Why does F@H fold the same prteins over and over and...

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Why does F@H fold the same prteins over and over and...

Postposted on Tue Jun 04, 2002 2:21 am

Well, the topic is my question, pretty simple. :)

I run F@H in screensaver mode, which allows you to see which protein it is folding, how much progress you have made on the WU, etc. I found it curious though that I am on proteinA for the third time that I can remember. Anyone know what's up with that?
MadManOriginal
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Postposted on Tue Jun 04, 2002 2:45 am

Different parts of the animation. One single protein fold animation, done beginning to end on one PC, would take years, IIRC. It may seem to be the exact same protein, but it's more likely you're seeing parts 137, 141, and 165 of 11000 in the series. :)

The main F@H page has a results page with all the finished animations, kind of cool to look at.
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Postposted on Tue Jun 04, 2002 9:27 am

isn't the whole idea that protiens can fold in many different ways and things go wrong when they fold "incorrectly" and that we are simulating the (various) folding processes so that they can be studied/compared...
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Postposted on Tue Jun 04, 2002 12:00 pm

JohnnyQ wrote:isn't the whole idea that protiens can fold in many different ways and things go wrong when they fold "incorrectly" and that we are simulating the (various) folding processes so that they can be studied/compared...


True, but it takes a LONG time to even get ONE instance done. Unfortunately the feedback we get from stanford regaring where we are is somewhat ambiguous, theres really no sure way for us to know.

But yes, they run each protein 10-15 times, to see how it folds, over several thousand packets.

.:Ttocs
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Postposted on Wed Jun 05, 2002 2:29 am

incidentally, it is my most humble opinion that the screensaver just renders the same two images from different angles and distances...

i havn't bothered finding this out for sure, but staring at the damn thing going for over an hour has pretty much convinced me, any challenges will be summarily ignored! </zealot mode>

so now i just use the command line client...

JQ
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Postposted on Wed Jun 05, 2002 3:12 am

Well, I didn't mean to imply that it was the same protein b/c I was staring at the picture, nor that I was trying to watch it 'fold' :) In the screensaver version the name of the protein is written on the side of the screen. I am not talking about frames though, but the fact that this is the third (or more) time I have been on proteinA. I understand each WU has multiple frames, and frames are the 1-100 (or whatever) that get counted toward a WU progress.

Forge's explanation makes sense, but I think he should use the word 'run' (as in: each protein has multiple runs.) Look in your logfile at the start of a WU to see what I mean.
MadManOriginal
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Postposted on Wed Jun 05, 2002 9:09 am

From the Folding @ Home FAQ:

I just finished a WU and now I got another for the same protein. Is there something wrong?

No, most likely everything is fine. We're studying the dynamics of a few proteins, so you're likely to get the same protein to work on multiple times. Each WU gives us additional information about the dynamics of that protein, so it is important to us. Indeed, if we did only 1 WU per protein, we would not learn very much.

So in other words, it's supposed to do that. Just checked my stats and I've done 125 WU's of Protien A myself... ;)
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Postposted on Wed Jun 05, 2002 5:21 pm

If I remember right, each WU computes a 5ns section fo the protein folding... so you will get the same protein many many times...

I too have been wondering the same thing as I look at my standings on F@H :-(,
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