Obtaining Code

Full Code from GitHub

The ChimeraX repository is hosted on GitHub. To get the full codebase:

# If you have SSH access
git clone git@github.com:RBVI/ChimeraX.git
# If not
git clone https://github.com/RBVI/ChimeraX.git

Alternatively, you can make a clone of the repo to your GitHub account and add the RBVI repo as an upstream repository.

# If you have SSH access
git remote add upstream git@github.com:RBVI/ChimeraX.git
# If not
git remote add upstream https://github.com/RBVI/ChimeraX.git

From there you can issue pull requests for the RBVI ChimeraX repository.

Code from the ChimeraX Distribution

Most of ChimeraX is written in Python and that code is included in the ChimeraX distribution:

Windows: ChimeraX/bin/Lib/site-packages/chimerax
macOS: ChimeraX.app/Contents/lib/python3.x/site-packages/chimerax
Linux: chimerax/lib/python3.x/site-packages/chimerax

The ‘3.x’ in the latter two lines depends on the exact version of Python 3 being used by your version of ChimeraX, but is not less than 3.7. Typing, for example, chimerax/lib/python3.<TAB> should cause your shell to auto-complete the path for you.

Small modifications to the code can be tested by simply editing the Python code and restarting ChimeraX.

There is documentation for how to use a ChimeraX distribution to develop bundles elsewhere on this website.

Git Cheat Sheet

Here are a minimal set of commands to get started using git:

  1. Git associates a user name and email address with all check-ins. The defaults are based on your USERNAME and your computer’s hostname. The email address is usually wrong. To explicitly set those values:

    git config --global user.name "Your Name"
    git config --global user.email you@example.com
  2. Make local copy of repository:

    git clone https://github.com/RBVI/ChimeraX.git
  3. Use the develop branch (the master branch is only used for releases):

    git switch develop
  4. To update repository to latest version:

    git pull
  5. Add current state of file to the repository:

    git add "filename(s)"
  6. Commit all changes to repository (added files and changes to those added files):

    git commit -a
  7. Copy local repository changes to master repository:

    git push
  8. Diff from previous to current revision of file (ignores additions):

    git whatchanged -n 1 -p <file>
  9. Diff to previous commit of file:

    git diff HEAD^ <file>