Opened 3 years ago

Closed 3 years ago

Last modified 3 years ago

#8135 closed defect (can't reproduce)

Crash in event loop

Reported by: chimerax-bug-report@… 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-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 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 0x00000002048d52c0 (most recent call first):
  File "/private/var/folders/w6/zdps7fvn2rn75f4z76gqyr_m0000gn/T/AppTranslocation/4E347525-8FF4-4C9E-970A-17B110D9424D/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
  File "/private/var/folders/w6/zdps7fvn2rn75f4z76gqyr_m0000gn/T/AppTranslocation/4E347525-8FF4-4C9E-970A-17B110D9424D/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
  File "/private/var/folders/w6/zdps7fvn2rn75f4z76gqyr_m0000gn/T/AppTranslocation/4E347525-8FF4-4C9E-970A-17B110D9424D/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in 
  File "/private/var/folders/w6/zdps7fvn2rn75f4z76gqyr_m0000gn/T/AppTranslocation/4E347525-8FF4-4C9E-970A-17B110D9424D/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/private/var/folders/w6/zdps7fvn2rn75f4z76gqyr_m0000gn/T/AppTranslocation/4E347525-8FF4-4C9E-970A-17B110D9424D/d/ChimeraX-1.5.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" : 140000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro18,3",
  "coalitionID" : 5379,
  "osVersion" : {
    "train" : "macOS 13.0.1",
    "build" : "22A400",
    "releaseType" : "User"
  },
  "captureTime" : "2022-12-07 00:08:31.0398 +0900",
  "incident" : "422C1B06-CA1F-4B66-9BFB-D3C98365A8C5",
  "pid" : 23696,
  "translated" : true,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2022-12-06 23:22:50.8918 +0900",
  "procStartAbsTime" : 3521144340184,
  "procExitAbsTime" : 3586908705599,
  "procName" : "ChimeraX",
  "procPath" : "\/private\/var\/folders\/*\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.5.0","CFBundleVersion":"1.5.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"4C8306D6-0E23-537F-AB9C-2E3A7682B445","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "305AB122-AC9D-70CD-47A1-4B28D546E446",
  "wakeTime" : 2776,
  "sleepWakeUUID" : "7AAC5444-D730-4105-9A52-16E89EFD396C",
  "sip" : "enabled",
  "vmRegionInfo" : "0x40 is not in any region.  Bytes before following region: 140722949930944\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      mapped file              7ffc9d714000-7ffca45cc000 [110.7M] r-x\/r-x SM=COW  ...t_id=67877bed",
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000040","rawCodes":[1,64],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000040"},
  "vmregioninfo" : "0x40 is not in any region.  Bytes before following region: 140722949930944\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      mapped file              7ffc9d714000-7ffca45cc000 [110.7M] r-x\/r-x SM=COW  ...t_id=67877bed",
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  "faultingThread" : 0,
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===== Log before crash start =====
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open /Users/kunwoong/Desktop/M393T/cholesterol.cxs

Opened TMEM175_WT_2.77_P5_J329_zflip (1).mrc as #2, grid size 400,400,400,
pixel 0.553, shown at level 0.0787, step 1, values float32  
Log from Mon Dec 5 11:03:58 2022 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/kunwoong/Desktop/hs/TMEM175_WT_2.77_P5_J329_zflip-coot-0
> (3).pdb"

Chain information for TMEM175_WT_2.77_P5_J329_zflip-coot-0 (3).pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> set bgColor white

> open "/Users/kunwoong/Desktop/hs/TMEM175_WT_2.77_P5_J329_zflip (1).mrc"

Opened TMEM175_WT_2.77_P5_J329_zflip (1).mrc as #2, grid size 400,400,400,
pixel 0.553, shown at level 0.0394, step 2, values float32  

> volume #2 step 1

> volume #2 level 0.06713

> transparency 50

> ui tool show "Color Actions"

> color bychain

> surface dust #2 size 5.53

Alignment identifier is 1/A  
Alignment identifier is 1/B  

> select
> /A:35-47,50-57,67-100,107-132,137-162,165-168,172-175,181-201,258-274,277-280,288-291,293-295,299-331,339-362,373-395,416-438,442-457,459-469

