id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
15799	Crash on Mac waking from sleep	kelvin.lau@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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    ""CFBundleShortVersionString"" : ""6.9"",
    ""CFBundleIdentifier"" : ""com.apple.CoreFoundation"",
    ""size"" : 5083136,
    ""uuid"" : ""84b539d5-22c9-3f8c-84c8-903e9c7b8d29"",
    ""path"" : ""\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation"",
    ""name"" : ""CoreFoundation"",
    ""CFBundleVersion"" : ""2503.1""
  },
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    ""source"" : ""P"",
    ""arch"" : ""arm64e"",
    ""base"" : 6872043520,
    ""CFBundleShortVersionString"" : ""2.1.1"",
    ""CFBundleIdentifier"" : ""com.apple.HIToolbox"",
    ""size"" : 2899968,
    ""uuid"" : ""7db6c397-563f-3756-908c-e25b019a1848"",
    ""path"" : ""\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox"",
    ""name"" : ""HIToolbox""
  },
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    ""source"" : ""P"",
    ""arch"" : ""arm64e"",
    ""base"" : 6691831808,
    ""size"" : 559640,
    ""uuid"" : ""37bbc384-0755-31c7-a808-0ed49e44dd8e"",
    ""path"" : ""\/usr\/lib\/dyld"",
    ""name"" : ""dyld""
  },
  {
    ""size"" : 0,
    ""source"" : ""A"",
    ""base"" : 0,
    ""uuid"" : ""00000000-0000-0000-0000-000000000000""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""arm64e"",
    ""base"" : 6695534592,
    ""size"" : 53248,
    ""uuid"" : ""386b0fc1-7873-3328-8e71-43269fd1b2c7"",
    ""path"" : ""\/usr\/lib\/system\/libsystem_pthread.dylib"",
    ""name"" : ""libsystem_pthread.dylib""
  },
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    ""arch"" : ""arm64e"",
    ""base"" : 6695292928,
    ""size"" : 241660,
    ""uuid"" : ""9b8b53f9-e2b6-36df-98e9-28d8fca732f2"",
    ""path"" : ""\/usr\/lib\/system\/libsystem_kernel.dylib"",
    ""name"" : ""libsystem_kernel.dylib""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""arm64e"",
    ""base"" : 6694600704,
    ""size"" : 577528,
    ""uuid"" : ""ec33cd83-7098-3ad6-82c8-bc03ac81e87b"",
    ""path"" : ""\/usr\/lib\/libc++.1.dylib"",
    ""name"" : ""libc++.1.dylib""
  }
],
  ""sharedCache"" : {
  ""base"" : 6691078144,
  ""size"" : 4220698624,
  ""uuid"" : ""3406ad1b-2469-30eb-9863-5dce861e6dea""
},
  ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=12.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=12.4G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               256K        2 \nActivity Tracing                   256K        1 \nCG image                          1008K       59 \nColorSync                          624K       31 \nCoreAnimation                     3808K      176 \nCoreGraphics                        64K        4 \nCoreServices                       624K        2 \nCoreUI image data                 5392K       37 \nFoundation                          48K        2 \nKernel Alloc Once                   32K        1 \nMALLOC                            11.6G      255 \nMALLOC guard page                  192K       12 \nMach message                        64K        3 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                       56.7M       46 \nStack                            166.6M       46 \nVM_ALLOCATE                      460.6M      420 \nVM_ALLOCATE (reserved)           192.0M        4         reserved VM address space (unallocated)\n__AUTH                            2210K      408 \n__AUTH_CONST                      31.9M      626 \n__CTF                               824        1 \n__DATA                            22.3M      785 \n__DATA_CONST                      42.8M      794 \n__DATA_DIRTY                      2032K      234 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__INFO_FILTER                         8        1 \n__LINKEDIT                       563.2M      163 \n__OBJC_RO                         71.9M        1 \n__OBJC_RW                         2199K        1 \n__TEXT                           941.9M      811 \ndyld private memory                592K        5 \nmapped file                      569.9M       99 \nshared memory                     3168K       25 \n===========                     =======  ======= \nTOTAL                             14.7G     5061 \nTOTAL, minus reserved VM space    14.5G     5061 \n"",
  ""legacyInfo"" : {
  ""threadTriggered"" : {
    ""name"" : ""CrBrowserMain"",
    ""queue"" : ""com.apple.main-thread""
  }
},
  ""logWritingSignature"" : ""b3c12fdfe0f10e1b40e7c3bf2a175d9f903c6ac7"",
  ""trialInfo"" : {
  ""rollouts"" : [
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      ""rolloutId"" : ""648c94d4ebdf9e3e398fa708"",
      ""factorPackIds"" : {
        ""SIRI_UNDERSTANDING_NL_OVERRIDES"" : ""65a8104b6712a43e7922cab8""
      },
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      ""factorPackIds"" : {
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      },
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  ""experiments"" : [
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      ""treatmentId"" : ""c47ab4cc-c9c3-4b5d-a87c-e2433ce02597"",
      ""experimentId"" : ""6639bc6ba73d460582162323"",
      ""deploymentId"" : 400000006
    },
    {
      ""treatmentId"" : ""45f4e2a5-551b-4bc2-a2dc-19c244dda8f8"",
      ""experimentId"" : ""6643969b3099cf28e049862f"",
      ""deploymentId"" : 400000007
    }
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}
}
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  

