Does the graphics show the lowest energy you found during the WU or just the one being relaxed?

Anyway, is there a "typical" low energy that most proteins approach in their natural stage? Perhaps its related to how big it is?
And a comparison to the current lowest enrgy found (and a RMSD-Model?) would be interesting.

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Have you read the quick guide to Rosetta graphics? https://boinc.bakerlab.org/rosetta/rah_graphics.php

Have you read the quick guide to Rosetta graphics? https://boinc.bakerlab.org/rosetta/rah_graphics.php

I don't understand the
"Accepted" shows the most recently accepted move.
"Low Energy" shows the lowest energy shape seen in the current trajectory.

"accepted move" means a lower energy than the current lowest?
"trajectory" is the whole WU or decoy?

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G'day Avi and welcome to Rosetta@Home.

I don't understand the
"Accepted" shows the most recently accepted move.
"Low Energy" shows the lowest energy shape seen in the current trajectory.

"accepted move" means a lower energy than the current lowest?
"trajectory" is the whole WU or decoy?

Have a read of this first so what I have writen makes sence.

You have asked some pretty hard questions here, so I'll answer them as best I can:

"Accepted" shows the most recently accepted move. Yes
"Low Energy" shows the lowest energy shape seen in the current trajectory. Yes.
"accepted move" means a lower energy than the current lowest? Not necessarily, to use Dr DB analogy you may have to climb a hill to find out if the valley on the other side is lower than the valley that you are in.
"trajectory" is the whole WU or decoy? Per decoy.

If I got any of that wrong someone will correct me :)

Happy crunching.

G'day Avi and welcome to Rosetta@Home.

I don't understand the
"Accepted" shows the most recently accepted move.
"Low Energy" shows the lowest energy shape seen in the current trajectory.

"accepted move" means a lower energy than the current lowest?
"trajectory" is the whole WU or decoy?

Have a read of this first so what I have writen makes sence.

You have asked some pretty hard questions here, so I'll answer them as best I can:

"Accepted" shows the most recently accepted move. Yes
"Low Energy" shows the lowest energy shape seen in the current trajectory. Yes.
"accepted move" means a lower energy than the current lowest? Not necessarily, to use Dr DB analogy you may have to climb a hill to find out if the valley on the other side is lower than the valley that you are in.
"trajectory" is the whole WU or decoy? Per decoy.

If I got any of that wrong someone will correct me :)

Happy crunching.

So during relax, why would the Accepted Energy ever go up?
(and the first two lines were a quote from the FAQ, the 2nd two were my questions)

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So during relax, why would the Accepted Energy ever go up?

The accepted energy in the graphics while doing a (full atom) relax, jumps around all over the place as the slightest move in an atom position can have huge ramifications to the energy. The thing to watch out for in the (full atom) relax is the red dot, which will be at the lowest enrergy that Rosetta@Home can produce for that decoy.

A quote from Dr David Baker:

the landscape is extremely bumpy since small changes in atom positions can cause huge clashes

This was to a question that I asked here.

(and the first two lines were a quote from the FAQ, the 2nd two were my questions)

That would explain the lack of question marks, that I completly missed :oops: :)

Hugo, actually, the red dot is your own prior model's prediction(s). If you are crunching model 1 you'll not see a red dot. Other times you may be on model 25 and only see a few red dots, that's because the others are so much lower (better) on the scale then your present model, that the graphic hasn't scaled to include them yet.

So you aren't watching for a red dot... you're making a new one. And if your new red dot is lower then the others, then your current model is better then the ones you ran previously on the same protein.

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Hugo, actually, the red dot is your own prior model's prediction(s). If you are crunching model 1 you'll not see a red dot. Other times you may be on model 25 and only see a few red dots, that's because the others are so much lower (better) on the scale then your present model, that the graphic hasn't scaled to include them yet.

So you aren't watching for a red dot... you're making a new one. And if your new red dot is lower then the others, then your current model is better then the ones you ran previously on the same protein.

Is the placement of the red dot too fast to see before the next ab initio (I haven't watched the graphics in a while)?

Is the placement of the red dot too fast to see before the next ab initio (I haven't watched the graphics in a while)?

Yes I think so.

I have only seen it(them)in the folowing decoys.

Anders n

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Yes I think so.

I have only seen it(them)in the folowing decoys.

Anders n

Thanks for the info.

Edit: because a smiley face seemed inappropriate, dang, it's hard to talk to people with only text (for me anyway). And then couldn't spell "anyway" :)