![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#9409 closed defect (duplicate)
Crash handling QTimer callback
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | 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-13.4.1-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00000004005a7000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x00000001eb7dde00 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/color_button.py", line 147 in
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
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{
"uptime" : 89000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,2",
"coalitionID" : 602,
"osVersion" : {
"train" : "macOS 13.4.1",
"build" : "22F770820d",
"releaseType" : "User"
},
"captureTime" : "2023-07-19 16:23:27.0880 -0400",
"incident" : "5AF6A7E2-A810-4D45-92C0-78993FB666AE",
"pid" : 17438,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-07-19 13:30:03.3043 -0400",
"procStartAbsTime" : 1887017874788,
"procExitAbsTime" : 2136707397530,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.1","CFBundleVersion":"1.6.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"32B13DDB-F408-570B-BF11-58BEA8459E37","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "9E68BBFB-41E2-9468-5E03-195041F4BA66",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 22894,
"sleepWakeUUID" : "AA1EE3E9-2ECA-4454-9594-C6075B291B9D",
"sip" : "enabled",
"vmRegionInfo" : "0x82b is not in any region. Bytes before following region: 105557813884885\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 600118000000-600120000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)",
"exception" : {"codes":"0x0000000000000001, 0x000000000000082b","rawCodes":[1,2091],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000000000000082b"},
"vmregioninfo" : "0x82b is not in any region. Bytes before following region: 105557813884885\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 600118000000-600120000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)",
"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,
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"path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/linalg\/lapack_lite.cpython-39-darwin.so",
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===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/edk4001/Library/Mobile Documents/com~apple~CloudDocs/bps2023
> site1.cxs"
Opened HCN1_21july08_j230_run_class001_highRes_mask.mrc as #19, grid size
340,340,340, pixel 0.815, shown at level 0.399, step 1, values float32
Opened HCN1_21july08_j230_run_class001_highRes_mask.mrc copy as #21, grid size
340,340,340, pixel 0.815, shown at level 0.147, step 1, values float32
opened ChimeraX session
> ui mousemode right "play map series"
> ui mousemode right "map eraser"
> volume erase #21 center 130.59,147.81,122.15 radius 2.0103
> volume erase #21 center 131.39,147.67,122.1 radius 2.0103
> volume erase #21 center 129.54,145.42,124.29 radius 2.0103
> volume erase #21 center 131.33,145.46,124.19 radius 2.0103
> volume erase #21 center 131.44,143.72,123.47 radius 1.0051
> volume erase #21 center 132.96,148.28,121.87 radius 1.0051
> volume erase #21 center 132.97,149.69,122.42 radius 1.0051
> open "/Users/edk4001/Library/CloudStorage/Dropbox/ekim_nimigeanlab/final em
> maps/21july08_HCN1_WT_nanodisc_1mMDIPP/HCN1_21july08_j230_run_class001_highRes_mask.mrc"
Opened HCN1_21july08_j230_run_class001_highRes_mask.mrc as #23, grid size
340,340,340, pixel 0.815, shown at level 0.0458, step 2, values float32
> volume #23 step 1
> volume #23 level 0.1705
> volume #23 level 0.1938
> volume #23 level 0.2094
> volume erase #23 center 131.87,148.61,121.88 radius 0.97001
Opened HCN1_21july08_j230_run_class001_highRes_mask.mrc copy as #24, grid size
340,340,340, pixel 0.815, shown at step 1, values float32
> volume erase #24 center 131.95,148.41,121.24 radius 0.97001
> volume erase #24 center 132.15,148.36,122.56 radius 0.97001
