688b: error reading: problem with non polymer bonds.

Case number:845829-994816
Topic:Crash/Hang
Opened by:truestone
Status:Closed
Type:Bug
Opened on:Sunday, March 24, 2013 - 12:37
Last modified:Thursday, October 3, 2013 - 01:02

I introduced a few disulfide bond in my 688b solution until I found one that seemed to stick. It happens to be between the monomeres. I settled everything until close to my best. Then when restarting foldit, it refuses to load the solution saying "problem with non polymer bonds." Log says:

loading solution: puzzle_994769_time_1364091890.ir_solution
core.conformation.symmetry.SymmData: Setting weight of master jump ( jump-id=1 ) to 1.0 (was undefined)
core.conformation.symmetry.SymmData: Setting jump_group GJDB: [master 1] 2:0
core.conformation.symmetry.SymmData: symmetry name: c2
core.conformation.symmetry.SymmData: number of subunits: 2
core.conformation.symmetry.SymmData: number of interfaces: 1
core.conformation.symmetry.SymmData: score subunit number: BD11
core.conformation.symmetry.SymmData: anchor the subunits at residue: 42
core.conformation.symmetry.SymmData: Virtual coordinate system BD11
core.conformation.symmetry.SymmData: x: 1 0 0
core.conformation.symmetry.SymmData: y: 0 1 0
core.conformation.symmetry.SymmData: origin: 0 0 0
core.conformation.symmetry.SymmData: Virtual coordinate system BD12
core.conformation.symmetry.SymmData: x: -1 0 0
core.conformation.symmetry.SymmData: y: 0 -1 0
core.conformation.symmetry.SymmData: origin: 0 0 0
core.conformation.symmetry.SymmData: Dof for jump: 1
core.conformation.symmetry.SymmData: x 0:0,0:0,0 n2c
core.conformation.symmetry.SymmData: y 1:0,0:0,0 n2c
core.conformation.symmetry.SymmData: z 1:0,0:0,0 n2c
core.conformation.symmetry.SymmData: x_angle 1:0,0:0,0 n2c
core.conformation.symmetry.SymmData: y_angle 1:0,0:0,0 n2c
core.conformation.symmetry.SymmData: z_angle 1:0,0:0,0 n2c
core.conformation.symmetry.SymmData: Jump J1 BD11 BD12
core.conformation.symmetry.SymmData: Jump JDB11 BD11 SUBUNIT
core.conformation.symmetry.SymmData: Jump JDB12 BD12 SUBUNIT
core.conformation.symmetry.SymmData: Include subunit: 1 2
core.conformation.symmetry.SymmData: Output subunit: 1 2
core.conformation.symmetry.SymmData: SlideType: RANDOM
core.conformation.symmetry.SymmData: SlideCriteriaType: CEN_DOCK_SCORE
core.conformation.symmetry.SymmData: SlideCriteriaVal: AUTOMATIC
core.conformation.symmetry.SymmData: SlideOrder: none
core.conformation.symmetry.SymmData: Setting weight of master jump ( jump-id=1 ) to 1.0 (was undefined)
core.conformation.symmetry.SymmData: Setting jump_group GJDB: [master 1] 2:0
core.conformation.symmetry.SymmData: symmetry name: c2
core.conformation.symmetry.SymmData: number of subunits: 2
core.conformation.symmetry.SymmData: number of interfaces: 1
core.conformation.symmetry.SymmData: score subunit number: BD11
core.conformation.symmetry.SymmData: anchor the subunits at residue: 42
core.conformation.symmetry.SymmData: Virtual coordinate system BD11
core.conformation.symmetry.SymmData: x: 1 0 0
core.conformation.symmetry.SymmData: y: 0 1 0
core.conformation.symmetry.SymmData: origin: 0 0 0
core.conformation.symmetry.SymmData: Virtual coordinate system BD12
core.conformation.symmetry.SymmData: x: -1 0 0
core.conformation.symmetry.SymmData: y: 0 -1 0
core.conformation.symmetry.SymmData: origin: 0 0 0
core.conformation.symmetry.SymmData: Dof for jump: 1
core.conformation.symmetry.SymmData: x 0:0,0:0,0 n2c
core.conformation.symmetry.SymmData: y 1:0,0:0,0 n2c
core.conformation.symmetry.SymmData: z 1:0,0:0,0 n2c
core.conformation.symmetry.SymmData: x_angle 1:0,0:0,0 n2c
core.conformation.symmetry.SymmData: y_angle 1:0,0:0,0 n2c
core.conformation.symmetry.SymmData: z_angle 1:0,0:0,0 n2c
core.conformation.symmetry.SymmData: Jump J1 BD11 BD12
core.conformation.symmetry.SymmData: Jump JDB11 BD11 SUBUNIT
core.conformation.symmetry.SymmData: Jump JDB12 BD12 SUBUNIT
core.conformation.symmetry.SymmData: Include subunit: 1 2
core.conformation.symmetry.SymmData: Output subunit: 1 2
core.conformation.symmetry.SymmData: SlideType: RANDOM
core.conformation.symmetry.SymmData: SlideCriteriaType: CEN_DOCK_SCORE
core.conformation.symmetry.SymmData: SlideCriteriaVal: AUTOMATIC
core.conformation.symmetry.SymmData: SlideOrder: none
core.pose.util: WARNING: conf2pdb_chain(): PDBInfo does not exist, returning empty map
core.conformation.symmetry.util: =================== SYM FOLD TREE, jump notation: =symfixed= *indep* #symdof# jump[=follows] ========================
BD11(85)
|----#j5#---->Sub1

(Sun, 03/24/2013 - 12:37  |  6 comments)


Joined: 12/06/2008
Groups: Contenders
Topic: General » Crash/Hang

Bumping this feedback up to the top, since it was never resolved, and I'm having the exact problem on puzzle # 783. Anyone else?

brow42's picture
User offline. Last seen 51 weeks 4 days ago. Offline
Joined: 09/19/2011
Groups: None

This is a HIGH priority error. Once you close your client, you cannot load your solution. Every time I have loaded this puzzle, I've started back at the denovo, with no best in the track.

