Opened 3 years ago

Last modified 3 years ago

#7286 accepted defect

Unknown crash

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

Description (last modified by Eric Pettersen) 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.


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{
  "uptime" : 1400000,
  "procLaunch" : "2022-07-07 16:16:48.3421 +0200",
  "procRole" : "Background",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro17,1",
  "procStartAbsTime" : 32037086705931,
  "coalitionID" : 73622,
  "osVersion" : {
    "train" : "macOS 12.4",
    "build" : "21F79",
    "releaseType" : "User"
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  "captureTime" : "2022-07-14 13:47:51.4949 +0200",
  "incident" : "B162DD4D-E8C7-47BD-95F1-AD5E9DBA6DB5",
  "bug_type" : "309",
  "pid" : 92276,
  "procExitAbsTime" : 33778630527872,
  "translated" : true,
  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/private\/var\/folders\/*\/ChimeraX-1.4.app\/Contents\/MacOS\/ChimeraX",
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "BB9D28C0-3EF2-B744-F9A6-E850B445ECA8",
  "wakeTime" : 2302,
  "sleepWakeUUID" : "B630B6E8-4B69-4705-B59E-EB3777D6ECE4",
  "sip" : "enabled",
  "vmRegionInfo" : "0x10adcc1d0 is in 0x10abcd000-0x10ae36000;  bytes after start: 2093520  bytes before end: 433711\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      Rosetta Generic             10abcc000-10abcd000    [    4K] rw-\/rwx SM=PRV  \n--->  mapped file                 10abcd000-10ae36000    [ 2468K] r-x\/rwx SM=COW  ...t_id=a7219d71\n      mapped file                 10ae36000-10ae70000    [  232K] rw-\/rwx SM=COW  ...t_id=a3a1b271",
  "isCorpse" : 1,
  "exception" : {"codes":"0x000000000000000a, 0x000000010adcc1d0","rawCodes":[10,4477206992],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_MEMORY_ERROR at 0x000000010adcc1d0"},
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  "ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
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    "path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
    "name" : "libsystem_platform.dylib"
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  {
    "size" : 0,
    "source" : "A",
    "base" : 0,
    "uuid" : "00000000-0000-0000-0000-000000000000"
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  {
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    "arch" : "x86_64",
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    "CFBundleIdentifier" : "com.apple.CoreFoundation",
    "size" : 5246976,
    "uuid" : "9c8908f2-e5e0-35b7-9f41-fdf8d7476d8b",
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    "name" : "CoreFoundation",
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    "arch" : "x86_64",
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    "size" : 442368,
    "uuid" : "b70ce1ec-b902-3852-8268-05de00bfa8d5",
    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 140703126843392,
    "size" : 196608,
    "uuid" : "0ee8ce32-639c-316a-9551-dab9a2e0c8a5",
    "path" : "\/usr\/libexec\/rosetta\/runtime",
    "name" : "runtime"
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    "arch" : "x86_64",
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    "size" : 229376,
    "uuid" : "61711d11-e776-3bc3-b9a2-6f9f37cb8499",
    "path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
    "name" : "libsystem_kernel.dylib"
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    "arch" : "x86_64",
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    "size" : 49152,
    "uuid" : "bc574849-1aae-31e7-b350-916dda999d97",
    "path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
    "name" : "libsystem_pthread.dylib"
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],
  "sharedCache" : {
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  "size" : 15220686848,
  "uuid" : "53b6853f-0bc3-33f5-be72-1aca3a188ff8"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=205.8M resident=0K(0%) swapped_out_or_unallocated=205.8M(100%)\nWritable regions: Total=4.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=4.4G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               384K        3 \nActivity Tracing                   256K        1 \nCG backing stores                 9552K       11 \nCG image                           928K       83 \nColorSync                          236K       28 \nCoreAnimation                     3280K       84 \nCoreGraphics                        52K       12 \nCoreServices                       624K        2 \nCoreUI image data                 5376K       46 \nFoundation                          36K        2 \nKernel Alloc Once                 1296K        3 \nMALLOC                             3.1G      905 \nMALLOC guard page                  192K        9 \nMALLOC_MEDIUM (reserved)         768.0M        8         reserved VM address space (unallocated)\nMach message                        16K        4 \nOpenGL GLSL                        384K        4 \nRosetta Arena                     4096K        2 \nRosetta Generic                   1688K      419 \nRosetta IndirectBranch            2048K        1 \nRosetta JIT                      128.0M        1 \nRosetta Return Stack               720K       72 \nRosetta Thread Context             720K       72 \nSTACK GUARD                         36K        9 \nStack                            145.6M       36 \nStack Guard                       56.1M       27 \nVM_ALLOCATE                      172.4M      252 \nVM_ALLOCATE (reserved)            96.1M       11         reserved VM address space (unallocated)\n__DATA                             355K       46 \n__DATA_CONST                      3033K       40 \n__DATA_DIRTY                        79K       24 \n__LINKEDIT                       192.9M        7 \n__OBJC_RO                         82.7M        1 \n__OBJC_RW                         3200K        2 \n__TEXT                            13.0M       50 \n__UNICODE                          592K        1 \ndyld private memory               1184K        3 \nmapped file                        7.0G     1038 \nshared memory                     5620K       42 \nunshared pmap                     12.6M        9 \n===========                     =======  ======= \nTOTAL                             11.7G     3370 \nTOTAL, minus reserved VM space    10.9G     3370 \n",
  "legacyInfo" : {
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  "rollouts" : [
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}
}
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/tomkunde/Documents/Work/Untitled Folder/A4H4_optimized.mol2"