> volume erase #24 center 132.53,148.17,123.23 radius 0.97001
> close #24
> open "/Users/edk4001/Library/CloudStorage/Dropbox/ekim_nimigeanlab/final em
> maps/21july08_HCN1_WT_nanodisc_1mMDIPP/HCN1_21july08_j230_run_class001_highRes_mask.mrc"
Opened HCN1_21july08_j230_run_class001_highRes_mask.mrc as #24, grid size
340,340,340, pixel 0.815, shown at level 0.0458, step 2, values float32
> show #!23 models
> hide #!23 models
> volume #24 step 1
> close #23
> volume #24 level 0.2912
> volume #24 level 0.2172
> volume erase #24 center 132.53,144.4,124.7 radius 0.97001
Opened HCN1_21july08_j230_run_class001_highRes_mask.mrc copy as #23, grid size
340,340,340, pixel 0.815, shown at step 1, values float32
> volume erase #23 center 133.39,144.94,124.55 radius 0.97001
> volume erase #23 center 132.03,148.53,121.41 radius 0.97001
> volume erase #23 center 132.77,147.85,122.26 radius 0.97001
> volume erase #23 center 129.19,145.84,123.95 radius 6.3743 outside true
> volume erase #23 center 130.56,149.57,125.61 radius 2.0786
> volume erase #23 center 129.35,151.49,124.45 radius 2.0786
> volume erase #23 center 126.8,151.64,123.48 radius 2.0786
> ui tool show "Side View"
> volume erase #23 center 131.89,149.95,126.39 radius 2.0786
> volume erase #23 center 130.76,151.99,126.98 radius 2.0786
> volume erase #23 center 126.87,149.85,128.3 radius 2.0786
> volume erase #23 center 127.03,148.83,128.95 radius 2.0786
> volume erase #23 center 126.16,151.47,123.57 radius 2.0786
> volume erase #23 center 130.82,145.39,128.5 radius 2.0786
> volume erase #23 center 130.36,144.33,128.79 radius 2.0786
> volume erase #23 center 131.67,146.02,128.05 radius 2.0786
> volume erase #23 center 131.48,146.52,127.65 radius 2.0786
> volume erase #23 center 131.36,147.05,127.43 radius 2.0786
> volume erase #23 center 131.71,148.37,125.28 radius 2.0786
> volume erase #23 center 132.57,144.72,128.65 radius 2.0786
> volume erase #23 center 129.4,140.93,123.21 radius 2.0786
> volume erase #23 center 128.17,140.73,125.55 radius 2.0786
> volume erase #23 center 127.34,141.06,125.18 radius 2.0786
> volume erase #23 center 130.26,140.29,123.68 radius 2.0786
> volume erase #23 center 129.95,140.14,122.22 radius 2.0786
> volume erase #23 center 127.4,141.47,119.9 radius 2.0786
> volume erase #23 center 126.22,143.71,120.64 radius 2.0786
> volume erase #23 center 126.14,141.51,121.83 radius 2.0786
> volume erase #23 center 125.83,145.18,120.08 radius 2.0786
> volume erase #23 center 132.34,143.94,119.7 radius 2.0786
> volume erase #23 center 134.08,142.97,123.95 radius 2.0786
> volume erase #23 center 134.58,142.73,124.53 radius 2.0786
> volume erase #23 center 135.68,145.34,125.45 radius 2.0786
> volume erase #23 center 133.06,149.87,120.48 radius 2.0786
> volume erase #23 center 133.39,150.29,121.73 radius 2.0786
> volume erase #23 center 131.96,142,125.33 radius 2.0786
> volume erase #23 center 133.94,146.56,124.48 radius 2.0786
> volume erase #23 center 133.76,147.34,123.92 radius 2.0786
> show #!21 models
> color #23 #941100ff models
> select add #23
4 models selected
> ui tool show "Color Actions"
> color sel fire brick
> color sel maroon
> color sel dark red
> color sel fire brick
> color #23 #9411003e models
> color #23 #94110029 models
> color #23 #94110028 models
> color #23 #94110026 models
> select clear
> color #21 #b2b2b22a models
> color #21 #b2b2b227 models
> color #21 #b2b2b222 models
> color #21 #b2b2b21c models
> color #21 #b2b2b218 models
> color #21 #b2b2b21a models
> hide #!23 models
> hide #!21 models
> select #1/C:380
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/C:383
13 atoms, 11 bonds, 2 residues, 2 models selected
> select add #1/C:384
20 atoms, 17 bonds, 3 residues, 2 models selected
> select add #1/B:357
28 atoms, 24 bonds, 4 residues, 2 models selected
> select add #1/B:386
40 atoms, 36 bonds, 5 residues, 3 models selected
> select add #1/B:389
51 atoms, 47 bonds, 6 residues, 3 models selected
> select add #1/B:302
59 atoms, 54 bonds, 7 residues, 3 models selected
