Sophia Installation and Startup
1. If you don't have Chimera installed, download and install it (https://www.cgl.ucsf.edu/chimera/).
Sophia has been tested with Chimera v1.8.
2. Go to the Sophia homepage (http://sophia-web.appspot.com). Click the download button.
3. Move Sophia to an appropriate directory and unzip it.
4. Launch Chimera.
5. Within Chimera, click File, then Open...
6. Navigate to the Sophia directory and double-click on launch_sophia.py.
(If you don't see that file, click on the File type bar at the bottom of the window and select "Python".)
7. The Sophia icon should appear in the tool bar on the left side of the main Chimera window.
Click it. This will open the Sophia Main window.