Opened 3 years ago

Closed 3 years ago

Last modified 3 years ago

#7247 closed defect (can't reproduce)

Crash saving atomic session state

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Sessions Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5.dev202207070159 (2022-07-07 01:59:45 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x000000020440e600 (most recent call first):
  File "/private/var/folders/pv/p4r5cqd171v6y9ds5gwfnqz80000gn/T/AppTranslocation/F062FF2E-9862-4476-86EB-04FC767BDA39/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molobject.py", line 1900 in save_state
  File "/private/var/folders/pv/p4r5cqd171v6y9ds5gwfnqz80000gn/T/AppTranslocation/F062FF2E-9862-4476-86EB-04FC767BDA39/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/structure.py", line 209 in take_snapshot
  File "/private/var/folders/pv/p4r5cqd171v6y9ds5gwfnqz80000gn/T/AppTranslocation/F062FF2E-9862-4476-86EB-04FC767BDA39/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/structure.py", line 1389 in take_snapshot
  File "/private/var/folders/pv/p4r5cqd171v6y9ds5gwfnqz80000gn/T/AppTranslocation/F062FF2E-9862-4476-86EB-04FC767BDA39/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/session.py", line 285 in process
  File "/private/var/folders/pv/p4r5cqd171v6y9ds5gwfnqz80000gn/T/AppTranslocation/F062FF2E-9862-4476-86EB-04FC767BDA39/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/session.py", line 262 in discovery
  File "/private/var/folders/pv/p4r5cqd171v6y9ds5gwfnqz80000gn/T/AppTranslocation/F062FF2E-9862-4476-86EB-04FC767BDA39/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/session.py", line 625 in save
  File "/private/var/folders/pv/p4r5cqd171v6y9ds5gwfnqz80000gn/T/AppTranslocation/F062FF2E-9862-4476-86EB-04FC767BDA39/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/session.py", line 896 in save
  File "/private/var/folders/pv/p4r5cqd171v6y9ds5gwfnqz80000gn/T/AppTranslocation/F062FF2E-9862-4476-86EB-04FC767BDA39/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core_formats/__init__.py", line 84 in save
  File "/private/var/folders/pv/p4r5cqd171v6y9ds5gwfnqz80000gn/T/AppTranslocation/F062FF2E-9862-4476-86EB-04FC767BDA39/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/save_command/cmd.py", line 90 in provider_save
  File "/private/var/folders/pv/p4r5cqd171v6y9ds5gwfnqz80000gn/T/AppTranslocation/F062FF2E-9862-4476-86EB-04FC767BDA39/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
  File "/private/var/folders/pv/p4r5cqd171v6y9ds5gwfnqz80000gn/T/AppTranslocation/F062FF2E-9862-4476-86EB-04FC767BDA39/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/save_command/cmd.py", line 75 in cmd_save
  File "/private/var/folders/pv/p4r5cqd171v6y9ds5gwfnqz80000gn/T/AppTranslocation/F062FF2E-9862-4476-86EB-04FC767BDA39/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
  File "/private/var/folders/pv/p4r5cqd171v6y9ds5gwfnqz80000gn/T/AppTranslocation/F062FF2E-9862-4476-86EB-04FC767BDA39/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38 in run
  File "/private/var/folders/pv/p4r5cqd171v6y9ds5gwfnqz80000gn/T/AppTranslocation/F062FF2E-9862-4476-86EB-04FC767BDA39/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/save_command/dialog.py", line 51 in display
  File "/private/var/folders/pv/p4r5cqd171v6y9ds5gwfnqz80000gn/T/AppTranslocation/F062FF2E-9862-4476-86EB-04FC767BDA39/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/save_command/dialog.py", line 127 in show_save_file_dialog
  File "/private/var/folders/pv/p4r5cqd171v6y9ds5gwfnqz80000gn/T/AppTranslocation/F062FF2E-9862-4476-86EB-04FC767BDA39/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/save_command/dialog.py", line 116 in 
  File "/private/var/folders/pv/p4r5cqd171v6y9ds5gwfnqz80000gn/T/AppTranslocation/F062FF2E-9862-4476-86EB-04FC767BDA39/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 332 in event_loop
  File "/private/var/folders/pv/p4r5cqd171v6y9ds5gwfnqz80000gn/T/AppTranslocation/F062FF2E-9862-4476-86EB-04FC767BDA39/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 870 in init
  File "/private/var/folders/pv/p4r5cqd171v6y9ds5gwfnqz80000gn/T/AppTranslocation/F062FF2E-9862-4476-86EB-04FC767BDA39/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1021 in 
  File "/private/var/folders/pv/p4r5cqd171v6y9ds5gwfnqz80000gn/T/AppTranslocation/F062FF2E-9862-4476-86EB-04FC767BDA39/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/private/var/folders/pv/p4r5cqd171v6y9ds5gwfnqz80000gn/T/AppTranslocation/F062FF2E-9862-4476-86EB-04FC767BDA39/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main


