Prototype of Rosetta "game"

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Ian Davis

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Message 44975 - Posted: 14 Aug 2007, 22:33:55 UTC

Hi R@H community,

I've been working with several others in the lab on an "interactive Rosetta" project. The vision is that one day, you'll be able to interact with Rosetta as it runs, both (1) to help it produce better results and (2) to learn about what it's doing.

We're not there yet, but we have an early prototype for #2, the educational side. This is a simple "game" you can play in your web browser (using Java) to find the missing side chain for a designed protein that might be used to fight cancer. In this case, there's a small number of choices and the right answer should be obvious. However, it illustrates one of the basic steps that Rosetta performs thousands of times every time it designs a protein.

More "levels" for the game will be coming in the future. Also we're already planning to change the interface on the Java applet and to add a "score board" so you can compete against others, but if you try it out and have other comments or ideas to share, please post them here.

Here's the link: the Rotamer Game

Thanks!
Ian
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FluffyChicken
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Message 45006 - Posted: 15 Aug 2007, 20:34:16 UTC

Right first time :)

I took the obvious choice, err guess.


Team mauisun.org
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Nickhorsky

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Message 45018 - Posted: 16 Aug 2007, 0:43:52 UTC

I have the latest JAVA but I don't get the game...
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hugothehermit

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Message 45028 - Posted: 16 Aug 2007, 7:23:22 UTC

Actually your demo has helped me understand just how difficult all of this is, considering that it's only one side chain, that has already been fixed in place by the proteins / molecules placement.


A few questions:

Will the game allow abinito structure design? A lot of the abinito designs produced by Rosetta seem a little off to me and I would like to play with them, especially if PDB's could be swapped between other players.

If so would Rosetta be able to do the full atom relax on the abinito structures? So you didn't have to set every side chain by hand.

Please have 3D glasses in mind when writing the programme, even if it never happens, it would be better that having to rewrite it all when it does come up :)

Great job, will be looking forward to the next levels.

I have the latest JAVA but I don't get the game...


It doesn't work with Firefox with NoScript installed, but it's only a demo. If you have another browser give that a go.

I got it right the first time too :)
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Ian Davis

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Message 45070 - Posted: 16 Aug 2007, 23:44:46 UTC - in response to Message 45018.  

I have the latest JAVA but I don't get the game...

Could you tell me which OS (Windows XP, Windows 2000, OS X, Linux, etc) you're using and what web browser (including version number) you're using? I can't promise I'll be able to fix it but I'll try...
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Ian Davis

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Message 45071 - Posted: 16 Aug 2007, 23:48:06 UTC - in response to Message 45028.  

Actually your demo has helped me understand just how difficult all of this is, considering that it's only one side chain, that has already been fixed in place by the proteins / molecules placement.


Great! That was a really important goal for this project.


Will the game allow abinito structure design? A lot of the abinito designs produced by Rosetta seem a little off to me and I would like to play with them, especially if PDB's could be swapped between other players.

If so would Rosetta be able to do the full atom relax on the abinito structures? So you didn't have to set every side chain by hand.


Yes -- eventually. The "full" game will be a program you download, and should allow you to do all kinds of crazy things to the structures Rosetta is predicting :) We're planning to allow all the things you mention here. This more limited version I'm demoing on the web is intended more as a training ground, to help people understand the principles they'll need for playing the full game (when it becomes available later).

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agge

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Message 45083 - Posted: 17 Aug 2007, 15:04:18 UTC

i got it wrong :(
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r0b

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Message 45108 - Posted: 18 Aug 2007, 8:22:46 UTC
Last modified: 18 Aug 2007, 8:25:34 UTC

doesn't work for me, too

Vista Business 32Bit, tested with Opera 9.23 ( Java Sun 1.6 ) and Firefox 2.0.0.6

Firefox says "error: java.lang.ExceptionInInitializerError"
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mewbysea

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Message 45114 - Posted: 18 Aug 2007, 15:17:01 UTC - in response to Message 45108.  
Last modified: 18 Aug 2007, 15:20:15 UTC

doesn't work for me, too

Vista Business 32Bit, tested with Opera 9.23 ( Java Sun 1.6 ) and Firefox 2.0.0.6

Firefox says "error: java.lang.ExceptionInInitializerError"



No luck with latest Java in either IE (7.0.6) or (as expected) Firefox (2.0.0.6). IE requests "click to activate this control", but nothing happens post-click. Other Java apps (including the Jave home page "game" intro) run fine in both.

Running WIN XP MCE on Intel Quad core 2.4 Ghz.