> graphics silhouettes true

> lighting soft

> windowsize 800 800

> ui tool hide ""command line interface""

> ui tool show clix

UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open ""/Users/kelvinlau/Desktop/RhGB07-full/RBD zoomed in-more.cxs"" format
> session

Opened 103_zflipped.ccp4 as #2, grid size 300,300,300, pixel 1.38, shown at
level 0.184, step 1, values float32  
Opened 103_sharp_zflipped.ccp4 as #3, grid size 300,300,300, pixel 1.38, shown
at level 0.239, step 1, values float32  
Opened 103_zflipped.ccp4 1 as #6.2, grid size 300,300,300, pixel 1.38, shown
at level 0.19, step 1, values float32  
opened ChimeraX session  

> ui tool show ""Command Line Interface""

> ui tool show clix

> center #1

Unknown command: center #1  

> ui tool show clix

> show #!1 models

> view list

Named views: overview  

> view overview

> select clear

> show #!4 models

> hide #!1 models

> select add #7/A:64

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

> select up

182 atoms, 186 bonds, 26 residues, 1 model selected  

> select up

4881 atoms, 5034 bonds, 609 residues, 1 model selected  

> select up

4895 atoms, 5049 bonds, 610 residues, 1 model selected  

> select up

5440 atoms, 5609 bonds, 682 residues, 1 model selected  

> select up

5441 atoms, 5609 bonds, 683 residues, 1 model selected  

> select up

6761 atoms, 6971 bonds, 859 residues, 1 model selected  

> select down

5441 atoms, 5609 bonds, 683 residues, 1 model selected  

> hide sel

> hide sel cartoons

Drag select of 147 atoms, 57 residues, 141 bonds  

> select clear

> select add #7/B:436

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

> show sel atoms

> select clear

> hide (#4,7-8 & (protein|nucleic)) target a

> cartoon hide #4,7-8

> show (#4,7-8 & ((protein&@ca)|(nucleic&@p))) target ab

Drag select of 13 atoms, 11 pseudobonds  

> select up

104 atoms, 102 bonds, 11 pseudobonds, 13 residues, 2 models selected  

> select up

616 atoms, 627 bonds, 11 pseudobonds, 81 residues, 2 models selected  

> select up

4881 atoms, 5034 bonds, 11 pseudobonds, 609 residues, 2 models selected  

> hide sel

> ui tool show ""Side View""

> save /Users/kelvinlau/Desktop/RhGB07-full/RBDdiff-prd0038-zoom3.tiff
> supersample 4

> hide #!7 models

> hide #!8 models

> show #!4 atoms

> show #!4 cartoons

> hide #!4 atoms

> undo

> select ::name=""BMA""::name=""MAN""::name=""NAG""::name=""ZN""