> select add #1/B:305
67 atoms, 61 bonds, 8 residues, 3 models selected
> select add #1/B:306
75 atoms, 68 bonds, 9 residues, 3 models selected
> select add #1/B:309
81 atoms, 73 bonds, 10 residues, 3 models selected
> select add #1/B:353
89 atoms, 80 bonds, 11 residues, 3 models selected
> ui tool show "Color Actions"
> color sel dark slate blue
> select #1/?:1@@serial_number=12
1 atom, 1 residue, 1 model selected
> select add #1/C:384
8 atoms, 6 bonds, 2 residues, 2 models selected
> select add #1/C:383
13 atoms, 10 bonds, 3 residues, 3 models selected
> select add #1/C:380
21 atoms, 17 bonds, 4 residues, 3 models selected
> select add #1/B:357
29 atoms, 24 bonds, 5 residues, 3 models selected
> select add #1/B:353
37 atoms, 31 bonds, 6 residues, 4 models selected
> select add #1/B:309
43 atoms, 36 bonds, 7 residues, 4 models selected
> select add #1/B:306
51 atoms, 43 bonds, 8 residues, 4 models selected
> select add #1/B:305
59 atoms, 50 bonds, 9 residues, 4 models selected
> select add #1/B:302
67 atoms, 57 bonds, 10 residues, 4 models selected
> select add #1/B:389
78 atoms, 68 bonds, 11 residues, 4 models selected
> select add #1/B:386
90 atoms, 80 bonds, 12 residues, 4 models selected
> select up
102 atoms, 95 bonds, 12 residues, 4 models selected
> size sel stickRadius 0.27
Changed 95 bond radii
> select clear
> show #!21 models
> show #!23 models
> save "/Users/edk4001/Desktop/HCN1 pfl site 1 zoom.png" width 3000 height
> 2481 supersample 4 transparentBackground true
> graphics silhouettes width 6
> lighting soft
> lighting full
> lighting simple
> lighting shadows true
> lighting shadows false
> save "/Users/edk4001/Desktop/HCN1 pfl site 1 zoom.png" width 4000 height
> 3307 supersample 4 transparentBackground true
> volume #23 level 0.2021
> save "/Users/edk4001/Desktop/HCN1 pfl site 1 zoom.png" width 4000 height
> 3307 supersample 4 transparentBackground true
> open /Users/edk4001/Desktop/phenix_HCN1_21july08/21july08_isolde5-coot-5.pdb
Chain information for 21july08_isolde5-coot-5.pdb #22
---
Chain | Description
A B C D | No description available
> hide #!1 models
> show #!1 models
> select add #22
14613 atoms, 14977 bonds, 4 pseudobonds, 1941 residues, 2 models selected
> hide #!23 models
> hide #!21 models
> select #22/A,D
7300 atoms, 7482 bonds, 2 pseudobonds, 970 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #22/b
3663 atoms, 3754 bonds, 1 pseudobond, 486 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light slate gray
> color sel slate gray
> color sel light slate gray
> select #22/C
3650 atoms, 3741 bonds, 1 pseudobond, 485 residues, 2 models selected
> ui tool show "Color Actions"
> color sel pale goldenrod
> hide #!1 models
> show #!1 models
> select #22/B:601@C7
1 atom, 1 residue, 1 model selected
> select up
13 atoms, 13 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel dark red
> color sel maroon
> color sel fire brick
> color sel maroon
> select #22/B:302
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #22/B:305
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #22/B:306
24 atoms, 21 bonds, 3 residues, 1 model selected
> select add #22/B:309
30 atoms, 26 bonds, 4 residues, 1 model selected
> select add #22/B:357
38 atoms, 33 bonds, 5 residues, 1 model selected
> select add #1/B:354
44 atoms, 38 bonds, 6 residues, 2 models selected
> select subtract #1/B:354
38 atoms, 33 bonds, 5 residues, 2 models selected
> select add #1/B:353
46 atoms, 40 bonds, 6 residues, 2 models selected
> select add #22/B:353
54 atoms, 47 bonds, 7 residues, 3 models selected
> select subtract #1/B:353
46 atoms, 40 bonds, 6 residues, 2 models selected
> select subtract #22/B:353
38 atoms, 33 bonds, 5 residues, 1 model selected
> select add #22/B:353
46 atoms, 40 bonds, 6 residues, 1 model selected
> select subtract #22/B:357
38 atoms, 33 bonds, 5 residues, 1 model selected
> select add #1/B:357
46 atoms, 40 bonds, 6 residues, 2 models selected
> select subtract #1/B:357
38 atoms, 33 bonds, 5 residues, 2 models selected