2287 atoms, 2325 bonds, 294 residues, 1 model selected  

> select clear

> select /A:93

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

> select /A:93

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

> style sel stick

Changed 5 atom styles  

> style sel stick

Changed 5 atom styles  

> show sel atoms

> select clear

> ui mousemode right zoom

> select /A:93

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

> show sel atoms

> hide sel atoms

> show sel atoms

> select clear

> select /A:93,97

16 atoms, 14 bonds, 2 residues, 1 model selected  

> show sel atoms

> select clear

> select /A:93,97,339

27 atoms, 24 bonds, 3 residues, 1 model selected  

> show sel atoms

> select clear

> lighting soft

> graphics silhouettes true

> select /A:92-93,97,339

41 atoms, 40 bonds, 4 residues, 1 model selected  

> show sel atoms

> select /A:90,92-93,97,339

48 atoms, 46 bonds, 5 residues, 1 model selected  

> show sel atoms

> select /A:86,90,92-93,97,339

56 atoms, 53 bonds, 6 residues, 1 model selected  

> show sel atoms

> select /A:86,90,92-93,97,339,343

64 atoms, 60 bonds, 7 residues, 1 model selected  

> show sel atoms

> select clear

> ui tool show "Side View"

> ui mousemode right "contour level"

> volume #2 level 0.08146

> ui tool show "Color Actions"

> color byelement target a

> color byhetero target a

> color bynucleotide target a

> color bychain target a

> color bypolymer target a

> ui tool show "Color Actions"

> color dodger blue target a

> color turquoise target a

> ui tool show "Color Actions"

> color byelement target a

> color light salmon target a

> color byelement target a

> color byhetero target a

> color byelement target a

> color bynucleotide target a

> color bypolymer target a

> color turquoise target a

> save /Users/kunwoong/Desktop/image1.png supersample 3

> volume #2 level -0.05741

> volume #2 level -0.4989

> volume #2 level -0.7445

> volume #2 level -0.6764

> volume #2 level -0.6087

> volume #2 level -0.4212

> volume #2 level -0.2114

> volume #2 level -0.2222

> volume #2 level -0.279

> volume #2 level -0.3249

> ui mousemode right zoom

> ui mousemode right "contour level"

> volume #2 level -0.7142

> volume #2 level -0.6487

> volume #2 level -0.002813

> volume #2 level 0.02368

> volume #2 level 0.03998

> volume #2 level 0.06036

> volume #2 level 0.1011

> ui mousemode right zoom

> volume #2 level 0.07872

> save /Users/kunwoong/Desktop/image2.png supersample 3

> open /Users/kunwoong/Downloads/rcsb_pdb_7P0K.fasta

Summary of feedback from opening /Users/kunwoong/Downloads/rcsb_pdb_7P0K.fasta  
---  
note | Alignment identifier is rcsb_pdb_7P0K.fasta  
  
Opened 1 sequences from rcsb_pdb_7P0K.fasta  

> save /Users/kunwoong/Desktop/hs/cholesterol.cxs includeMaps true

——— End of log from Mon Dec 5 11:03:58 2022 ———

opened ChimeraX session  

> ui mousemode right "contour level"

> volume #2 level 0.08239

> ui mousemode right "pick blobs"

> measure blob #!2.1 triangleNumber 356755 color #30cdb5ff

Surface TMEM175_WT_2.77_P5_J329_zflip (1).mrc #2.1 blob:  
volume = 43.23  
area = 84.212  
size = 8.7856 4.8655 3.171  
  

> measure blob #!2.1 triangleNumber 215257 color #30cdb5ff

Surface TMEM175_WT_2.77_P5_J329_zflip (1).mrc #2.1 blob:  
volume = 21266  
area = 33751  
size = 68.575 67.308 59.659  
  

> volume #2 level 0.08239

> measure blob #!2.1 triangleNumber 342734 color #30cdb5ff

Surface TMEM175_WT_2.77_P5_J329_zflip (1).mrc #2.1 blob:  
volume = 43.23  
area = 84.212  
size = 8.7856 4.8655 3.171  
  

> ui mousemode right "contour level"

> volume #2 level 0.1

> ui mousemode right "pick blobs"