Opened A4H4_optimized.mol2 containing 1 structures (336 atoms, 360 bonds)  

> set bgColor white

> style balls

Expected a keyword  

> style ball

Changed 336 atom styles  

> hide H

Drag select of 15 atoms, 15 bonds  
Drag select of 15 atoms, 16 bonds  

> name frozen Amines sel

> color C orange

> color Amines orchid

> select clear

> lighting soft

> lighting shadows true intensity 0.5

> graphics silhouettes true

> save "/Users/tomkunde/Documents/Work/Untitled Folder/A4H4 full on
> picture.png" transparentBackground true

> style sphere

Changed 336 atom styles  

> save "/Users/tomkunde/Documents/Work/Untitled Folder/A4H4 sphere window
> view.png" transparentBackground true

> save "/Users/tomkunde/Documents/Work/Untitled Folder/A4H4.cxs"

> close session

> open "/Users/tomkunde/Documents/Work/Untitled Folder/A4H1F3 optimized.mol2"

Opened A4H1F3 optimized.mol2 containing 1 structures (336 atoms, 360 bonds)  

> hide H

> style balls

Expected a keyword  

> style ball

Changed 336 atom styles  
Drag select of 15 atoms, 16 bonds  
Drag select of 15 atoms, 17 bonds  
Drag select of 15 atoms, 16 bonds  

> name frozen Amines sel

> select clear

> select /?:1@@serial_number=-1

336 atoms, 360 bonds, 1 residue, 1 model selected  

> select clear

Drag select of 1 atoms  

> select add /?:1@@serial_number=-1

336 atoms, 360 bonds, 1 residue, 1 model selected  

> select clear

Drag select of 1 atoms  
Drag select of 1 atoms, 2 bonds  
Drag select of 2 atoms, 1 bonds  
Drag select of 1 atoms, 1 bonds  
Drag select of 2 atoms, 2 bonds  
Drag select of 2 atoms, 1 bonds  
Drag select of 1 atoms  
Drag select of 2 atoms, 3 bonds  
Drag select of 2 atoms, 1 bonds  
Drag select of 2 atoms, 2 bonds  
Drag select of 1 atoms, 1 bonds  

> name frozen H-aldehyde sel

> color C dodger blue

> color Amines orchid

> color H-aldehyde orange

> color F pale green

> select clear

> lighting soft

> lighting shadows true intensity 0.5

> graphics silhouettes false

> graphics silhouettes true

> save "/Users/tomkunde/Documents/Work/Untitled Folder/A4H1F3 full on.png"
> transparentBackground true

> style sphere

Changed 336 atom styles  

> save "/Users/tomkunde/Documents/Work/Untitled Folder/A4H1F3 sphere window
> view.png" transparentBackground true

> save "/Users/tomkunde/Documents/Work/Untitled Folder/A4H1F3.cxs"

> close session

> open "/Users/tomkunde/Documents/Work/Untitled Folder/A4H2F2 optimized.mol2"

Opened A4H2F2 optimized.mol2 containing 1 structures (336 atoms, 360 bonds)  

> hide H

> style ball

Changed 336 atom styles  
Drag select of 15 atoms, 15 bonds  
Drag select of 15 atoms, 16 bonds  

> name frozen Amines sel

> select clear

Drag select of 27 atoms, 31 bonds  
Drag select of 1 atoms  
Drag select of 25 atoms, 30 bonds  
Drag select of 1 atoms, 1 bonds  

> name frozen H-Aldehyde sel

> color C dodger blue

> color Amines orchid

> color H-Aldehyde orange

> select clear

> lighting soft

> lighting shadows true intensity 0.5

> save "/Users/tomkunde/Documents/Work/Untitled Folder/A4H2F2 full on.png"
> transparentBackground true

> show H

> style sphere

Changed 336 atom styles  

> hide H

> show H

> save "/Users/tomkunde/Documents/Work/Untitled Folder/A4H2F2 window view.png"
> transparentBackground true

> save "/Users/tomkunde/Documents/Work/Untitled Folder/A4H2F2.cxs"

> close session

> open "/Users/tomkunde/Documents/Work/Untitled Folder/A4H3F1 optimized.mol2"

Opened A4H3F1 optimized.mol2 containing 1 structures (336 atoms, 360 bonds)  

> hide H

> style ball

Changed 336 atom styles  
Drag select of 15 atoms, 17 bonds  
Drag select of 15 atoms, 16 bonds  
Drag select of 15 atoms, 15 bonds  