3405 atoms, 3521 bonds, 254 residues, 5 models selected  

> select up

58944 atoms, 60670 bonds, 7507 residues, 5 models selected  

> select down

3405 atoms, 3521 bonds, 254 residues, 5 models selected  

> select add #4/A:334@CG

3406 atoms, 3521 bonds, 255 residues, 5 models selected  

> select up

3408 atoms, 3522 bonds, 256 residues, 5 models selected  

> select up

3421 atoms, 3537 bonds, 256 residues, 5 models selected  

> invert sel

Unknown command: invert sel  

> ui tool show clix

> select invert

Expected an objects specifier or a keyword  

> ui tool show clix

> select ~sel & ##selected

59166 atoms, 60861 bonds, 449 pseudobonds, 7738 residues, 12 models selected  

> hide sel & #!4 atoms

> select clear

> select ::name=""BMA""::name=""MAN""::name=""NAG""::name=""ZN""

3405 atoms, 3521 bonds, 254 residues, 5 models selected  

Populating font family aliases took 171 ms. Replace uses of missing font
family ""Poppins"" with one that exists to avoid this cost.  

> color sel #4ECDC4

> select clear

> color #4 byhetero

> save /Users/kelvinlau/Desktop/RhGB07-full/RBD.tiff supersample 4

> hide #!4 models

> show #!1 models

> open ""/Users/kelvinlau/Library/CloudStorage/GoogleDrive-
> kelvin.lau@epfl.ch/Shared drives/new-bat-stuff-2024-uk/EM-
> Full/RealSpaceRefine_40/trimer30B_real_space_refined_006-coot-1_real_space_refined_040.pdb""

Chain information for
trimer30B_real_space_refined_006-coot-1_real_space_refined_040.pdb #9  
---  
Chain | Description  
A B C | No description available  
  

> select #9/B,C

18068 atoms, 18578 bonds, 4 pseudobonds, 2266 residues, 2 models selected  

> delete sel

> hide #!1 models

> select #9

9034 atoms, 9289 bonds, 2 pseudobonds, 1133 residues, 2 models selected  

> hide pbonds

> select clear

> open
> /Users/kelvinlau/Downloads/clustalo-I20240820-165439-0398-26224244-p1m.aln-
> clustal_num

Unrecognized file suffix '.aln-clustal_num'  

> open
> /Users/kelvinlau/Downloads/clustalo-I20240820-165439-0398-26224244-p1m.aln

Summary of feedback from opening
/Users/kelvinlau/Downloads/clustalo-I20240820-165439-0398-26224244-p1m.aln  
---  
notes | Alignment identifier is clustalo-I20240820-165439-0398-26224244-p1m.aln  
Associated trimer30B_real_space_refined_006-coot-1_real_space_refined_040.pdb
chain A to RhGB07_WDQ27002.1_UK with 8 mismatches  
Associated trimer30B_real_space_refined_006-coot-1_real_space_refined_040.pdb
chain B to RhGB07_WDQ27002.1_UK with 8 mismatches  
Associated trimer30B_real_space_refined_006-coot-1_real_space_refined_040.pdb
chain C to RhGB07_WDQ27002.1_UK with 8 mismatches  
Associated 30B-RBD-only.pdb chain A to RhGB07_WDQ27002.1_UK with 4 mismatches  
Associated 8u29 chain A to PRD-0038_QTJ30153.1_Rwanda with 78 mismatches  
Associated 8u29 chain B to PRD-0038_QTJ30153.1_Rwanda with 78 mismatches  
Associated 8u29 chain C to PRD-0038_QTJ30153.1_Rwanda with 78 mismatches  
Associated 8u29 chain A to PRD-0038_QTJ30153.1_Rwanda with 78 mismatches  
Associated trimer30B_real_space_refined_006-coot-1_real_space_refined_040.pdb
chain A to RhGB07_WDQ27002.1_UK with 8 mismatches  
Showing conservation header (""seq_conservation"" residue attribute) for
alignment clustalo-I20240820-165439-0398-26224244-p1m.aln  
  
Opened 121 sequences from clustalo-I20240820-165439-0398-26224244-p1m.aln  
Traceback (most recent call last):  
File ""/Users/kelvinlau/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/clix/widgets/main.py"",
line 203, in _on_text_changed  
self._update_completion_state(False)  
File ""/Users/kelvinlau/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/clix/widgets/main.py"",
line 45, in _update_completion_state  
self._current_completion_state =
self._get_completion_list(cursor.selectedText())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/kelvinlau/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/clix/widgets/main.py"",
line 147, in _get_completion_list  
return self._completion_for_chain(last_word, current_command)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/kelvinlau/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/clix/widgets/main.py"",
line 193, in _completion_for_chain  
f""/{_i}"" for _i in model.chains.chain_ids if _i.startswith(last_word[1:])  
^^^^^^^^^^^^  
AttributeError: 'PseudobondGroup' object has no attribute 'chains'  
  
