Now I can run Folding@Home on my PS3 and fold proteins myself on the computer!

Shoulda gone with pontifex, bridge building in 3d >P

Re: Foldit Review - is "conformation" a word? I am confusated...

Oops.

"Chemical conformation, in chemistry, is the chemical structure of a molecule. In polymer chemistry, it's the three-dimensional shape of the macromolecular chain."

My bad.

Tip for Penny Arcade Episode One: Be sure you've done everything you wanted to do before defeating

I'd like to add that Foldit was deliberately created not only to test if combined human pattern recognition can outmatch a supercomputer, but also in hope that it can lead to real cellular biologcal discoveries and maybe even breakthrus. So, if you add your bit - you're literally doing more than just some fun - it's time not "wasted"!

The bridge builder game looks like the good old Pontifex, a game I liied a lot in its days.

Hey Jay and the team,
I think it would be nice to have mini '5-star-raters' beside each Weekend Download and Link Dump Friday game. Just so it would be a little easier to voice our opinion on the games. Thanks, these are all great little time-wasters.

The link for the bridge builder is not working for me. it keeps coming up IE cannot display this webpage.

I'd love to play foldit, but it doesn't seem to run correctly on my computer. :( I've successfully folded two proteins, but I have no idea what I did -- I clicked utterly randomly on the molecule displayed in the middle of an utterly blank screen with the upper-right quadrant greyed out. No instructions, no menus, no way to quit or go to the next level when I finish. My laptop IS rather old, I confess, but this didn't look like a game that would strain its capabilities.

update to my last: On the foldit forums there is a suggestion from someone having the same issue, stating that updating the graphics driver solved the problem. Unfortunately mine is up-to-date, so it doesn't help me, but if any other users here are having the same problem, I offer the information.

On another forum years ago (archives seem lost) we competed to get lowest costs for bridges. I remember the tricks and tried to go for low cost, so these should be close to minimums except for the big levels.

01: 300
02: 700
03: 1600
04: 2500
05: 700
06: 3200
07: 10700
08: 11900
09: 3800
10: 1400
11: 17700
12: 10700
13: 3400
14: 4200
15: 1900

I'll post screenshots later if there are questions and other people dont come up with better minimums.

Ew, The Jackyard is 12MB zipped and over 100MB unzipped? Someone needs to learn how to compress their executables.

LS
I have had the same experience.

Anyone?

Thanks LS

I didnt have your latest post when I posted. Updating my graphics driver worked for me. It all makes a lot more sense now!

The Foldit game sounds so cool.. waiting for it to download..

Just awesome to combine my work field with gaming :)

Foldit looks cool.... unfortunately though it doesn't run on my Mac because "It is not supported by the architecture".

Has anyone got up to level 7 in Bridge Building Game level set 2? Unless I'm missing something, it doesn't seem to be possible to build any of the white links (the ones the train doesn't go through), so I don't see how it can be possible to finish the level...?

Anyway it has been pretty good so far, Foldit is great too.

Yeah bridge building game link definitely borked. I can't connect either with FF.

foldit seemed interesting but i'm stuck on the first unguided helices level. i don't really understand the whole "hiding hydrophobic sidechains" business. sometimes it'll tell me something like "good hiding!" or whatever but i don't really understand why.

Well, I also downloaded Fold It and joined the JIG team...my question for zho or whoever is on the team is how the points accrue. Is it automatic or do I have to submit after each fold?

And I agree that some of the instructions are a bit arcane, but I seem to have been fairly successful, even if I didn't always understand why I had to move 4 pieces when moving 2 appeared to do away with the clash.

Some answers for Foldit questions:

Hiding hydrophobic sidechains means putting the little orange glowy bits as much as possible into the interior of the folded protein. You might need to adjust your display options using the menu at the bottom of the screen to highlight the hydrophobic parts.

As for performance, keep in mind that there are a lot of calculations and optimization going on behind the scenes, so it's not necessarily going to run as fast as you might think. Still, it should be playable on most machines.

As long as you are connected to the internet, your top score is automatically recorded and saved. There is an option to play offline, but I've never tried that out.

The color guides seem to be a bit misleading -- red only shows the really bad parts, so although it may look like the clash is gone, it's not gone enough. The score is a better indicator of progress.

Thanks to everyone who joined the Jayisgames team! Like bioLarzen said, the ultimate goal is to nail down just how all these complex proteins work, and eventually to aid in the design of new proteins!

Oh and for anyone who is interested in the actual science behind the game, the fold.it website has some good info.

"Hiding hydrophobic sidechains means putting the little orange glowy bits as much as possible into the interior of the folded protein."

Yeah. The tutorial told me that. But, and maybe I'm just dense or slow... I don't exactly understand what it means to put them "into the interior of the folded protein." How do I do that? How do it know if it's in the interior?