> name frozen Amines sel

> select clear

Drag select of 11 atoms, 12 bonds  
Drag select of 19 atoms, 21 bonds  
Drag select of 1 atoms  
Drag select of 2 atoms, 1 bonds  
Drag select of 11 atoms, 13 bonds  
Drag select of 1 atoms, 1 bonds  
Drag select of 1 atoms  

> color frozen F-Aldehyde sel

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> name frozen F-Aldehyde sel

> color C orange

> color F-Aldehyde dodger blue

> color F pale green

> color Amines orchid

> select clear

> lighting soft

> lighting shadows true intensity 0.5

> graphics silhouettes false

> graphics silhouettes true

> save "/Users/tomkunde/Documents/Work/Untitled Folder/A4H3F1 full on.png"
> transparentBackground true

> style sphere

Changed 336 atom styles  

> show H

> save "/Users/tomkunde/Documents/Work/Untitled Folder/A4H3F1 window view.png"
> transparentBackground true

> save "/Users/tomkunde/Documents/Work/Untitled Folder/A4H3F1.cxs"

> close session

> open "/Users/tomkunde/Documents/Work/Untitled Folder/A4H4.cxs" format
> session

opened ChimeraX session  

> open "/Users/tomkunde/Documents/Work/Untitled Folder/A4H4 cavity_cav1.dx"

Opened A4H4 cavity_cav1.dx as #2, grid size 96,97,98, pixel 0.2, shown at
level -6,6, step 1, values float32  

> volume #2 level 0.3878 level 6

> volume #2 color #ff9f3f color #b2b2b2

> volume #2 color #ff9856 color #b2b2b2

> volume #2 color #ff9f3f color #b2b2b2

> style stick

Changed 336 atom styles  

> volume #2 level 3.803 level 6

> movie record

> turn y 2 180

> wait 180

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

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

> close session

> open "/Users/tomkunde/Documents/Work/Untitled Folder/A4H1F3.cxs" format
> session

opened ChimeraX session  

> style stick

Changed 336 atom styles  

> open "/Users/tomkunde/Documents/Work/Untitled Folder/A4H1F3 cavity_cav1.dx"

Opened A4H1F3 cavity_cav1.dx as #2, grid size 94,92,85, pixel 0.2, shown at
level -6,6, step 1, values float32  

> volume #2 level 0.2585 level 6

> volume #2 color #8ed243 color #ffffb2

> volume #2 color #ff9f3f color #ffffb2

> volume #2 color #ffd159 color #ffffb2

> volume #2 level 0.377 level 6

> movie record

> turn y 2 180

> wait 180

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

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

> close session

> open "/Users/tomkunde/Documents/Work/Untitled Folder/A4H2F2.cxs" format
> session

opened ChimeraX session  

> style stick

Changed 336 atom styles  

> hide H

> open "/Users/tomkunde/Documents/Work/Untitled Folder/A4H2F2 cavity_cav1.dx"

Opened A4H2F2 cavity_cav1.dx as #2, grid size 98,91,93, pixel 0.2, shown at
level -6,6, step 1, values float32  

> volume #2 level 0.5494 level 6

> volume #2 color #e9ff52 color #b2ffff

> volume #2 color #cbdf47 color #b2ffff

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/tomkunde/Desktop/movie5.mp4

Movie saved to /Users/tomkunde/Desktop/movie5.mp4  
  

> close session

> open "/Users/tomkunde/Documents/Work/Untitled Folder/A4H3F1.cxs" format
> session

opened ChimeraX session  

> style stick

Changed 336 atom styles  

> hide H

> open "/Users/tomkunde/Documents/Work/Untitled Folder/A4H3F1 cavity_cav1.dx"

Opened A4H3F1 cavity_cav1.dx as #2, grid size 81,100,97, pixel 0.2, shown at
level -6,6, step 1, values float32  

> volume #2 level 1.228 level 6

> volume #2 color #ff9f3f color #b2b2ff

> volume #2 color #a6ff53 color #b2b2ff

> volume #2 color #8ad445 color #b2b2ff

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/tomkunde/Desktop/movie6.mp4

Movie saved to /Users/tomkunde/Desktop/movie6.mp4  
  

> close session

> open "/Users/tomkunde/Documents/Work/MOL-files Cages/Stacked FF24 .cxs"

opened ChimeraX session  

> open "/Users/tomkunde/Documents/Work/Crystal structures/FF24 cavity
> maps_cav1.dx"

Opened FF24 cavity maps_cav1.dx as #2, grid size 29,29,36, pixel 0.2, shown at
level -4,4, step 1, values float32  

> volume #2 level 0.3555 level 4

> volume #2 color #dffb81 color #ffb2ff

> open "/Users/tomkunde/Documents/Work/Crystal structures/FF24 cavity
> maps_cav2.dx"

Opened FF24 cavity maps_cav2.dx as #3, grid size 27,24,29, pixel 0.2, shown at
level -4,4, step 1, values float32  

