1221: Disordered Electron Density: Round 1

Closed since almost 10 years ago

Summary

• Created: April 17, 2016
• Expires: April 24, 2016 at 23:00 UTC
• Max points: 100

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!

Top groups

• 1. Go Science 100 pts. 10,353
• 2. Contenders 77 pts. 10,328
• 3. Beta Folders 58 pts. 10,313
• 4. Anthropic Dreams 43 pts. 9,849
• 5. BOINC@Poland 31 pts. 9,820
• 6. Gargleblasters 22 pts. 9,755
• 7. L'Alliance Francophone 15 pts. 9,282
• 8. HMT heritage 11 pts. 8,863
• 9. Italiani Al Lavoro 7 pts. 8,661
• 10. Deleted group pts. 8,308

Top soloists

• 1. dcrwheeler 100 pts. 10,450
• 2. Bruno Kestemont 97 pts. 10,353
• 3. Bletchley Park 94 pts. 10,328
• 4. bertro 91 pts. 10,313
• 5. pauldunn 88 pts. 10,257
• 6. gloverd 85 pts. 10,253
• 7. mirp 82 pts. 9,936
• 8. mimi 79 pts. 9,919
• 9. jamiexq 76 pts. 9,849
• 10. kitek314_pl 74 pts. 9,820

Comments

[bertro]

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.

[bertro]

===»> Log.txt

args passed:
'F:\FolditNEW\Main A\Foldit\Foldit.exe'
starting the init thread!..
boinc base url: https://fold.it
checking updates…
binary
local: 'c2642c6c2819dc6eb1eccc7dfce6539b'
remote: 'c2642c6c2819dc6eb1eccc7dfce6539b'
database
local: '45bbcddcbd4174e67b82569775fde821'
remote: '45bbcddcbd4174e67b82569775fde821'
resources
local: 'f3f5689675a05a73fb3d5d1f6e8950e6'
remote: 'f3f5689675a05a73fb3d5d1f6e8950e6'
cleaning up old components:
binary 00000000000000000000000000000000
binary c2642c6c2819dc6eb1eccc7dfce6539b
database 45bbcddcbd4174e67b82569775fde821
resources 00000000000000000000000000000000
resources f3f5689675a05a73fb3d5d1f6e8950e6
SoundTheme::load: cmp-resources-f3f5689675a05a73fb3d5d1f6e8950e6\resources\sounds/organic_01
loading: cmp-resources-f3f5689675a05a73fb3d5d1f6e8950e6\resources\sounds/organic_01/rotamer_land_00.ogg
loading: cmp-resources-f3f5689675a05a73fb3d5d1f6e8950e6\resources\sounds/organic_01/rotamer_land_01.ogg
loading: cmp-resources-f3f5689675a05a73fb3d5d1f6e8950e6\resources\sounds/organic_01/rotamer_land_02.ogg
loading: cmp-resources-f3f5689675a05a73fb3d5d1f6e8950e6\resources\sounds/organic_01/rotamer_land_03.ogg
loading: cmp-resources-f3f5689675a05a73fb3d5d1f6e8950e6\resources\sounds/organic_01/rotamer_land_04.ogg
loading: cmp-resources-f3f5689675a05a73fb3d5d1f6e8950e6\resources\sounds/organic_01/rotamer_land_05.ogg
SVM classifier successfully loaded
Feature list successfully loaded
Valid classifier feature list
[0mcore.conformation.Conformation: [0m[ WARNING ] missing heavyatom: OXT on residue LEU:CtermProteinFull 21
[0mcore.conformation.Conformation: [0m[ WARNING ] missing heavyatom: OXT on residue GLU:CtermProteinFull 21
[0mcore.conformation.Conformation: [0m[ WARNING ] missing heavyatom: OXT on residue LYS:CtermProteinFull 21
[0mcore.conformation.Conformation: [0m[ WARNING ] missing heavyatom: OXT on residue ARG:CtermProteinFull 21
[0mcore.conformation.Conformation: [0m[ WARNING ] missing heavyatom: OXT on residue ASP:CtermProteinFull 21
[0mcore.conformation.Conformation: [0m[ WARNING ] missing heavyatom: OXT on residue LEU:CtermProteinFull 17
[0mcore.conformation.Conformation: [0m[ WARNING ] missing heavyatom: OXT on residue THR:CtermProteinFull 16
[0mcore.conformation.Conformation: [0m[ WARNING ] missing heavyatom: OXT on residue VAL:CtermProteinFull 17
[0mcore.conformation.Conformation: [0m[ WARNING ] missing heavyatom: OXT on residue ARG:CtermProteinFull 17
[0mcore.conformation.Conformation: [0m[ WARNING ] missing heavyatom: OXT on residue LYS:CtermProteinFull 16
[0mcore.conformation.Conformation: [0m[ WARNING ] missing heavyatom: OXT on residue ASN:CtermProteinFull 16
[0mcore.conformation.Conformation: [0m[ WARNING ] missing heavyatom: OXT on residue GLU:CtermProteinFull 16
[0mcore.conformation.Conformation: [0m[ WARNING ] missing heavyatom: OXT on residue ASP:CtermProteinFull 13
[0mcore.conformation.Conformation: [0m[ WARNING ] missing heavyatom: OXT on residue ARG:CtermProteinFull 12
[0mcore.conformation.Conformation: [0m[ WARNING ] missing heavyatom: OXT on residue GLU:CtermProteinFull 12
[0mcore.conformation.Conformation: [0m[ WARNING ] missing heavyatom: OXT on residue ASN:CtermProteinFull 12
buildid: 20160331-69bf47620a-win_x86-devprev
about to create view_options_button_
Duplicate hotkey Shift+L (Show outlines, )
setting side chain mode to: 0 Don't Show (Fast)
Playing: sounds/organic_01/splashscreen.ogg
Converting any old-style quicksaves and autosaves…
Deleting any old temporary autosaves and quicksaves…
Reading in vall_torsions file: cmp-database-45bbcddcbd4174e67b82569775fde821\database\sampling/rna/1jj2.torsions
Lines read from vall_torsions file: 2754
Sending SOPs:

