1)
Message boards :
Number crunching :
Minirosetta 2.00
(Message 64232)
Posted 26 Nov 2009 by darkpella Post: I'm also seeing a considerable number of WUs with errors similar to those posted by others recently. Similar here with the following WUs: 299885240 299643164 299547442 298811740 stderr is slightly different though. stderr from my WUs is like: <core_client_version>6.6.38</core_client_version> while the one from some of bruce's WUs is like: <core_client_version>6.10.18</core_client_version> |
2)
Message boards :
Number crunching :
Problems with web site
(Message 49208)
Posted 29 Nov 2007 by darkpella Post: Hi, guess this doesn't belong right here but, as you will see, I got no chance to post it where it belongs.. In the last couple of days RALPH is totally unreachable: can't report WU that were already uploaded, cant upload newly finished WUs, cant' fetch scheduler list, can't access website itself... Any idea about what's going on and how long this will last? Bye darkpella |
3)
Message boards :
Rosetta@home Science :
Help me explain the science behind Rosetta@home!
(Message 45543)
Posted 28 Aug 2007 by darkpella Post: Hi, I do have two points I could not really understand in the explanation I found here about what rosetta basically does. In this page, if I understood it right, it is told that, starting from one point in the trajectory (current "accepted" configuration) Rosetta will try to move a bit some part of the amino-acid chain in a random manner and then decide whether this new configuration can become the new "accepted" one based on the energy of this "trial" configuration. If so, the "trial" becomes the new "accepted" configuation and the process starts again modifying this new "accepted" configuration", otherwise the old "accepted" configuration is modified again in a different way to get a new "trial" one, the energy of which is then calculated to see whether this new "trial" can be taken as the new "accepted" and so on. The subsequent "accepted" configurations form a trajecory. Rosetta keeps track of what the lowest energy "accepted" configuration found along the trajecory is, then, when the trajecory calculation end, takes this lowest energy configuration as the best prediction for that trajectory. 5 to 20 trajectories are calculated for each WU and lowest energy configuration found among them all is returned as the best prediction for that particular WU. Now the points I don't get are:
|
4)
Message boards :
Rosetta@home Science :
CASP7 T0363 top predictions posted
(Message 28491)
Posted 25 Sep 2006 by darkpella Post: From the front page. Hi, I noticed that the comparison in this picture is made among 3 different structures: 1. Native (green) structure, as published by CASP I guess, letting no questions arise about whre it comes from and why it takes part to this comparison. 2. Lowest energy (blue) R@H prediction, hence R@H best guess for the protein structure, also letting no basic questions arise. 3. A template (red) structure, the origin of which is not very clear to me... could someone tell me where this structure comes froma, and what should it add to the comparison between the native (or, better, CASP-published) structure and the R@H best guess one? Thanks darkpella |
5)
Message boards :
Rosetta@home Science :
Lowest energy structure and distance to true structure
(Message 27572)
Posted 19 Sep 2006 by darkpella Post: Hi darkpella, Guess the optimization is done against the 6 DOF of a rigid body in the 3D space, ain't it?
My aerodynamics teacher at college always told that, when experiments don't agree with predictions, it might be that predictions are wrong or that experiments are wrong (or both). Guess that's the case...
I'll let my PC go on crunching for R@H then (and for Predictor@Home either, as soon as they get back with their new prediction scheme) Thanks for the explanation! Bye darkpella |
6)
Message boards :
Rosetta@home Science :
Lowest energy structure and distance to true structure
(Message 27555)
Posted 19 Sep 2006 by darkpella Post: Hi, I had a look at the top prediction page (http://boinc.bakerlab.org/rosetta/rah_top_predictions.php) and a pair of questions arose: 1. How is distance of a predicted structure to the true structure calculated (i.e. what does RMSD stand for)? 2. I noticed that the lowet energy structure and the lowets distance to true structure one are never the same . Does this mean that natural protein folding does not pursue lowest energy? What pursues R@H then? How can one possibly choose which prediction is the most accurate one among the many ones that come in, if the lowest energy criterion is not the right one? bye you all! darkpella |
7)
Message boards :
Number crunching :
Question on results of latest CASP
(Message 27549)
Posted 19 Sep 2006 by darkpella Post: Hi, Two shots, two kills, very good. Thanks a lot for your prompt reply! darkpella |
8)
Message boards :
Number crunching :
Question on results of latest CASP
(Message 27544)
Posted 19 Sep 2006 by darkpella Post: Hi, does anyone know wether and where the results of the latest CASP can be found to see how R@H performed? I read a messaage through RSS on R@H newsboard stating that the native protein structers of latest CASP proteins were eginning to be released, but didn't hear anything more about it therefater. Bye you all darkpella |
9)
Message boards :
Cafe Rosetta :
Dr. Baker's plea...
(Message 21203)
Posted 26 Jul 2006 by darkpella Post: Hi Dr. Baker, on July 15 you asked the crunching community to increase the CPU % devoted to R@H for a couple of weeks, since a lot of CASPs were due in a short time. Since the 2 weeks are coming to an end, I would like to know whether R@H will (likely) meet the delivery deadline for those CASPs. By the way, could you notice any increase in resources devoted to R@H? Apart from them, a small poll: - Did you (crucnchers) read DB's request? (I did ;) - Did you actually increase R@H resource share? to what extent? (I prevented all other BOINC-projects from getting new tasks). That's all folks! darkpella |
10)
Message boards :
Number crunching :
David, how's it going with the CASP due?
(Message 21202)
Posted 26 Jul 2006 by darkpella Post: Hi David, on July 15 you asked the crunching community to increase the CPU % devoted to R@H for a couple of weeks, since a lot of CASPs were due in a short time. Since the 2 weeks are coming to an end, I would like to know whether R@H will (likely) meet the delivery deadline for those CASPs. By the way, could you notice any increase in resources devoted to R@H? Apart from them, a small poll: - Did you (crucnchers) read DB's request? (I did ;) - Did you actually increase R@H resource share? to what extent? (I prevented all other BOINC-projects from getting new tasks). That's all folks! darkpella |
11)
Questions and Answers :
Windows :
Not getting any further workunit
(Message 12607)
Posted 24 Mar 2006 by darkpella Post: Hello, Since some days I'm not getting any further workunit from any boinc project. I got Boinc 5.2.13 on Win2k Pro and subscribed the following projects: BBC Climate Change Experiment rosetta@home boincsimap climateprediction.net Einstein @home LHC@home QMC@home SETI@home SZTAKI Desktop Grid I try updating these projects and/or rebooting, scheduler requests (when I update) succeed, but no new workunit is downloaded. The only project running now is climateprediction.net, since it doesn't often require new workunits to work on. Any idea about what the problem is? Thanks darkpella |
©2025 University of Washington
https://www.bakerlab.org