id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
18280	Crash in Qt waking from sleep on Mac, multiple displays	gyanamahapatra2@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-15.5-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault

Current thread 0x00000001f86c9f00 (most recent call first):
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 368 in event_loop
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1057 in init
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1220 in 
  File """", line 88 in _run_code
  File """", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, chimerax.surface._surface, psutil._psutil_osx, psutil._psutil_posix, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, PIL._imaging, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath (total: 56)


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    ""size"" : 5500928,
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    ""path"" : ""\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation"",
    ""name"" : ""CoreFoundation"",
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    ""CFBundleIdentifier"" : ""com.apple.HIToolbox"",
    ""size"" : 3174368,
    ""uuid"" : ""9286e29f-fcee-31d0-acea-2842ea23bedf"",
    ""path"" : ""\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox"",
    ""name"" : ""HIToolbox""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""arm64e"",
    ""base"" : 6612402176,
    ""size"" : 636112,
    ""uuid"" : ""9cf0401a-a938-389e-a77d-9e9608076ccf"",
    ""path"" : ""\/usr\/lib\/dyld"",
    ""name"" : ""dyld""
  },
  {
    ""size"" : 0,
    ""source"" : ""A"",
    ""base"" : 0,
    ""uuid"" : ""00000000-0000-0000-0000-000000000000""
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  {
    ""source"" : ""P"",
    ""arch"" : ""arm64e"",
    ""base"" : 6639685632,
    ""CFBundleShortVersionString"" : ""6.9"",
    ""CFBundleIdentifier"" : ""com.apple.Foundation"",
    ""size"" : 14586624,
    ""uuid"" : ""e8f6a451-0acc-3e05-b18f-fec6618ce44a"",
    ""path"" : ""\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation"",
    ""name"" : ""Foundation"",
    ""CFBundleVersion"" : ""3502.1.401""
  },
  {
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    ""arch"" : ""arm64e"",
    ""base"" : 6804766720,
    ""CFBundleShortVersionString"" : ""372.5.2"",
    ""CFBundleIdentifier"" : ""com.apple.IOSurface"",
    ""size"" : 102112,
    ""uuid"" : ""2b84e9fb-3fce-3520-ae9b-6211cd70ad88"",
    ""path"" : ""\/System\/Library\/Frameworks\/IOSurface.framework\/Versions\/A\/IOSurface"",
    ""name"" : ""IOSurface"",
    ""CFBundleVersion"" : ""372.5.2""
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    ""CFBundleIdentifier"" : ""com.apple.framework.IOKit"",
    ""size"" : 926528,
    ""uuid"" : ""d1ba721b-4309-3caf-81c7-595aef32f6a9"",
    ""path"" : ""\/System\/Library\/Frameworks\/IOKit.framework\/Versions\/A\/IOKit"",
    ""name"" : ""IOKit""
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],
  ""sharedCache"" : {
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  ""size"" : 5047205888,
  ""uuid"" : ""d7397d7f-8df9-3920-81a7-c0a144be9c51""
},
  ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=4.4G written=31.8M(1%) resident=2939K(0%) swapped_out=29.0M(1%) unallocated=4.4G(99%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               512K        4 \nActivity Tracing                   256K        1 \nCG image                           656K       31 \nColorSync                          640K       32 \nCoreAnimation                     3680K      206 \nCoreGraphics                        64K        4 \nCoreImage                           32K        1 \nCoreServices                       624K        2 \nCoreUI image data                 4176K       32 \nFoundation                          48K        2 \nKernel Alloc Once                   32K        1 \nMALLOC                             3.7G      136 \nMALLOC guard page                  288K       18 \nMach message                        64K        3 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        688K       43 \nStack                            203.0M       44 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      313.4M      159 \nVM_ALLOCATE (reserved)           192.0M        2         reserved VM address space (unallocated)\n__AUTH                            5452K      693 \n__AUTH_CONST                      77.0M      940 \n__CTF                               824        1 \n__DATA                            37.1M     1077 \n__DATA_CONST                      37.1M     1094 \n__DATA_DIRTY                      2777K      341 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__INFO_FILTER                         8        1 \n__LINKEDIT                       646.5M      148 \n__OBJC_RO                         61.4M        1 \n__OBJC_RW                         2396K        1 \n__TEXT                             1.3G     1111 \n__TEXT (graphics)                  736K        3 \n__TPRO_CONST                       128K        2 \ndyld private memory               1840K       17 \nmapped file                      369.8M       71 \npage table in kernel              2939K        1 \nshared memory                     3744K       27 \n===========                     =======  ======= \nTOTAL                              7.0G     6257 \nTOTAL, minus reserved VM space     6.8G     6257 \n"",
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},
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}
===== Log before crash start =====
> buttonpanel Volume_series rows 3 columns 4

