In the rosetta beta graphics the energy is positive or negative. Is the 0 energy point the energy of the starting molecule?

(Perhaps this should be at the science board, my apologies.)

Well, I personally don't know all the details of the energy calculations. But let me try to express what I understand of it.

The energy levels shown are calculated based on the positions of the atoms in your current model. A higher positive number basically means that structure is very unstable and is about to fall apart. A zero basically means these atoms are just as happy to be in the orientation of your model as they are to stand by themselves. And a negative number indicates that the atoms are attracting each other. The larger the negative value, the better the attraction. A strong attraction indicates a strong structure that won't tend to fall apart. Since proteins are pretty stable in nature, a structure with a larger negative value is probably closer to the actual native form of the protein.

So, no, zero holds no special meaning. What Rosetta is searching for is the structure with the most negative value it can find.

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Rosetta Moderator: Mod.Sense

i would presume 0 is the starting point, and the energy release from this point is calculated (i.e. the negative values...)

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