AttributeError: 'PseudobondGroup' object has no attribute 'chains'  
  
File ""/Users/kelvinlau/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/clix/widgets/main.py"",
line 193, in _completion_for_chain  
f""/{_i}"" for _i in model.chains.chain_ids if _i.startswith(last_word[1:])  
^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> color byattribute seq_conservation #9 & protein range -1.5,3 noValueColor
> gray

8473 atoms, 1091 residues, atom seq_conservation range -2.5 to 0.869  

> color byattribute seq_conservation #9

9034 atoms, 1133 residues, atom seq_conservation range -2.5 to 0.869  

> color byattribute seq_conservation #9 range -2.5,0.1

9034 atoms, 1133 residues, atom seq_conservation range -2.5 to 0.869  

> color byattribute seq_conservation #9 range -1,0.1

9034 atoms, 1133 residues, atom seq_conservation range -2.5 to 0.869  

> color byattribute seq_conservation #9 palette blue:white:red range -1,0.1

9034 atoms, 1133 residues, atom seq_conservation range -2.5 to 0.869  

> color byattribute seq_conservation #9 palette blue:white:red

9034 atoms, 1133 residues, atom seq_conservation range -2.5 to 0.869  

> select add #9/A:480

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

> select add #9/A:342

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

> select clear

> color byattribute seq_conservation #9 palette ""cheer up emo kid""

9034 atoms, 1133 residues, atom seq_conservation range -2.5 to 0.869  

> color byattribute seq_conservation #9 palette #C44D58:#C7F464:#556270

9034 atoms, 1133 residues, atom seq_conservation range -2.5 to 0.869  

> color byattribute seq_conservation #9 palette #C44D58:#C7F464:#556270 range
> -2,0.5

9034 atoms, 1133 residues, atom seq_conservation range -2.5 to 0.869  

> color byattribute seq_conservation #9 palette #C44D58:#C7F464:#556270 range
> -1,0.1

9034 atoms, 1133 residues, atom seq_conservation range -2.5 to 0.869  

> select #9/A:480

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

> select clear

> show #!9 surfaces

> color byattribute seq_conservation #9 palette #C44D58:#C7F464:#556270 range
> -1,0.1

9034 atoms, 1133 residues, 1 surfaces, atom seq_conservation range -2.5 to
0.869  

> select ::name=""BMA""::name=""MAN""::name=""NAG""::name=""ZN""

3966 atoms, 4104 bonds, 296 residues, 6 models selected  

> hide sel & #!9 atoms

> select clear

> lighting soft

> save /Users/kelvinlau/conservationsurface.cxs

> save /Users/kelvinlau/Desktop/RhGB07-full/FL_con.tiff supersample 4

> save /Users/kelvinlau/Desktop/RhGB07-full/FL_con2.tiff supersample 4

> ui tool show clix

> color byattribute seq_conservation #4 palette #C44D58:#C7F464:#556270 range
> -1,0.1

1521 atoms, 186 residues, atom seq_conservation range -2.49 to 0.869  

> hide #!9 models

> show #!4 models

> show #!4 surfaces

> color byattribute seq_conservation #4 palette #C44D58:#C7F464:#556270 range
> -1,0.1

1521 atoms, 186 residues, 1 surfaces, atom seq_conservation range -2.49 to
0.869  

> color byattribute seq_conservation #4 palette #C44D58:#C7F464:#556270 range
> -1,0.1

1521 atoms, 186 residues, 1 surfaces, atom seq_conservation range -2.49 to
0.869  

> hide #!4 surfaces

> select clear

Drag select of 1 atoms, 175 residues, 1 bonds  

> color sel #556270

> select clear

> color byattribute seq_conservation #4 palette #C44D58:#C7F464:#556270 range
> -1,0.1