Sending SOPs:

About to show the puzzle screen…
Trying to get the puzzle list…
Loading cache…
Parsing puzzle URL…
Parsing contests…
Parsing macros…
Saving the cache…
Parsing level completion…
Sending SOPs:

Initting the list…
Got the puzzles…
Sending SOPs:

Finished show_puzzle_screen…
has key .odensity
has key .owts
has key .params
has key .2.params
has key .opdb
has key .opuzzle_setup
has key .ocnstr
starting score : 7164.54
puzzle loaded
[0mWarning: [0mUnable to locate database file chemical/gasteiger/default/atom_type_data.txt
[0m[1m[31m
ERROR: Unable to open gasteiger atom type file: cmp-database-45bbcddcbd4174e67b82569775fde821\database\chemical/gasteiger/default/atom_type_data.txt
ERROR:: Exit from: ......\source\src\core\chemical\gasteiger\GasteigerAtomTypeSet.cc line: 58
[0m
UNHANDLED EXCEPTION
1: RaiseException +72 bytes (no line)
2: library_main +46809519 bytes (no line)
3: library_main +44830496 bytes (no line)
4: library_main +44218969 bytes (no line)
5: library_main +42812450 bytes (no line)
6: library_main +4279842 bytes (no line)
7: library_main +4138407 bytes (no line)
8: library_main +3254560 bytes (no line)
9: library_main +3251722 bytes (no line)
10: library_main +407818 bytes (no line)
11: library_main +663143 bytes (no line)
12: library_main +3310807 bytes (no line)
13: library_main +3386333 bytes (no line)
14: library_main +678689 bytes (no line)
15: library_main +675098 bytes (no line)
16: library_main +841039 bytes (no line)
17: library_main +480242 bytes (no line)
18: library_main +861729 bytes (no line)
19: library_main +549791 bytes (no line)
20: library_main +404801 bytes (no line)
21: library_main +4356837 bytes (no line)
22: library_main +4357291 bytes (no line)
23: BaseThreadInitThunk +36 bytes (no line)
24: RtlUnicodeStringToInteger +595 bytes (no line)
25: RtlUnicodeStringToInteger +542 bytes (no line)

===»> Debug.txt

version: 1
{
"build_id" : "20160331-69bf47620a-win_x86-devprev"
"crash_id" : "cd7681d6-1aa9-4671-b5a1-aefb58761187"
"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" : "2002315"
"puzzle_running_time" : "0"
"running_time" : "2.5774e+006"
"timestamp" : "1461162818"
}
verify: bed796190956960a92ef109636f44c5a

[alcor29]

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

[dizzywings]

Will puzzle still affect achievements like moves and top 10, 20, 30? If not I may just save and wait on it.

[inkycatz]

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.

[inkycatz]

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

[inkycatz]

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!

[inkycatz]

Appreciate your positive attitude here! :)

[Bruno Kestemont]

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.

[Bruno Kestemont]

1) Zero points means that it will not change anything in our overall ranking (=> indeed you may save and wait)

2) If they technically succeed "allowing players to load solutions from this puzzle", then the ones with a high solution for this puzzle would have an advantage on the others for second round.

From an overall ranking point of view, playing this puzzle is thus a "small positive sum game". :D