Hi Kyle,
Here is the fixed script avalnogui.py to report density map values at atom positions. It is also at the Chimera Python scripts web page (I sent this before with a wrong URL that required a password)
I made it take the file paths on the command line, for instance,
$ chimera --nogui --silent --script "avalnogui.py 1a0m.pdb 1a0m.omap"
#1:1.A@N 3.722
#1:1.A@CA 3.345
#1:1.A@C 4.04
...
Tom