{"app_name":"ChimeraX","timestamp":"2022-07-08 15:03:36.00 -0400","app_version":"1.5.0","slice_uuid":"9596eff5-d2be-396c-9c4e-6177235c3dae","build_version":"1.5.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.1 (21C52)","incident_id":"7CB60D32-1622-47F1-B4E2-AB9540BA1F83","name":"ChimeraX"}
{
  "uptime" : 52000,
  "procLaunch" : "2022-07-08 14:56:25.0138 -0400",
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro18,1",
  "procStartAbsTime" : 1246489074682,
  "coalitionID" : 1550,
  "osVersion" : {
    "train" : "macOS 12.1",
    "build" : "21C52",
    "releaseType" : "User"
  },
  "captureTime" : "2022-07-08 15:03:36.4226 -0400",
  "incident" : "7CB60D32-1622-47F1-B4E2-AB9540BA1F83",
  "bug_type" : "309",
  "pid" : 26011,
  "procExitAbsTime" : 1256842745332,
  "translated" : true,
  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Volumes\/VOLUME\/*\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.5.0","CFBundleVersion":"1.5.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"4CB50F8F-CD57-53CB-88FE-678E01604455","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "3ED55E4F-3DB6-4500-AA2B-4EC43B8C2983",
  "wakeTime" : 8233,
  "sleepWakeUUID" : "2622EEAA-7912-4B13-9323-3510BE1679BD",
  "sip" : "enabled",
  "vmRegionInfo" : "0x270 is not in any region.  Bytes before following region: 4365417872\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      104330000-104331000    [    4K] r-x\/r-x SM=COW  ...acOS\/ChimeraX",
  "isCorpse" : 1,
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000270","rawCodes":[1,624],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000270"},
  "ktriageinfo" : "VM - pmap_enter failed with resource shortage\nVM - pmap_enter failed with resource shortage\n",
  "vmregioninfo" : "0x270 is not in any region.  Bytes before following region: 4365417872\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      104330000-104331000    [    4K] r-x\/r-x SM=COW  ...acOS\/ChimeraX",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
  "threads" : 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  "vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=6.7G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=6.7G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               640K        5 \nActivity Tracing                   256K        1 \nCG backing stores                 1344K        4 \nCG image                            88K       22 \nColorSync                          240K       28 \nCoreAnimation                      132K       25 \nCoreGraphics                        12K        2 \nCoreUI image data                 2272K       31 \nDispatch continuations            80.0M        1 \nFoundation                          36K        2 \nKernel Alloc Once                    8K        1 \nMALLOC                             5.7G     1340 \nMALLOC guard page                  192K        9 \nMALLOC_MEDIUM (reserved)          48.0M        1         reserved VM address space (unallocated)\nMach message                        16K        4 \nOpenGL GLSL                        384K        4 \nRosetta Arena                     4096K        2 \nRosetta Generic                   1504K      373 \nRosetta IndirectBranch            2048K        1 \nRosetta JIT                      128.0M        1 \nRosetta Return Stack               840K       84 \nRosetta Thread Context             840K       84 \nSTACK GUARD                         44K       11 \nStack                            171.1M       42 \nStack Guard                       56.1M       31 \nVM_ALLOCATE                      317.4M      842 \nVM_ALLOCATE (reserved)           192.1M       13         reserved VM address space (unallocated)\n__DATA                            43.6M      665 \n__DATA_CONST                      30.1M      339 \n__DATA_DIRTY                      1622K      213 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       730.9M      151 \n__OBJC_RO                         81.8M        1 \n__OBJC_RW                         3136K        2 \n__TEXT                           771.8M      667 \n__UNICODE                          588K        1 \ndyld private memory               1184K        3 \nmapped file                        5.2G     1144 \nshared memory                     3004K       20 \nunshared pmap                     11.3M        8 \n===========                     =======  ======= \nTOTAL                             13.6G     6180 \nTOTAL, minus reserved VM space    13.3G     6180 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
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},
  "trialInfo" : {
  "rollouts" : [
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      "factorPackIds" : {
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}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.5.dev202206160031 (2022-06-16)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/lmillervedam/Documents/Dteam_LMV/Dteam_sessions/PocketFinding/20220627_indivsubunits_sitemap/pockets26S_vs_indivSubunits_V2.cxs
> format session

