On Mon, Oct 10, 2011 at 6:51 AM, R.M. Garavito
So my question is does Phenix store the absolute paths in its various project indices?
Yes. Fixing this is on my to-do list (hopefully it will happen before we release version 1.7.3), but I can pretty much guarantee that whatever I end up doing will not be a perfect solution - there are simply too many places where absolute paths are used and it is not as simple as substituting "$PROJECT_DIR" in all of the various parameter files. I don't think there is an easy fix for your problem anyway; in my experience, it is always less trouble to fix the UIDs on the computer being added to the collective than it is debugging the many issues (not just in Phenix) that will arise if your users have multiple identities. -Nat