Opened 3 years ago

Closed 3 years ago

#8003 closed defect (can't reproduce)

Crash adjusting window sizes

Reported by: chai.gopalasingam@… Owned by: pett
Priority: normal Milestone:
Component: Window Toolkit 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: 1.4 (2022-06-03 23:39:42 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Attempting to drag down some of the pop up windows to make them larger (i.e., volume viewer, log windows) within the right hand side panel and it suddenly crashed. Prior to this many of the windows were not in the panel (by choice), but fixing them back into the right hand panel led to many of them being to small to view.
Fatal Python error: Segmentation fault

Current thread 0x0000000200c5c600 (most recent call first):
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2317 in destroy
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2185 in _destroy
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 807 in remove_tool
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 370 in remove_tool
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/tools.py", line 154 in delete
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/map/volume_viewer.py", line 114 in delete
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 674 in close_request
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2283 in 
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 318 in event_loop
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 870 in init
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1021 in 
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/Applications/ChimeraX-1.4.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" : 4500000,
  "procLaunch" : "2022-11-09 14:07:34.8871 +0900",
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro17,1",
  "procStartAbsTime" : 107930964618494,
  "coalitionID" : 38525,
  "osVersion" : {
    "train" : "macOS 12.2.1",
    "build" : "21D62",
    "releaseType" : "User"
  },
  "captureTime" : "2022-11-10 11:01:13.4965 +0900",
  "incident" : "3F4E974F-5FA2-48F4-8AA0-A135A290AF61",
  "bug_type" : "309",
  "pid" : 12694,
  "procExitAbsTime" : 109201084857793,
  "translated" : true,
  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.4.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.4.0","CFBundleVersion":"1.4.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"061F1F98-3CB4-5333-A8CF-31DCC056ED77","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "1F6D094E-BB51-A896-68D3-B8012DF55E08",
  "wakeTime" : 538,
  "sleepWakeUUID" : "65725B7C-F7AF-45EA-A7D2-CDE93F8D1249",
  "sip" : "enabled",
  "vmRegionInfo" : "0xa76e187c728 is not in any region.  Bytes after previous region: 11024669853481  Bytes before following region: 94047410075864\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  ...(unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV  ",
  "isCorpse" : 1,
  "exception" : {"codes":"0x0000000000000001, 0x00008a76e187c728","rawCodes":[1,152243194545960],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00008a76e187c728 -> 0x00000a76e187c728 (possible pointer authentication failure)"},
  "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",
  "vmregioninfo" : "0xa76e187c728 is not in any region.  Bytes after previous region: 11024669853481  Bytes before following region: 94047410075864\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  ...(unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV  ",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
  "threads" : 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        "SIRI_TEXT_TO_SPEECH" : "622657ce37186c771d5404ad"
      },
      "deploymentId" : 240000414
    },
    {
      "rolloutId" : "60186475825c62000ccf5450",
      "factorPackIds" : {

      },
      "deploymentId" : 240000026
    },
    {
      "rolloutId" : "60f8ddccefea4203d95cbeef",
      "factorPackIds" : {

      },
      "deploymentId" : 240000021
    },
    {
      "rolloutId" : "63582c5f8a53461413999550",
      "factorPackIds" : {

      },
      "deploymentId" : 240000002
    },
    {
      "rolloutId" : "5ffde50ce2aacd000d47a95f",
      "factorPackIds" : {

      },
      "deploymentId" : 240000215
    },
    {
      "rolloutId" : "5fc94383418129005b4e9ae0",
      "factorPackIds" : {

      },
      "deploymentId" : 240000537
    },
    {
      "rolloutId" : "5fb4245a1bbfe8005e33a1e1",
      "factorPackIds" : {

      },
      "deploymentId" : 240000020
    }
  ],
  "experiments" : [

  ]
}
}
===== Log before crash start =====
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/chaig/Desktop/Hyogo_Postdoc_Shiro_Dec2019/Manuscripts/Monomer_qNOR_dimer_transition/for_paper/Figures/Figure2/monomer.cxs
> format session