> measure blob #!2.1 triangleNumber 205434 color #30cdb5ff

Surface TMEM175_WT_2.77_P5_J329_zflip (1).mrc #2.1 blob:  
volume = 52.621  
area = 105.67  
size = 15.053 3.2253 3.067  
  

> measure blob #!2.1 triangleNumber 287060 color #30cdb5ff

Surface TMEM175_WT_2.77_P5_J329_zflip (1).mrc #2.1 blob:  
volume = 35.094  
area = 73.53  
size = 8.419 4.532 2.8658  
  

> volume #2 level 0.1061

> measure blob #!2.1 triangleNumber 289446 color #30cdb5ff

Surface TMEM175_WT_2.77_P5_J329_zflip (1).mrc #2.1 blob:  
volume = 32.545  
area = 70.109  
size = 8.3169 4.4226 2.7597  
  

> measure blob #!2.1 triangleNumber 175039 color #30cdb5ff

Surface TMEM175_WT_2.77_P5_J329_zflip (1).mrc #2.1 blob:  
volume = 48.929  
area = 100.54  
size = 14.512 3.1301 2.992  
  

> ui tool show "Color Actions"

> color byelement target a

> color cyan target a

> color byelement target a

> color byhetero target a

> color cyan target a

> color byhetero target a

> select #2

4 models selected  

> select #2

4 models selected  

> select clear

> measure blob #!2.1 triangleNumber 254567 color #0000ccff outline true

Surface TMEM175_WT_2.77_P5_J329_zflip (1).mrc #2.1 blob:  
volume = 1153.3  
area = 2061.3  
size = 48.656 23.736 14.389  
  

> ui tool show "Volume Viewer"

> measure blob #!2.1 triangleNumber 295216 color #26d2caff

Surface TMEM175_WT_2.77_P5_J329_zflip (1).mrc #2.1 blob:  
volume = 32.545  
area = 70.109  
size = 8.3169 4.4226 2.7597  
  

> volume #2 level 0.1081

> measure blob #!2.1 triangleNumber 197688 color #26d2caff

Surface TMEM175_WT_2.77_P5_J329_zflip (1).mrc #2.1 blob:  
volume = 47.788  
area = 99.029  
size = 14.437 3.1389 2.9703  
  

> measure blob #!2.1 triangleNumber 290902 color #26d2caff

Surface TMEM175_WT_2.77_P5_J329_zflip (1).mrc #2.1 blob:  
volume = 31.741  
area = 69.015  
size = 8.2855 4.384 2.7255  
  

> ui tool show "Side View"

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/kunwoong/Desktop/movie3.mp4

Movie saved to /Users/kunwoong/Desktop/movie3.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/kunwoong/Desktop/movie4.mp4

Movie saved to /Users/kunwoong/Desktop/movie4.mp4  
  

> close session

> open
> /Users/kunwoong/Desktop/enpp2_new/662/cryosparc_P11_J662_012_volume_map_sharp.mrc

Opened cryosparc_P11_J662_012_volume_map_sharp.mrc as #1, grid size
224,224,224, pixel 0.901, shown at level 0.146, step 1, values float32  

> volume #1 level 0.1894

> open
> "/Users/kunwoong/Desktop/enpp2_new/662/cryosparc_P11_J662_012_volume_map_sharp_cryonet
> (1)-coot-0.pdb"

Summary of feedback from opening
/Users/kunwoong/Desktop/enpp2_new/662/cryosparc_P11_J662_012_volume_map_sharp_cryonet
(1)-coot-0.pdb  
---  
warning | Ignored bad PDB record found on line 4  
REMARK INFO: [occupancy]=sse [bfactor]=score  
  
Chain information for cryosparc_P11_J662_012_volume_map_sharp_cryonet
(1)-coot-0.pdb #2  
---  
Chain | Description  
A | No description available  
  

> transparency 50

> set bgColor white

> surface dust #1 size 9.01

> color zone #1 near #2 distance 5.41

> hide atoms

> color zone #1 near #2 distance 5.41

> surface dust #1 size 9.01

> volume #1 color #bfbeba80

Alignment identifier is 2/A  

> select
> /A:81-83,90-94,105-107,124-127,134-139,144-146,176-181,187-195,210-219,223-226,248-250,252-254,260-267,282-294,312-318,323-346,373-375,405-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853