opened ChimeraX session  

> open
> /Users/lmillervedam/Documents/Budapest_LMV/Bteam_sessions/ESR1_PDBs_monomers_v3.cxs.20437.tmp

Unrecognized file suffix '.tmp'  

> open
> /Users/lmillervedam/Documents/Budapest_LMV/Bteam_sessions/esr1_agonist_antagonist_pdbs_H12poses.cxs

opened ChimeraX session  

> show #!276 models

> mmaker #276/D to #8/A

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
BUD-026_co_xtal_with_0.525mM_RTX_1289659-1_C2_2.00A_refmac2_tmp.pdb, chain A
(#8) with 6PFM.pdb, chain D (#276), sequence alignment score = 1113.9  
RMSD between 195 pruned atom pairs is 0.532 angstroms; (across all 228 pairs:
7.870)  
  
Drag select of 128 atoms, 106 residues, 115 bonds  

> select up

1254 atoms, 1245 bonds, 113 residues, 2 models selected  

> select up

1322 atoms, 1319 bonds, 113 residues, 2 models selected  

> select up

2117 atoms, 2152 bonds, 178 residues, 2 models selected  

> select up

5390 atoms, 5463 bonds, 464 residues, 2 models selected  

> delete sel

> hide #!276 models

> show #!330 models

> show #!329 models

> hide #!330 models

Drag select of 116 atoms, 213 residues, 101 bonds  

> select up

1748 atoms, 1762 bonds, 219 residues, 1 model selected  

> select up

1774 atoms, 1794 bonds, 219 residues, 1 model selected  

> select up

3039 atoms, 3092 bonds, 374 residues, 1 model selected  

> select up

4760 atoms, 4842 bonds, 592 residues, 1 model selected  

> select up

5765 atoms, 5696 bonds, 865 residues, 1 model selected  

> delete sel

> hide #!329 models

> show #!328 models

> show #!327 models

> show #!326 models

> select add #328/C:349

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #327/D:477

19 atoms, 17 bonds, 2 residues, 2 models selected  

> select add #326/C:321

27 atoms, 24 bonds, 3 residues, 3 models selected  

> select add #326/B:425

38 atoms, 35 bonds, 4 residues, 3 models selected  

> select add #326/B:337

49 atoms, 46 bonds, 5 residues, 3 models selected  

> select add #327/B:337

60 atoms, 57 bonds, 6 residues, 3 models selected  

> select up

853 atoms, 864 bonds, 108 residues, 3 models selected  

> select up

6526 atoms, 6653 bonds, 818 residues, 3 models selected  

> select up

6534 atoms, 6660 bonds, 819 residues, 3 models selected  

> delete sel

Drag select of 234 atoms, 345 residues, 227 bonds  
Drag select of 65 atoms, 128 residues, 58 bonds  
Drag select of 19 atoms, 114 residues, 22 bonds  
Drag select of 10 residues  

