Hi Jeff

Easy.
When you load 2 files, Jmol puts them in 2 "frames" (or "models"). You have 
found that you 
can select them, using 1.1 and 1.2, but that doesn't make them visible.
You must use the "frame" command, see
http://www.stolaf.edu/academics/chemapps/jmol/docs//index.htm#frame

Example: 
frame 1.1 # displays 1st file loaded
frame 1.2 # displays 2nd file loaded
frame all # displays both




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