> select add #22/B:357
46 atoms, 40 bonds, 6 residues, 1 model selected
> select add #22/C:380
54 atoms, 47 bonds, 7 residues, 1 model selected
> select add #22/C:384
61 atoms, 53 bonds, 8 residues, 1 model selected
> select add #22/C:383
66 atoms, 57 bonds, 9 residues, 1 model selected
> select add #22/B:389
77 atoms, 68 bonds, 10 residues, 1 model selected
> select add #22/B:386
89 atoms, 80 bonds, 11 residues, 1 model selected
> show sel atoms
> ui tool show "Color Actions"
> color sel dark slate blue
> hide #!1 models
> select add #22/B:601@C1
90 atoms, 80 bonds, 12 residues, 1 model selected
> select up
102 atoms, 95 bonds, 12 residues, 1 model selected
> size sel stickRadius 0.27
Changed 95 bond radii
> show #!23 models
> show #!21 models
> select clear
> lighting soft
> lighting simple
> lighting full
> lighting shadows false
> lighting shadows true
> lighting simple
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting full
> lighting shadows false
> save "/Users/edk4001/Desktop/HCN1 pfl site 1 zoom.png" width 4000 height
> 3307 supersample 4 transparentBackground true
> volume #23 level 0.1672
> volume #23 level 0.1486
> save "/Users/edk4001/Desktop/HCN1 pfl site 1 zoom.png" width 4000 height
> 3307 supersample 4 transparentBackground true
> save "/Users/edk4001/Desktop/HCN1 pfl site 1 zoom.cxs" includeMaps true
> save "/Users/edk4001/Desktop/HCN1 pfl site 1 zoom.png" width 4000 height
> 3307 supersample 4 transparentBackground true
> volume #23 level 0.09513
> hide #!21 models
> show #!21 models
> hide #!21 models
> ui mousemode right "map eraser"
> volume erase #23 center 124.31,151.58,122.4 radius 2.6818
> volume erase #23 center 128.65,152.95,123.27 radius 2.6818
> volume erase #23 center 132.01,152.78,124.92 radius 2.6818
> surface dust #23 size 8.15
> show #!21 models
> graphics silhouettes width 6
> color #23 #ff2600ff models
> color #23 #ff26002a models
> color #23 #ff260024 models
> color #23 #ff26001b models
> color #23 #ff260027 models
> color #23 #ff260026 models
> save "/Users/edk4001/Desktop/HCN1 pfl site 1 zoom.png" width 4000 height
> 3307 supersample 4 transparentBackground true
> save "/Users/edk4001/Desktop/HCN1 pfl site 1 zoom.cxs" includeMaps true
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> open /Users/edk4001/Desktop/phenix_HCN1_21july08/21july08_isolde5-coot-5.pdb
Chain information for 21july08_isolde5-coot-5.pdb #25
---
Chain | Description
A B C D | No description available
> hide #!23 models
> hide #!22 models
> hide #!21 models
> show #!23 models
> hide #!23 models
> show #!24 models
> volume #24 level 0.1549
> surface dust #24 size 8.15
> color #24 #d6d6d6ff models
> color #24 #d6d6d616 models
> color #24 #d6d6d631 models
> color #24 #d6d6d61f models
> color #24 #d6d6d61a models
> color #24 #d6d6d672 models
> color #24 #d6d6d62c models
> color #24 #d6d6d62e models
> color #24 #d6d6d634 models
> color #24 #d6d6d633 models
> hide #!24 models
> select #25/B
3663 atoms, 3754 bonds, 1 pseudobond, 486 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light slate gray
> lighting soft
> lighting full
> lighting simple
> lighting full
> select clear
> select #25/A,C,D
10950 atoms, 11223 bonds, 3 pseudobonds, 1455 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select clear
> select #25/B:602@C1
1 atom, 1 residue, 1 model selected
> select up
13 atoms, 13 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel maroon
> size sel stickRadius 0.27
Changed 13 bond radii
> select clear
> show #!24 models
> volume #24 level 0.1705
> color #24 #d6d6d6ff models
> show #!1 models
> hide #!24 models
> hide #!25 models
> hide #!1 models
> show #!25 models
> show #!24 models
> show #!23 models
> hide #!23 models
> hide #!24 models
> show #!24 models
> hide #!25 models
> ui mousemode right "map eraser"
> volume erase #24 center 146.24,181.09,136.81 radius 7.6004 outside true
Opened HCN1_21july08_j230_run_class001_highRes_mask.mrc copy as #27, grid size
340,340,340, pixel 0.815, shown at step 1, values float32