A possible work-around is to manually rotate your cysteines to break bridges before saving. I cannot test this, because I cannot load my solution.

brow42's picture
User offline. Last seen 51 weeks 4 days ago. Offline
Joined: 09/19/2011
Groups: None

Operation ID: ClientInformation Correlation ID: 61880
SOP Success Operation ID: ReportAchievements Correlation ID: 61879
core.pose.util: WARNING: conf2pdb_chain(): PDBInfo does not exist, returning default map 1=A, 2=B, ...
core.conformation.symmetry.Conformation: Found disulfide between residues 1 26
core.conformation.symmetry.Conformation: current variant for 1 CYD
core.conformation.symmetry.Conformation: current variant for 26 CYD
core.conformation.symmetry.Conformation: current variant for 1 CYD
core.conformation.symmetry.Conformation: current variant for 26 CYD
core.conformation.symmetry.Conformation: Found disulfide between residues 12 49
core.conformation.symmetry.Conformation: current variant for 12 CYD
core.conformation.symmetry.Conformation: current variant for 49 CYD
core.conformation.symmetry.Conformation: current variant for 12 CYD
core.conformation.symmetry.Conformation: current variant for 49 CYD
core.conformation.symmetry.Conformation: Found disulfide between residues 22 44
core.conformation.symmetry.Conformation: current variant for 22 CYD
core.conformation.symmetry.Conformation: current variant for 44 CYD
core.conformation.symmetry.Conformation: current variant for 22 CYD
core.conformation.symmetry.Conformation: current variant for 44 CYD
core.conformation.symmetry.Conformation: Found disulfide between residues 39 100
core.conformation.symmetry.Conformation: current variant for 39 CYD
core.conformation.symmetry.Conformation: current variant for 100 CYD
core.conformation.symmetry.Conformation: current variant for 39 CYD
core.conformation.symmetry.Conformation: current variant for 100 CYD
core.conformation.symmetry.Conformation: Found disulfide between residues 50 118
core.conformation.symmetry.Conformation: current variant for 50 CYD
core.conformation.symmetry.Conformation: current variant for 118 CYD
core.conformation.symmetry.Conformation: current variant for 50 CYD
core.conformation.symmetry.Conformation: current variant for 118 CYD
core.conformation.symmetry.Conformation: Found disulfide between residues 57 111
core.conformation.symmetry.Conformation: current variant for 57 CYD
core.conformation.symmetry.Conformation: current variant for 111 CYD
core.conformation.symmetry.Conformation: current variant for 57 CYD
core.conformation.symmetry.Conformation: current variant for 111 CYD
core.conformation.Conformation: Connecting residues: 62 ( CYD_p:NtermProteinFull ) and 87 ( CYD ) at atoms SG and SG
core.conformation.Conformation: with mututal distances: 3.44072 and 1.49822
core.conformation.Conformation: Connecting residues: 73 ( CYD ) and 110 ( CYD ) at atoms SG and SG
core.conformation.Conformation: with mututal distances: 0.737511 and 2.09003
core.conformation.Conformation: Connecting residues: 83 ( CYD ) and 105 ( CYD ) at atoms SG and SG
core.conformation.Conformation: with mututal distances: 0.0471812 and 2.30072
RSD CYD_p:NtermProteinFull 1 (6 2), 26 OTHER CONN INDEX OUT OF BOUNDS
RSD CYD 12 (6 3), 49
RSD 13 CYS -
RSD CYD 22 (6 3), 44
RSD CYD 26 (6 3), 1 OTHER CONN INDEX OUT OF BOUNDS
RSD CYD 39 (6 3), 100
RSD CYD 44 (6 3), 22
RSD CYD 49 (6 3), 12
RSD CYD 50 (6 3), 118
RSD 53 CYS -
RSD CYD 57 (6 3), 111
RSD CYD_p:NtermProteinFull 62 (6 2), 87 OTHER CONN INDEX OUT OF BOUNDS
RSD CYD 73 (6 3), 110
RSD 74 CYS -
RSD CYD 83 (6 3), 105
RSD CYD 87 (6 3), 62 OTHER CONN INDEX OUT OF BOUNDS
RSD CYD 100 (6 3), 39
RSD CYD 105 (6 3), 83
RSD CYD 110 (6 3), 73
RSD CYD 111 (6 3), 57
RSD 114 CYS -
RSD CYD 118 (6 3), 50
Error reading puzzle_995989_time_1380631567.ir_solution[BUFFER]; problem with non polymer bonds.
(..\..\..\source\src\interactive\util\rosetta_util.cc:1124)

brow42's picture
User offline. Last seen 51 weeks 4 days ago. Offline
Joined: 09/19/2011
Groups: None
Joined: 05/28/2012

I just had this happen to me, though i had quite a bit more cysteines than normal. and all 4 were between the bridges. I cannot open my save at all and it re started me off as a de-novo.

Joined: 12/06/2008
Groups: Contenders
Status: Open » Closed

Closing this thread, as it is a duplicate, as shown by brow42.

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