> select add #327/B:489

4788 atoms, 314 bonds, 609 residues, 3 models selected  

> select up

4947 atoms, 5012 bonds, 609 residues, 3 models selected  

> select up

4994 atoms, 5068 bonds, 609 residues, 3 models selected  

> select up

7016 atoms, 7143 bonds, 858 residues, 3 models selected  

> select up

8335 atoms, 8498 bonds, 1025 residues, 3 models selected  

> select up

9554 atoms, 9017 bonds, 1794 residues, 3 models selected  

> select up

17834 atoms, 16904 bonds, 3293 residues, 3 models selected  

> select clear

> select add #326/D:409

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #326/D:548

19 atoms, 17 bonds, 2 residues, 1 model selected  

> select add #328/D:313

27 atoms, 24 bonds, 3 residues, 2 models selected  

> select add #328/D:544

35 atoms, 31 bonds, 4 residues, 2 models selected  

> select add #328/C:512

41 atoms, 36 bonds, 5 residues, 2 models selected  

> select add #327/D:317

47 atoms, 41 bonds, 6 residues, 3 models selected  

> select add #327/D:532

55 atoms, 48 bonds, 7 residues, 3 models selected  

> select add #327/C:477

66 atoms, 58 bonds, 8 residues, 3 models selected  

> select add #327/C:544

74 atoms, 65 bonds, 9 residues, 3 models selected  

> select up

1035 atoms, 1038 bonds, 130 residues, 3 models selected  

> select up

5450 atoms, 5555 bonds, 684 residues, 3 models selected  

> delete sel

> select add #328/C:541

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #328/C:458

15 atoms, 13 bonds, 2 residues, 1 model selected  

> select add #328/D:503

26 atoms, 23 bonds, 3 residues, 1 model selected  

> select add #328/D:485

33 atoms, 29 bonds, 4 residues, 1 model selected  

> select add #328/C:426

41 atoms, 36 bonds, 5 residues, 1 model selected  

> select add #326/D:432

47 atoms, 41 bonds, 6 residues, 2 models selected  

> select add #326/D:602@C28

48 atoms, 41 bonds, 7 residues, 2 models selected  

> select up

79 atoms, 76 bonds, 7 residues, 2 models selected  

> select up

913 atoms, 925 bonds, 108 residues, 2 models selected  

> select up

1298 atoms, 1317 bonds, 158 residues, 2 models selected  

> select up

2697 atoms, 2347 bonds, 670 residues, 2 models selected  

> delete sel

> hide #!327 models

> hide #!328 models

> hide #!326 models

> show #!325 models

> show #!324 models

> show #!323 models

> show #!322 models

> show #!321 models

Drag select of 142 atoms, 276 residues, 133 bonds  
Drag select of 567 atoms, 1235 residues, 518 bonds  

> select up

12308 atoms, 12479 bonds, 1533 residues, 5 models selected  

> select up

12479 atoms, 12681 bonds, 1533 residues, 5 models selected  

> select up

15846 atoms, 16139 bonds, 1950 residues, 5 models selected  

> select up

18162 atoms, 18502 bonds, 2246 residues, 5 models selected  

> select up

19167 atoms, 18838 bonds, 2961 residues, 5 models selected  

> delete sel

Drag select of 167 atoms, 391 residues, 137 bonds  

> select up

3171 atoms, 3192 bonds, 405 residues, 5 models selected  

> select up

3369 atoms, 3416 bonds, 405 residues, 5 models selected  

> select up

4866 atoms, 4967 bonds, 596 residues, 5 models selected  

> select up

9085 atoms, 9249 bonds, 1123 residues, 5 models selected  

> delete sel

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select up

43 atoms, 12 bonds, 31 residues, 1 model selected  

> delete sel

> show #!320 models

> hide #!321 models

> hide #!322 models

> hide #!323 models

> hide #!324 models

> hide #!325 models

> show #!319 models

> show #!318 models

> show #!317 models

> show #!316 models

Drag select of 69 atoms, 452 residues, 62 bonds  

> select up

3598 atoms, 3636 bonds, 457 residues, 2 models selected  

> select up

3677 atoms, 3726 bonds, 457 residues, 2 models selected  

> select up

5468 atoms, 5563 bonds, 677 residues, 2 models selected  

> select up

6904 atoms, 7026 bonds, 863 residues, 2 models selected  

> delete sel

Drag select of 55 atoms, 147 residues, 43 bonds  

> select up

1627 atoms, 1637 bonds, 152 residues, 3 models selected  

> select up

3003 atoms, 3041 bonds, 273 residues, 3 models selected  

> select up

6050 atoms, 6122 bonds, 498 residues, 3 models selected  

> delete sel

> select add #319/B:438

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

10 atoms, 8 bonds, 2 residues, 2 models selected  

> select up

45 atoms, 48 bonds, 2 residues, 2 models selected  

> select up

178 atoms, 183 bonds, 18 residues, 2 models selected  

> select up

358 atoms, 366 bonds, 41 residues, 2 models selected  

> select up

1889 atoms, 1758 bonds, 368 residues, 2 models selected  

> delete sel

> show #!315 models

> hide #!316 models

> hide #!317 models

> hide #!318 models

> hide #!319 models

> hide #!320 models

> show #!314 models

> show #!313 models

> show #!312 models

> show #!311 models

Drag select of 142 atoms, 439 residues, 134 bonds  
Drag select of 144 residues  
Drag select of 82 residues  

