Unfortunately our ChimeraX git repository is not clonable outside our UCSF lab.  We plan to remedy this by moving the ChimeraX source code to GitHub -- currently it is in a git repository on our lab's servers.  It is visible in a not very useful way one file at a time through a web interface

For some purposes it is adequate to look at the Python code which is all included in the ChimeraX distributions.  ChimeraX is 80% Python and 20% C++. The ChimeraX API is described in the Programming Manual:

  Tom