Hi Virginia,
    Another thing to note is that in the target field, the path to the Chimera executable is embedded in double quotes (e.g. it is something like: "C:\....\chimera.exe").  To add the --stereo option, you need to add it outside the ending double quote and separated by a space, like this:  "C:\...\chimera.exe" --stereo .

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        pett@cgl.ucsf.edu
                        http://www.cgl.ucsf.edu