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I'm trying to lay out a big undirected graph—*this worked great in Omnigraffle 3 creating really nice graphs that were evenly laid out, had smooth boundaries etc.. but I can't get Omnigraffle 5 to make the graphs look good. There are always weird nodes poking way out on the edges, with everything else clumped in the middle, overlapping etc... I've tried every possible combination of line length and repulsion and it doesn't seem to work.

Any suggestions on how to make those nice looking graphs with the new system?

Thanks!