> volume erase #27 center 145.13,182.93,142.46 radius 2.4943
> volume erase #27 center 145.05,182.34,142.37 radius 2.4943
> volume erase #27 center 140.81,178.09,139.5 radius 2.4943
> volume erase #27 center 139.76,177.9,137.68 radius 2.4943
> volume erase #27 center 144.01,180.05,142.55 radius 2.4943
> volume erase #27 center 143.96,179.97,142.41 radius 2.4943
> volume erase #27 center 141.89,176.39,132.27 radius 2.4943
> color #27 #ff2600ff models
> color #27 #ff260010 models
> color #27 #ff260025 models
> color #27 #ff260026 models
> color #27 #ff260027 models
> show #!25 models
> color #27 #ff260026 models
> show #!24 models
> hide #!24 models
> hide #!25 models
> hide #!27 models
> show #!24 models
> ui mousemode right "map eraser"
> volume erase #24 center 145.88,164.03,135.58 radius 18.953 outside true
Opened HCN1_21july08_j230_run_class001_highRes_mask.mrc copy as #28, grid size
340,340,340, pixel 0.815, shown at step 1, values float32
> show #!27 models
> show #!24 models
> color #28 #fffc79ff models
> hide #!27 models
> hide #!24 models
> volume erase #28 center 140.65,178.1,137.91 radius 5.8201
> volume erase #28 center 142.43,180.15,140.89 radius 5.8201
> volume erase #28 center 132.71,175.9,130.96 radius 5.8201
> volume erase #28 center 133.14,177.14,137.65 radius 5.8201
> volume erase #28 center 133.89,177.06,140.13 radius 5.8201
> volume erase #28 center 134.09,177.26,141.05 radius 5.8201
> volume erase #28 center 138.02,180.64,133.77 radius 5.8201
> volume erase #28 center 133.47,172.71,133.77 radius 5.1272
> volume erase #28 center 134.21,175.85,137.09 radius 5.1272
> volume erase #28 center 136.35,177.14,135.72 radius 5.1272
> volume erase #28 center 135.61,176.86,128.88 radius 5.1272
> volume erase #28 center 137.17,173.83,125.71 radius 5.1272
> volume erase #28 center 142.08,176.32,129.09 radius 5.1272
> volume erase #28 center 148.5,168.2,148.12 radius 5.1272
> volume erase #28 center 136.19,167.82,148.77 radius 5.1272
> volume erase #28 center 131.52,172.79,144.77 radius 5.1272
> volume erase #28 center 131.84,171.09,148.14 radius 5.1272
> volume erase #28 center 126.52,167.55,138.8 radius 5.1272
> volume erase #28 center 128.13,160.02,139.17 radius 4.0186
> volume erase #28 center 129.42,167,134.45 radius 4.0186
> volume erase #28 center 128.32,163.71,134.03 radius 4.0186
> volume erase #28 center 129.01,165.62,131.38 radius 4.0186
> volume erase #28 center 129.5,167.34,128.3 radius 4.0186
> volume erase #28 center 131.42,169.69,125.91 radius 4.0186
> volume erase #28 center 132.47,170.27,123.91 radius 4.0186
> surface dust #28 size 8.15
> volume erase #28 center 140.26,152.03,120.22 radius 4.0186
> volume erase #28 center 153.87,148.28,142.38 radius 14.827
> volume erase #28 center 155.39,146.15,138.27 radius 14.827
> show #!27 models
> show #!24 models
> show #!25 models
> color #24 #d6d6d61b models
> color #24 #d6d6d621 models
> color #24 #d6d6d61e models
> color #24 #d6d6d61b models
> color #24 #d6d6d618 models
> color #24 #d6d6d619 models
> color #24 #d6d6d61a models
> color #28 #fffc794a models
> color #28 #fffc7928 models
> color #28 #fffc7924 models
> color #28 #fffc7923 models
> color #28 #fffc7926 models
> hide #!24 models
> hide #!27 models
> hide #!28 models
> select #25/B:219
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #25/B:220
10 atoms, 8 bonds, 2 residues, 1 model selected
> select add #25/B:221
24 atoms, 23 bonds, 3 residues, 1 model selected
> select add #25/B:222
35 atoms, 34 bonds, 4 residues, 1 model selected
> select add #25/B:223
42 atoms, 40 bonds, 5 residues, 1 model selected
> select add #25/B:218
47 atoms, 44 bonds, 6 residues, 1 model selected
> show sel atoms
> ui tool show "Color Actions"
> color sel dark slate blue
> size sel stickRadius 0.27
Changed 49 bond radii
> select clear
> show #!24 models
> hide #!25 models
> color #24 #d6d6d6ff models
> ui mousemode right "map eraser"
> surface dust #24 size 8.15
> volume erase #24 center 140.78,168.83,138.18 radius 3.1748
