My thoughts exactly, I was looking into how to organise the Q. in that format, it's too big and too repeditive.

Hugo, if you need a way to set up the FAQ in sections, contact me via the email link on my team website. I may be able to set something up for it, which can later be exported to a html page for the Rosetta site.

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*** Join BOINC@Australia today ***

Hugo, if you need a way to set up the FAQ in sections, contact me via the email link on my team website. I may be able to set something up for it, which can later be exported to a html page for the Rosetta site.

I would like to, but I've had some bad news about a family member, so I'm probibly going to be away for a while, so this will be my last revision for the forseeable future. I'll also have posted the file here it dosn't like Mozilla.

The best of luck, to Rosetta@Home and it's crunchers.

Catch ya all later Hugo,
I'll still crunch :)

Q. What is the URL of Rosetta@Home?
A. https://boinc.bakerlab.org/rosetta

Q. Is Rosetta@Home non-profit? / Is someone going to make money out of my donated computer time?
A. The Univerity of Washinton makes available the source code (the actual Rosetta algothim, which our donated computer power is helping improve) available to academics and other universities for free, and will eventually make the source code available to the puplic, when the possible cheating problem on BOINC is addressed. Dr David Baker "Everything will be public domain ... No, I do not believe in patenting naturally ocurring genes, proteins, etc."

All of these questions are addressed by the answer below, the * means if Rosetta@Home is being left in memory additional steps are listed.
Q. How do I set Rosetta@Home to stay in memory?
Q. Why am I getting an error every time BOINC switches tasks?
Q. Why am I getting a 'Reason: Access Violation (0xc0000005) error'? *
Q. Why is my computer stuck on 1% ? *
Q. Why am I getting an error every time BOINC runs a benchmark? *

A. To change your preferences to leave Rosetta@Home in memory, General Preferences Log in (if your not already) -> Edit Preferences (down the bottom) -> Leave applications in memory while preempted? Check yes and click the update preferences button, also remember to update BOINC. BOINC Manager and select "Projects"(tab) , select "Rosetta@home", and click "Update"

Q. Why am I getting an error every time BOINC runs a benchmark?*
A. Update your BOINC version to 5.2.13 or higher as it no longer removes applications from memory when doing a benchmark.

Q. Why is my computer stuck on 1% ? *
A. This is another known BOINC and Rosetta@Home issue, there are a couple of things you can do about it, they should be done in the order here:
1. suspend the Work Unit, BOINC Manager -> Work (tab) -> click on the Work Unit click the Suspend button (on the left hand side) then Resume button, wait for the computer to re-start the Work Unit (it will need to finish the new Work Unit it started, if it had another available) and see if it's still stuck, give it about 20min.
2. Shutdown BOINC, restart BOINC see if the Work Unit is still stuck, give it about 20min.
3. Reboot your computer. See if the Work Unit is still stuck, give it about 20min.
4. Abort the Work Unit, BOINC Manager -> Work (tab) -> click on the Work Unit that's stuck click the Abort button (on the left hand side).

Q. Why am I getting a 'Reason: Access Violation (0xc0000005) error'? *
A. An error occurred somewhere on the computer, it could have been BOINC or Rosetta@Home or any programme that your computer was doing at the time. This is not a Rosetta@Home specific error, as far as I am aware it happens, on occasion, in all of the BOINC applications. Keep Rosetta@Home in memory and ignore this problem if it's not getting out of hand.

Q. What is the difference between Rosetta@Home and Folding@Home / Predictor@home ?
A. Dr David Baker "The Rosetta@home project goals are very different from those of Folding@home. The goal of Folding@home, I believe, is to determine how long proteins take to fold, given the sequence of the protein and knowledge of its three dimensional structure. The goal of Rosetta@home is to predict the three dimensional structure from the amino acid sequence." Dr David Kim "Our project is similar to Predictor@home, in that we are trying to improve our methods by conducting research that is only possible with the computing power that a grid computing project can provide."

Q. Can I move work from one computer to another?
A. Yes. If you copy the ENTIRE Boinc folder to a thumb drive, take that to a different system, plug it in and run, it will continue to work. The only downside to doing this is that your "view computers" display may get a little confused if you upload a WU from the new system. This can be prevented by running BOINC Manager from the thumbdrive initially after the copy, and setting network access to never available.