Level 7 of Bridge Building Game has a Build Deck option.

I hadn't realized that BBG was a newer version of Bridge Builder. I figured the name was just changed. The update is great! I like the simplicity of BB compared to Pontifex.

141 ... there is a "build deck" option available in level 7... with this you can make blocking tiles, and with this the level becomes quite easy..

BTW: a wonderfull weekend download, with 2 games at once I really like (foldit and bridgebuilder)

got a cost of 2300 on bridge game level 4,
but 3500 on level 3.
Such a simple game, with awful, well, with NO graphics to speak of. But really interesting.
The penny arcade game doesn't work, something about no compatible display device? No great loss, I've got this bridge game.

I am loving foldit. I've leapt to the top 10 in a couple of challenges and I'm taking you all with me!

Good addition to my protein folding screensaver!

@fnord3125

You have to imagine the protein as a 3D object. What you see on the foldit screen is a representation of the protein that isn't 3D in the same way. For example, check out this image: http://www.cbs.dtu.dk/courses/27617.struc/protein_blue_brown.gif

The brown protein at the bottom is shown as foldit would show it. But the blue protein above is shown as it would appear to an observer.

A protein is a long chain of amino acids. Foldit shows you proteins as a long chain, but the chain may curl up on itself. You have to imagine its 3D structure from what foldit shows you. You can then see which bits face outwards (exterior) and which are buried inside the protein by other parts of the protein.

You have to make sure the parts of the protein chain that face out (e.g. towards you) have the blue glowy bits on, and the parts that face in have the orange glowy bits.

Oh I'm terrible at fold-it. I was hoping I'd be good at it, since I have good 3D visualization talent, but I think there's something subtle that's just not doing it for me. I think one problem is that there isn't good incremental feedback for how "happy" the hydrophobic side-chains are. If I could more easily/instantly see that some are happier than others, I might be able to help the bad areas more selectively. Also, I know this part is hard to do on the screen, but it is hard to tell where a given request will bend the model, and how much it will actually move (as opposed to how much you requested). There are a lot of cases where I try to move something, and I just can't see where the hang-up is. Of course, that is the sort of thing where physical intuition works best.

Ooh, make a construction set for them (like Legos, Connex, etc)! Give them accurate joints according to how they can bend and fold. Then publish diagrams on the Internet for how to build the latest puzzle, and have them be kids' toys or those little workplace desk trinkets. Bets that one of these on a secretary's desk would find an optimum solution pretty quickly? And only some of the players need to know the intent, the others will actually be helpful randomizers. The only trouble would inputing them back into virtual space to be sent off to the scientists. Hmmm. Well, 3D scanning technology is getting cheaper every day, right?

The more I try to talk/think about Foldit the less it sounds like fun and the more it sounds like work. :) Thanks for the advice anyway, zxo and Tom. I've never had very good spatial relation sense, so it probably just isn't the thing for me.

hey i need help for Jackyard.

its very confusing.

help?

Some cents on FoldIt:

I think its a great idea, beside any insights the creators might get, I think its an excellent tool to what some (e.g. northern european countries) consider nowadays the forth task of university: public communication / dissemination of knowledge. This tool gives a wonderful insight to laymans on some concepts of how proteins work. I'd appreciate it however if it would come with more info, thrown as bits here and there, like what I'm doing. How the proteins structure effects this or that or biology. Whatever... Right now the "game" is only interested in the solutions I provide, and hardly gives me anything (like knowledge) for it...

About the protein, I guess the "hands" are quite important altough they are hidden by default, if I take a protein at any position pull a bit around it, and wiggle it, it will wiggle back into the orignal position. If I shake it however while pulled apart, thus move the hands, it will not go back into the previous position.

However on the other hand, I'd wish to be able to "turn off" hands completly when starting. And also to be able to run wiggle without it worrying about the hands at all. So when I got the spine in the position I consider good, I can start worring about what the hands will do...

I also have problems with the input, often enough I just would want to put my hands into the screen and push/twist the thing how I want it to be, and I guess it would be better, However the main problem is using pull and/or rubbers to get through the interface the object you created in head... I don't know how to solve that, buy a 3D-mouse? :-) (Do be exact, I don't miss 3D vision stuff out of this Virtual reality bushwa, I just dearly miss 3D input when working with foldit)

I'd wish for a rubber thats not like a rubber, but one which would provide a constant force instead one increasing with distance. This way I could make more alterations by pulling two appart things gently together . But the rubbers force will be too great if things are too far apart, destroying the object or it will be too week if they are already quite close, but you want to pull to hydrogen bridges together over wiggle default reculance to keep them apart, because of collisions.

