Here is another suggestion. Since we are working on known protein why not rotate the current best energy to where it would have the least distance between points of the two proteins.

Yes, this is a great idea. We've been discussing it ourselves. I think we will implement it by rotating the native so that it is optimally aligned to the current lowest energy. And then allow the user to rotate all in tandem. I'm looking into this right now.

i agree, plz do not start to move the whole thing around like seti, i just hate that too. make it an option if you ever do it if possible.

I also lean against having the whole display rotate. If somebody is extremely worried about monitor burn-in, they probably should just turn off the graphics.

Also, the seti logo does not rotate with the rest of the display, so I don't think their graphics are completely burn-in proof.

- dislay the name of the protein (and not just something like 1acf - is this the PDB-ID?)

Yes, the 4 letter codes, like "1acf" are the Protein DataBank IDs. Currently the true name of the protein is not something that is included in the application anywhere, so it would require some modifcations to tell the work unit about it. But you can always look it up if you are curious in the PDB. Here is a link to 1acf (Acanthamoeba Castellanii Profilin Ib)

- would it be possible to display helices / sheets?

We are looking into this. One question is whether we can maintain the same framerates.

As for the Colour's suggested by dgnuff, shouldn't these setting and actually all screensaver/graphics settings go in the respective section in the profiles.



Then when the Boinc coders eventualy get around to central settings and local setting (well it's on there boinc's to-do page) it'll just flow easier ?

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Team mauisun.org

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It would be interesting to have user configurable rainbow schemes. Perhaps with some kind of interactive interface.

I think the graphics are great.

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Secret team meetings and the sharing of 3.2Terabytes of free software -->HERE!... Don't spy, we don't like spies!

^^

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Graphics look really nice. Great work done there.
But i think there's missing something:

The "smallest accepted Energy found in this WU" should be written somewhere in the statistics at the bottom, especially when we start with proteins where the native form is unknown.

And i have one question about the algorithm: What are the criterias for it to stop with relaxing phase and starting again with ab initio for an other aproach?
I've seen relaxing phases that only lasted 1 min and others going about 30 min at the same WU without anything else active on my PC.

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But i think there's missing something:

The "smallest accepted Energy found in this WU" should be written somewhere in the statistics at the bottom, especially when we start with proteins where the native form is unknown.

I agree, and will try to include this in the next version of the graphics.

And i have one question about the algorithm: What are the criterias for it to stop with relaxing phase and starting again with ab initio for an other aproach?
I've seen relaxing phases that only lasted 1 min and others going about 30 min at the same WU without anything else active on my PC.

Most protocols use a fixed number of steps in the Full Atom Relax stage. Without knowing which Work Unit you were running, I don't know the explanation for the differences in times. But, because the algorithm is not determinstic, it is possible for there to be significant variance in behavior even when running identical protocols.

the differences in the amount of time spent in relax is due to filters we put in to increase
efficiency. In an initial set of runs, we recorded the energy not only at the end of relax, but also
at two stages about 5% and 40% through the trajectory. In the set of runs you are doing now, we are bailing out early at one of these two stages if the energy at the stage is higher than the median energy observed in the initial trajectories at this stage. In this way, unpromising trajectories are terminated early.

we will soon be starting a new round of runs in which each trajectory is directed towards low energy regions of the landscape identified in the runs you are doing now

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we will soon be starting a new round of runs in which each trajectory is directed towards low energy regions of the landscape identified in the runs you are doing now

You mean the good stuff is coming soon. hehe :-)

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How many Graphics WU's are being sent out, I still have yet to recieve one. Not that I am complaining just very very anxoius, I have process over 75 WU's since the graphical WU's have been released, and I can't hardly believe believe my bad luck.

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Open the BOINC Manager, click on the Work tab, click on the job in progress, and then click on the Show graphics pushbutton. All current jobs will show the graphics.

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How many Graphics WU's are being sent out, I still have yet to recieve one. Not that I am complaining just very very anxoius, I have process over 75 WU's since the graphical WU's have been released, and I can't hardly believe believe my bad luck.

As far as I can tell from the systems I'm running Boinc and Rosetta on, all new WU's are 4.80 and have graphics. That being said, a couple of my systems are still flushing old 4.79 WU's from their caches, although this is because I maintain a good sized cache.

I expect those units to be completed in the next few days, at which point I'll be running graphics on all my Win32 system.

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How many Graphics WU's are being sent out, I still have yet to recieve one. Not that I am complaining just very very anxoius, I have process over 75 WU's since the graphical WU's have been released, and I can't hardly believe believe my bad luck.

I took a look at your results, it looks like you just finished returning W/Us downloaded on Nov 15. It looks like all the W/Us currently on your system were downloaded today (5 Dec) and *should* have graphics.

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Yup I am getting them now, I waited a while and reduced my chache size and now all my WU's are graphical, yeah!!!

But here is a thought. WIth the graphical portain, here is an idea, for each unit, could there be an explaination of the unit in plain english as too waht it is? persay, test unit, bovine protein, aids protein, alszymers protein, that would be cool and maybe a little sentance about what its purpose will be. IE: "we are searching this particualar protein becuase it has these features, yad yada," or "this is the result of a prevoius test that showed remarkable results and we are further testing it becuase it is promissing yada yada yada.", It would fit very nicely in a small box with 8 or 10 point font. I can imagine that it would be easy to implement with a small text file the GUI will load. very easy to implement,

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Good idea about the text box, but more for the future I think. Right now, all the proteins are chosen solely because they have already been mapped to a very high resolution. That allows the developers to see how close the application is actually getting to the final result.

When they stop working primarily on the code and attempt to map unknown proteins, that would be a great addition to allow members to see what they were actually working on.

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When they stop working primarily on the code and attempt to map unknown proteins, that would be a great addition to allow members to see what they were actually working on.

You know, I actually do read the forums and attempt to learn all I can from them, I must admit that the project developers do the best job I have ever seen in a project on keeping the members updated. But honestly as much as I try to learn it, its in one ear and out the other.

I looked back through the forums and what you have said has been said before. None the less the WU info would be a great idea. Here is a thought I just read anouther post about these new topology units comming out, well here is an shinning example of how to keep us informed. Or at least a simple page of upcomming units and we will be calling them this...

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Graphics seem to be down today? Am I the only one or is this a Boinc problem?

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