puzzle picture
1221: Disordered Electron Density: Round 1
Status: Closed

Summary

Name: 1221: Disordered Electron Density: Round 1
Status: Closed
Created: 04/17/2016
Points: 0
Expired: 04/24/2016 - 23:00
Difficulty: Advanced
Description: NOTE: Because many players have had trouble playing this puzzle, the puzzle has been made worth zero points, and it will not contribute to player rankings. However, this puzzle is still of unique scientific interest, and we encourage players to work on it if they are able!

This is a big one! This electron density puzzle features two proteins: the first is a large well-ordered helical protein that is mostly frozen in place. This binder protein has two flexible loops that bind a second, mostly disordered, substrate protein. The substrate protein is provided here as an extended chain, and is completely flexible. We know that the substrate protein is bound to the binder protein somewhere in this crystal structure. But it seems that the substrate is able to adopt several different shapes, making the electron density very difficult to interpret. We’re asking Foldit players to help us find the ways that the substrate protein can bind to the binder protein! Fold up the extended chain and dock it next to the flexible loops of the binder to improve your score!
Categories:

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RankGroupScorePoints
1Go Science10,3530
2Contenders10,3270
3Beta Folders10,3130
4Anthropic Dreams9,8480
5BOINC@Poland9,8190

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Comments

Joined: 10/23/2014
Groups: Contenders
Crashed

Tried opening and crashed. Tried again and crashed. Running Windows 10.

Joined: 10/30/2012
Groups: Beta Folders
moi Aussie

moi Aussie

Joined: 06/24/2008
Groups: Void Crushers
Unhappy puzzle

It took me 5 attempts to load the puzzle

spvincent's picture
User offline. Last seen 18 hours 20 min ago. Offline
Joined: 12/07/2007
Groups: Contenders
opens on mac os x: crashes

opens on mac os x: crashes when trying to open on linux/wine. Main versions

Susume's picture
User offline. Last seen 1 hour 36 min ago. Offline
Joined: 10/02/2011
server timeout error

I and some others are getting this message when trying to load 1221:
"A timeout was reached due to excessive server load. Sorry for the inconvenience, please try again later."

Win 7 devprev

LociOiling's picture
User offline. Last seen 16 min 17 sec ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
check "disable network timeouts"

By checking "disable network timeouts" on the login screen, I was able to get this puzzle open.

I'd love to hear the explanation of why that is, but good enough for now.

Not sure if there's a good reason to leave "disable network timeouts" unchecked. Having it unchecked did not prevent clients from hanging after the most recent server outage.

gitwut's picture
User offline. Last seen 20 weeks 2 days ago. Offline
Joined: 05/18/2012
Groups: Contenders
This should've have been a devprev, optional puzzle

The description for this puzzle is very poor. What is the deal with the scattered, partial hydrophobes seemingly unattached to any protein yet they have unique segment numbers? The ease with which it crashes makes it unworkable.

bkoep's picture
User offline. Last seen 15 hours 12 min ago. Offline
Joined: 11/15/2012
Groups: None
Small molecules

Yes, in addition to protein, this crystal structure does include some well-ordered small molecules. The small spheres represent Zn atoms, and the ringed molecules are imidazole (which is very similar to the side chain of histidine). These small molecules occupy strong density in the electron density map, but they are frozen in place, and can mostly be ignored in this puzzle.

smilingone's picture
User offline. Last seen 2 hours 16 min ago. Offline
Joined: 09/19/2011
Groups: Beta Folders
Can't open on win10 devprev

No comments as reported by some. Simply crashes while trying to open.

jamiexq's picture
User offline. Last seen 1 hour 4 min ago. Offline
Joined: 07/31/2011
puzzle won't load

win 7 main client - just stays stuck on Loading screen

LociOiling's picture
User offline. Last seen 16 min 17 sec ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
Finally opened OK on Win 10, both main and devprev

Checking "disable network timeouts" on the login screen let it download without the timeout message.

Even with no scripts running, the 1221 client is using nearly twice the memory of a client with EDRW running on puzzle 1220. Check your memory usage on the performance tab of task manager, anything above 90% might be an issue.

