Since 2 days the accepted energy is between -270 -280. Before it was +280 and more.

I dont know why, please help.

Sorry for bad englisch, not learn it so long ;)

A negative number for accepted energy is a good thing. It indications the model you are working on will not fall apart if you made one like it in the real world.

Moving this to Science forum.

---

Rosetta Moderator: Mod.Sense

But if the accepted energy is negative its working slower, so why its better ^^

But if the accepted energy is negative its working slower, so why its better ^^

You are wrong, the "accepted energy" is a number that refer to the energy used by the protein to fold in this model

Lower energy is required-->more easily the protein will fold in this model

And the number can be negative, the minimum isn't 0

So less energy means a good model

---

You are wrong, the "accepted energy" is a number that refer to the energy used by the protein to fold in this model

I don't think TEKNO's wrong - he doesn't state anything wrong - just ask a question!

There might well be a relationship between the negative energy models and running more slowly as the 'fine-tuning' that transient mentions is more compute-intensive and so runs more slowly.

HTH
Danny

---

The models often have two phases. The first is "fast" and you see lots of activity in the graphic. The second is "slow" and only minor changes are observed to the structure. In between these two phases, there seems to be a point where they begin counting the energy levels of all of the side chains in addition to the main backbone. This is a lot more points to calculate, and is a much more details analysis. Thus it seems slower, and it results in a much lower energy level.

It could be perceived as being caused by encountering a lower energy level. But I think it is just confusion here about cause and effect. The full atom relax stage appears slower, and accounts for energy at a more granular level. So you will see your energy graph drop significantly at the point where the model progresses to the full atom relax stage.

It's all normal. It is how Rosetta is doing the search for the shape most likely to occur in nature.

---

Add this signature to your EMail:
Running Microsoft's "System Idle Process" will never help cure cancer, AIDS nor Alzheimer's. But running Rosetta@home just might!
https://boinc.bakerlab.org/rosetta/

This has probably been asked before but since I am new to this i will ask anyway.
What do the red dots in the final box, in the lower right hand corner, that plots the energy and RMSD of each accepted move mean. There were seven of them in one of my models and it was the first time I have seen it.

Thanks
Dave

What are the little red dots in the graphic for?
Why don't I see the red dots from my prior runs in the graphic?

Welcome to Rosetta Dave! Be sure to post any other questions.

---

Add this signature to your EMail:
Running Microsoft's "System Idle Process" will never help cure cancer, AIDS nor Alzheimer's. But running Rosetta@home just might!
https://boinc.bakerlab.org/rosetta/