puzzle picture
1315: Electron Density Reconstruction 2
Status: Closed

Summary

Name: 1315: Electron Density Reconstruction 2
Status: Closed
Created: 12/07/2016
Points: 0
Expired: 12/14/2016 - 23:00
Difficulty: Intermediate
Description: Note: This puzzle was closed early due to a large number of crash reports.

The structure of this protein has already been solved and published, but close inspection suggests that there are some problems with the published solution. We'd like to see if Foldit players can use the same electron density data to reconstruct a better model! For this particular target, we have some key experimental data that may provide hints about the structure: This protein contains three cysteines, two of which oxidize to form a disulfide bond. This structure also contains a copper ion, which has been already been placed in the density for you. Three residues are known to interact with this copper ion: HIS 46, CYS 112, and HIS 117. Secondary structure predictions (from PSIPRED) are marked on the starting structure, and provide clues about where the protein might form helices and sheets!

Sequence:
AECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHSWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGHSALLKGTLTLK
Categories:

Top Groups

RankGroupScorePoints
1Go Science10,0010
2Anthropic Dreams9,0760
3xkcd8,7530
4Gargleblasters8,7300
5L'Alliance Francophone8,6860

Top Soloists

RankPlayerGroupScorePoints
1Glen B 74 1616  10,2070
2ZeroLeak7 74 78 Go Science10,0010
3caglar 74 443 Go Science9,8770
4g_b 74 25  9,7850
5YeshuaLives 74 1616  9,5300


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Comments

bertro's picture
User offline. Last seen 41 weeks 4 days ago. Offline
Joined: 05/02/2011
Groups: Beta Folders
Cannot reload the puzzle

Cannot reload the puzzle once I played it and close the client. It crashes...

log.txt:

Finished show_puzzle_screen...
has key .ocmdline
has key .odensity
has key .owts
has key .params
has key .opdb
has key .opuzzle_setup
has key .ofilters
core.scoring.electron_density.xray_scattering: [ WARNING ] Unknown atom CU
starting score : 20542.8
puzzle loaded

ERROR: Cannot type atom with element 'Cu'
ERROR:: Exit from: ..\..\..\source\src\core\chemical\atomtype_support.cc line: 277

UNHANDLED EXCEPTION
1: RaiseException +98 bytes (no line)
2: alIsAuxiliaryEffectSlot +611704 bytes (no line)
3: library_main +36595372 bytes (no line)
4: library_main +35457859 bytes (no line)
5: library_main +3582435 bytes (no line)
6: library_main +3127156 bytes (no line)
7: library_main +1521280 bytes (no line)
8: library_main +1518378 bytes (no line)
9: library_main +1584645 bytes (no line)
10: library_main +1729308 bytes (no line)
11: library_main +2301806 bytes (no line)
12: library_main +2354829 bytes (no line)
13: library_main +1738511 bytes (no line)
14: library_main +1733631 bytes (no line)
15: library_main +103682 bytes (no line)
16: library_main +210778 bytes (no line)
17: library_main +124959 bytes (no line)
18: library_main +317096 bytes (no line)
19: library_main +3236885 bytes (no line)
20: library_main +3237339 bytes (no line)
21: BaseThreadInitThunk +36 bytes (no line)
22: RtlSubscribeWnfStateChangeNotification +1081 bytes (no line)
23: RtlSubscribeWnfStateChangeNotification +1028 bytes (no line)

LociOiling's picture
User offline. Last seen 45 min 5 sec ago. Offline
Joined: 12/27/2012
Copper the culprit?

On Windows, I see debug.txt with the message "Cannot type atom with element 'Cu'".

See also feedback 2003188.

SaraL's picture
User offline. Last seen 1 year 22 weeks ago. Offline
Joined: 09/20/2011
Groups: Gargleblasters
crash

I''m also crashing.