Joined: 05/19/2009
Groups: Contenders
loads but it does consume a lot of memory

While loading it briefly peaked to 1.4 Gigabyte, while running it uses around 920 Megabyte.

Joined: 12/01/2011
Groups: Go Science
Crash

Checking "disable network timeouts" on the login screen let it download without the timeout message.

But then it crashes into a grinding halt

Susume's picture
User offline. Last seen 1 hour 36 min ago. Offline
Joined: 10/02/2011
Same

Same here: disabling network timeouts prevents the server timeout message, but the game loads the 1221 score boards (can't tell if it loads the protein, as I can't see the protein on the screen) and then promptly crashes. Win 7 devprev.

Also, before crashing it says we have over 52 million days left on the puzzle (and 19 hours).

Joined: 09/24/2012
Groups: Go Science
only crashed on opening more than 1 window

Not crashed the first time. All attempts to open another new window crashed

Joined: 09/24/2012
Groups: Go Science
saved ok

trying to share= > crash
trying to open it again 20 times= always crash
restard computer: crash on all attempts
It's like this computer is definitively not able to open it anymore.
==================

Loading on another computer (also Windows): OK first time, crash on other attempts

Loading on a new DEVPREV same computer: OK

Batz's picture
User offline. Last seen 4 days 21 hours ago. Offline
Joined: 02/16/2012
Groups: Go Science
Exactly the same for me... It

Exactly the same for me... It ran smoothly until I started to try sharing my solution. Now I cannot play it at all anymore. The other puzzles are working, but this won't open. :(

grogar7's picture
User offline. Last seen 8 hours 10 min ago. Offline
Joined: 10/03/2011
No crash!

I did not have any errors opening this puzzle (although it did take a while to load) and it seems to be running fine. And I have an older Core i5 (first generation) ASUS running Windows 10. Go figure ...

Joined: 10/23/2014
Groups: Contenders
Crash

Yesterday my fourth attempt to open the puzzle crashed in about 1/2 second. Today I got to the screen initializing before crashing. Susume reported over 52 million days left, I only get 48,798,575 days 1 hours left till the puzzle expires. What gives?

Visual Studio reports the following error:

Unhandled exception at 0x75D2DAD8 in Foldit.exe: Microsoft C++ exception: std::bad_alloc at memory location 0x0018F298.

Joined: 09/24/2012
Groups: Go Science
segs 234-251

are these molecules? ligands? what is their role?

frood66's picture
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Joined: 09/20/2011
Groups: Marvin's bunch
crash

thought it was my lucky day - then I tried creating a new track - machine crash

jamiexq's picture
User offline. Last seen 1 hour 4 min ago. Offline
Joined: 07/31/2011
update

Was able to play puzzle until servers went down - and now cannot get it to open again - crashes foldit win 7 main

gitwut's picture
User offline. Last seen 20 weeks 2 days ago. Offline
Joined: 05/18/2012
Groups: Contenders
Reopen as devprev

As I suggested earlier, this puzzle should be closed and re-opened as a devprev puzzle. It is unworkable for too many people.

jamiexq's picture
User offline. Last seen 1 hour 4 min ago. Offline
Joined: 07/31/2011
crashes in devprev also

puzzle wont' open in devprev either win 7

Joined: 04/19/2011
constantly crashes except the first time

Just as others said it opened once without problem, then never again. Neither in main nor in deprev clients. Tried on three different computers at least 20 times: Win 7, Win 8 even on Vista. The one with Win 8 has 32 GB memory and a 3rd gen i7 CPU - the crash cannot be a resource problem.
I second gitwut suggestion: Close it and re-post as a devprev puzzle, unless it can be fixed and made playable for everyone.

Joined: 09/24/2012
Groups: Go Science
Conclusion: only once

-(re) install Foldit (and Devprev)
-open only once
-never share, never change track (you can save)

LociOiling's picture
User offline. Last seen 16 min 18 sec ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
possible solution to crashiness

One client kept crashing on opening the puzzle.