Opened postprocess.mrc as #1, grid size 288,288,288, pixel 0.752, shown at
level 0.017, step 1, values float32  
Opened run_class001.mrc as #3, grid size 288,288,288, pixel 0.752, shown at
level 0.00905, step 1, values float32  
Opened relion_locres_filtered.mrc as #5, grid size 288,288,288, pixel 0.752,
shown at level 0.0327, step 1, values float32  
opened ChimeraX session  

> close #2,4

> hide #!1 models

> show #!1 models

> show #!3 models

> hide #!1 models

> surface unzone #2

> surface unzone #3

> volume #3 level 0.008599

> view #3 clip false

> surface unzone #3

> close #3

> close #1

> open
> /Users/chaig/Desktop/Hyogo_Postdoc_Shiro_Dec2019/Manuscripts/Monomer_qNOR_dimer_transition/for_paper/Refine3D/2nd_polish/run_class001.mrc

Opened run_class001.mrc as #1, grid size 288,288,288, pixel 0.752, shown at
level 0.00575, step 2, values float32  

> view #1 clip false

> ui tool show "Side View"

> lighting simple

> open
> /Users/chaig/Desktop/Hyogo_Postdoc_Shiro_Dec2019/Cryo_EM/cryoEM_NmqNOR_monomer/Data_collection/220122_cryoARM300/RealSpaceRefine_48/edits/edit_pp_maps/Polish2nd_tm10del_add6_rama_real_space_refined_048_v7.pdb
> format pdb

Chain information for
Polish2nd_tm10del_add6_rama_real_space_refined_048_v7.pdb #2  
---  
Chain | Description  
A | No description available  
  

> hide #!1 models

> show #!1 models

> color #2 #fedd1d transparency 0

> hide #!1 models

> show #!1 models

> color #2 #f5c66c transparency 0

> hide #!1 models

> lighting soft

> lighting simple

> show #!1 models

> volume #1 step 1

> color zone #1 near #2 distance 3

> color zone #1 near #2 distance 2.8

> color zone #1 near #2 distance 3.5

> color zone #1 near #2 distance 4

> lighting soft

> volume splitbyzone #1

Opened run_class001.mrc 0 as #3.1, grid size 288,288,288, pixel 0.752, shown
at level 0.00575, step 1, values float32  
Opened run_class001.mrc 1 as #3.2, grid size 288,288,288, pixel 0.752, shown
at level 0.00575, step 1, values float32  

> hide #!3 models

> show #!3 models

> hide #!3.1 models

> show #!3.1 models

> hide #!3.1 models

> hide #!3.2 models

> show #!3.1 models

> show #!3.2 models

> hide #!2 models

> volume #3.2 level 0.007225

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> volume #3.1 level 0.006212

> volume #3.1 color #a0a0bf

> volume #3.1 color #a2a2bf

> volume #3.1 color #9191ab72

> volume #3.1 color #9191ab00

> volume #3.1 color #9191abb9

> volume #3.1 color #9191ab

> volume #3.1 color #9191abf4

> volume #3.1 color #9191ab84

> volume #3.1 color #9191ab5d

> volume #3.1 color #bfc0e35d

> volume #3.1 color #babadc5d

> volume #3.1 color #9cb0dc5d

> volume #3.1 color #726fdc5d

> volume #3.1 color #747edc5d

> volume #3.1 color #747edc5e

> lighting simple

> lighting soft

> volume #3.1 color #747edc

> volume #3.1 color #747edc8c

> volume #3.1 color #747edc33

> volume #3.2 level 0.008922

> hide #!3.2 models

> show #!2 models

> volume #3.1 color #747edc

> volume #3.1 color #747edcf6

> volume #3.1 color #747edc

> volume #3.1 level 0.004291

> surface dust #3.1 size 7.52

> show #!3.2 models

> volume #3.1 level 0.005069

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!3.1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!3.1 models

