Opened 8 months ago

Closed 8 months ago

#17144 closed defect (duplicate)

Crash on Mac waking from sleep

Reported by: halle.andrews-clark@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Window Toolkit Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-13.0.1-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
  "uptime" : 72000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 502,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro17,1",
  "coalitionID" : 677,
  "osVersion" : {
    "train" : "macOS 13.0.1",
    "build" : "22A400",
    "releaseType" : "User"
  },
  "captureTime" : "2025-03-20 13:35:16.9617 +0100",
  "incident" : "BC4A8C2D-677C-4659-BDC6-DA9B813FBBAE",
  "pid" : 73606,
  "translated" : true,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-03-20 11:22:48.1895 +0100",
  "procStartAbsTime" : 1611944914889,
  "procExitAbsTime" : 1728991040204,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"33116714-09C9-5A00-BCA9-4034A28E2E8E","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "02E04C25-79CA-2EF6-F248-C1774882463F",
  "wakeTime" : 59,
  "sleepWakeUUID" : "E3394F2E-8239-4BD5-B5EC-7F295DA7C759",
  "sip" : "disabled",
  "exception" : {"codes":"0x0000000000000002, 0x0000000000000000","rawCodes":[2,0],"type":"EXC_BREAKPOINT","signal":"SIGTRAP"},
  "termination" : {"flags":0,"code":5,"namespace":"SIGNAL","indicator":"Trace\/BPT trap: 5","byProc":"exc handler","byPid":73606},
  "os_fault" : {"process":"ChimeraX"},
  "ktriageinfo" : "VM - pmap_enter retried due to resource shortage\nVM - pmap_enter retried due to resource shortage\nVM - pmap_enter retried due to resource shortage\nVM - pmap_enter retried due to resource shortage\nVM - pmap_enter retried due to resource shortage\n",
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  "faultingThread" : 0,
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===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with
> 25S rRNA /exit tunnel
> /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_0.cif"
> "/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with 25S
> rRNA /exit tunnel
> /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_1.cif"
> "/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with 25S
> rRNA /exit tunnel
> /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_2.cif"
> "/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with 25S
> rRNA /exit tunnel
> /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_3.cif"
> "/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with 25S
> rRNA /exit tunnel
> /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_4.cif"

Chain information for fold_snd1_ribs_exit_interact_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
  
Chain information for fold_snd1_ribs_exit_interact_model_1.cif #2  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
  
Chain information for fold_snd1_ribs_exit_interact_model_2.cif #3  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
  
Chain information for fold_snd1_ribs_exit_interact_model_3.cif #4  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
  
Chain information for fold_snd1_ribs_exit_interact_model_4.cif #5  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
  

> select

413705 atoms, 457795 bonds, 23350 residues, 5 models selected  

> cartoon sel

> hide sel target a

> open "/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with
> 25S rRNA /20250221_scSND1-ribosome.cxs"

Opened cryosparc_P26_J86_005_volume_map.mrc as #1, grid size 320,320,320,
pixel 1.34, shown at level 0.3, step 1, values float32  
Opened emdb 16191 as #5, grid size 420,420,420, pixel 1.08, shown at level
0.0247, step 2, values float32  
opened ChimeraX session  

> hide #!1 models

> hide #2 models

> hide #3 models

> open "/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with
> 25S rRNA /exit tunnel
> /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_0.cif"

Chain information for fold_snd1_ribs_exit_interact_model_0.cif #7  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
  

> open "/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with
> 25S rRNA /exit tunnel
> /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_1.cif"

Chain information for fold_snd1_ribs_exit_interact_model_1.cif #8  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
  

> open "/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with
> 25S rRNA /exit tunnel
> /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_2.cif"

Chain information for fold_snd1_ribs_exit_interact_model_2.cif #9  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
  

> open "/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with
> 25S rRNA /exit tunnel
> /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_3.cif"

Chain information for fold_snd1_ribs_exit_interact_model_3.cif #10  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
  

> open "/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with
> 25S rRNA /exit tunnel
> /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_4.cif"

Chain information for fold_snd1_ribs_exit_interact_model_4.cif #11  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
  