After some experimentation, I tried deleting the the autosave files under

*foldit*\puzzles\002002315\*userid*\autosave*.ir_solution

where *foldit* is the foldit install folder, 002002315 is the nodeid of puzzle 1221, *userid* is your numeric userid (it should be the only directory at this level), and autosave*.ir_solution is all the autosaved solution files.

I hadn't done anything on this client, so the autosaved files were worthless.

Deleting these files allowed the client to open the puzzle without crashing.

I suspect this files were corrupted in one of the previous crashes.

Joined: 01/01/2016
Groups: Gargleblasters
Also crashing at 2nd attempt

Yesterday loaded fine (albeit a bit slowly) then was fine until server blip. Today can't open it and it crashes. Loci's solution sadly didn't work for me unless I delete all the quicksaves as well, then it does open although the puzzle has been reset. Not ideal...

grogar7's picture
User offline. Last seen 8 hours 10 min ago. Offline
Joined: 10/03/2011
update

1221 was playing without problems 10 minutes ago. I saved current solution and tried to open an earlier saved solution. Immediate crash!

Now I cannot reload the puzzle, even with 'disable server timeouts' checked.

I agree with those who say, "Get rid of this one until problem is solved."

Joined: 04/24/2014
Groups: None
Some recommendations on crashing

While it may be a memory associated issue, or maybe not, the team has passed along these helpful suggestions:

Closing other programs.
Start the puzzle on a fresh client, so that it has loaded the minimal set of data in to memory.
Upgrading any hardware, if possible. (We know that's probably not a great solution or all that practical for a lot of you so we put it last.)

In the meantime, we appreciate all the reports and your patience with this puzzle!

Joined: 10/23/2014
Groups: Contenders
Still Crashes

Followed your recommendations. I even shut down my PC and the first thing I did once up again was start foldit. Still crashed. I seriously doubt it's a memory issue.

I have a one year old i7 3.6 GHz, 12 GB ram PC running Windows 10. Unless foldit needs more than 10 GB of memory it should be fine. Other players have commented about having less powerful PCs and being able to work on the puzzle.

bendbob's picture
User offline. Last seen 3 weeks 6 days ago. Offline
Joined: 05/06/2011
Just wondering (the old

Just wondering (the old software QA guy in me is asking):
1. can you move the quicksaves to a temporary fold
2. start game
3. move the quicksaves back to the correct location
4. attempt to open a quicksave

Will the client crash now?

Joined: 04/24/2014
Groups: None
It would be interesting

It would be interesting to see the results of this if anyone wants to try it out and report back.

LociOiling's picture
User offline. Last seen 16 min 18 sec ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
deleted autosaves only

@bendbob, in this case, the puzzle was crashing upon loading. I hadn't run any scripts, so I didn't have any quicksave files in the puzzles directory.

All I had was four autosaves:

autosave.ir_solution
autosave-best.ir_solution
autosave-creditbest.ir_solution
autosave-recentbest.ir_solution

I saved the files from another crashy client and took a look.

All were about 120 KB, slightly smaller than the ones from a client running on the same puzzle. The files looked reasonable on inspection. They are most binary, with a few eyecatchers such as "VRFY" near the end. I'm assuming "VRFY" is similar to the "verify" keyword found in various other foldit files.

I tried deleting the files one-by-one in the order shown. The client wouldn't start until all four were gone.

I did a shake and wiggle once the client was running and compared the new autosave files to the old ones. I don't see any obvious differences in the overall structure. It appears autosave.ir_solution gets updated from time to time, even with the client sitting idle. There is some move information (references to ActionGlobalMinimize, ActionRepack) near the end of the new file, before the PHAS, ALGN, SCOR, and VRFY eyecatchers. Bottom line, the bad files aren't obviously corrupted or truncated.

I'll be glad to share the "bad" files with the developers.

Joined: 09/24/2012
Groups: Go Science
yes it still crashes

Answer is here:
http://fold.it/portal/node/2002315#comment-32249

All we can do is deleting the puzzle map, start again from scratch.

