I always do a nice suspend and wait until it clears from memory

dag was talking about suspending the projects in the BOINC manager I presume. You might want to try using the hybernate shutdown on your portable. This basically pushes everything in memory out to disk, leaves the programs active and when you power up again, everything is where you left off. Not sure how that would work for BOINC. But it sure works great for word processors, browsers etc.

---

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/

I always do a nice suspend and wait until it clears from memory

...
You might want to try using the hybernate shutdown on your portable.
...

Putting it in standby mode may work for a Linux system, but we're talking about Windoz here. I depend on the daily reboot to clear the accumulated cruft. Also, it doesn't seem to do well with going to sleep on a docking station with wired LAN and waking up all alone with wireless LAN, different keyboard, mouse, etc., and vise-versa. (XP Pro w/SP2+)

dag

---

dag
--Finding aliens is cool, but understanding the structure of proteins is useful.

Would it be possible to run sample batches of new WUs through Ralph, and to post a notice here that a test run on Ralph is happening - i.e. it's own moderator-only thread (so those that shut off Ralph when they see no work can turn it back on?)

But these failures bring up a science related question or two. When looking at last month's WUs that ended up failing in less than a minute on 2Ghz machines, almost all of the ones reported failed 3 times and were discarded. At least one of them got picked up after two Windows client failures and finished fine on a Linux client. Was this because mostly because the Win clients so far outnumber the Linux clients, or more of the fact that the Linux clients were actually producing results for 2+ hours, while the Win clients were failing almost instantly and grabbing more WUs to fail?

What's different with the clients that allows Mac and Linux clients to handle these WUs that almost instantly fail on Windows clients?

What's different with the WUs themselves? I assume that biology doesn't allow amino acid/protein chains #87 and #88 in a 109 AA protein chain to be encrypted with "Bill Gates Suxx0rs" :) It'd be funny if it could be proven, but not likely. *grin* Are these larger or smaller than the WUs we've been working on - or have some unique visual feature? i.e. it looks like two plates held together in the middle with a few atoms that look like a rod - a yo-yo. (Yes, I know that's probably not even possible.)

You've mentioned that for some WUs that we've turned in 10,000 models for, that we haven't come close to the native structure. (You mentioned approaches that will allow us to go through the process twice.. and hopefully get close to those structures without having to run through 100,000 models/decoys or more..) I see at C562_EColi (the last result on the home page) that it lists the size as 106 AA; which is how we got used to having protein's size described at DF. At what size does the Rosetta client fail to get close enough to the native structure with 10,000 models/decoys? Or is it just that the longer the protein chain is, the more likely it has complex structures?

---

I read a post over in setiathome about Rosetta being mentioned in the newsletter of 'Livescience'. Good job, guys.

---

Founder of BOINC GROUP - Objectivists - Philosophically minded rational data crunchers.

Mostly to David Baker, but if you're looking in, the last couple of posts you've made in your journal cover 95% of the reason I'm here. There's somthing I really like about being in right at startup, and knowing that the crunching I'm doing is helping to actually fine tune the tools that someday might find a cure for HIV, or Malaria.

Keeping that in mind, in your last note you talk about sidechain sampling. Is it possible to explain in layman's terms what this is? So far, you've been able to do a great job of explaining the search methodologies, talking about explorerers on a planet, or explaining how the HIV search will go: trying to design a custom protein that will allow our immune system to generate antibodies effective against the "static" portions of the virus. Etc.

Any chance of an explanation of that sort for sidechains? Enquiring minds want to know. :)

---

Mostly to David Baker, but if you're looking in, the last couple of posts you've made in your journal cover 95% of the reason I'm here. There's somthing I really like about being in right at startup, and knowing that the crunching I'm doing is helping to actually fine tune the tools that someday might find a cure for HIV, or Malaria.

Keeping that in mind, in your last note you talk about sidechain sampling. Is it possible to explain in layman's terms what this is? So far, you've been able to do a great job of explaining the search methodologies, talking about explorerers on a planet, or explaining how the HIV search will go: trying to design a custom protein that will allow our immune system to generate antibodies effective against the "static" portions of the virus. Etc.

Any chance of an explanation of that sort for sidechains? Enquiring minds want to know. :)

Sure (and thanks for the words of encouragement!). sorry about the jargon. proteins are chains of amino acids. there are 20 types of amino acids. they have a common backbone, but differ in the "sidechains". when they are spliced together, the resulting protein has a linear "backbone" with "sidechains" coming off, one for each amino acid. these sidechains can adopt a number of different possible conformations (shapes). the improvement is to try out many different possibiities for each of these shapes at each step in our sampling processs. as I said in the journal, this helps the search, but before we can deploy this on rosetta@home we need to track down and fix the windows specific problem.

---

Good news today:

second, David Kim has awarded credits to those who lost valuable time during the problems last weekend.

Suppose it will be handled just as fast as those credits for time exceeding WU's and in that case : just don't bother as I will not bother to report them anymore.
Already written those off.
Counting the days "17".