> volume #3.1 color #747edc58

> show #!1 models

> volume #1 level 0.01028

> volume #3.1 level 0.005801

> volume #3.1 level 0.005572

> save monomer_micelle_map_trans.jpg

> save monomer_micelle_map_trans2.jpg

> volume #1 level 0.009827

> volume #1 level 0.009601

> surface dust #1 size 7.52

> volume #1 level 0.008809

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> colour #2 byhet

> lighting simple

> colour #2:801 crimson

> colour #2:801 crimson byhet

> color #2:801 crimson byhet

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> colour #2 byhet

> colour #2:802 cadet blue

> colour #2:802 by het

> color #2:802 by het

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

> colour #2 byhet

> select clear

> lighting soft

> lighting simple

> show #!3.1 models

> show #!3.2 models

> hide #!2 models

> lighting soft

> show #!1 models

> hide #!1 models

> show #!1 models

> save monomer_micelle_map_trans3.jpg

> save monomer_micelle_map_trans4.jpg

> show #!2 models

> hide #!1 models

> hide #!3.1 models

> show #!3.1 models

> hide #!3.2 models

> volume #3.1 color #747edc00

> preset cartoons/nucleotides cylinders/stubs

Using preset: Cartoons/Nucleotides / Cylinders/Stubs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> volume #3.1 color #747edc00

> volume #3.1 color #747edc

> volume #3.1 color #747edc00

> volume #3.1 color #747edc0a

> volume #3.1 color #747edc00

> volume #3.1 color #747edc

> volume #3.1 color #747edc35

> volume #3.1 color #747edc00

> save bottom_monomer_micelle_trans.jpg

> show #!3.1 models

> save bottom_monomer_micelle_trans.jpg

> hide #!3.1 models

> save bottom_monomer_new.jpg

> save top_monomer_new.jpg

> lighting gentle

> save front_monomer_new.jpg

> save side_monomer_new.jpg

> lighting simple

> show #!1 models

> hide #!2 models

> hide #!3 models

> ui mousemode right "tape measure"

> marker segment #4 position 114.2,66.12,141.6 toPosition 69.45,120.2,85.02
> color yellow radius 0.188 label 90.19 labelHeight 9.019 labelColor yellow

> marker delete #4

> marker segment #4 position 86.88,143.7,98.58 toPosition 115.6,91.83,165.3
> color yellow radius 0.188 label 89.28 labelHeight 8.928 labelColor yellow

> marker segment #4 position 90.33,81.61,119.8 toPosition 146.5,91.91,103
> color yellow radius 0.188 label 59.5 labelHeight 5.95 labelColor yellow

> show #!3.1 models

> marker segment #4 position 86.37,95.73,133.2 toPosition 73.49,120.9,95.6
> color yellow radius 0.188 label 47.01 labelHeight 4.701 labelColor yellow

> marker delete #4

> ui mousemode right zoom

> ui mousemode right translate

> show #!2 models

> hide #!1 models

> lighting soft

> color #3.1 #747edc00 models

> color #3.1 #747edc3f models

> color #3.1 #747edc models transparency 0

> color #3.1 #747edc14 models

> color #3.1 #747edc00 models

> save front_monomer_trans.jpg

> show #6 models

> hide #6 models

> show #!5 models

> hide #!2 models

> volume #5 level 0.0251

> hide #!3 models

> hide #!3.1 models

> volume #5 level 0.02092

> surface dust #5 size 7.52

> open
> /Users/chaig/Desktop/Hyogo_Postdoc_Shiro_Dec2019/Manuscripts/Monomer_qNOR_dimer_transition/for_paper/Refine3D/2nd_polish/relion_locres.mrc

Opened relion_locres.mrc as #4, grid size 288,288,288, pixel 0.752, shown at
level 24.1, step 2, values float32  

> select subtract #7

Nothing selected  

> hide #7 models

> show #7 models

> hide #7 models

> hide #!4 models

> select subtract #7

Nothing selected  

> ui tool show "Surface Color"