Forbidden:: share, close, shut down, change track, overload of the computer (e.g. using too much memory, 100% CPU etc), computer crash for other reasons (electricity disruption etc)

Allowed: save (locally), stop and start recipes, lock or screensaver, windows sleep mode, play other puzzles in other windows in parallel, hide notifications (ONLY if the network is connected !!), reset the puzzle, undos and all other tools

Risky: to play with the density map (reports of crashes when changing the threshold) but I suspect this is another (memory) problem.

In case of network disruption (no credit on the server) or hang ("freezed window", "non responding") never try anything on this client. Try to reconnect using other client, other puzzle and wait until the puzzle responds itself.

Joined: 09/24/2012
Groups: Go Science
Other forbidden

If you saved a solution, don't try to edit your comments afterwards: crash !

Joined: 09/24/2012
Groups: Go Science
crash on save

Finally I also crashed on saving local.

Joined: 09/24/2012
Groups: Go Science
aarg !

I loose my best solution rank 5 after a computer stop.

Loci's solution doesn't work for me.

log says:
CRASH: 447652

When trying to open any new Foldit client, windows7 says
"The game has previously not started up corectly.If this problem persists, please install the latest version"

Completely deleted map *foldit*\puzzles\002002315

Opening: ok, a rest puzzle :(

Trying to load a saved solution: crash

frood66's picture
User offline. Last seen 2 hours 50 min ago. Offline
Joined: 09/20/2011
Groups: Marvin's bunch
perhaps obvious advice

this puzzle is currently not fit for purpose.

Bonus science chat is after it's closure.

I suggest the puzzle is removed and fixed - then we can have the science chat. Then the puzzle can be reposted when it's fixed. This has to be more productive than what we have now?

Joined: 04/24/2014
Groups: None
Moving Chat/Puzzle Comments

Unfortunately, we're just not able to move the chat due to its last minute nature - and we do plan on working on a Round 2, as noted in the news.

Thanks for the feedback as we work on making the best of a rough situation!

LociOiling's picture
User offline. Last seen 16 min 18 sec ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
latest crashing advice

First, there was an omission in my previous post, the saved solutions are under:

*foldit*\puzzles\002002315\*userid*\*trackname*\*.ir_solution

The previous post left out *trackname*, which is "default" or the name of the track you're using.

The next part is a long sad story.

I tried stopping a client to share. Of course, the client hung due to yesterday's network outage. Anticipating this problem, I was running the procmon utility, but unfortunately it didn't give me a good idea of where the hang is. Also, I saw some Norton Security activity on the process, so I need to see what that's about. (I thought I had excluded the foldit directories from Norton's scanning, but I guess not.) I do have the procmon log if anyone's interested.

After closing the hung client, it of course crashed on restart. Deleting the autosave files in the above directory did not help. I had to delete the quicksave files as well to restart the client.

After restarting, I tried copying the quicksave files back in. There were quite a few, as the client had been running TvdL Enchanted DRW 2.8.1. Foldit apparently only checks these files at startup, so things like "save.Quickload(50)" didn't change the pose of the protein.

After closing the client again, it of course crashed again on startup. So it appears that the work done on this client has been lost, unless I can figure something out.

jamiexq's picture
User offline. Last seen 1 hour 4 min ago. Offline
Joined: 07/31/2011
am I missing something?

Why leave a puzzle up that is so obviously broken - even if it is now for zero points?

Joined: 04/24/2014
Groups: None
Zero points

While we understand that the puzzle is not very functional for a number of players, we feel the unique scientific interest of this puzzle still makes it worth exploring for those who can, without penalizing those who can't participate with it at this time. As noted in the news post, we're hoping for a simplified Round 2 that will widen the circle of participants.

Additionally, it helps us collect data and hopefully pin down the real issues behind all the trouble. Just taking it down also limits that source of data.

Appreciate the perspective, though, we know it's a tough situation for the community to be in.

alcor29's picture
User offline. Last seen 1 hour 50 min ago. Offline
Joined: 11/16/2012
think about the current status of folding 1221

74 people have been able to log in and do some work on it. Out of that maybe 15 or 25 have been able to take it pretty far. The rest are probably locked out after crashing trying to make a new track, share etc. In fact since the scores don't seem to have moved, it is possible that everyone is now locked out. So why keep it active?