> hide #7 models

> show #7 models

> select add #7

82741 atoms, 91559 bonds, 4670 residues, 1 model selected  

> select add #8

165482 atoms, 183118 bonds, 9340 residues, 2 models selected  

> select add #9

248223 atoms, 274677 bonds, 14010 residues, 3 models selected  

> select add #10

330964 atoms, 366236 bonds, 18680 residues, 4 models selected  

> select add #11

413705 atoms, 457795 bonds, 23350 residues, 5 models selected  

> hide sel target a

> cartoon sel

> show #3 models

> show #2 models

> show #!4 models

> select clear

> ui tool show Matchmaker

> matchmaker #7 to #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 8bqx, chain BQ (#4) with fold_snd1_ribs_exit_interact_model_0.cif,
chain E (#7), sequence alignment score = 19589.3  
RMSD between 2794 pruned atom pairs is 0.843 angstroms; (across all 3301
pairs: 9.094)  
  

> ui tool show Matchmaker

> matchmaker #8 to #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 8bqx, chain BQ (#4) with fold_snd1_ribs_exit_interact_model_1.cif,
chain E (#8), sequence alignment score = 19589.3  
RMSD between 2734 pruned atom pairs is 0.939 angstroms; (across all 3301
pairs: 8.192)  
  

> ui tool show Matchmaker

> matchmaker #9 to #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 8bqx, chain BQ (#4) with fold_snd1_ribs_exit_interact_model_2.cif,
chain E (#9), sequence alignment score = 19589.3  
RMSD between 2703 pruned atom pairs is 0.914 angstroms; (across all 3301
pairs: 6.995)  
  

> ui tool show Matchmaker

> matchmaker #10 to #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 8bqx, chain BQ (#4) with fold_snd1_ribs_exit_interact_model_3.cif,
chain E (#10), sequence alignment score = 19589.3  
RMSD between 2720 pruned atom pairs is 0.870 angstroms; (across all 3301
pairs: 9.636)  
  

> ui tool show Matchmaker

> matchmaker #11 to #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 8bqx, chain BQ (#4) with fold_snd1_ribs_exit_interact_model_4.cif,
chain E (#11), sequence alignment score = 19589.3  
RMSD between 2737 pruned atom pairs is 0.854 angstroms; (across all 3301
pairs: 8.399)  
  

> select add #7

82741 atoms, 91559 bonds, 4670 residues, 1 model selected  

> select add #8

165482 atoms, 183118 bonds, 9340 residues, 2 models selected  

> select add #9

248223 atoms, 274677 bonds, 14010 residues, 3 models selected  

> select add #10

330964 atoms, 366236 bonds, 18680 residues, 4 models selected  

> select add #11

413705 atoms, 457795 bonds, 23350 residues, 5 models selected  

> cartoon sel

> hide #!4 models

> show #!4 models

> save "/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with
> 25S rRNA /exit tunnel /exit tunnel AF3 snd1.cxs"

> cartoon sel

> select add #2

416078 atoms, 460209 bonds, 23646 residues, 6 models selected  

> select subtract #2

413705 atoms, 457795 bonds, 23350 residues, 5 models selected  

> close session

> open "/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with
> 25S rRNA /exit tunnel /exit tunnel AF3 snd1.cxs" format session

Opened cryosparc_P26_J86_005_volume_map.mrc as #1, grid size 320,320,320,
pixel 1.34, shown at level 0.3, step 1, values float32  
Opened emdb 16191 as #5, grid size 420,420,420, pixel 1.08, shown at level
0.0247, step 2, values float32  
opened ChimeraX session  

> select add #1

413705 atoms, 457795 bonds, 23350 residues, 7 models selected  

> select subtract #1

413705 atoms, 457795 bonds, 23350 residues, 5 models selected  

> show #!1 models

> hide #!1 models

> cartoon sel

> show sel target ab

> close session

> open "/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with
> 25S rRNA /exit tunnel
> /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_0.cif"
> "/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with 25S
> rRNA /exit tunnel
> /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_1.cif"
> "/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with 25S
> rRNA /exit tunnel
> /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_2.cif"
> "/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with 25S
> rRNA /exit tunnel
> /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_3.cif"
> "/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with 25S
> rRNA /exit tunnel
> /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_4.cif"

Chain information for fold_snd1_ribs_exit_interact_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
  