> color sample #5.1 map #4 palette #ff0000:#ffffff:#0000ff

Map values for surface "surface": minimum 2.748, mean 3.052, maximum 4.756  

> color sample #5.1 map #4 palette 2.748,#0fc7cf:3.752,#ffffff:4.756,#9e205e

Map values for surface "surface": minimum 2.748, mean 3.052, maximum 4.756  

> color sample #5.1 map #4 palette 2.748,#0fc7cf:3.752,#ffffff:4.756,#9e205e

Map values for surface "surface": minimum 2.748, mean 3.052, maximum 4.756  

> key cyan-white-maroon :2.75 :3.75 :4.76 showTool true

> ui mousemode right "color key"

> key accent-3 :2.75 :3.75 :4.76

> key size 0.01734,0.20656

> key size 0.00734,0.20656

> key accent-3 :2.75 :3.75 :4.76 white:

> key #7fc97f:2.75 #beaed4:3.75 #fdc086:4.76 white: white:

> color sample #5.1 map #4 palette accent-5

Map values for surface "surface": minimum 2.748, mean 3.052, maximum 4.756  

> color sample #5.1 map #4 palette accent-5 key true

Map values for surface "surface": minimum 2.748, mean 3.052, maximum 4.756  

> key accent-5 :2.75 :3.25 :3.75 :4.25 :4.76 showTool true

> key pos 0.774224,0.523094 size 0.0694128,0.163264

> show #6 models

> key pos 0.753861,0.381839 size 0.0876194,0.337057

> graphics silhouettes false

> graphics silhouettes true

> key pos 0.707768,0.398519 size 0.0666459,0.280276

> key accent-5 :2.75 :3.25 :3.75 :4.25 :4.7

> key accent-5 :2.75 :3.25 :3.75 :4.25 :4.75

> save monomer_locres_Accent5_1.jpg

> hide #!5 models

> show #!5 models

> hide #5.1.1 models

> hide #5.1.2 models

> show #5.1.2 models

> show #5.1.1 models

> hide #5.1.1 models

> show #5.1.1 models

> hide #5.1.1 models

> key pos 0.69777,0.39852

> key pos 0.68777,0.39852

> key pos 0.67777,0.39852

> hide #6 models

> show #5.1.1 models

> hide #5.1.1 models

> show #5.1.1 models

> hide #5.1.1 models

> hide #5.1.2 models

> show #5.1.2 models

> hide #5.1.2 models

> show #5.1.1 models

> hide #5.1.1 models

> color sample #5.1.1#5.1.2 map #4 palette
> 2.748,#0fc7cf:3.752,#ffffff:4.756,#9e205e

Map values for surface "cap near": minimum 2.753, mean 2.925, maximum 3.396  
Map values for surface "cap far": minimum 2.817, mean 2.95, maximum 3.513  

> color single #5.1.1#5.1.2

> color sample #5.1.1#5.1.2 map #4 palette
> 2.748,#0fc7cf:3.752,#ffffff:4.756,#9e205e

Map values for surface "cap near": minimum 2.765, mean 2.968, maximum 3.626  
Map values for surface "cap far": minimum 2.775, mean 2.938, maximum 3.432  