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Profile dcdc

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Message 45116 - Posted: 18 Aug 2007, 15:42:53 UTC

these problems anything to do with java not being compatible with the latest firefox update?
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Profile Greg_BE
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Message 45119 - Posted: 18 Aug 2007, 16:13:45 UTC

firefox doesn't work and IE says error:java.lang.NoClassDefFoundError: Could not initialize class sun.awt.shell.Win32ShellFolder2$ComTaskExecuter.

i checked my java install, its ok
version 6 update 2
and it verifys ok on java's site.
so whats up with this?
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Message 45124 - Posted: 18 Aug 2007, 17:16:31 UTC
Last modified: 18 Aug 2007, 17:19:18 UTC

IE7 latest Java, get a blank box with the red cross, (prettily done mind), in the the top left.
Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.
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Profile Malcolm Cole

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Message 45126 - Posted: 18 Aug 2007, 17:25:32 UTC

Regret the X in the box does not activate for me either. I am using Microsoft Internet Explorer 7.0 and Java 6 Update 2, which I think are the latest in the UK. Is the game working with these versions anywhere else?
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Koen

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Message 45127 - Posted: 18 Aug 2007, 17:53:41 UTC

Worked fine with Java 5 Update 4 (+ Firefox).
Had to update Java today to version 6 Update 2 and all I get to see now is that darn red X.
(On the game-screen it said: "If you're having trouble loading the game, update Java to the latest version". Oops :))

Regret the X in the box does not activate for me either. I am using Microsoft Internet Explorer 7.0 and Java 6 Update 2, which I think are the latest in the UK. Is the game working with these versions anywhere else?

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Message 45128 - Posted: 18 Aug 2007, 18:10:31 UTC - in response to Message 45126.  

Regret the X in the box does not activate for me either. I am using Microsoft Internet Explorer 7.0 and Java 6 Update 2, which I think are the latest in the UK. Is the game working with these versions anywhere else?


your using the same software as me IE and java, i'm over in belgium, but use US software, shouldn't be any different. English is English in software.
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Profile Greg_BE
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Message 45213 - Posted: 20 Aug 2007, 17:54:42 UTC

why is it with firefox and the latest java software all this does is do the java display and then show a red X and then lock up my browser?
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Ian Davis

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Message 45255 - Posted: 21 Aug 2007, 23:29:27 UTC - in response to Message 45127.  
Last modified: 22 Aug 2007, 17:43:48 UTC

Worked fine with Java 5 Update 4 (+ Firefox).
Had to update Java today to version 6 Update 2 and all I get to see now is that darn red X.
(On the game-screen it said: "If you're having trouble loading the game, update Java to the latest version". Oops :))


Based on the feedback here, I'd say that Java 1.6 (aka Java 6) isn't working with the game, at least on Windows. I don't know why, but am trying to figure it out. If I can figure it out I'll post something here and try to fix the game.

So, if you're having trouble, maybe try one of the older Java 1.5 versions instead of Java 1.6. If that solves the problem for you, please let me know! I apologize for the inconvenience but greatly appreciate the help from all of you in tracking down the problem.

Best,
Ian

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Ian Davis

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Message 45278 - Posted: 22 Aug 2007, 20:35:59 UTC - in response to Message 45255.  

Yes, it's a bug in Java 6 under Windows (http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6570445, if you're interested).

The temporary fix is to remove Java 6 and fall back to Java 5 (JRE 5.0):

http://java.sun.com/javase/downloads/index_jdk5.jsp

There is no workaround listed in the bug database, but I'll see if I can figure one out...

-Ian
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Ian Davis

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Message 45280 - Posted: 22 Aug 2007, 21:21:36 UTC - in response to Message 45255.  

Based on the feedback here, I'd say that Java 1.6 (aka Java 6) isn't working with the game, at least on Windows. I don't know why, but am trying to figure it out. If I can figure it out I'll post something here and try to fix the game.


OK, I believe it's fixed now. Totally quit out of your browser and/or clear your cache and/or reboot if you're still having trouble. Does that fix the problem for everyone who tried Java 6 under Windows and got the red X?

Best,
Ian

PS *Much thanks* for helping track down this bug! I never would have caught it on my own...
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Koen

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Message 45304 - Posted: 23 Aug 2007, 8:30:41 UTC

OK, I believe it's fixed now. Totally quit out of your browser and/or clear your cache and/or reboot if you're still having trouble. Does that fix the problem for everyone who tried Java 6 under Windows and got the red X?

Best,
Ian

PS *Much thanks* for helping track down this bug! I never would have caught it on my own...


Problem fixed! Well done!
Glad I could 'help'.

Koen
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Message boards : Rosetta@home Science : Prototype of Rosetta "game"



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