Q. Master file fetch failed?
A1. This means the Rosetta@Home 's server is down. Give it a few hours and then try again.
A2. Your internet connectivity may not be working properly, try to brows the Rosetta@Home web site, have a look at the Server statis{--- staris or statistics need to check ---}, the link is on the Rosetta@Home home page. To fix your internet connectivity (generally shut down everything including your router (if you have one), modem, DHCP server (if you have one) etc... start every thing up in the correct order and and try again).

Q Exited with zero status but no 'finished' file.
A. This is a BOINC problem, it's harmless, just ignore it.

Q. Which ports does Rosetta@Home need open?
A. Port 80 (http) is used for most communications with the project servers. Port 443 (https) is used if the password is being exchanged . Ports 1043 and 31416 are used for local control as well as for remote control of a BOINC client. 1043 is preferred and 31416 is a fall back. Unless you are RPC'ing over the Internet don't open 1043 and 31416 in your non-local firewall specifically for BOINC.

Q. Should I use Hyper Threading?
A. Yes, it gets you a small gain over not using it. If you are very low on memory and don't want to use more than x CPUs then Log in (if your not already) -> Edit Preferences (down the bottom) -> On multiprocessors, use at most N CPUs.

Q. Why can't I get new Work Units from Rosetta@Home ?
A. If your computer is doing more than one science application (Seti@Home and Rosetta@Home for example) BOINC decides how much work you can have so that that the Work Unit deadlines are not reached. Either allow BOINC to do this or if you are more interested in one of the science applications you can change the resource share [url=https://boinc.bakerlab.org/rosetta/prefs.php?subset=project]Rosetta@Home preferences ->Edit Rosetta@Home preferences and change the resource share. Alternatively you can suspend the other application(s), BOINC Manager -> Projects (tab) click on the application you would like to suspend and either click on the Suspend button or the No New Work button (to allow BOINC to finish the Work Units it has on hand but not to get new ones), on the left hand side.

Q. I don't receive an E-mail? / My ISP is blocking my E-mail from Rosetta@Home?
A. This is usually caused by your ISP blocking the E-mail as spam, Even though you can join up without it I would suggest that you get a free E-mail account and use that, remembering that if you don't log on to these free E-mail accounts every so often then some of them will delete your account. I also as a general suggestion that I give to everybody (no inference that Rosetta@home could or would contribute to this should be taken) that you never use you ISP E-mail account for anything else than talking to your ISP as it's not funny being spammed on an account that you actually need.

Q. Why is it reported that I have more computers than I actually do? / How do I merge my computers?
A. When you detach and then re-attach to the same project, BOINC assumes that it's a different computer, You can merge these computers so they are one again, Your computers click on the computer you would like merge click Merge this computer (down the bottom of the page).

Q. Why do I have ghost Work Units? / Why do I have Work Units assigned to me that I don't have?
A This seems to be caused by BOINC and the Rosetta@Home server losing the ability to communicate properly, and it can safely be ignored.

Q. Is Rosetta@Home concentrating on a particular disease?
A. Dr David Baker "My research group is involved both in fundamental methods development research and in trying to fight disease more directly...

Malaria: We are part of a collaborative project headed by Austin Burt at Imperial College in London that is one of the Gates Foundation "Grand Challenge Projects in Global Health". Malaria is caused by a parasite that spends part of its life cycle inside the mosquito, and is passed along to humans by mosquito bites. The idea behind the project is to make mosquitos resistant to the parasite by eliminating genes required in the mosquito for the parasite to live. Our part of the project is to use our computer based design methods (rosetta) to engineer new enzymes that will specifically target and inactivate these genes.

Anthrax: We are helping a research group at Harvard build models of anthrax toxin that should contribute to the development of treatments. You can read the abstract of a paper describing some of this work at
http://www.pnas.org/cgi/content/abstract/102/45/16409

HIV: One of the reasons that HIV is such a deadly virus is that it has evolved to trick the immune system. We are collaborating with researchers in Seattle and at the NIH to try to develop a vaccine for HIV. Our role in this project is central--we are using rosetta to design small proteins that display the small number of critical regions of the HIV coat protein in a way that the immune system can easily recognize and generate antibodies to. Our goal is to create small stable protein vaccines that can be made very cheaply and shipped all over the world "

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I have un-stickied this thread and created a new one with just the latest revision. This one was getting a bit long for new users to wade through.

GREAT progress on this!

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