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This is actually what I do, when I open Pathway Tools I select my PGDB in the Organism Summary Page. This opens me the Single Database Page of the PGDB I selected. Then I invoke the Tools menu in the Navigator and I don't see the 'Propagate MetaCyc Data Updates' in the menu. It doesn't seem disabled, it's just not there.

I'm on Pathway Tools version 19.5 on Mac OSX 10.9.5

Any ideas? Is there a way to run this tool on the command-line?