripts/
            │   ├── organized_6iok_design_motifscaffolding_2.sh
            │   └── 6iok_design_ppi.sh
            └── logs

Setup the overall directory structure like above.

If you already have RFdiffusion, don't worry about setting up that directory. Clone this repo in the same parent directory as your RFdiffusion repo.

Instructions for cloning:

In your iGEM parent directory, run the following commands:

git clone https://github.com/uwigem/Protein-Modeling-2025.git
cd Protein-Modeling-2025

Usage

We've included some aliases/functions in /aliases.sh to make things easier. To be able to use these on your system, run the following commands:

On mac (in Protein-Modeling-2025):

echo "source $(pwd)/aliases.sh" >> ~/.zshrc; source ~/.zshrc

On windows git bash (in Protein-Modeling-2025):

echo "source $(pwd)/aliases.sh" >> ~/.bashrc; source ~/.bashrc

Keep in mind that this will let you use the aliases across your system. Below is a breakdown of the aliases:

gupdate

Definition:

git stash
git pull
git stash pop

Usage: Run gupdate before making any new changes to the repo or right before pushing new changes. In summary, this command stores away (stashes) your new changes, pulls new changes from the upstream repo, and then reimplements your changes.

gpush

Definition:

git add .
git commit -m "$1"
git push 

Usage: Run gpush *insert commit message here* when making changes

Scripts