> volume #3 level 1.928 level 4

> volume #3 color #dffb81 color #ffb2b2

> open "/Users/tomkunde/Documents/Work/Crystal structures/FF24 cavity
> maps_cav3.dx" "/Users/tomkunde/Documents/Work/Crystal structures/FF24 cavity
> maps_cav5.dx" "/Users/tomkunde/Documents/Work/Crystal structures/FF24 cavity
> maps_cav4.dx"

Opened FF24 cavity maps_cav3.dx as #4.1, grid size 25,26,21, pixel 0.2, shown
at level -4,4, step 1, values float32  
Opened FF24 cavity maps_cav5.dx as #4.2, grid size 9,19,16, pixel 0.2, shown
at level -4,4, step 1, values float32  
Opened FF24 cavity maps_cav4.dx as #4.3, grid size 16,22,20, pixel 0.2, shown
at level -4,4, step 1, values float32  

> volume #4.1 level 0.4436 level 4

> volume #4.1 color #dffb81 color #b2ffb2

> volume #4.2 level 0.61 level 4

> volume #4.2 color #dffb81 color #e5bf99

> volume #4.3 level 0.4104 level 4

> volume #4.3 color #dffb81 color #99bfe5

> style stick

Changed 396 atom styles  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/tomkunde/Desktop/movie7.mp4

Movie saved to /Users/tomkunde/Desktop/movie7.mp4  
  

> open "/Users/tomkunde/Documents/Work/Crystal structures/FF24 H2
> cavity_cav1.dx"

Opened FF24 H2 cavity_cav1.dx as #5, grid size 85,55,56, pixel 0.2, shown at
level -6,6, step 1, values float32  

> hide #!4 models

> hide #!3 models

> hide #!2 models

> volume #5 level 0.6654 level 6

> volume #5 color #ff6875 color #cccc99

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/tomkunde/Desktop/movie8.mp4

Movie saved to /Users/tomkunde/Desktop/movie8.mp4  
  

> close session

> open "/Users/tomkunde/Documents/Work/Untitled Folder/GC2_optimized.mol"

> hdie H

Unknown command: hdie H  

> hide H

> style ball

Changed 336 atom styles  
Drag select of 15 atoms, 16 bonds  
Drag select of 15 atoms, 17 bonds  
Drag select of 15 atoms, 18 bonds  
Drag select of 15 atoms, 15 bonds  

> name frozen Amines sel

> select clear

> color C dodger blue

> color Amines orchid

> color F pale green

> select clear

> lighting soft

> lighting shadows true intensity 0.5

> graphics silhouettes false

> graphics silhouettes true

> open "/Users/tomkunde/Documents/Work/Untitled Folder/A4F4 cavities_cav1.dx"

Opened A4F4 cavities_cav1.dx as #2, grid size 97,103,99, pixel 0.2, shown at
level -6,6, step 1, values float32  

> volume #2 color #dffb81 color #b2b2b2

> volume #2 level 4.61 level 6

> volume #2 level 1.282 level 6

> volume #2 color #bad06b color #b2b2b2

> volume #2 level 4.998 level 6

> hide #1 models

> volume #2 color #79834c58 color #b2b2b2

> volume #2 color #79834cc0 color #b2b2b2

> volume #2 color #a7b469c0 color #b2b2b2

> volume #2 color #8ed243 color #b2b2b2

> volume #2 color #8ed24390 color #b2b2b2

> volume #2 color #ff9f3f color #b2b2b2

> volume #2 color #ff9f3fe2 color #b2b2b2

> volume #2 color #ff9f3f00 color #b2b2b2

> volume #2 color #ff9f3f24 color #b2b2b2

> volume #2 color #ffb04e color #b2b2b2

> show #1 models

> close session

> open "/Users/tomkunde/Documents/Work/MOL-files Cages/Stacked FF24 .cxs"
> format session

opened ChimeraX session  

> open "/Users/tomkunde/Documents/Work/Crystal structures/FF24 H2
> cavity_cav1.dx"

Opened FF24 H2 cavity_cav1.dx as #2, grid size 85,55,56, pixel 0.2, shown at
level -6,6, step 1, values float32  

> volume #2 level 5 level 6

> volume #2 color #e5371a color #ffffb2

> volume #2 color #e54f52 color #ffffb2

> volume #2 level 3 level 6

> color #1 #1e90ff1e

> style sphere

Changed 396 atom styles  

> undo

> color Amines orchid

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color DACH orchid

> color F pale green

> style sphere

Changed 396 atom styles  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/tomkunde/Desktop/movie9.mp4

Movie saved to /Users/tomkunde/Desktop/movie9.mp4  
  

> close session

> open "/Users/tomkunde/Documents/Work/Untitled Folder/2+2-PTO-
> MC_optimized.mol2"

Opened 2+2-PTO-MC_optimized.mol2 containing 1 structures (104 atoms, 112
bonds)  

> hide H

Drag select of 6 atoms, 7 bonds  

> name frozen DACH sel

> color C doger blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color C dodger blue

