From what I read here the graph with the red/turquoise dots shows rmsd/energy pairs.

The red dot shows the best pair found so far on my computer, i.e. lowest RMSD/lowest energy.

The turquiose dots show the results of calculations done on the basis of the experimentically determined structure. Is that true?

But then I don't get why there are that many green dots. There should only be one native dot, being the one with RMSD=0 and energy=lowest. But why are there that many?


And did I get it right that what we currently do here is not searching for actual structures but testing the model itself? So a successful run would be one where the model comes up with the a RMSD=0 and lowest energy structure. Or the red dot being identical to a green dot. But which green dot?

well a WU consisct of multiple models, so multiple dots...

Okay, but each model refers to the same protein, or doesn't it? So when the dots show the "real" data there should only be one. Or how are those green ones acquired?

It also looks like the the model running on my computer adds green dots all the time. Is that true? But I think I read the dots are from earlier experiments.

A green dot is generated each time a configuration is tested. So there are many generated per model.

A red dot represents the best configuration in a model. The protein and your run time preference determine how many models are in a task. So you will see different numbers of red dots in different tasks.

---

BOINC WIKI

BOINCing since 2002/12/8

Thanks, I was confused because it said

"The turquoise points are from calculations we did here where we cheated and started with the actual structure."

on this page: https://boinc.bakerlab.org/rosetta/rah_top_predictions.php


And where is the "zero line" (don't know the correct english term) for the RMSD in that picture? Lowest energy is at the very bottom, but RMSD should be zero for the best result. Is it on the very right?

Thanks, I was confused because it said

"The turquoise points are from calculations we did here where we cheated and started with the actual structure."

on this page: https://boinc.bakerlab.org/rosetta/rah_top_predictions.php


And where is the "zero line" (don't know the correct english term) for the RMSD in that picture? Lowest energy is at the very bottom, but RMSD should be zero for the best result. Is it on the very right?

i believe its at the right, you can try to open the graphics mode and watch to the number that is given after rmsd: and look what the graph dous at the same time, then you know for shure ;)

It seems the lowest RMSD is at the very left. So the optimal result (RMSD=0 and energe=min) would be in the lower left.

It seems the lowest RMSD is at the very left. So the optimal result (RMSD=0 and energe=min) would be in the lower left.

correct