---

I'm curious to see the source code.
When I read in the e-mails the names of the functions [get_the_hell_out()]
I guess the complete source code must be an equivalent :p

---

Member of Dutch Power Cows

Could the watchdog message be revised?
Rather than:
Rosetta score stayed the same too long. Watchdog is killing the run!

How about:
Rosetta score stayed the same too long. Watchdog is ending the run!

or, keeping inline with the programmer humor going here, perhaps:
Watchdog is barking. Postman ending delivery.

---

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/

How embarrassing... both the watchdog "killing" and get_the_hell_out() are my silly recent contributions. Its not representative of the rest of the code -- I didn't expect these error messages and functions to get broadcast to such a wide audience! I assure you that the rest of the code is totally dry and scientific. We'll change "killing" to "ending" in the release after the next (I read the message too late).

Could the watchdog message be revised?
Rather than:
Rosetta score stayed the same too long. Watchdog is killing the run!

How about:
Rosetta score stayed the same too long. Watchdog is ending the run!

or, keeping inline with the programmer humor going here, perhaps:
Watchdog is barking. Postman ending delivery.

---

I had a friend that worked in tech support at Microsoft - who had a noose dangling from the ceiling and inside the noose was a picture frame. It was in reference to "My windows is hung."

Now I can picture Rhiu's workspace with a 12 inch blade dangling from the ceiling and stained in catchup.. :)

In reference to "terminating a process with extreme prejudice".. *grin*

Here's hoping the code helps eliminate most of the remaining bugs that are frustrating the users.. so we can run through CASP with as few problems as possible.

---

Why embarrassing? I like the name of the function ;)

---

Member of Dutch Power Cows

Just a comment to Davids last entry. I would strongly suggest to delay the release of the new app till Monday and use the Weekend for thorough testing. Failing WUs are a real burden for the project since they are sent out again for several weeks. We all hope that this won't happen with the new watchdog but you never know.

---

I agree with tralala!
If there happens anything now, the project will lose more power than with 2 days delay of a new version...

---

Member of Dutch Power Cows

Imho, a weekend release is OK if the project team has a strong feeling of confidence in the new release, and importantly, if someone on the Project Team can commit to monitoring the release very carefully over the entire weekend.

In this way if problems do arise, someone on the Team can jump in immediately and make fixes before things snowball and turn into big problems.

Thanks!

---

Regards,
Bob P.

And he's glad to see to number of pc's rising, i think it will drop a bit at the end of the Stampede

---

If you know the amino acid sequances, and you know the structures of mutiple proteins then why don't you combine the two?

Like this: amino acid n is usually folded x fasion.

If you see my point, you could make a database of all the known structures for that sequence, then weight the probability of an amio acid structure, so as to have a most probable to least probable structure for each of the amino acids sequances, test each to find the energy levels for the overall protein that you are trying to predict.

Of course this wouldn't find a structure that to date is unknown but it maybe a shortcut for the others.

You may do something like this already. It was just a thought that struck me so I thought I'd bounce it off the R@H team.

Edit: clarity

---

I believe this is what they try to do. . but consider the following. . if you have a 20 aa (amino acid) sequence. . you might know how the first and second interact by themselves. . but what happens when 6 and 7 in the chain loop around and interact with the start? Now, an assumption you made at the beggining (they fold like x) is not true since something external is acting opon them.

I think you're right in that it's worth having a database of these types of things. . and I seem to remember the lab folks mentioning that is what took up some of our disk space. . . but:

I could be wrong :)

-E

---

Great thoughts! You are definitely on the right track of a general protocol for structure prediction. The approach you described - the comparative modeling approach - is actually being routinely used by biologists nowadays.

One aspect of the Rosetta@Home project is to develope methods to improve the template-based structure models. Some of the work units you are currently running are doing extractly this type of work! You can read a little more about these work units here.

If you know the amino acid sequances, and you know the structures of mutiple proteins then why don't you combine the two?

Like this: amino acid n is usually folded x fasion.

If you see my point, you could make a database of all the known structures for that sequence, then weight the probability of an amio acid structure, so as to have a most probable to least probable structure for each of the amino acids sequances, test each to find the energy levels for the overall protein that you are trying to predict.

Of course this wouldn't find a structure that to date is unknown but it maybe a shortcut for the others.

You may do something like this already. It was just a thought that struck me so I thought I'd bounce it off the R@H team.

Edit: clarity

---

Thanks for the info Dr(?) Bin Qian I hadn't even thought of using the families of the protein, because I didn't know they existed :), very clever I must say.

That begs the question: Is it possible to group all of the unknown proteins into families?

I had a look on wikipedia X-Ray Crystallography (under Biological structures) and found that ~100 proteins have been solved by electron microscope, so is it possible to get another Rosetta shortcut by getting a rough estimate of what the protein shape or family is this way or perhaps a even early data from x-ray crystallography, or it's chemical reactions etc... ?

As I understand it, any type of reduction in the search space is a very good thing.

That's enough for me, I'm using your time that is better spent elsewhere.

Edit to make more sense

---