1521 atoms, 186 residues, 1 surfaces, atom seq_conservation range -2.49 to
0.869  

> show #!4 surfaces

Drag select of 30B-RBD-only.pdb_A SES surface, 43263 of 188138 triangles, 1
atoms, 55 residues  

> color sel #556270

> color byattribute seq_conservation #4 palette #C44D58:#C7F464:#556270 range
> -1,0.1

1521 atoms, 186 residues, 1 surfaces, atom seq_conservation range -2.49 to
0.869  

> color byattribute seq_conservation #4 palette #C44D58:#C7F464:#556270 range
> -1,0.1

1521 atoms, 186 residues, 1 surfaces, atom seq_conservation range -2.49 to
0.869  

> select clear

> ui mousemode right ""color key""

> key blue:min white: #c44d58:max

> key blue:min #c7f464: #c44d58:max

> key #556270:min #c7f464: #c44d58:max

> key colorTreatment distinct

> key colorTreatment blended

> key pos 0.694819,0.118868 size 0.204635,0.0495277

> key #556270:min #c7f464: #c44d58:L

> key #556270:min #c7f464: #c44d58:LE

> key #556270:min #c7f464: #c44d58:LEA

> key #556270:min #c7f464: #c44d58:LEAS

> key #556270:min #c7f464: #c44d58:LEAST

> key #556270:min #c7f464: ""#c44d58:LEAST ""

> key #556270:min #c7f464: #c44d58:LEAST

> key #556270:min #c7f464: #c44d58:LEAS

> key #556270:min #c7f464: #c44d58:LEA

> key #556270:min #c7f464: #c44d58:LE

> key #556270:min #c7f464: #c44d58:L

> key #556270:min #c7f464: #c44d58:

> key #556270:min #c7f464: #c44d58:l

> key #556270:min #c7f464: #c44d58:

> key #556270:min #c7f464: #c44d58:L

> key #556270:min #c7f464: #c44d58:Le

> key #556270:min #c7f464: #c44d58:Lea

> key #556270:min #c7f464: #c44d58:Leas

> key #556270:min #c7f464: #c44d58:Least

> key #556270:min #c7f464: ""#c44d58:Least ""

> key #556270:min #c7f464: ""#c44d58:Least c""

> key #556270:min #c7f464: ""#c44d58:Least co""

> key #556270:min #c7f464: ""#c44d58:Least con""

> key #556270:min #c7f464: ""#c44d58:Least cons""

> key #556270:min #c7f464: ""#c44d58:Least conse""

> key #556270:min #c7f464: ""#c44d58:Least conser""

> key #556270:min #c7f464: ""#c44d58:Least conserv""

> key #556270:min #c7f464: ""#c44d58:Least conserve""

> key #556270:min #c7f464: ""#c44d58:Least conserver""

> key #556270:min #c7f464: ""#c44d58:Least conserverd""

> key #556270:min #c7f464: ""#c44d58:Least c""

> key #556270:min #c7f464: ""#c44d58:Least co""

> key #556270:min #c7f464: ""#c44d58:Least con""

> key #556270:min #c7f464: ""#c44d58:Least cons""

> key #556270:min #c7f464: ""#c44d58:Least conse""

> key #556270:min #c7f464: ""#c44d58:Least conser""

> key #556270:min #c7f464: ""#c44d58:Least conserv""

> key #556270:min #c7f464: ""#c44d58:Least conserve""

> key #556270:min #c7f464: ""#c44d58:Least conserved""

> key #556270:M #c7f464: ""#c44d58:Least conserved""

> key #556270:Mo #c7f464: ""#c44d58:Least conserved""

> key #556270:Mos #c7f464: ""#c44d58:Least conserved""

> key #556270:Most #c7f464: ""#c44d58:Least conserved""

> key ""#556270:Most "" #c7f464: ""#c44d58:Least conserved""

> key ""#556270:Most c"" #c7f464: ""#c44d58:Least conserved""

> key ""#556270:Most co"" #c7f464: ""#c44d58:Least conserved""

> key ""#556270:Most con"" #c7f464: ""#c44d58:Least conserved""

> key ""#556270:Most cons"" #c7f464: ""#c44d58:Least conserved""

> key ""#556270:Most conse"" #c7f464: ""#c44d58:Least conserved""

