Bridges in Symmetry Crash during rebuild

Case number:954892-993709
Topic:Developer Preview
Opened by:brow42
Status:Open
Type:Bug
Opened on:Wednesday, October 10, 2012 - 19:32
Last modified:Saturday, July 13, 2013 - 08:51

For 638, I've shared LonelySulfideCrasher. A simple rebuild on 33-35 will soon crash the program. My view options are clashes, exposed, sheet bonds, loop bonds, ligand constraints, score coloring, cartoon (all are loops), show all sidechains, outlines. Crash happens if show sidechain bonds is on OR off.

Originally reported by marie_s in http://fold.it/portal/node/993658#comment-20033 , however, I am in main, not devprev. I think she has reported it before on an earlier design puzzle, as well.

I get two log files. One has an unhelpful no-symbol traceback. The other has the same assertion error that marie reported. It seems the log file contents depend on which thread is running when there is a crash?

The only bridge showing in my save file is from 35 to 3, (mirrored 4 times). It is an all cysteine chain.

Tail of log:

core.conformation.Conformation: Found disulfide between residues 21 117
core.conformation.Conformation: current variant for 21 CYS
core.conformation.Conformation: current variant for 117 CYD
core.conformation.Conformation: current variant for 21 CYD
core.conformation.Conformation: current variant for 117 CYD
core.conformation.Conformation: Reverting out-of-date disulfide CYD to CYS at resid 26
core.conformation.Conformation: Found disulfide between residues 27 158
core.conformation.Conformation: current variant for 27 CYS
core.conformation.Conformation: current variant for 158 CYD
core.conformation.Conformation: current variant for 27 CYD
core.conformation.Conformation: current variant for 158 CYD
core.conformation.Conformation: Found disulfide between residues 35 103
core.conformation.Conformation: current variant for 35 CYD
core.conformation.Conformation: current variant for 103 CYD
core.conformation.Conformation: current variant for 35 CYD
core.conformation.Conformation: current variant for 103 CYD
core.conformation.Conformation: Reverting out-of-date disulfide CYD to CYS at resid 62
core.conformation.Conformation: Reverting out-of-date disulfide CYD to CYS at resid 68
core.conformation.Conformation: Found disulfide between residues 76 144
core.conformation.Conformation: current variant for 76 CYD
core.conformation.Conformation: current variant for 144 CYS
core.conformation.Conformation: current variant for 76 CYD
core.conformation.Conformation: current variant for 144 CYD
ERROR: Could not find disulfide partner for residue 21
ERROR:: Exit from: ..\..\..\rosetta_source\src\core\scoring\disulfides\FullatomDisulfideEnergyContainer.cc line: 576
ERROR: Rosetta exit unexpectedly

(Wed, 10/10/2012 - 19:32  |  7 comments)


marie_s's picture
User offline. Last seen 1 year 45 weeks ago. Offline
Joined: 05/18/2008
Groups: None

My cysteine lost its partner in hub puzzle also.
I put my log in the comment of the puzzle.

beta_helix's picture
User offline. Last seen 2 days 3 hours ago. Offline
Joined: 05/09/2008
Groups: None

assigning...

Joined: 03/18/2012
Groups: Gargleblasters

I get the same error log, about 10 seconds into a run of recipe "QuickMutate V4.53 Ligand" on a solution for 644 ("4B1.3", created by frood66). Three out of 4 runs died like this, one completed successfully.

Joined: 03/18/2012
Groups: Gargleblasters

Oh and this is on devprev, on both Windows and Mac.

tamirh's picture
User offline. Last seen 6 years 14 weeks ago. Offline
Joined: 05/11/2012

Looks like the same issue as http://fold.it/portal/node/993664 & http://fold.it/portal/node/993740

The fix will come with the next devprev version (coming soon).

brow42's picture
User offline. Last seen 6 days 16 hours ago. Offline
Joined: 09/19/2011
Groups: None
Status: Open » Closed

Probably fixed...beta said the disulfide crasher was fixed, and didn't see any problems in recent 70 segment symmetry dimer in which I put disulfide bonds.

Joined: 05/19/2009
Groups: Contenders
Topic: Crash/Hang » Developer Preview
Status: Closed » Open

Reopened, as it reappeared...

Client: 20130702-6bc01bba0e-win_x86-devprev

core.optimization.LineMinimizer: Inaccurate G! step= 7.62939e-008 Deriv= -8.71981 Finite Diff= 3.03291
core.optimization.LineMinimizer: Inaccurate G! step= 1.90735e-008 Deriv= -8.71981 Finite Diff= 3.03286
core.optimization.LineMinimizer: Inaccurate G! step= 4.76837e-009 Deriv= -8.71981 Finite Diff= 3.04212
core.optimization.LineMinimizer: Inaccurate G! step= 1.19209e-009 Deriv= -8.71981 Finite Diff= 3.03756
core.optimization.LineMinimizer: Inaccurate G! step= 2.98023e-010 Deriv= -8.71981 Finite Diff= 3.02134
core.optimization.LineMinimizer: Inaccurate G! step= 7.45058e-011 Deriv= -8.71981 Finite Diff= 3.15228
core.optimization.LineMinimizer: Inaccurate G! step= 1.86265e-011 Deriv= -8.71981 Finite Diff= 3.45955
core.optimization.LineMinimizer: Inaccurate G! step= 4.65661e-012 Deriv= -8.71981 Finite Diff= 0.138855
core.optimization.LineMinimizer: Inaccurate G! step= 1.16415e-012 Deriv= -8.71981 Finite Diff= 2.06299
CB: 0.0657299 1
TB: -43.8143 -359.921
CB: 0.000394597 1
TB: -370.345 -359.921
ERROR: Could not find disulfide partner for residue 50
ERROR:: Exit from: ..\..\..\source\src\core\scoring\disulfides\FullatomDisulfideEnergyContainer.cc line: 586

UNHANDLED EXCEPTION
1: RaiseException +88 bytes (no line)
2: library_main +29811989 bytes (no line)
3: library_main +27776607 bytes (no line)
4: library_main +25744667 bytes (no line)
5: library_main +25746319 bytes (no line)
6: library_main +22603826 bytes (no line)
7: library_main +22604263 bytes (no line)
8: library_main +20108858 bytes (no line)
9: library_main +20275740 bytes (no line)
10: library_main +4349725 bytes (no line)
11: library_main +5362453 bytes (no line)
12: library_main +3667870 bytes (no line)
13: library_main +3671206 bytes (no line)
14: BaseThreadInitThunk +18 bytes (no line)
15: RtlInitializeExceptionChain +99 bytes (no line)
16: RtlInitializeExceptionChain +54 bytes (no line)

Problem signature:
Problem Event Name: APPCRASH
Application Name: Foldit.exe
Application Version: 0.0.0.0
Application Timestamp: 4e761405
Fault Module Name: KERNELBASE.dll
Fault Module Version: 6.1.7601.17965
Fault Module Timestamp: 506dbe50
Exception Code: e06d7363
Exception Offset: 0000c41f
OS Version: 6.1.7601.2.1.0.256.48
Locale ID: 1043
Additional Information 1: 0a9e
Additional Information 2: 0a9e372d3b4ad19135b953a78882e789
Additional Information 3: 0a9e
Additional Information 4: 0a9e372d3b4ad19135b953a78882e789

Sitemap

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