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World Community Grid Forums
Category: Retired Forums
Forum: Member-to-Member Support [Read Only]
Thread: 0% completed but molecule displays |
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Thread Status: Active Total posts in this thread: 4
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Took a peek at the agent and after almost 2 hrs elapsed time it says: 0% progress completed, but the molecule displays and rotates. The i icon shows 0.0% completed. According the the Known Issues Thread:
http://www.worldcommunitygrid.org/forums/wcg/viewthread?thread=1984 "If the progress shows 0%, and the agent has been actively running for at least 10 minutes, and if you leave and reenter the graphics screen and it does NOT show a molecule within about 2 minutes, then you have one of the two problem gene sequences which cause this problem in Rosetta. Otherwise, your agent is working normally and you should disregard this." Since the graphics screen does show a rotating molecule, do I conclude that the agent is working normally and let it continue to run? I feel foolsih leaving the agent running when it claims that 0% progress has been made.  Thanks. |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
julied,
No need to feel foolish. It sounds as though you have a non-convergent work unit. Not all attempts to fold a protein succeed. Sometimes Rosetta will try to fold a protein for several hours, then give up and return that information to the server. Then it will get a new Work Unit. If a whole day goes by with 0.0% progress, then you have a problem, but the first thing to assume is that you will just spend a few hours trying to fold the protein, then return a code telling the server that the protein will not fold using that seed number. Lawrence |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Sometimes Rosetta will try to fold a protein for several hours, then give up and return that information to the server. That's exactly what happened, Lawrence. Oddly, it alloted both points and a return. Nice, but iffy.  Thanks for getting back to me yet ANOTHER time.  |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
julied,
Of course you were awarded points. What we are doing is using a parameter range with about 10,00 values and attemting to fold a protein using a particular value. We return a description of the protein folded using each value. But if the protein will not fold for the range of values in a Work Unit, that is valuable information too. There is a post-processing step that looks at all 10,000 returned structures created by Rosetta for a protein and decides whether or not a fold prediction can be made for that protein within a given confidence interval. Reading Dr. Bonneau's posts, apparently we get a fold prediction within a 90% confidence interval for about half the proteins we are investigating. A Work Unit usually has a range of 50 - 500 seed values to try, so we do not run 10,000 Work Units per protein. Keep on crunching! Lawrence |
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