Chain information for fold_snd1_ribs_exit_interact_model_1.cif #2  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
  
Chain information for fold_snd1_ribs_exit_interact_model_2.cif #3  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
  
Chain information for fold_snd1_ribs_exit_interact_model_3.cif #4  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
  
Chain information for fold_snd1_ribs_exit_interact_model_4.cif #5  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
  

> open "/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with
> 25S rRNA /20250221_scSND1-ribosome.cxs"

Opened cryosparc_P26_J86_005_volume_map.mrc as #1, grid size 320,320,320,
pixel 1.34, shown at level 0.3, step 1, values float32  
Opened emdb 16191 as #5, grid size 420,420,420, pixel 1.08, shown at level
0.0247, step 2, values float32  
opened ChimeraX session  

> hide #!1 models

> open "/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with
> 25S rRNA /exit tunnel
> /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_0.cif"

Chain information for fold_snd1_ribs_exit_interact_model_0.cif #7  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
  

> open "/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with
> 25S rRNA /exit tunnel
> /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_1.cif"

Chain information for fold_snd1_ribs_exit_interact_model_1.cif #8  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
  

> open "/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with
> 25S rRNA /exit tunnel
> /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_2.cif"

Chain information for fold_snd1_ribs_exit_interact_model_2.cif #9  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
  

> open "/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with
> 25S rRNA /exit tunnel
> /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_3.cif"

Chain information for fold_snd1_ribs_exit_interact_model_3.cif #10  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
  

> open "/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with
> 25S rRNA /exit tunnel
> /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_4.cif"

Chain information for fold_snd1_ribs_exit_interact_model_4.cif #11  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
  

> ui tool show Matchmaker

> matchmaker #7 to #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 8bqx, chain BQ (#4) with fold_snd1_ribs_exit_interact_model_0.cif,
chain E (#7), sequence alignment score = 19589.3  
RMSD between 2794 pruned atom pairs is 0.843 angstroms; (across all 3301
pairs: 9.094)  
  

> ui tool show Matchmaker

> matchmaker #8 to #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 8bqx, chain BQ (#4) with fold_snd1_ribs_exit_interact_model_1.cif,
chain E (#8), sequence alignment score = 19589.3  
RMSD between 2734 pruned atom pairs is 0.939 angstroms; (across all 3301
pairs: 8.192)  
  

> ui tool show Matchmaker

> matchmaker #9 to #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 8bqx, chain BQ (#4) with fold_snd1_ribs_exit_interact_model_2.cif,
chain E (#9), sequence alignment score = 19589.3  
RMSD between 2703 pruned atom pairs is 0.914 angstroms; (across all 3301
pairs: 6.995)  
  

> ui tool show Matchmaker

> matchmaker #10 to #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 8bqx, chain BQ (#4) with fold_snd1_ribs_exit_interact_model_3.cif,
chain E (#10), sequence alignment score = 19589.3  
RMSD between 2720 pruned atom pairs is 0.870 angstroms; (across all 3301
pairs: 9.636)  
  

> ui tool show Matchmaker

> matchmaker #11 to #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 8bqx, chain BQ (#4) with fold_snd1_ribs_exit_interact_model_4.cif,
chain E (#11), sequence alignment score = 19589.3  
RMSD between 2737 pruned atom pairs is 0.854 angstroms; (across all 3301
pairs: 8.399)  
  