> color F pale green

> color DACH orchid

> style sphere

Changed 104 atom styles  

> lighting simple

> lighting soft

> lighting shadows true intensity 0.5

> graphics silhouettes false

> graphics silhouettes true

> select clear

> save "/Users/tomkunde/Documents/Work/Untitled Folder/2+2 PTO-MC
> speheres.png" transparentBackground true

> save "/Users/tomkunde/Documents/Work/Untitled Folder/2+2 PTO-MC.cxs"

> close session

> open "/Users/tomkunde/Documents/Work/Untitled Folder/3+3-PTO-
> MC_optimized.mol2"

Opened 3+3-PTO-MC_optimized.mol2 containing 1 structures (156 atoms, 168
bonds)  

> hdie H

Unknown command: hdie H  

> hide H

Drag select of 6 atoms, 6 bonds  
Drag select of 6 atoms, 8 bonds  

> name frozen DACH sel

> style sphere

Changed 156 atom styles  

> color C dodger blue

> color DACH orchid

> color F pale green

> show H

> select clear

> lighting soft

> lighting shadows true intensity 0.5

> graphics silhouettes false

> graphics silhouettes true

> save "/Users/tomkunde/Documents/Work/Untitled Folder/3+3 PTO-MC spheres.png"
> transparentBackground true

> save "/Users/tomkunde/Documents/Work/Untitled Folder/3+3 PTO-MC.cxs"

> close session

> open "/Users/tomkunde/Documents/Work/Untitled Folder/4+4-PTO-
> MC_optimized.mol2"

Opened 4+4-PTO-MC_optimized.mol2 containing 1 structures (208 atoms, 224
bonds)  

> hdie H

Unknown command: hdie H  

> hide H

Drag select of 6 atoms, 7 bonds  
Drag select of 6 atoms, 8 bonds  
Drag select of 6 atoms, 6 bonds  

> name frozen DACH sel

> color C dodger blue

> color DACH orchid

> color F pale green

> show H

> style sphere

Changed 208 atom styles  

> lighting soft

> lighting shadows true intensity 0.5

> select clear

> save "/Users/tomkunde/Documents/Work/Untitled Folder/4+4 PTO-MC spheres.png"
> transparentBackground true

> save "/Users/tomkunde/Documents/Work/Untitled Folder/4+4 PTO-MC.cxs"

> open "/Users/tomkunde/Documents/Work/Untitled Folder/3+3 PTO-MC.cxs"

opened ChimeraX session  

> open "/Users/tomkunde/Documents/Work/Untitled Folder/4+4 PTO-MC.cxs"

opened ChimeraX session  

> open "/Users/tomkunde/Documents/Work/Untitled Folder/3+3-PTO-
> MC_optimized.mol2"

Opened 3+3-PTO-MC_optimized.mol2 containing 1 structures (156 atoms, 168
bonds)  

> open "/Users/tomkunde/Documents/Work/Untitled Folder/2+2-PTO-
> MC_optimized.mol2"

Opened 2+2-PTO-MC_optimized.mol2 containing 1 structures (104 atoms, 112
bonds)  

> select add #2

156 atoms, 168 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,-1.5242,0,1,0,0.22619,0,0,1,0.21368

> select add #3

260 atoms, 280 bonds, 2 residues, 2 models selected  

> view matrix models
> #2,1,0,0,-2.996,0,1,0,2.1086,0,0,1,0.51162,#3,1,0,0,-1.4718,0,1,0,1.8824,0,0,1,0.29794

> select subtract #2

104 atoms, 112 bonds, 1 residue, 1 model selected  

> view matrix models #3,1,0,0,-1.1602,0,1,0,1.4321,0,0,1,0.23202

> select subtract #3

Nothing selected  

> select add #2

156 atoms, 168 bonds, 1 residue, 1 model selected  

> view matrix models #2,1,0,0,-0.62681,0,1,0,-1.0957,0,0,1,0.022435

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.99495,0.1002,0.0061834,-0.83994,-0.10028,0.99488,0.012957,-1.3562,-0.0048533,-0.013511,0.9999,0.036232

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.99495,0.1002,0.0061834,-1.1189,-0.10028,0.99488,0.012957,-0.55543,-0.0048533,-0.013511,0.9999,0.11714

> select subtract #2

Nothing selected  

> select add #3

104 atoms, 112 bonds, 1 residue, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.97326,0.22718,0.033986,-1.1611,-0.2274,0.9738,0.0027125,1.3391,-0.032479,-0.010368,0.99942,0.21844

> hide #1 models

> view matrix models
> #3,0.9753,0.21348,0.056662,-1.2002,-0.21557,0.97591,0.033704,1.2946,-0.048102,-0.045086,0.99782,0.20578

> view matrix models
> #3,-0.05356,0.98428,0.16831,-1.5335,-0.9981,-0.057892,0.020932,0.74892,0.030347,-0.16687,0.98551,0.21983

> view matrix models
> #3,-0.047196,0.9978,0.046546,-1.3339,-0.99837,-0.048612,0.029766,0.73734,0.031964,-0.045065,0.99847,0.23345