I wonder in the completly other direction of public commincation, I wonder if this thing would benefit if translated into an alternative more playfull atmosphere than being so obviously close to chemistry. I don't know how about a roman altering vines? Or an alien playing around with stuff to create energy for his vessel.... I don't know.

One thing I tried to get other solutions was instead of starting to optimize with the version I get when starting the puzzle was to first pull the whole protein apart into a single line with rubbers, and then to fold it in a new way.... Problem is pulling the helixes will destroy them! (make them straight) and there is hardly any way I can twist them again once lined out. IMHO another issue of limited input capabilities....

Oh, Fold-it is just too slow on my computer. I have a pretty recent one too, though not totally suped-up in the graphics department. Once they get big, it gets slow. There must be a better way to optimize it (yeah, I know, you can turn some parts off, but then you're working blind). I definitely think this should be integrated into a physical toy. The speed and ease of human interaction in trying different combinations on a physical object just can't be beat. And hey, then they not only will get the work done for free, they can MAKE money off it by selling little toys . . .

Out of curiosity, is anyone having trouble with Bridge Builder's UI? I'm running it on OS X 10.5.3, and the lower-right hand corner options except undo/redo (delete, flip-x, etc) are always greyed out. I also can't seem to click anywhere without the interface thinking I want to build a long chain of girders in the general direction of the mouse.

Bridge Builder is annoyingly slow and laggy for me. For a supposedly "simple" game, it takes too long. What's it do, run an unoptimised loop all the time, or something?

Foldit is too confusing for me, I'm afraid..

Yes Bridge Builder's UI can be tricky. To de-select a beam try clicking way down out the bottom of the sea into the grey area. You'll know when you can't see a line popping out anymore.

As to the other buttons, you can click and drag a selection box, maybe from there you can flip/rotate?

Hmm... Penny Arcade keeps freezing on my Mac before it even gets through the intro. Anyone else had problems?

Oh, thanks fuzzyface, I didn't notice that.

Why do all the best games seem to get hidden away in Weekend Downloads and Link Dump Fridays? :)

The Penny Arcade game "On the Rain-Slick Precipice of Darkness" was excellent! I cannot wait until the second installment. The graphics and gameplay reminded me of Psychonauts, which was also a great game. Precipice was funnier (with some adult humor added), and a little more engaging. Thanks a lot for the link!

Did anyone finish level-09 from the 2nd Map Pack for the Bridge Building Game?
You have to hold a weight of 160.000 but you only 40.000 of budget for a massively wide river.
Damn! My iron bars just crack like toothpicks no matter what design I go for.

Stefano, I also couldn't do it, I found a solution on youtube however:

http://de.youtube.com/watch?v=ytFxrDZsy7c

This bridge also worked for me, somehow I did something wrong, but when I tried to recreate exactly that bridge I missed 200$... Well I found two non so important bars, and it went over fine.

http://de.youtube.com/watch?v=RngIVlpj9q0

Thats a solution I just found added only 2 days before. this one is IMHO much nicer.

I did 09-Level with 33500. But the bridge was prettier at 38000, before I started to refine it.

11-Level was quite a hard one. I'm down to 18200.

I'm just starting 13-Level. It is the biggest span so far (15 Deck lengths between the anchors)

A few of my Bridge Building Game records so far...
map pack 2:
7- 1500
9- 29900
11- 18000
12- 7600
13- 26500
14- 6000

I'm really liking the new version. The Copy, Paste, and Flip X options really make designing go a lot faster.

Hey, thanks a lot fuzzyface! It didn't occur to me that people would have posted videos on youtube. But makes sense, since it's a fairly old and interesting game...
BTW, the second solution is my favorite too, although I think the extremities could use a little refinement.
Thanks again.

David, how did you design your level 9 bridge? I like keeping my budget to a minimum, but cool and clever designs are definitely my biggest concern!

Personally, I would like to propose a different version of highscore for bridg-builder.
Use all your money (or as much as you want) and then use the progressive test to see how much your bridge can hold .
I like watching the stress colors and going, "you can hold a bit more, just a bit more".

And here's what I was doing before fuzzyface posted the 2 possible working solutions (mine was too expensive):
http://www.youtube.com/watch?v=10_eVPDVD3s

gah. can't do level 15 of the bridge building... help?

stefano, whats that for a funny spike on start of your bridge?

here is my $29900 level 9 bridge:
http://lcdlagtester.googlepages.com/9_29900.gif
$32600, but a much cleaner design:
http://lcdlagtester.googlepages.com/9_32600.gif

Ok...I am confused and frustrated... Is anyone else having troouble with Map Pack "02-New" starting on Level 6. The train keeps going under the bridge and I cannot seem to get it to work.

Ok...figured out half the problem...solid white lines only made on the yellow line on edit board...still doesn't help me with the second gap yet...but working on it