> show #5.1.1 models

> show #5.1.2 models

> hide #5.1.1 models

> hide #5.1.2 models

> show #5.1.1 models

> show #5.1.2 models

> color sample #5.1 map #4 palette 2.748,#0fc7cf:3.752,#ffffff:4.756,#9e205e

Map values for surface "surface": minimum 2.748, mean 3.052, maximum 4.756  

> color sample #5.1 map #4 palette 2.748,#0fc7cf:3.752,#ffffff:4.756,#9e205e

Map values for surface "surface": minimum 2.748, mean 3.052, maximum 4.756  

> hide #5.1.1 models

> hide #5.1.2 models

> show #5.1.2 models

> show #5.1.1 models

> color sample #5.1 map #4 palette accent-5 key true

Map values for surface "surface": minimum 2.748, mean 3.052, maximum 4.756  

> key accent-5 :2.75 :3.25 :3.75 :4.25 :4.76 showTool true

Map values for surface "cap near": minimum 2.76, mean 2.904, maximum 3.31  

> key accent-5 :2.76 :2.90 :3.03 :3.17 :3.31 showTool true

Map values for surface "cap far": minimum 2.798, mean 2.969, maximum 3.502  

> key accent-5 :2.80 :2.97 :3.15 :3.33 :3.50 showTool true

> show #6 models

> hide #6 models

> color sample #5.1 map #4 palette 2.748,#0fc7cf:3.752,#ffffff:4.756,#9e205e

Map values for surface "surface": minimum 2.748, mean 3.052, maximum 4.756  
Map values for surface "cap near": minimum 3.167, mean 3.234, maximum 3.334  
Map values for surface "cap far": minimum 2.796, mean 2.943, maximum 3.359  

> color sample #5.1 map #4 palette accent-5 key true

Map values for surface "surface": minimum 2.748, mean 3.052, maximum 4.756  

> key accent-5 :2.75 :3.25 :3.75 :4.25 :4.76 showTool true

Map values for surface "cap near": minimum 3.167, mean 3.234, maximum 3.334  

> key accent-5 :3.17 :3.21 :3.25 :3.29 :3.33 showTool true

Map values for surface "cap far": minimum 2.796, mean 2.943, maximum 3.359  

> key accent-5 :2.80 :2.94 :3.08 :3.22 :3.36 showTool true

> color single #5.1.1#5.1.2

> color sample #5.1 map #4 palette accent-5 key true

Map values for surface "surface": minimum 2.748, mean 3.052, maximum 4.756  

> key accent-5 :2.75 :3.25 :3.75 :4.25 :4.76 showTool true

Map values for surface "cap near": minimum 3.167, mean 3.234, maximum 3.334  

> key accent-5 :3.17 :3.21 :3.25 :3.29 :3.33 showTool true

Map values for surface "cap far": minimum 2.796, mean 2.943, maximum 3.359  

> key accent-5 :2.80 :2.94 :3.08 :3.22 :3.36 showTool true

> color single #5.1.1#5.1.2

> hide #5.1.1 models

> show #5.1.1 models

> hide #5.1.2 models

> show #5.1.2 models

> color sample #5.1 map #4 palette accent-5 key true

Map values for surface "surface": minimum 2.748, mean 3.052, maximum 4.756  

> key accent-5 :2.75 :3.25 :3.75 :4.25 :4.76 showTool true

Map values for surface "cap near": minimum 3.167, mean 3.234, maximum 3.334  

> key accent-5 :3.17 :3.21 :3.25 :3.29 :3.33 showTool true

Map values for surface "cap far": minimum 2.796, mean 2.943, maximum 3.359  

> key accent-5 :2.80 :2.94 :3.08 :3.22 :3.36 showTool true

> color sample #5 map #4 palette accent-5 key true

Map values for surface "surface": minimum 2.748, mean 3.052, maximum 4.756  

> key accent-5 :2.75 :3.25 :3.75 :4.25 :4.76 showTool true

Map values for surface "cap near": minimum 3.167, mean 3.234, maximum 3.334  

> key accent-5 :3.17 :3.21 :3.25 :3.29 :3.33 showTool true

Map values for surface "cap far": minimum 2.796, mean 2.943, maximum 3.359  

> key accent-5 :2.80 :2.94 :3.08 :3.22 :3.36 showTool true

> color sample #5 map #4 palette accent-5 key true

Map values for surface "surface": minimum 2.748, mean 3.052, maximum 4.756  

> key accent-5 :2.75 :3.25 :3.75 :4.25 :4.76 showTool true

Map values for surface "cap near": minimum 3.046, mean 3.227, maximum 3.521  

> key accent-5 :3.05 :3.17 :3.28 :3.40 :3.52 showTool true

Map values for surface "cap far": minimum 2.797, mean 2.942, maximum 3.461  

> key accent-5 :2.80 :2.96 :3.13 :3.29 :3.46 showTool true

> key accent-5 :2.75 :3.25 :3.75 :4.25 :4.76 showTool true

> hide #!5.1 models

> show #!3.1 models

> hide #!3.1 models

> hide #!3 models

> show #5.1 models

> key accent-5 :2.75 :3.25 :3.75 :4.25 :4.76 showTool true

> color single #5.1.1#5.1.2

> key accent-5 :2.75 :3.25 :3.75 :4.25 :4.76 showTool true

> hide #5.1.1 models

> show #5.1.1 models

> color sample #5 map #4 palette accent-5 key true

Map values for surface "surface": minimum 2.748, mean 3.052, maximum 4.756  

> key accent-5 :2.75 :3.25 :3.75 :4.25 :4.76 showTool true

Map values for surface "cap near": minimum 2.871, mean 2.982, maximum 3.248  

> key accent-5 :2.87 :2.97 :3.06 :3.15 :3.25 showTool true

Map values for surface "cap far": minimum 2.774, mean 2.91, maximum 3.477  

> key accent-5 :2.77 :2.95 :3.13 :3.30 :3.48 showTool true

> color single #5.1.1#5.1.2

> color sample #5 map #4 palette accent-5 key true

Map values for surface "surface": minimum 2.748, mean 3.052, maximum 4.756  

> key accent-5 :2.75 :3.25 :3.75 :4.25 :4.76 showTool true

Map values for surface "cap near": minimum 2.864, mean 2.988, maximum 3.35  

> key accent-5 :2.86 :2.99 :3.11 :3.23 :3.35 showTool true

Map values for surface "cap far": minimum 2.775, mean 2.914, maximum 3.462  

> key accent-5 :2.77 :2.95 :3.12 :3.29 :3.46 showTool true

> color sample #5 map #4 palette accent-5 key true

Map values for surface "surface": minimum 2.748, mean 3.052, maximum 4.756  

> key accent-5 :2.75 :3.25 :3.75 :4.25 :4.76 showTool true

Map values for surface "cap near": minimum 2.761, mean 2.925, maximum 3.399  

> key accent-5 :2.76 :2.92 :3.08 :3.24 :3.40 showTool true

Map values for surface "cap far": minimum 2.796, mean 2.95, maximum 3.792  

> key accent-5 :2.80 :3.05 :3.29 :3.54 :3.79 showTool true

> color sample #5.1 map #4 palette accent-5 key true

Map values for surface "surface": minimum 2.748, mean 3.052, maximum 4.756  

> key accent-5 :2.75 :3.25 :3.75 :4.25 :4.76 showTool true

Map values for surface "cap near": minimum 2.761, mean 2.925, maximum 3.399  

> key accent-5 :2.76 :2.92 :3.08 :3.24 :3.40 showTool true

Map values for surface "cap far": minimum 2.796, mean 2.95, maximum 3.792  

> key accent-5 :2.80 :3.05 :3.29 :3.54 :3.79 showTool true

> hide #5.1.1 models

> hide #5.1.2 models

> show #5.1.2 models

> show #5.1.1 models

> hide #5.1.1 models

> show #5.1.1 models

> hide #5.1.1 models

> hide #5.1.2 models

> show #5.1.2 models

> hide #5.1.2 models

> color sample #5.1.1 map #4 palette accent-5 key true

Map values for surface "cap near": minimum 2.761, mean 2.913, maximum 3.405  

> key accent-5 :2.76 :2.92 :3.08 :3.24 :3.41 showTool true

> show #5.1.1 models

> hide #5.1.1 models

> show #5.1.1 models

> hide #5.1.1 models

> show #5.1.2 models

> hide #5.1.2 models

> show #5.1.1 models

> hide #5.1.1 models

> show #5.1.1 models

> hide #5.1.1 models

> show #5.1.1 models

> hide #5.1.1 models

> show #5.1.1 models

> hide #5.1.1 models

> show #5.1.1 models

> hide #5.1.2 models

> show #5.1.2 models

> color sample #5.1 map #4 palette accent-5 key true

Map values for surface "surface": minimum 2.748, mean 3.052, maximum 4.756  

> key accent-5 :2.75 :3.25 :3.75 :4.25 :4.76 showTool true

Map values for surface "cap near": minimum 2.759, mean 2.929, maximum 3.408  

> key accent-5 :2.76 :2.92 :3.08 :3.25 :3.41 showTool true

Map values for surface "cap far": minimum 2.983, mean 3.165, maximum 3.639  

> key accent-5 :2.98 :3.15 :3.31 :3.47 :3.64 showTool true

> save monomer_locres_Accent5_12jpg

Cannot determine format for 'monomer_locres_Accent5_12jpg'  

> save monomer_locres_Accent5_2.jpg

> lighting simple

> show #7 models

> hide #!5 models

> show #!1 models

> set bgColor black

> ui mousemode right translate

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> ui mousemode right "tape measure"

> marker segment #8 position 115.4,65.63,140.7 toPosition 82.91,117.8,74.64
> color yellow radius 0.188 label 90.18 labelHeight 9.018 labelColor yellow

> marker delete #8

> marker segment #8 position 146.1,101.4,104.9 toPosition 86.87,97.7,129.8
> color yellow radius 0.188 label 64.39 labelHeight 6.439 labelColor yellow

> show #!3.1 models

> set bgColor white

> marker segment #8 position 139,87.2,102.2 toPosition 123.9,109.6,69.48 color
> yellow radius 0.188 label 42.46 labelHeight 4.246 labelColor yellow

> show #!5 models

> hide #!3.1 models

> hide #!3 models

> hide #!8 models

> hide #!1 models

> volume #5 level 0.01328

> volume splitbyzone #5

Volume relion_locres_filtered.mrc #5 does not have zone coloring  

> show #!2 models

> marker delete #8

> ui mousemode right translate

> ui mousemode right zoom

> hide cartoons

> show cartoons

> select #2:490,541,542,494,335,635,633

69 atoms, 69 bonds, 7 residues, 1 model selected  

> show sel atoms

> select clear

> hide cartoons

> show #!1 models

> hide #!1 models

> show cartoons

> hide cartoons

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> surface zone #5 nearAtoms #2:490,541,542,494,335,635,633 distance 2.8

> show #!5 models

> surface zone #5 nearAtoms #2:490,541,542,494,335,635,633,801,802,803,804
> distance 2.8

> volume #5 level 0.06749

> volume #5 color #ffb2b231

> volume #5 color #ffb2b21e

> volume #5 color #ffb2b21f

> volume #5 level 0.05985

> surface zone #5 nearAtoms #2:490,541,542,494,335,635,633,801,802,803,804
> distance 3

> surface zone #5 nearAtoms #2:490,541,542,494,335,635,633,801,802,803,804
> distance 2.5

> lighting simple


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

Log:
Startup Messages  
---  
note | Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database.json  
  
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: 8 GB

Software:

    System Software Overview:

      System Version: macOS 12.2.1 (21D62)
      Kernel Version: Darwin 21.3.0
      Time since boot: 102 days 4:50

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:
        PHL 328P6VU:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 3840 x 2160 @ 30.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


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-Clipper: 0.18.0
    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-ISOLDE: 1.4
    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 (2)

comment:1 by pett, 3 years ago

Cc: Tom Goddard added
Component: Unassigned → Window Toolkit
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash adjusting window sizes

comment:2 by pett, 3 years ago

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

Hi Chai,

Thanks for reporting this problem. From the code traceback, it seems like you may have accidentally hit a window's close button while trying to adjust its size. At least it looks that way. I tried a lot of window resizings and/or window closings to try to reproduce this problem without success. Nonetheless, the report is helpful because it gives us another clue as to how to look for it -- and this problem is reported at least a fw times a week (mostly anonymously).

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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