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

Don`t know. I have all WUs (new one) with graphics :o

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

Same here - just attached new machine to the project and downlaoded rosetta_4.80_windows_intelx86.exe
But the graphics is there - it is just not name "graphics" as - I assume -application with graphics becomes a standard version.

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just a few obsevations,

When watching the graphics I notice that where a certain area should be straight and pulled out, I tend to notice that in the searching part that one part is normally a very tight helix shape. also I find that the end of the chain say the blue part, if it should be on the bottom then its mostly on the top and vice versa for the red. I also find that no matter how loud I yell at it; it doesnt want to listen to me, ha ha

Also just a little curious, [if its in anouther post, i missed it] What are the little grey boxes in the plot? are they the native structure locations?

does anyone else notice anything particualr about the units ????

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Yeah mine step out of bounds sometimes. I see the same thing you are seeing on some of my WU's also. I tried yelling, I tried time outs nothing seems to make them do what I want them to do. Go figure I don't like doing what some people tell me to do either. But I do enjoy this project very much. I enjoy the Admins contributions as well as all the chat here. I just really hope this project stays around for along time. Kudo's to Paul, Jack, Ingleside, Stepahan T., David and anyone else I forgot. And Ace you crack me up.

Have a Great Day All and may the higher power of your understanding Bless you richly in this Christmas season.

Ecaf

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Newbie observations and a question or two.

Folding Image migrates/exceeds display box (Searching, Accepted, Lowest) boundaries.

Multiple Red Dots in results splatter graph.

Both seem to be explained in posts in this forum, although multiple low energy reports back to you seem odd if we are only looking for lowest energy state.

Where can we ( or is it possible to ) view the splatter graph for work units we have completed and sent back to rosetta@home?

Is any information retained on our local systems which we can review completed work units and the results?

Are larger work units allocated to more capable processor platforms or are work units generally similiar in size? ( ie 3+GHz systems get larger work units while 1.5Ghz and below are sent smaller work units )

To overcome color impairements, perhaps a crosshatch or dot pattern fill for the segments.

Phil - on an old K6-2 500MHZ

Newbie observations and a question or two.

Folding Image migrates/exceeds display box (Searching, Accepted, Lowest) boundaries.

This is a known issue. The solution will probably, eventually, come by allowing the user to reposition, and even rotate, the protein.

Multiple Red Dots in results splatter graph.

Both seem to be explained in posts in this forum, although multiple low energy reports back to you seem odd if we are only looking for lowest energy state.

This is a good point. It helps us refine our algorithm to see the end point of every folding run.

Where can we ( or is it possible to ) view the splatter graph for work units we have completed and sent back to rosetta@home?

We haven't had time to update as often as we'd like, but you can view what's been done so far at

https://boinc.bakerlab.org/rosetta/rah_results.php

https://boinc.bakerlab.org/rosetta/rah_top_predictions.php

Is any information retained on our local systems which we can review completed work units and the results?

Not that I know of, though this is a good idea.

Are larger work units allocated to more capable processor platforms or are work units generally similiar in size? ( ie 3+GHz systems get larger work units while 1.5Ghz and below are sent smaller work units )

Currrently, most work units are desinged to be the same size.

To overcome color impairements, perhaps a crosshatch or dot pattern fill for the segments.

We have several color blind people in lab who I think can help us with this design.

Phil - on an old K6-2 500MHZ

Thanks for the feedback!

A couple more inquiries, please bear with me. I'm like a curious George.

> > Multiple Red Dots in results splatter graph.

> > Both seem to be explained in posts in this forum, although multiple low
> > energy reports back to you seem odd if we are only looking for lowest energy
> > state.

> This is a good point. It helps us refine our algorithm to see the end point
> of every folding run.

Alright, just for clarity, each folding run generates a low energy 'red dot' in the local graph on local system. There are generally multiple folding runs per work unit so multiple 'red dots' are expected, just not all visible at the same time due to the shifting of the local splatter graph window to accommodate the range of energy levels. The resulting 'red dots' are sent back to rosetta to be consolidated into the 'results' splatter graph along with other completed WUs. All the 'green points' the local computer has generated in the local splatter graph are discarded.

The link you gave for viewing results:

https://boinc.bakerlab.org/rosetta/rah_results.php

shows several different graphs, none of which specifically match the work unit name ( we have only 1 WU returned to rosetta ) completed so far. Within the graphs themselves there seems to be no blue "*" ( designates point found by the WU completed here ) which would indicate we weren't able to contribute or our run was some type of verifying run for results already obtained (is this done as follows - double checking only on 'red dot' results?).

The "RESULTS" link on the "HOME" page takes me to the link above. The "VIEW" link beside "RESULTS" on the "YOUR ACCOUNT" page under the "Account statistics" heading gives details on the WU status. It would be nice to have something in this table which would link us to the splatter graph for the particular WU.