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.047196,0.9978,0.046546,-2.6652,-0.99837,-0.048612,0.029766,-0.080139,0.031964,-0.045065,0.99847,0.022365

> view matrix models
> #3,-0.047196,0.9978,0.046546,-1.2526,-0.99837,-0.048612,0.029766,-0.10783,0.031964,-0.045065,0.99847,-0.077005

> style sticks

Expected a keyword  

> style stick

Changed 468 atom styles  

> show #1 models

> hide #3 models

> select subtract #3

Nothing selected  

> select add #2

156 atoms, 168 bonds, 1 residue, 1 model selected  

> view matrix models
> #2,0.99495,0.1002,0.0061834,-0.30089,-0.10028,0.99488,0.012957,-0.70809,-0.0048533,-0.013511,0.9999,0.33853

> select subtract #2

Nothing selected  

> show #3 models

> color #1 #dffb81 transparency 0

> color #1 #8ed243 transparency 0

> color #2 #8ed243 transparency 0

> color #2 #b4d28e transparency 0

> color #2 #bad29a transparency 0

> color #3 #8ed243 transparency 0

> color #3 #d2d0c5 transparency 0

> select add #2

156 atoms, 168 bonds, 1 residue, 1 model selected  

> view matrix models
> #2,0.99495,0.1002,0.0061834,-0.70304,-0.10028,0.99488,0.012957,-0.99916,-0.0048533,-0.013511,0.9999,-8.5279

> select subtract #2

Nothing selected  

> select add #3

104 atoms, 112 bonds, 1 residue, 1 model selected  

> view matrix models
> #3,-0.047196,0.9978,0.046546,-2.1282,-0.99837,-0.048612,0.029766,-0.70898,0.031964,-0.045065,0.99847,-18.327

> select subtract #3

Nothing selected  

> style sphere

Changed 468 atom styles  

> select add #3

104 atoms, 112 bonds, 1 residue, 1 model selected  

> view matrix models
> #3,-0.047196,0.9978,0.046546,-2.4058,-0.99837,-0.048612,0.029766,-0.84975,0.031964,-0.045065,0.99847,-20.738

> select subtract #3

Nothing selected  

> select add #2

156 atoms, 168 bonds, 1 residue, 1 model selected  

> view matrix models
> #2,0.99495,0.1002,0.0061834,-1.0333,-0.10028,0.99488,0.012957,-1.0874,-0.0048533,-0.013511,0.9999,-10.862

> view matrix models
> #2,0.99495,0.1002,0.0061834,-1.9012,-0.10028,0.99488,0.012957,-0.47925,-0.0048533,-0.013511,0.9999,-11.345

> select subtract #2

Nothing selected  

> select add #3

104 atoms, 112 bonds, 1 residue, 1 model selected  

> view matrix models
> #3,-0.047196,0.9978,0.046546,-2.5378,-0.99837,-0.048612,0.029766,-0.83539,0.031964,-0.045065,0.99847,-21.337

> ui mousemode right translate

> select clear

> save "/Users/tomkunde/Documents/Work/Untitled Folder/PTO-MC comparison
> spheres side.png" transparentBackground true

> ui mousemode right "translate selected models"

> select add #3

104 atoms, 112 bonds, 1 residue, 1 model selected  

> view matrix models
> #3,-0.047196,0.9978,0.046546,-3.7209,-0.99837,-0.048612,0.029766,-0.89114,0.031964,-0.045065,0.99847,-21.222

> ui mousemode right "rotate selected models"

> select subtract #3

Nothing selected  

> select add #2

156 atoms, 168 bonds, 1 residue, 1 model selected  

> view matrix models
> #2,0.98411,0.17751,0.0036814,-2.0689,-0.17755,0.98391,0.020004,-0.65197,-7.1303e-05,-0.02034,0.99979,-11.321

> select subtract #2

Nothing selected  

> ui mousemode right translate

> save "/Users/tomkunde/Documents/Work/Untitled Folder/Comparison PTO-MC
> spheres back view.png" transparentBackground true

> style ball

Changed 468 atom styles  

> select add #1

208 atoms, 224 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #1,1,0,0,-1.6214,0,1,0,-0.034575,0,0,1,-0.039284

> select subtract #1

Nothing selected  

> save "/Users/tomkunde/Documents/Work/Untitled Folder/Comparison PTO-MC
> sideview balls.png" transparentBackground true

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/tomkunde/Desktop/movie10.mp4

Movie saved to /Users/tomkunde/Desktop/movie10.mp4  
  

> style sphere

Changed 468 atom styles  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/tomkunde/Desktop/movie11.mp4

Movie saved to /Users/tomkunde/Desktop/movie11.mp4  
  

> open "/Users/tomkunde/Documents/Work/Untitled
> Folder/PTOnew2+3cage_optimized.mol2"

Opened PTOnew2+3cage_optimized.mol2 containing 1 structures (180 atoms, 192
bonds)  

> close session

> open "/Users/tomkunde/Documents/Work/Untitled
> Folder/PTOnew2+3cage_optimized.mol2" format mol2

