How do I prevent the view in the clipping planes window from zooming in when I fit a selected residue to the screen?
This can be done with a preference. Open the Preferences panel, and under Workspace – Clipping planes, deselect the option "Zoom clipping planes with Workspace".
You can also do this with a Maestro command. First, ensure that the Commands text box is displayed (Window → Command Input Area or Ctrl+Shift+I), then enter the following command: