As of r376, I removed the compatibility-with-old-lab-people feature of checking for Modeller in $MODINSTALLSVN. If you want to build IMP with support for Modeller, either specify this on the command line, i.e.

scons modeller=/my/modeller/location

or (recommended) make a file called config.py in the top-level IMP directory and set it like any other Python variable in there: modeller="/my/modeller/location"

The same is true for EM/emlib/EMBED; set its location with the embed variable: embed="/my/embed/location"

Ben