1894 atoms, 1906 bonds, 225 residues, 1 model selected  

> select
> /A:81-83,90-94,105-107,124-127,134-139,144-146,176-181,187-195,210-219,223-226,248-250,252-254,260-267,282-294,312-318,323-346,373-375,405-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853

1894 atoms, 1906 bonds, 225 residues, 1 model selected  

> select
> /A:81-83,90-94,105-107,124-127,134-139,144-146,176-181,187-195,210-219,223-226,248-250,252-254,260-267,282-294,312-318,323-346,373-375,405-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853

1894 atoms, 1906 bonds, 225 residues, 1 model selected  

> select clear

> select
> /A:81-83,90-94,105-107,124-127,134-139,144-146,176-181,187-195,210-219,223-226,248-250,252-254,260-267,282-294,312-318,323-346,373-375,405-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853

1894 atoms, 1906 bonds, 225 residues, 1 model selected  

> select clear

> select
> /A:81-83,90-94,105-107,124-127,134-139,144-146,176-181,187-195,210-219,223-226,248-250,252-254,260-267,282-294,312-318,323-346,373-375,405-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853

1894 atoms, 1906 bonds, 225 residues, 1 model selected  

> select
> /A:81-83,90-94,105-107,124-127,134-139,144-146,176-181,187-195,210-219,223-226,248-250,252-254,260-267,282-294,312-318,323-346,373-375,405-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853

1894 atoms, 1906 bonds, 225 residues, 1 model selected  

> select
> /A:81-83,90-94,105-107,124-127,134-139,144-146,176-181,187-195,210-219,223-226,248-250,252-254,260-267,282-294,312-318,323-346,373-375,405-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853

1894 atoms, 1906 bonds, 225 residues, 1 model selected  

> select
> /A:81-83,90-94,105-107,124-127,134-139,144-146,176-181,187-195,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,405-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853

1908 atoms, 1922 bonds, 226 residues, 1 model selected  

> select clear

> select
> /A:81-83,90-94,105-107,124-127,134-139,144-146,176-181,187-195,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,405-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853

1908 atoms, 1922 bonds, 226 residues, 1 model selected  

> select
> /A:81-83,90-94,105-107,124-127,134-139,144-146,176-181,187-195,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,405-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853

1908 atoms, 1922 bonds, 226 residues, 1 model selected  

> select
> /A:81-83,90-94,105-107,124-127,134-139,144-146,176-181,187-195,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,405-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853

1908 atoms, 1922 bonds, 226 residues, 1 model selected  

> select
> /A:81-83,90-94,105-107,124-127,134-139,144-146,176-181,187-195,207,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,405-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853

1915 atoms, 1929 bonds, 227 residues, 1 model selected  

> select
> /A:81-83,90-94,105-107,124-127,134-139,144-146,176-181,187-195,207,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,405-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853

1915 atoms, 1929 bonds, 227 residues, 1 model selected  

> select clear

> select
> /A:81-83,90-94,105-107,124-127,134-139,144-146,158-163,176-181,187-195,207,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,405-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853

1960 atoms, 1975 bonds, 233 residues, 1 model selected  

> select
> /A:81-83,90-94,105-107,113-118,124-127,134-139,144-146,158-163,176-181,187-195,207,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,405-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853

2005 atoms, 2019 bonds, 239 residues, 1 model selected  

> select
> /A:81-83,90-94,105-107,109-119,124-127,134-139,144-146,158-163,176-181,187-195,207,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,405-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853

2019 atoms, 2033 bonds, 241 residues, 1 model selected  

> select
> /A:81-83,90-94,105-107,109-119,124-127,134-139,144-146,158-163,176-181,187-195,207,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,391-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853

2087 atoms, 2101 bonds, 249 residues, 1 model selected  

> select
> /A:81-83,90-94,105-107,109-119,124-127,134-139,144-146,158-163,176-181,187-195,207,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,391-412,426-428,431-433,482-484,506-517,532-534,543-554,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853

