One idea is use the Chimera note pad that lets you write any text notes and they are saved in the session, menu Tools / Utilities / Notepad.  You could put position names and notes about those positions in using note pad.

  If you don’t like that I’d say the real issue is user interface, how will you type the notes in and how will you view them.  If you plan on providing that user interface in your own dialog then I’d suggest you can just keep a Python dictionary mapping names to notes and your tool will save these in sessions.

  Using the iPad to control Chimera so it can be passed around during a group visualization session is cool.  When I show Chimera stereo visualization to visiting students I usually pass around a wireless space navigator so they can change the view point.  I wonder what they would do if the controller allowed them to change molecule display styles, clip the model, change colors.  Seems like changing view points (flying around) is the main interesting thing.  Probably the second most interesting capability would be to blow things up!

Tom