Looking at the detail for my WU there is an entry:

max # of error/total/success results 10, 20, 10

What does this tell us? We never like to see a number > 0 in an error field.

Although not related to graphics ( don't mean to hijack this thread ), does rosetta fold proteins in isolation, restraints are the ones imposed by segments repelling or attracting each other, or are there such things as catalysts in the mix which might enable lower energy folds to take place without the catalysts becoming part of the protein? Is this thinking too far out of the box? Noticing a lot of void area in the result splatter graphs prompted this idea.

Phil

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Looking at the detail for my WU there is an entry:

max # of error/total/success results 10, 20, 10

What does this tell us? We never like to see a number > 0 in an error field.

I was going to refer you to the Wiki's description of that page only to find that is one of the features not documented yet ... :(

However, the meaning of the values are partly covered in quorum of results, though this is another place where we need more ... :(

==== edit

I did at least get all of the parameters pointing in the correct places. Look at max success results for a page image reference ...
sigh ...

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Looking at the detail for my WU there is an entry:

max # of error/total/success results 10, 20, 10

What does this tell us? We never like to see a number > 0 in an error field.

Wow... lots of good questions, and only one I can answer! Most projects, other than Rosetta and CPDN, issue the same Work Unit to multiple people to form a "quorum", so, for example, they'll send it out to 4 people, and when 3 of those have returned the result, a validator runs and sees if they "match". Then credit is calculated, etc., etc., etc. This line on that page was put in _more_ for those projects benefit, but it is still relevant here as follows:

If you have an error on the WU, it will be sent out to someone else to give it a try. The numbers up there say that this is allowed to happen 10 times, and then the project gives up, assuming that WU is "bad", or needs to be looked at by a human, or something. The project can raise or lower this number, depending on the number of errors that are likely based on history, and the number of participants available.

The limits on total and success are just the defaults, and don't apply here, because the first "success" finishes it out. At other projects, besides errors, you can have "success but not valid", and "past deadline" returns, and those numbers come into play.

EDIT:: Yeah, Paul, I was too, then I remembered how new that line was and realized it hadn't made it in there yet. Too many more important things right now!

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EDIT:: Yeah, Paul, I was too, then I remembered how new that line was and realized it hadn't made it in there yet. Too many more important things right now!

well, it is a little better now ...

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Although not related to graphics ( don't mean to hijack this thread ), does rosetta fold proteins in isolation, restraints are the ones imposed by segments repelling or attracting each other, or are there such things as catalysts in the mix which might enable lower energy folds to take place without the catalysts becoming part of the protein? Is this thinking too far out of the box? Noticing a lot of void area in the result splatter graphs prompted this idea.

Phil

You might want to try asking this in the science section of the forum. David Baker is really good about answering questions of this sort that relate directly to the science of Rosetta

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I see now that the results are from Nov 15th not Dec 15th, so there wouldn't be any blue "*" for WU completed here ( member since three days ago).

I have perused the boards a little more and posed a supposition on directed random selection ( You asked for feedback thread ). The science of folding is unfamiliar to me as my path took me down the inorganic route. Chaperones ( in another thread ) seem to provide a kind of scaffolding for building the protein until the end pieces are in place then, similiar to the space shuttle gantries detaching and setting the shuttle free, protein folding ( relaxing ) begins to take place.

Thanks again,

Phil

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I'm interested in a different graphic - The graph you find in the statistics tab in the BOINC manager, I would like to know what it means??. I understand the Days axis means the amount od days you have belomged to the project??, but the other number I don't know what it means

Many Thanks

Alan

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Basically they show various looks at your credit earnings over time.

I don't find the graphs all that useful, but, there *MAY* be a change in the future to make the tab contain better data and graphing.

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Mostly to Jack, regarding the graphics in 4.81. The ability to spin the native form is nice, but a little hard to control, in my humble opinion.

You're doing a rotation, but the center of rotation seems to be a fair distance from the molecule, which means that as I rotate, the molecule tends to swing out of the viewport.

Is there any way you can make the following three points always conincident:

The center of the viewport, the "center" of the molecule, and the center of rotation. That might make things a little more useful.

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Mostly to Jack, regarding the graphics in 4.81. The ability to spin the native form is nice, but a little hard to control, in my humble opinion.

You're doing a rotation, but the center of rotation seems to be a fair distance from the molecule, which means that as I rotate, the molecule tends to swing out of the viewport.

Is there any way you can make the following three points always conincident:

The center of the viewport, the "center" of the molecule, and the center of rotation. That might make things a little more useful.

Please see this thread:

https://boinc.bakerlab.org/rosetta/forum_thread.php?id=755

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