> key ""#556270:Most conser"" #c7f464: ""#c44d58:Least conserved""

> key ""#556270:Most conserv"" #c7f464: ""#c44d58:Least conserved""

> key ""#556270:Most conserve"" #c7f464: ""#c44d58:Least conserved""

> key ""#556270:Most conserved"" #c7f464: ""#c44d58:Least conserved""

> ui mousemode right translate

> save /Users/kelvinlau/Desktop/RhGB07-full/RBD_con1.tiff supersample 4

> save /Users/kelvinlau/Desktop/RhGB07-full/RBD_con2.tiff supersample 4

> save /Users/kelvinlau/Desktop/RhGB07-full/RBD_con3.tiff supersample 4

> hide #!4 surfaces

> show #!8 models

> hide #!8 models

> hide #10 models

> hide #!4 models

> show #!4 models

> show #!5 models

> hide #!5 models

> show #!7 models

> show #!8 models

> show #!4,7-8 cartoons

> hide #!7 models

> hide #!8 models

> show #!8 models

Alignment identifier is 1  
Alignment identifier is 4/A  
Alignment identifier is 2  
Alignment identifier is 7/A  
Alignment identifier is 7/B  

> select #4/A:483

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

> select #4/A:483-489

46 atoms, 47 bonds, 7 residues, 1 model selected  

> select clear

> select add #4/A:439

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select add #4/A:435

17 atoms, 16 bonds, 2 residues, 2 models selected  

> select #8/A:434

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

> select add #8/A:440

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

> select #4/A:435

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

> select add #4/A:436

15 atoms, 13 bonds, 2 residues, 2 models selected  

> select add #4/A:437

24 atoms, 21 bonds, 3 residues, 2 models selected  

> select #4/A:466

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #4/A:466-470

34 atoms, 34 bonds, 5 residues, 1 model selected  

> select clear

> show #!7 models

> select #4/A:465-466

11 atoms, 10 bonds, 2 residues, 1 model selected  

> select #4/A:465-470

38 atoms, 38 bonds, 6 residues, 1 model selected  

> select #4/A:466

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #4/A:466-469

27 atoms, 27 bonds, 4 residues, 1 model selected  

> select #4/A:470

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #4/A:470

7 atoms, 6 bonds, 1 residue, 1 model selected  

> hide (#!4 & sel-residues & (protein|nucleic)) target a

> cartoon hide (#!4 & sel-residues)

> show (#!4 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab

> select clear

> hide (#4,7-8 & (protein|nucleic)) target a

> cartoon hide #4,7-8

> show (#4,7-8 & ((protein&@ca)|(nucleic&@p))) target ab

> select add #7/A:33@CA

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

272 atoms, 278 bonds, 34 residues, 1 model selected  

> select up

4881 atoms, 5034 bonds, 609 residues, 1 model selected  

> hide sel

> select clear

> ui tool show ""Side View""

> color #4 #556270

> select clear

> save /Users/kelvinlau/Desktop/RhGB07-full/RBDdiff-prd0038-zoom4.tiff
> supersample 4

> select #4/A:466

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #4/A:466-469

27 atoms, 27 bonds, 3 pseudobonds, 4 residues, 2 models selected  

> select #4/A:470-471

16 atoms, 15 bonds, 1 pseudobond, 2 residues, 2 models selected  

> select #4/A:466-471

43 atoms, 43 bonds, 5 pseudobonds, 6 residues, 2 models selected  

> select #4/A:466

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #4/A:466-470

34 atoms, 34 bonds, 4 pseudobonds, 5 residues, 2 models selected  


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

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  

> graphics silhouettes true

> lighting soft

> windowsize 800 800

> ui tool hide ""command line interface""

> ui tool show clix

UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

Failed to send bug report. Possibly no internet connection.  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,4
      Model Number: Z15H00063SM/A
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 10151.121.1
      OS Loader Version: 10151.121.1

Software:

    System Software Overview:

      System Version: macOS 14.5 (23F79)
      Kernel Version: Darwin 23.5.0
      Time since boot: 20 days, 19 hours, 41 minutes

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 24
      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: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-clix: 0.1.1
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
}}}
"	defect	closed	normal		Window Toolkit		duplicate						all	ChimeraX