2186 atoms, 2203 bonds, 261 residues, 1 model selected  

> select clear

> select
> /A:81-83,90-94,105-107,109-119,124-127,134-139,144-146,158-163,176-181,187-195,207,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,391-412,426-428,431-433,482-484,506-517,532-534,543-554,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853

2186 atoms, 2203 bonds, 261 residues, 1 model selected  

> select
> /A:81-83,90-94,105-107,109-119,124-127,134-139,144-146,158-163,176-181,187-195,207,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,391-412,426-428,431-433,482-484,506-517,532-534,543-554,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853

2186 atoms, 2203 bonds, 261 residues, 1 model selected  

> select
> /A:81-83,90-94,105-107,109-119,124-127,134-139,144-146,158-163,176-181,187-195,207,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,391-412,426-428,431-433,482-484,506-517,532-534,543-554,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853

2186 atoms, 2203 bonds, 261 residues, 1 model selected  

> select
> /A:81-83,90-94,105-107,109-119,124-127,134-139,144-146,158-163,176-181,187-195,207,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,391-412,426-428,431-433,482-484,506-517,532-534,543-554,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853

2186 atoms, 2203 bonds, 261 residues, 1 model selected  

> select
> /A:81-83,90-94,105-107,109-119,124-127,134-139,144-146,158-163,176-181,187-195,207,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,391-412,426-428,431-433,482-484,506-517,532-534,543-554,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853

2186 atoms, 2203 bonds, 261 residues, 1 model selected  

> select
> /A:81-83,90-94,105-107,109-119,124-127,134-139,144-146,158-163,176-181,187-195,207,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,391-412,426-428,431-433,482-484,506-517,532-534,543-554,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853

2186 atoms, 2203 bonds, 261 residues, 1 model selected  

> select
> /A:81-83,90-94,105-107,109-119,124-127,134-139,144-146,158-163,176-181,187-195,207,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,391-412,426-428,431-433,482-484,506-517,532-534,543-554,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853

2186 atoms, 2203 bonds, 261 residues, 1 model selected  

> select
> /A:81-83,90-94,105-107,109-119,124-127,134-139,144-146,158-163,176-181,187-195,207,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,391-412,426-428,431-433,482-484,506-517,532-534,543-554,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853

2186 atoms, 2203 bonds, 261 residues, 1 model selected  

> select /A:255

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select /A:255

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select /A:252,255

24 atoms, 25 bonds, 2 residues, 1 model selected  

> select /A:252,255,261

38 atoms, 40 bonds, 3 residues, 1 model selected  

> style sel stick

Changed 38 atom styles  

> show sel atoms

> select clear

> ui tool show "Color Actions"

> color byhetero target a

> color byelement target a

> color cyan target a

> color byhetero target a

> color hot pink target c

> color light sea green target c

> color purple target c

> color salmon target c

> ui mousemode right "contour level"

> volume #1 level 0.2784

> volume #1 level 0.6169

> volume #1 level 0.6579

> volume #1 level 0.6438

> volume #1 level 0.6582

> ui mousemode right "pick blobs"

> measure blob #!1.1 triangleNumber 85971 color #18cdbcff

Surface cryosparc_P11_J662_012_volume_map_sharp.mrc #1.1 blob:  
volume = 8606.1  
area = 19289  
size = 63.452 50.169 38.552  
  

> volume #1 level 0.6731

> measure blob #!1.1 triangleNumber 82371 color #18cdbcff

Surface cryosparc_P11_J662_012_volume_map_sharp.mrc #1.1 blob:  
volume = 8167.3  
area = 18452  
size = 63.407 49.698 39.081  
  

> volume #1 level 0.8215

> measure blob #!1.1 triangleNumber 62799 color #18cdbcff

Surface cryosparc_P11_J662_012_volume_map_sharp.mrc #1.1 blob:  
volume = 3317.4  
area = 7966  
size = 52.89 40.4 34.138  
  

> volume #1 level 1.267

> measure blob #!1.1 triangleNumber 25443 color #18cdbcff

Surface cryosparc_P11_J662_012_volume_map_sharp.mrc #1.1 blob:  
volume = 37.55  
area = 100.94  
size = 9.4419 6.9629 3.1214  
  

> volume #1 level 0.5841

> volume #1 level 0.7473

> ui mousemode right "pick blobs"