> select up

5628 atoms, 3670 bonds, 670 residues, 5 models selected  

> select up

9467 atoms, 9603 bonds, 1037 residues, 5 models selected  

> select up

19349 atoms, 19632 bonds, 1934 residues, 5 models selected  

> delete sel

> select add #311/B:314

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select add #313/D:488

19 atoms, 18 bonds, 2 residues, 2 models selected  

> select up

296 atoms, 297 bonds, 42 residues, 2 models selected  

> select up

695 atoms, 704 bonds, 92 residues, 2 models selected  

> select up

700 atoms, 708 bonds, 93 residues, 2 models selected  

> select up

1155 atoms, 1170 bonds, 151 residues, 2 models selected  

> select up

1358 atoms, 1237 bonds, 296 residues, 2 models selected  

> select up

5226 atoms, 4927 bonds, 1003 residues, 2 models selected  

> select down

1358 atoms, 1237 bonds, 296 residues, 2 models selected  

> delete sel

Drag select of 219 atoms, 30 residues, 203 bonds  

> select up

453 atoms, 205 bonds, 71 residues, 4 models selected  

> select up

538 atoms, 291 bonds, 71 residues, 4 models selected  

> delete sel

> hide #!315 models

> hide #!314 models

> hide #!313 models

> hide #!312 models

> hide #!311 models

> show #!310 models

> show #!309 models

Drag select of 186 atoms, 281 residues, 162 bonds  

> select up

2236 atoms, 2260 bonds, 288 residues, 2 models selected  

> select up

2244 atoms, 2269 bonds, 288 residues, 2 models selected  

> select up

3063 atoms, 3112 bonds, 389 residues, 2 models selected  

> select up

3684 atoms, 3747 bonds, 471 residues, 2 models selected  

> delete sel

> save
> /Users/lmillervedam/Documents/Budapest_LMV/Bteam_sessions/ESR1_PDBs_singlechain_V3.cxs


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

OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.1
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,1
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 10
      L2 Cache: 20 MB
      Memory: 32 GB

Software:

    System Software Overview:

      System Version: macOS 12.1 (21C52)
      Kernel Version: Darwin 21.2.0
      Time since boot: 1 day 4:58

Graphics/Displays:

    Apple G13X:

      Chipset Model: Apple G13X
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        DELL U3419W:
          Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
          UI Looks like: 3440 x 1440 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.0.5
    Babel: 2.10.3
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.7.0
    certifi: 2021.10.8
    cftime: 1.6.1
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.5.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.6
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-CheckWaters: 1.0
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.5.dev202207070159
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.6
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.2.1
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.4
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.1
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.21.1
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.1
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    executing: 0.8.3
    filelock: 3.4.2
    fonttools: 4.34.2
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    ipykernel: 6.15.0
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.3.4
    jupyter-core: 4.10.0
    kiwisolver: 1.4.3
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.6.0
    networkx: 2.6.3
    numexpr: 2.8.3
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.12.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.30
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.1
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.1
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.2.0
    qtconsole: 5.3.1
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 62.6.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.3.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

Change History (3)

comment:1 by Eric Pettersen, 3 years ago

Cc: Tom Goddard added
Component: Unassigned → Sessions
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash saving atomic session state

comment:2 by Eric Pettersen, 3 years ago

Resolution: → can't reproduce
Status: accepted → closed

Seems to somehow be a lack of memory issue. Was using 13.6 GB at the time, hundreds of models open and gathering a Python representation of the atomic state. Error includes mention of "resource shortage".

comment:3 by Tom Goddard, 3 years ago

The machine has 32 Gbytes of memory so ChimeraX using 13.6 Gbytes does not seem like much. Hopefully we will get better C++ stack traces with a native M1 Mac ChimeraX that will show what is going on. Here they are running Intel ChimeraX under emulation on this M1 Mac and maybe that is why the crash report is missing all the C++ function names.

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