Hello All,

Just fired up Rosetta, have been crunching away at PP@H for quite a while now but since they are on hiatus (And ignore their users) I have moved here :)

Can someone please give me a lamens overview of the "Lowest energy"?

Does this mean the least amount of energy used to fold into a stable protein?

What is RMSD?

Perhaps a general explanation of the graphics would be lovely.

Are there any optimised applications?

Thanks for having me, and I hope my 4 PCs can make a healthy contribution :)

Scott

Edit: And if I should have posted this elsewhere, please let me know.

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Some of these topics are covered in the FAQ:
https://boinc.bakerlab.org/rosetta/forum_thread.php?id=669

For lowest energy, take a look at these charts:
https://boinc.bakerlab.org/rosetta/rah_top_predictions.php
You'll notice that the energy is highly negative. It's kind of like moving around on the couch until you find the comfortable spot that you've worn into the couch by sitting in it for years. And it requiring a fair amount of energy to get you out of that position. (i.e. watching the drink, snack, and remote control spontaneously migrate to the other side of the room).

What is RMSD?
Root Mean Squared Deviation. A measure of how close two things are. Identical = an RMSD of 0. For protein measurements, it's listed in Angstroms. Smaller proteins (42 amino acids long) are fairly easy to get a RMSD of 1.5A; while large proteins (196 amino acids long, for example) require at least 10 times the processing power to start to approach a RMSD that low.

Perhaps a general explanation of the graphics would be lovely.
I'll let someone that's actually seen the graphics explain what's being shown.

Are there any optimised applications?
Not at present.. although there was discussions with at least one of the major application optimizers on whether they would be interested in optimizing the Rosetta app(s).

Anyway... welcome aboard. :)

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G'day Scottatron welcome to Rosetta@Home.

Can someone please give me a lamens overview of the "Lowest energy"?

I'll do my best:

Lowest energy lamens overview: anything that is stable ie. dosn't wan't to change in it's natural environment will have the lowest energy for that environment, you could of course heat it up, cool it down, add other chemicals etc... that would mean that it has to change and no longer has the lowest energy, but within it's natural environment it will have the lowest energy possible, if it didn't (have the lowest energy) it will go (change) to the lowest energy in it environment.

Does this mean the least amount of energy used to fold into a stable protein?

Not as I think you mean it, but probably true anyway.

What is RMSD?

Root Mean Square Deviation, is way of judging a known structure to a predicted structure

Perhaps a general explanation of the graphics would be lovely.

here

Are there any optimised applications?

No.

You may notice that Rosetta@Home is going through it's growing pains (credits) it happens to all BOINC projects but please disreguard, the project staff are usually very willing to talk to everybody, it's just that they are trying to stamp out fires and no doubt scratching their heads as they are first time BOINC'ers :)

Edit: BennyRop beat me to it :) and I changed a couple of words for clarity and added a couple of n's cause I can't spell

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Nothing else to add other than
Welcome to Rosetta :-)

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Team mauisun.org

Thanks all, there is so much more scientific info to digest here compared with Predictor!

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G'day Hugo

Apologies to all for butting in on this thread. I notice you run win98 on one of your boxes.

One of our teams newer members asked if there were any pitfalls to this or any issues to watch out for, as win98 wasn't a supported os.

Is there anything I should warn him of?

Cheers, and once again sorry for butting in on this thread.

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I don't recall seeing notice that it was ever fixed, but Rosetta had a problem under Win98 and WinME where you got credit for the first WU you finish and upload, and after that, it requests 0 credits for every WU beyond the first.

Perhaps changing settings to 24 hours, and closing down Rosetta once a day will get around the problem until the new credit system is put into place.. (where you get credit for the decoys you've turned in..)

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I don't recall seeing notice that it was ever fixed, but Rosetta had a problem under Win98 and WinME where you got credit for the first WU you finish and upload, and after that, it requests 0 credits for every WU beyond the first.

Perhaps changing settings to 24 hours, and closing down Rosetta once a day will get around the problem until the new credit system is put into place.. (where you get credit for the decoys you've turned in..)

The new work unit credit should be fine though, since the server assigns it regardless of the claimed credit.

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G'day Trog Dog

I did have a problem with credits a while back. I think R@H put some fix in place for this, so they (98 machines) may have to wait a little longer to be granted credits, but I don't do anything differently with it compared to my XP machine.

Just sign up as usual, let it go. No reboots or anything, just let it chug away.

Just to stay off topic, when is the next Aussie Assault happening at R@H :)

Edit: I don't think that BOINC can be installed as a service on 98 machines, but that's about it for down falls with BOINC and R@H as far as I can tell.

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G'day Trog Dog

I did have a problem with credits a while back. I think R@H put some fix in place for this, so they (98 machines) may have to wait a little longer to be granted credits, but I don't do anything differently with it compared to my XP machine.

Just sign up as usual, let it go. No reboots or anything, just let it chug away.

Just to stay off topic, when is the next Aussie Assault happening at R@H :)

Edit: I don't think that BOINC can be installed as a service on 98 machines, but that's about it for down falls with BOINC and R@H as far as I can tell.

Cheers Hugo

I've passed back your advice.

We've got an Assault planned for the first of next month, but the target isn't decided yet - if I can get some good solid stats on the new credit system I will nominate it as a target.

Personally, I joined Rosetta & Predictor on the same day with the same resource share. After a while I realised that I was just spinning my wheels at Rosetta, Predictor was just more reliable and stable, so for a while I dropped Rosetta's share to next to nothing. Now that Rosetta has sorted things out as far as reliability goes I've upped the resource share again, having said that though the existing/old credit system just didn't cut it.

I'm hoping the new one fixes that problem.

As far as the Aussie Aussalt's go it's good that they are getting some attention, I know it really boosts the team spirit/camaraderie side of things and the projects benefit too. So far we've targeted Malaria Control and Tanpaku. There's even been talks about mounting joint Assaults with other teams.

Once again, thanks for your help - and maybe we might see you on an Assault down the track :)

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Scottatron,

You may also enjoy Dr. Baker's Rosetta journal. I found it to be inspiring because of how open he his to new ideas and different ways of doing things.

https://boinc.bakerlab.org/rosetta/forum_thread.php?id=1177