> volume #1 level 0.3466

> measure blob #!1.1 triangleNumber 172292 color #18cdbcff

Surface cryosparc_P11_J662_012_volume_map_sharp.mrc #1.1 blob:  
volume = 27253  
area = 51149  
size = 87.501 63.859 48.02  
  

> volume #1 level 0.3763

> ui mousemode right zoom

> volume #1 level 0.7324

> volume #1 level 0.6286

> volume #1 level 0.6582

> lighting soft

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> lighting full

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> graphics silhouettes false

> graphics silhouettes true

> lighting simple

> lighting soft

> lighting flat

> lighting full

> lighting flat

> lighting soft

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> graphics silhouettes false

> graphics silhouettes true

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting soft

> volume #1 level 0.6731

> ui tool show "Color Actions"

> color dodger blue target c

> color dark turquoise target c

> color medium spring green target c

> color cornflower blue target c

> ui tool show "Side View"

> save /Users/kunwoong/Desktop/image1.png supersample 3

> save /Users/kunwoong/Desktop/image2.png supersample 3

> ui tool show "Volume Viewer"

> volume #1 level 0.1543

> volume #1 level -0.06192

> volume #1 level -0.134

> volume #1 level -0.004273

> volume #1 level -0.2781

> volume #1 level -0.2637

> volume #1 level 0.356

> volume #1 level 0.1254

> surface dust #1 size 9.01

> ui tool show "Volume Viewer"

> volume #1 level 0.2119

> volume #1 level 0.3128

> volume #1 level 0.1543

> view orient

> turn y 90

> lighting soft

> transparency 0

> transparency 50

> transparency 0

> transparency 50

> transparency 0

> transparency 50

> transparency 0

> transparency 50

> transparency 0

> open "/Users/kunwoong/Desktop/enpp2_new/hs/P11_J330_zflip_ENPP2_Chem2.mrc 2"

Unrecognized file suffix '.mrc 2'  

> open /Users/kunwoong/Desktop/enpp2_new/hs/P11_J330_zflip_ENPP2_Chem2.mrc

Opened P11_J330_zflip_ENPP2_Chem2.mrc as #3, grid size 224,224,224, pixel
0.901, shown at level 0.208, step 1, values float32  

> surface dust #1 size 9.01

> surface dust #3 size 9.01

> open "/Users/kunwoong/Desktop/enpp2_new/hs/Chem02_real_space_refined_004
> (3).pdb"

Chain information for Chem02_real_space_refined_004 (3).pdb #4  
---  
Chain | Description  
A | No description available  
  

> view orient

> ui tool show "Volume Viewer"

> view

> ui tool show "DICOM Browser"

> ui tool show "Surface Zone"

> select add #3

2 models selected  

> select add #4

5720 atoms, 5887 bonds, 2 pseudobonds, 703 residues, 4 models selected  

> ui mousemode right translate

> ui mousemode right "translate selected models"

> view matrix models
> #3,1,0,0,-36.586,0,1,0,84.165,0,0,1,-4.7299,#4,1,0,0,-36.586,0,1,0,84.165,0,0,1,-4.7299


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

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 83
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: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Model Number: MKGR3KH/A
      Chip: Unknown
      Total Number of Cores: 8 (6 performance and 2 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: 8 days, 14 hours, 26 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 14
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    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: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 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-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: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    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-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    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: 2.7.2
    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
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    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: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    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: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

Change History (4)

comment:1 by pett, 3 years ago

Cc: Tom Goddard added
Component: Unassigned → Core
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in event loop

comment:2 by pett, 3 years ago

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

comment:3 by Tom Goddard, 3 years ago

I am puzzled why on this ARM Mac they are running the Intel Mac ChimeraX 1.5. They should have gotten the universal build and be running the ARM ChimeraX.

I'll test on my ARM Mac laptop tomorrow to make sure the universal build is working.

comment:4 by Tom Goddard, 3 years ago

Tested that Mac universal build for ChimeraX 1.5 does report ARM platform for M1 Mac and macOS 13.0.1, ticket #8146. I guess the user either downloaded the Intel Mac installer, or requested to run the universal build using Intel architecture. Both seem highly implausible.

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