what in the world is abrelaxmode all about ?

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It is a question generator ...

See ... you generated a question ... :)

Sorry, my sense of humor excaped again ... I really have no idea ...

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It is a question generator ...

See ... you generated a question ... :)

Sorry, my sense of humor excaped again ... I really have no idea ...

wow, Your really funny! thanks anyway

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David Kim or one of the other project people should be stopping by this week and maybe they can enlighten both of us ... :)

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Wild guess, alpha helix and beta sheets with some relaxation in their constraints?

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Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.

Hopefully with time we will be able to provide a full description.
Here is a very brief one:
abrelax = ab initio + relaxation

Ab initio is Latin for "from the beginning." It is scientific jargon used to describe theoretical predictions that do not rely on any experimental data. It is the name of the part of our algorithm that predicts the overall folds of proteins using only their sequence of amino acids as input. This method is very fast, because it usese a reduced representation of the protein.

"Relaxation" comes about because the ab initio mode uses a simplified model of the protein, without all of the atoms explicitly represented. When those atoms are added to the structure they may clash with each other, which is physically impossible. So we "relax" out these clashes, and try to optimize the structure given our fully atomically detailed energy function. This step is essential, because we must use all of the atoms when evaluating the probability that a structure has the correct fold. Optimizing with all atoms on is much slower, so we cannot perform the entire search in this representation.

Hence "abrelax" - global fold prediction, followed by high resolution optimization and evaluation.

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Hey I am back with more questions, hope you dont mind.
so I got little anxous for the new screensaver and must of pressed the update button around 100 times and now I have a plehtora of work units mostly called
1hz6A_abrelaxmode_random_length20_jitter02_omega_sim_aneal and then there are some from 1n0u,

I am going to take a wild guess and assume that the begining numbers are a series of a set of units???

Does random length mean that the length of the random seed or length of the amino acid sequence? or not at all?

Baffled by jitter, can only assume its a jiggly one, ha ha.

omega, last run of set maybe or the end of the sequence?

sim must mean simulation and aneal is a greek god? I dont know?

How about making a page in the science section of rosetta explaining this? That would be cool.

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Hey I am back with more questions, hope you dont mind.
so I got little anxous for the new screensaver and must of pressed the update button around 100 times and now I have a plehtora of work units mostly called
1hz6A_abrelaxmode_random_length20_jitter02_omega_sim_aneal and then there are some from 1n0u,

How about making a page in the science section of rosetta explaining this? That would be cool.

You're probably not the only only curious one. David Baker is the definitive source on these. But until the science page is set-up, I'll tell you what I know.

1hz6A: This is the Protein Databank code for the crystal structure of this protein.

abrelax: I explained down below.

random_length20_jitter02: The quick answer on these is that they represent the methods we are using to ensure that we are taking full advantage of the computational power of boinc. We are forcing each computer to work within constraints at certain random positions along the length of the chain. We are also adding extra jitters so that we search more possibilities, jiggling the chain around a little more, as you say. Essentially this all encourages each computer to explore different possible structures.

omega: This is the name for the angle of one of the torsional bonds in a protein. This particular bond is very stiff, and so doesn't rotate very much. But the breakthrough David announced earlier is related to letting this move more than we used to.

sim_anneal: An abbreviation for "simulated annealing." Real annealing is the process where something heated up, and then cooled very slowly, so that defects can have a chance to work themselves out. Simulated Annealing is a computationl optimization protocol inspired by this idea. It was developed in the early 80's that has proved useful in many contexts. You can read more about it here.