> show #!4 models

> hide #!4 models

> select add #7

82741 atoms, 91559 bonds, 4670 residues, 1 model selected  

> select add #8

165482 atoms, 183118 bonds, 9340 residues, 2 models selected  

> select add #9

248223 atoms, 274677 bonds, 14010 residues, 3 models selected  

> select add #10

330964 atoms, 366236 bonds, 18680 residues, 4 models selected  

> select add #11

413705 atoms, 457795 bonds, 23350 residues, 5 models selected  

> cartoon sel

> hide sel target a

> select subtract #7

330964 atoms, 366236 bonds, 18680 residues, 4 models selected  

> select subtract #8

248223 atoms, 274677 bonds, 14010 residues, 3 models selected  

> select subtract #9

165482 atoms, 183118 bonds, 9340 residues, 2 models selected  

> select subtract #10

82741 atoms, 91559 bonds, 4670 residues, 1 model selected  

> select subtract #11

Nothing selected  

> hide #2 models

> select add #7

82741 atoms, 91559 bonds, 4670 residues, 1 model selected  

> select add #8

165482 atoms, 183118 bonds, 9340 residues, 2 models selected  

> select add #9

248223 atoms, 274677 bonds, 14010 residues, 3 models selected  

> select add #10

330964 atoms, 366236 bonds, 18680 residues, 4 models selected  

> select add #11

413705 atoms, 457795 bonds, 23350 residues, 5 models selected  

> color sel dim gray

> select subtract #7

330964 atoms, 366236 bonds, 18680 residues, 4 models selected  

> select subtract #8

248223 atoms, 274677 bonds, 14010 residues, 3 models selected  

> select subtract #9

165482 atoms, 183118 bonds, 9340 residues, 2 models selected  

> select subtract #10

82741 atoms, 91559 bonds, 4670 residues, 1 model selected  

> select subtract #11

Nothing selected  

> select #7/A:1-877

6914 atoms, 7029 bonds, 877 residues, 1 model selected  

> color sel red

> select #8/A:1-877

6914 atoms, 7029 bonds, 877 residues, 1 model selected  

> select #8/A:1-877

6914 atoms, 7029 bonds, 877 residues, 1 model selected  

> color sel red

> select #9/A:1-877

6914 atoms, 7029 bonds, 877 residues, 1 model selected  

> color sel red

> select #10/A:1-877

6914 atoms, 7029 bonds, 877 residues, 1 model selected  

> color sel red

> select #11/A:1-877

6914 atoms, 7029 bonds, 877 residues, 1 model selected  

> color sel red

> select clear

> select #10/A:1-877

6914 atoms, 7029 bonds, 877 residues, 1 model selected  

> select #11/A:1-877

6914 atoms, 7029 bonds, 877 residues, 1 model selected  

> select #10/A:1-877

6914 atoms, 7029 bonds, 877 residues, 1 model selected  

> select #9/A:1-877

6914 atoms, 7029 bonds, 877 residues, 1 model selected  

> select ~sel

743421 atoms, 812636 bonds, 8431 pseudobonds, 50032 residues, 18 models
selected  

> select subtract #1

743421 atoms, 812636 bonds, 8431 pseudobonds, 50032 residues, 16 models
selected  

> select subtract #2

741048 atoms, 810222 bonds, 8431 pseudobonds, 49736 residues, 15 models
selected  

> select subtract #3

738675 atoms, 807808 bonds, 8431 pseudobonds, 49440 residues, 14 models
selected  

> select subtract #4

535766 atoms, 589798 bonds, 3276 pseudobonds, 32738 residues, 10 models
selected  

> select subtract #5

535766 atoms, 589798 bonds, 3276 pseudobonds, 32738 residues, 8 models
selected  

> select subtract #6

406791 atoms, 450766 bonds, 22473 residues, 5 models selected  

> select subtract #7

324050 atoms, 359207 bonds, 17803 residues, 4 models selected  

> select subtract #8

241309 atoms, 267648 bonds, 13133 residues, 3 models selected  

> select add #9

248223 atoms, 274677 bonds, 14010 residues, 3 models selected  

> select subtract #10

165482 atoms, 183118 bonds, 9340 residues, 2 models selected  

> select subtract #11

82741 atoms, 91559 bonds, 4670 residues, 1 model selected  

> select subtract #9

Nothing selected  

> select add #7

82741 atoms, 91559 bonds, 4670 residues, 1 model selected  

> select #7/B:1-188

1522 atoms, 1539 bonds, 188 residues, 1 model selected  

> select #7/C:1-109

891 atoms, 905 bonds, 109 residues, 1 model selected  

> hide #3 models

> hide #8 models

> hide #9 models

> hide #10 models

> hide #11 models

> select add #7

82741 atoms, 91559 bonds, 4670 residues, 1 model selected  

> select subtract #7

Nothing selected  

> select #7/A:1-877

6914 atoms, 7029 bonds, 877 residues, 1 model selected  

> select ~sel

743421 atoms, 812636 bonds, 8431 pseudobonds, 50032 residues, 18 models
selected  

> cartoon hide (#7 & sel)