Opened PTOnew2+3cage_optimized.mol2 containing 1 structures (180 atoms, 192
bonds)  

> hide H

Drag select of 15 atoms, 17 bonds  

> close session

> open "/Users/tomkunde/Documents/Work/Untitled
> Folder/PTOnew2+3cage_optimized.mol2"

Opened PTOnew2+3cage_optimized.mol2 containing 1 structures (180 atoms, 192
bonds)  

> hide H

Drag select of 15 atoms, 17 bonds  

> name frozen Amines sel

> color C dodger blue

> color Amines orchid

> color F pale green

> style sphere

Changed 180 atom styles  

> lighting soft

> lighting shadows true intensity 0.5

> select clear

> style ball

Changed 180 atom styles  

> open "/Users/tomkunde/Documents/Work/Untitled Folder/PTOne2+3
> cavity_cav1.dx"

Opened PTOne2+3 cavity_cav1.dx as #2, grid size 61,55,68, pixel 0.2, shown at
level -6,6, step 1, values float32  

> volume #2 level 3 level 6

> volume #2 color #8ed243 color #b2ffff

> volume #2 color #ff9f3f color #b2ffff

> style sphere

Changed 180 atom styles  

> color #1 #1e90ff74

> color #1 #1e90ff50

> color #1 #1e90ff43

> color C dodger blue

> color Amines orchid

> color F pale green

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/tomkunde/Desktop/movie12.mp4

Movie saved to /Users/tomkunde/Desktop/movie12.mp4  
  

> show H

> Color H white

Unknown command: Color H white  

> color H white

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> volume #2 level 5 level 6

> close session

> open "/Users/tomkunde/Documents/Work/Untitled
> Folder/PTOnew2+3cage_optimized.mol2" format mol2

No such file/path: /Users/tomkunde/Documents/Work/Untitled
Folder/PTOnew2+3cage_optimized.mol2  

> open "/Users/tomkunde/Documents/Work/Jupyter
> Notebooks/PTOnew2+3cage_optimized.mol2"

Opened PTOnew2+3cage_optimized.mol2 containing 1 structures (180 atoms, 192
bonds)  

> open "/Users/tomkunde/Documents/Work/Jupyter Notebooks/PTOne2+3
> cavity_cav1.dx"

Opened PTOne2+3 cavity_cav1.dx as #2, grid size 61,55,68, pixel 0.2, shown at
level -6,6, step 1, values float32  

> volume #2 level 3 level 6

> volume #2 level 5 level 6

> volume #2 level 3 level 6

> open "/Users/tomkunde/Documents/Work/Jupyter
> Notebooks/GC1TREN_optimized.mol2"

Opened GC1TREN_optimized.mol2 containing 1 structures (268 atoms, 288 bonds)  

> close session

> open "/Users/tomkunde/Documents/Work/Jupyter
> Notebooks/GC1TREN_optimized.mol2"

Opened GC1TREN_optimized.mol2 containing 1 structures (268 atoms, 288 bonds)  

> hide H

> style ball

Changed 268 atom styles  
Drag select of 1 atoms  
Drag select of 1 atoms, 1 bonds  
Drag select of 1 atoms  
Drag select of 2 atoms, 1 bonds  
Drag select of 2 atoms, 2 bonds  
Drag select of 3 atoms, 2 bonds  
Drag select of 2 atoms, 1 bonds  

> select add /?:1@@serial_number=-1

268 atoms, 288 bonds, 1 residue, 1 model selected  

> undo

Drag select of 1 atoms  
Drag select of 1 atoms, 1 bonds  
Drag select of 1 atoms  
Drag select of 2 atoms, 2 bonds  

> name frozen TREN sel

> color C dodger blue

> color TREN orchid

> color F pale green

> select clear

> lighting soft

> lighting shadows true intensity 0.5

> graphics silhouettes false

> graphics silhouettes true

> ui mousemode right "translate selected models"

> ui mousemode right zoom

> style sphere

Changed 268 atom styles  

> open "/Users/tomkunde/Documents/Work/Jupyter Notebooks/GC1TREN
> Cavity_cav1.dx"

Opened GC1TREN Cavity_cav1.dx as #2, grid size 89,83,89, pixel 0.2, shown at
level -6,6, step 1, values float32  

> volume #2 level 3 level 6

> style stick

Changed 268 atom styles  

> volume #2 color #ff9f3f color #ffb2ff

> save "/Users/tomkunde/Documents/Work/Jupyter Notebooks/GC1TREN w Cavity.cxs"

> close session

> open "/Users/tomkunde/Documents/Work/Jupyter
> Notebooks/GC1_A4H4_optimized.mol2"

Opened GC1_A4H4_optimized.mol2 containing 1 structures (268 atoms, 288 bonds)  