Opened HCN1_21july08_j230_run_class001_highRes_mask.mrc copy as #29, grid size
340,340,340, pixel 0.815, shown at step 1, values float32
> surface dust #29 size 8.15
> volume erase #29 center 146.23,177.22,134.83 radius 3.0486
> volume erase #29 center 147.49,177.85,136.46 radius 3.0486
> volume erase #29 center 146.14,177.23,137.89 radius 3.0486
> volume erase #29 center 145.13,179.91,138.37 radius 3.0486
> volume erase #29 center 143.8,179.27,141.63 radius 3.0486
> volume erase #29 center 143.19,179.37,141.67 radius 3.0486
> volume erase #29 center 122.83,190.28,141.38 radius 3.0486
> volume erase #29 center 138.56,164.03,133.03 radius 3.0486
> volume erase #29 center 137.84,164.09,134.7 radius 3.0486
> volume erase #29 center 135.89,163.85,136.88 radius 3.0486
> volume erase #29 center 138.1,164.94,127.97 radius 3.0486
> volume erase #29 center 138.02,159.54,131.18 radius 3.0486
> show #!28 models
> show #!27 models
> show #!25 models
> color #29 #d6d6d627 models
> color #29 #d6d6d61a models
> set bgColor black
> set bgColor white
> ui tool show "Side View"
> hide #!28 models
> show #!28 models
> hide #!27 models
> hide #!28 models
> hide #!29 models
> ui tool show Rotamers
No residues selected
> select #25/B:218@CA
1 atom, 1 residue, 1 model selected
> select clear
> show #!28 models
> show #!27 models
> show #!29 models
> save "/Users/edk4001/Desktop/HCN1 pfl site 2 zoom.png" width 4000 height
> 3301 supersample 4 transparentBackground true
> hide #!25 models
> hide #!28 models
> hide #!29 models
> ui mousemode right "map eraser"
> volume erase #27 center 143.51,182.72,140.9 radius 1.4669
> volume #23 color #ff260050
> volume #23 color #ff260043
> volume #23 color #ff260042
> color #27 #ff260080 models
> color #27 #ff260071 models
> color #27 #ff260066 models
> color #27 #ff26005c models
> color #27 #ff260058 models
> show #!25 models
> color #27 #ff260059 models
> show #!28 models
> color #28 #fffc7985 models
> color #28 #fffc795c models
> color #28 #fffc795a models
> show #!29 models
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,2
Model Number: Z14X000HSLL/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 64 GB
System Firmware Version: 8422.121.1
OS Loader Version: 8422.121.1
Software:
System Software Overview:
System Version: macOS 13.4.1 (c) (22F770820d)
Kernel Version: Darwin 22.5.0
Time since boot: 5 days, 10 hours, 57 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 32
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
G236HL:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.21.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
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: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.6.0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
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: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (4)
comment:1 by , 2 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash handling QTimer callback |
comment:2 by , 2 years ago
| Status: | accepted → feedback |
|---|
comment:3 by , 2 years ago
The crash was calling the color_pause signal for the color chooser 1 second after the color was last changed. Then it crashes trying to emit the signal apparently calling into Python. This might mean that a reference is not being held and Python garbage collects and then tries to call deleted Python objects. I know Qt Timer has this problem that it will get deleted if you don't hold a reference to it.
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/color_button.py", line 147
Crash is calling the lambda in this code in 1.6
def _set_pause_timer(self):
delay = self._pause_delay
if delay is None:
return
t = self._pause_timer
if t is not None:
t.stop()
from Qt.QtCore import QTimer
self._pause_timer = t = QTimer()
t.setSingleShot(True)
t.timeout.connect(lambda *, p=self.color_pause, c=self._color: p.emit(c))
t.start(int(1000*self._pause_delay))
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Hi Elizabeth,
--Eric