> hide #7 models

> show #8 models

> select #8/A:1-877

6914 atoms, 7029 bonds, 877 residues, 1 model selected  

> select ~sel

743421 atoms, 812636 bonds, 8431 pseudobonds, 50032 residues, 18 models
selected  

> cartoon hide (#8 & sel)

> hide #8 models

> show #9 models

> select #9/A:1-877

6914 atoms, 7029 bonds, 877 residues, 1 model selected  

> select ~sel

743421 atoms, 812636 bonds, 8431 pseudobonds, 50032 residues, 18 models
selected  

> cartoon hide (#9 & sel)

> hide #9 models

> show #10 models

> select #10/A:1-877

6914 atoms, 7029 bonds, 877 residues, 1 model selected  

> select ~sel

743421 atoms, 812636 bonds, 8431 pseudobonds, 50032 residues, 18 models
selected  

> cartoon hide (#10 & sel)

> hide #10 models

> show #11 models

> select #11/A:1-877

6914 atoms, 7029 bonds, 877 residues, 1 model selected  

> select ~sel

743421 atoms, 812636 bonds, 8431 pseudobonds, 50032 residues, 18 models
selected  

> cartoon hide (#11 & sel)

> show #10 models

> show #9 models

> show #8 models

> show #7 models

> show #3 models

> color #3 white

> color #3 #0100f5ff

> select subtract #1

743421 atoms, 812636 bonds, 8431 pseudobonds, 50032 residues, 16 models
selected  

> select subtract #2

741048 atoms, 810222 bonds, 8431 pseudobonds, 49736 residues, 15 models
selected  

> select subtract #3

738675 atoms, 807808 bonds, 8431 pseudobonds, 49440 residues, 14 models
selected  

> select subtract #4

535766 atoms, 589798 bonds, 3276 pseudobonds, 32738 residues, 10 models
selected  

> select subtract #5

535766 atoms, 589798 bonds, 3276 pseudobonds, 32738 residues, 8 models
selected  

> select subtract #6

406791 atoms, 450766 bonds, 22473 residues, 5 models selected  

> select subtract #7

324050 atoms, 359207 bonds, 17803 residues, 4 models selected  

> select subtract #8

241309 atoms, 267648 bonds, 13133 residues, 3 models selected  

> select subtract #9

158568 atoms, 176089 bonds, 8463 residues, 2 models selected  

> select subtract #10

75827 atoms, 84530 bonds, 3793 residues, 1 model selected  

> select add #11

82741 atoms, 91559 bonds, 4670 residues, 1 model selected  

> select subtract #11

Nothing selected  

> show #!4 models

> color #4 #4a4a4aff

> show #2 models

> hide #2 models

> save /Users/haandrew/Desktop/image36.png supersample 3

> save /Users/haandrew/Desktop/image37.png supersample 3

> save /Users/haandrew/Desktop/image38.png supersample 3

> show #2 models

> save /Users/haandrew/Desktop/image39.png supersample 3

> ui tool show "Side View"

> hide #7 models

> show #7 models

> hide #7 models

> hide #8 models

> hide #9 models

> hide #10 models

> show #10 models

> hide #11 models

> save /Users/haandrew/Desktop/image40.png supersample 3

> ui tool show "Side View"

> hide #2 models


===== Log before crash end =====

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro17,1
      Model Number: Z11D000L9D/A
      Chip: Unknown
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 8419.41.10
      OS Loader Version: 8419.41.10

Software:

    System Software Overview:

      System Version: macOS 13.0.1 (22A400)
      Kernel Version: Darwin 22.1.0
      Time since boot: 5 days, 3 hours, 2 minutes

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11

Change History (2)

comment:1 by Eric Pettersen, 8 months ago

Component: Unassigned → Window Toolkit
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash on Mac waking from sleep

comment:2 by Eric Pettersen, 8 months ago

Resolution: → duplicate
Status: assigned → closed

As per your previous report of this (ticket #17132):

ChimeraX 1.9 may encounter this crash less often. It is a bug in the Qt 6.7 window toolkit and ChimeraX 1.9 gives this message in its Report a Bug panel which explains what we know.

"This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here ​​​​https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX."

We have updated to Qt version 6.8 in the daily builds which may fix this problem, so you might consider trying the daily build.

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