> hide H

> style ball

Changed 268 atom styles  
Drag select of 2 atoms, 1 bonds  
Drag select of 2 atoms, 3 bonds  
Drag select of 2 atoms, 2 bonds  
Drag select of 2 atoms, 3 bonds  
Drag select of 1 atoms, 2 bonds  
Drag select of 2 atoms, 2 bonds  
Drag select of 1 atoms  
Drag select of 2 atoms, 2 bonds  
Drag select of 2 atoms, 1 bonds  
Drag select of 2 atoms, 2 bonds  

> name frozen TREN sel

> color C orange

> color TREN orchid

> lighting soft

> lighting shadows true intensity 0.5

> graphics silhouettes false

> graphics silhouettes true

> select /?:1@@serial_number=-1

268 atoms, 288 bonds, 1 residue, 1 model selected  

> select clear

> open "/Users/tomkunde/Documents/Work/Jupyter Notebooks/GC1 A4H4_cav1.dx"

Opened GC1 A4H4_cav1.dx as #2, grid size 88,86,86, pixel 0.2, shown at level
-6,6, step 1, values float32  

> volume #2 level 3 level 6

> volume #2 color #ff9f3f color #ffb2b2

> volume #2 color #8ed243 color #ffb2b2

> save "/Users/tomkunde/Documents/Work/Jupyter Notebooks/GC1A4H4 w cavity.cxs"

> close session

> open "/Users/tomkunde/Documents/Work/Jupyter
> Notebooks/GC1_A4H3F1_optimized.mol2"

Opened GC1_A4H3F1_optimized.mol2 containing 1 structures (268 atoms, 288
bonds)  

> hide H

> style ball

Changed 268 atom styles  
Drag select of 2 atoms, 1 bonds  
Drag select of 1 atoms  
Drag select of 1 atoms, 1 bonds  
Drag select of 2 atoms, 1 bonds  
Drag select of 2 atoms, 2 bonds  
Drag select of 2 atoms, 1 bonds  
Drag select of 1 atoms  

> name frozen TREN sel

> select clear

Drag select of 2 atoms, 4 bonds  
Drag select of 1 atoms, 1 bonds  
Drag select of 1 atoms  
Drag select of 1 atoms, 1 bonds  
Drag select of 1 atoms  
Drag select of 3 atoms, 3 bonds  
Drag select of 3 atoms, 2 bonds  
Drag select of 2 atoms, 4 bonds  
Drag select of 1 atoms  
Drag select of 1 atoms, 2 bonds  
Drag select of 1 atoms  
Drag select of 2 atoms, 1 bonds  
Drag select of 1 atoms  
Drag select of 1 atoms, 1 bonds  
Drag select of 1 atoms, 2 bonds  
Drag select of 2 atoms, 1 bonds  
Drag select of 1 atoms, 2 bonds  

> name frozen F-Aldehyde sel

> color C orange

> color TREN orchid

> color F-Aldehyde dodger blue

> color F pale green

> lighting soft

> lighting shadows true intensity 0.5

> select clear

> open "/Users/tomkunde/Documents/Work/Jupyter Notebooks/GC1A4H3F1
> cavity_cav1.dx"

Opened GC1A4H3F1 cavity_cav1.dx as #2, grid size 92,85,90, pixel 0.2, shown at
level -6,6, step 1, values float32  

> volume #2 level 3 level 6

> volume #2 color #8ed243 color #b2ffb2

> save "/Users/tomkunde/Documents/Work/Jupyter Notebooks/GC1A4H3F1 w
> cavity.cxs"

> close session

> open "/Users/tomkunde/Documents/Work/Jupyter
> Notebooks/GC1_A4H2F2_optimized.mol2"

Opened GC1_A4H2F2_optimized.mol2 containing 1 structures (268 atoms, 288
bonds)  

> style sphere

Changed 268 atom styles  

> close session

> open "/Users/tomkunde/Documents/Work/Untitled Folder/GC2_optimized.mol"
> format sdf

No such file/path: /Users/tomkunde/Documents/Work/Untitled
Folder/GC2_optimized.mol  

> open "/Users/tomkunde/Documents/Work/MOL-files Cages/Kwano Cage colored.cxs"
> format session

opened ChimeraX session  

> style sphere

Changed 345 atom styles  

> close session

> open "/Users/tomkunde/Documents/Work/Untitled Folder/A4H1F3.cxs" format
> session

No such file/path: /Users/tomkunde/Documents/Work/Untitled Folder/A4H1F3.cxs  


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

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




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

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro17,1
      Processor Name: Unknown
      Processor Speed: 2,4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache: 8 MB
      Memory: 16 GB

Software:

    System Software Overview:

      System Version: macOS 12.4 (21F79)
      Kernel Version: Darwin 21.5.0
      Time since boot: 33 days 3:28

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        HP 27fh:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    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: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 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: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    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: 1.1.5
    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: 2.1.2
    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: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    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-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: 2.6
    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: 1.18.3
    ChimeraX-uniprot: 2.2
    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: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    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: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    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: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    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
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

Change History (1)

comment:1 by Eric Pettersen, 3 years ago

Cc: Tom Goddard added
Component: Unassigned → Core
Description: modified (diff)
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Unknown crash

No Python backtrace. Was using 11.7GB at the time.

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