Problem signature:
Problem Event Name: APPCRASH
Application Name: Foldit.exe
Application Version: 0.0.0.0
Application Timestamp: 5795a631
Fault Module Name: KERNELBASE.dll
Fault Module Version: 6.1.7601.23569
Fault Module Timestamp: 57f7bc1f
Exception Code: e06d7363
Exception Offset: 0000c54f
OS Version: 6.1.7601.2.1.0.768.3
Locale ID: 1033
Additional Information 1: 0a9e
Additional Information 2: 0a9e372d3b4ad19135b953a78882e789
Additional Information 3: 0a9e
Additional Information 4: 0a9e372d3b4ad19135b953a78882e789

SaraL's picture
User offline. Last seen 1 year 22 weeks ago. Offline
Joined: 09/20/2011
Groups: Gargleblasters
additional information-

Debug.txt - looks like the same as above!
version: 1
{
"build_id" : "20161026-4422e3a127-win_x86"
"crash_id" : "c0cae7f5-fe61-4816-933e-f02aa351e4ec"
"current_actions" : ""
"current_tool" : ""
"file" : "core/chemical/atomtype_support.cc:277"
"machine_id" : "cc92676a-e14b-4fce-a9c8-c2c9716f244d"
"macro_id" : "-1"
"message" : "Cannot type atom with element 'Cu'"
"player_id" : "286843"
"puzzle_id" : "0"
"puzzle_running_time" : "1359"
"running_time" : "1359.16"
"timestamp" : "1481198902"
}
verify: 24d1f5bec3f8b6f29d43afb238e3ef3c

inkycatz's picture
User offline. Last seen 5 years 1 week ago. Offline
Joined: 04/24/2014
Groups: None
I've let the team know about

I've let the team know about the thread here and in feedback.

gitwut's picture
User offline. Last seen 3 years 20 weeks ago. Offline
Joined: 05/18/2012
Groups: Contenders
Feedback posted about segment 129

Puzzle 1315, segment 129 (?)

https://fold.it/portal/node/2003192

LociOiling's picture
User offline. Last seen 45 min 5 sec ago. Offline
Joined: 12/27/2012
Looks like segment 129 is the copper ion

Once you pointed it out, it's still kind of hard to see. I had to switch to light background and turn off the density to see it.

bkoep's picture
User offline. Last seen 2 hours 50 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Thanks for the feedback!

We're still not certain of the reason for these crashes. However, your shared logs and crash reports will be very helpful in tracking down the problem. We appreciate your patience!

LociOiling's picture
User offline. Last seen 45 min 5 sec ago. Offline
Joined: 12/27/2012
more on the copper ligand

For some reason, the copper ion at segment 129 reports five atoms.

print ( "atoms = " .. structure.GetAtomCount ( 129 ) )

atoms = 5

bkoep's picture
User offline. Last seen 2 hours 50 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Rosetta quirk

Yes, at some point in Rosetta's history, it seems that all residues were assumed to have more than one atom. In special cases like this, where it's desirable to have a "residue" with a single atom, the quick-and-dirty solution was simply to tack on a few virtual atoms. The virtual atoms aren't modeled with any physical properties, but they play nicely with some other constructs in the Rosetta code base.

LociOiling's picture
User offline. Last seen 45 min 5 sec ago. Offline
Joined: 12/27/2012
virtual atoms are still bandable...

I guess the virtual atoms do have a position in space.

Try this code for on the starting pose for puzzle 1315:

local ac129 = structure.GetAtomCount ( 129 )
print ( "segment 129 atom count = " .. ac129 )
for ii = 1, ac129 do
band.AddBetweenSegments ( 7, 129, 5, ii )
end

Unfortunately, I can't seem to post an image at the moment. The band to atom 1 of segment 129 goes to the ball representing the copper atom. The remaining bands go to points in space near the copper atom. Unlike normal spacebands, they are "headless".

brow42's picture
User offline. Last seen 2 years 2 weeks ago. Offline
Joined: 09/19/2011
Groups: None
Metalloproteins

I'm really glad you've tried to include the metal atom; I really can't see how we can fold accurately if they are missing. It's too bad that it's crashing Rosetta and showing other anomalies. I hope they can be worked out.

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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, Boehringer Ingelheim, RosettaCommons