Posts by StephenYavorsky

1) Message boards : Number crunching : Problems with Rosetta version 5.46 (Message 36808) Posted 15 Feb 2007 by StephenYavorsky Post: Please report here for problems you have observed with Rosetta version 5.46. "Waiting for memory" I have never seen this message previously, but two Rosetta units, the final one in the queue from 5.45 and the first from 5.46, have both just now stopped, with the message "waiting for memory." This has not happened before. There are two new setting in your "General Preferences". They are "use at most X percent ram while active", and "use at most X percent of ram when not active". By default they are set to 50 and 90 respectively. Try increasing them. tony Thanks, Tony, I've found the settings and I'm sure it will help.
2) Message boards : Number crunching : Problems with Rosetta version 5.46 (Message 36800) Posted 14 Feb 2007 by StephenYavorsky Post: Please report here for problems you have observed with Rosetta version 5.46. "Waiting for memory" I have never seen this message previously, but two Rosetta units, the final one in the queue from 5.45 and the first from 5.46, have both just now stopped, with the message "waiting for memory." This has not happened before.
3) Message boards : Number crunching : Report Rosetta screensaver problems here (Message 36273) Posted 8 Feb 2007 by StephenYavorsky Post: Stephen, this has been a quirk for some time. I've had similar oddities. I've even seen where I click the upper (lowest energy) small window and the lower (native) is the one that spins around. I have the same, improved results with a maximized screen. I had mentioned it briefly a few months ago. I guess I didn't press the issue because there were more important issues with the screen saver that were impacting users. But, yes, this needs to be investigated. Your computers are hidden. Am I correct to assume you are running Windows Stephen? My observations are from Win/XP Yes, I am using Windows XP.
4) Message boards : Number crunching : Report Rosetta screensaver problems here (Message 36246) Posted 7 Feb 2007 by StephenYavorsky Post: I do not use Rosetta as a "screensaver" so this is not a screensaver problem, but it is a graphics quirk. (I posted this previously in what may have been an incorrect spot.) With Rosetta 5.45 and the BOINC manager 5.8.8, I've noticed that if I want to move a protein around I can click either on the (a)"Searching_all_atoms" panel or the (b)"Accepted" panel and I can manipulate the protein orientation. BUT the moment I click on the smaller (c)"Low Energy" or (d)"Native" panels, I can no longer manipulate the first two (nor the latter two). Oddly, I can still manipulate the (b)"Accepted" panel by clicking on the far left of the (a)"Searching_all_atoms" panel, but can not manipulate the "Searching, etc.." panel at all. However, if I maximize the Rosetta window, then I can manipulate (b), (c), and (d) but not (a). So, there seems to be a quirk there to be noted.
5) Message boards : Number crunching : Odd graphics quirk, possibly (Message 36230) Posted 7 Feb 2007 by StephenYavorsky Post: With Rosetta 5.45 and the BOINC manager 5.8.8, I've noticed that if I want to move a protein around I can click either on the (A)"Searching_all_atoms" panel or the (B)"Accepted" panel and I can manipulate the protein orientation. BUT the moment I click on the smaller (C)"Low Energy" or (D)"Native" panels, I can no longer manipulate the first two (nor the latter two). Oddly, I can still manipulate the "Accepted" panel by clicking on the far left of the "Searching_all_atoms" panel, but can not manipulate the "Searching, etc.." panel at all. However, if I maximize the Rosetta window, then I can manipulate (B), (C), and (D) but not (A). So, there seems to be a quirk there to be noted.
6) Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (2) (Message 30484) Posted 2 Nov 2006 by StephenYavorsky Post: Regarding the upcoming interactive mode: How does the protein "sense" its own energy level, if it indeed does so? Could the interactive mode provide "feedback" about what the energy level is at each point of the manipulation so that the neophyte protein-artist could have an immediate sense of the usefulness of a particular move, in seeking the lowest level?
7) Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (2) (Message 29413) Posted 15 Oct 2006 by StephenYavorsky Post: Just read your mention about a possible interactive mode in which participants could try for themselves to find the best way to fold the protein with all its knotty branches. This caused me to remember hearing that some artists have to make chandeliers by interlocking antlers together, and that it is a difficult task, a test of their ability. Would some such people, (or others who work with interlocking puzzles), be worth tapping into for efforts in your new upcoming interactive mode?
8) Message boards : Number crunching : Report stuck & aborted WU here please - II (Message 13644) Posted 13 Apr 2006 by StephenYavorsky Post: This thread is for reporting Workunits that have hung (1% error), or that have been manually aborted for some reason. Please include the type of error in your report, and a link to the RESULT in your stats page. This thread replaces part one which is located here. Application: Rosetta 4.98 Project: TRUNCATE_TERMINI_FULLRELAX_1ptq__433_36_0 Stuck at 1.04% after 10h36m28s
9) Message boards : Number crunching : Meaning of little red squares in bottom-right of graphic? (Message 13187) Posted 7 Apr 2006 by StephenYavorsky Post: Before asking this question I searched as well as I could in the explanatory pages, as well as discussion threads. In the bottom-right segment of the Rosetta graphic, which shows the combined "Accepted Energy" plus "RMSD", occasionally there are small red squares. What do they indicate?