Joined: 04/24/2014
Groups: None
Instead of cutting and pasting

http://fold.it/portal/node/2002315#comment-32266 I think I hit a number of the points you're concerned about in this post.

Joined: 09/24/2012
Groups: Go Science
ok for a free challenge

I'm ok with the team decision to let this puzzle running for 0 points.

My investment would not be completely lost and no player would be penalized.

Moreover, I find it quite challenging to try a puzzle in one unique run at a time (no share, no parallel track, no stop). A kind of pure "hand fold" or "devprev-type" round without points.

A good way to train for this new type of puzzle.

Joined: 04/24/2014
Groups: None
Thanks Bruno!

Appreciate your positive attitude here! :)

Joined: 09/24/2012
Groups: Go Science
Suggestion of a new "Soloist" puzzle category

I would even make it a suggestion for the "hand fold" category (or a new "soloist only" category).

Hand fold is boring and time consuming because we cannot use any lua recipe.

A "no share" puzzle type round has some identical advantages like allowing for more diverse explorations to be evolved in a second round only.

bertro's picture
User offline. Last seen 4 hours 37 min ago. Offline
Joined: 05/02/2011
Groups: Beta Folders
Crash on changing Threshold in ED

This is the 2nd time it happens. I cannot change the Threshold in ED without crashing the puzzle.

I am running latest devprev under win10.

=====>>>> This the end of the log.txt:

Playing sound: 4
***** ENDING THREAD ActionRepack
***** STARTING THREAD ActionGlobalMinimize
Sending SOPs:

Entering IRC::run
updating surface...

UNHANDLED EXCEPTION
1: RaiseException +72 bytes (no line)
2: library_main +46809519 bytes (no line)
3: library_main +46800642 bytes (no line)
4: library_main +5260018 bytes (no line)
5: library_main +5259363 bytes (no line)
6: library_main +4929227 bytes (no line)
7: library_main +4342635 bytes (no line)
8: library_main +5222208 bytes (no line)
9: library_main +6508664 bytes (no line)
10: library_main +4688525 bytes (no line)
11: library_main +6292050 bytes (no line)
12: library_main +4003108 bytes (no line)
13: library_main +29675 bytes (no line)
14: library_main +21 bytes (no line)
15: no symbol (no line)
16: no symbol (no line)
17: no symbol (no line)
18: BaseThreadInitThunk +36 bytes (no line)
19: RtlUnicodeStringToInteger +595 bytes (no line)
20: RtlUnicodeStringToInteger +542 bytes (no line)
IRC::run error, code = 5, desc = Remote connection closed
Exiting IRC::run

=====>>> and debug.txt:

version: 1
{
"build_id" : "20160331-69bf47620a-win_x86-devprev"
"crash_id" : "0d9484aa-ec53-4618-926b-c5798dd8cb21"
"current_actions" : ""
"current_tool" : ""
"file" : "core/chemical/gasteiger/GasteigerAtomTypeSet.cc:58"
"machine_id" : "09edfe6b-95dc-4576-888d-aeeae5d74622"
"macro_id" : "-1"
"message" : "Unable to open gasteiger atom type file: cmp-database-45bbcddcbd4174e67b82569775fde821\\database\\chemical/gasteiger/default/atom_type_data.txt"
"player_id" : "253386"
"puzzle_id" : "0"
"puzzle_running_time" : "2503591"
"running_time" : "2.50359e+006"
"timestamp" : "1461089008"
}
verify: 41ed27e7cd12650289d5b4b361728802

====>>> Note that "cmp-database-45bbcddcbd4174e67b82569775fde821\\database\\chemical/gasteiger/default/atom_type_data.txt" does not exist on my foldit install. Under 'chemical' are only: atom_type_sets, carbohydrates, element_sets, mm_atom_type_sets, orbital_type_sets and residue_type_sets.

alcor29's picture
User offline. Last seen 1 hour 50 min ago. Offline
Joined: 11/16/2012
This is how I crashed after running ok for a few hours.

This is how I crashed after running ok for a few hours.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons