Hi Tom, Lower potential energy is better, so a minimization could go from positive to smaller positive, or positive to negative, or negative to larger negative. There isn't any knowledge of what the global minimum potential energy of the system might be (or even the energy of the closest local minimum, when initial energy is calculated), so no way to normalize relative to that. Basically, your initial instinct was right. I hope this clears it up! Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 20, 2012, at 10:16 AM, Thomas Sturgill wrote:

Elaine has explained that the initial energy is a total energy and not a free energy. Understood.

I want to verify that a negative energy is "better" than a positive energy, and a more negative energy is "better" still. This is what I assume now, but I had an angst that the energy value is somehow based on absolute value, so the "best" minimized energy is zero.

Humor my question, because I have to be 100% certain. No need to go into caveats about the ability of Chimera minimization to make models worse, and how difficult the energy parameter is to interpret.

Tom.