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1315: Electron Density Reconstruction 2

Closed since almost 6 years ago

Intermediate

Summary


Created
December 07, 2016
Expires
Max points
100
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

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Comments


bertro Lv 1

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)

SaraL Lv 1

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 Lv 1

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

LociOiling Lv 1

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 Staff Lv 1

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 Lv 1

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

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

atoms = 5

bkoep Staff Lv 1

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.