> buttonpanel Volume_series add Open_series command ""open browse vseries true""

> buttonpanel Volume_series add Play_1 command ""vseries play #1 direction
> oscillate loop true cacheFrames 20 maxFrameRate 20 normalize true""

> buttonpanel Volume_series add Stop_1 command ""vseries stop #1""

> buttonpanel Volume_series add Play_2 command ""vseries play #2 direction
> oscillate loop true cacheFrames 20 maxFrameRate 20 normalize true""

> buttonpanel Volume_series add Stop_2 command ""vseries stop #2""

> buttonpanel Volume_series add Play_3 command ""vseries play #3 direction
> oscillate loop true cacheFrames 20 maxFrameRate 20 normalize true""

> buttonpanel Volume_series add Stop_3 command ""vseries stop #3""

> buttonpanel Volume_series add Play_4 command ""vseries play #4 direction
> oscillate loop true cacheFrames 20 maxFrameRate 20 normalize true""

> buttonpanel Volume_series add Stop_4 command ""vseries stop #4""

> buttonpanel Volume_series add Play_5 command ""vseries play #5 direction
> oscillate loop true cacheFrames 20 maxFrameRate 20 normalize true""

> buttonpanel Volume_series add Stop_5 command ""vseries stop #5""

> buttonpanel Volume_series add Play_6 command ""vseries play #6 direction
> oscillate loop true cacheFrames 20 maxFrameRate 20 normalize true""

> buttonpanel Volume_series add Stop_6 command ""vseries stop #6""

> buttonpanel Volume_series add Record command ""movie record""

> buttonpanel Volume_series add Encode command ""movie encode output browse""

UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open ""/Users/gyanaprakashmahapatra/Library/CloudStorage/OneDrive-
> Personal/SYNMIKRO/Ph.D/Projects/Supercomplex/Chlamydomonas/Manuscript/Final
> Figures/Figure 3/Figure 3_A closer look_1.cxs""

Opened Composite Map.mrc as #2, grid size 512,512,512, pixel 0.73, shown at
level 0.0208, step 1, values float32  
Opened Composite Map.mrc 0 as #3.1, grid size 512,512,512, pixel 0.73, shown
at level 0.0208, step 1, values float32  
Opened Composite Map.mrc 1 as #3.2, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 2 as #3.3, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 3 as #3.4, grid size 512,512,512, pixel 0.73, shown
at level 0.04, step 1, values float32  
Opened Composite Map.mrc 4 as #3.5, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 5 as #3.6, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 6 as #3.7, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 7 as #3.8, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 8 as #3.9, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 9 as #3.10, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 10 as #3.11, grid size 512,512,512, pixel 0.73, shown
at level 0.04, step 1, values float32  
Opened Composite Map.mrc 11 as #3.12, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 12 as #3.13, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 13 as #3.14, grid size 512,512,512, pixel 0.73, shown
at level 0.03, step 1, values float32  
Opened Composite Map.mrc 14 as #3.15, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  

> view name session-start

opened ChimeraX session  

> hide #!3 models

> close #1-4

> open ""/Users/gyanaprakashmahapatra/Library/CloudStorage/OneDrive-
> Personal/SYNMIKRO/Ph.D/Projects/Supercomplex/Chlamydomonas/Manuscript/Final
> Figures/Figure 3/Figure 3_A closer look_2.cxs""

Opened Composite Map.mrc as #2, grid size 512,512,512, pixel 0.73, shown at
level 0.0208, step 1, values float32  
Opened Composite Map.mrc 0 as #3.1, grid size 512,512,512, pixel 0.73, shown
at level 0.0208, step 1, values float32  
Opened Composite Map.mrc 1 as #3.2, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 2 as #3.3, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 3 as #3.4, grid size 512,512,512, pixel 0.73, shown
at level 0.04, step 1, values float32  
Opened Composite Map.mrc 4 as #3.5, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 5 as #3.6, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 6 as #3.7, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 7 as #3.8, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 8 as #3.9, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 9 as #3.10, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 10 as #3.11, grid size 512,512,512, pixel 0.73, shown
at level 0.04, step 1, values float32  
Opened Composite Map.mrc 11 as #3.12, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 12 as #3.13, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 13 as #3.14, grid size 512,512,512, pixel 0.73, shown
at level 0.03, step 1, values float32  
Opened Composite Map.mrc 14 as #3.15, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  

> view name session-start

opened ChimeraX session  

> close #1-4

> open ""/Users/gyanaprakashmahapatra/Library/CloudStorage/OneDrive-
> Personal/SYNMIKRO/Ph.D/Projects/Supercomplex/Chlamydomonas/Manuscript/Final
> Figures/Figure 3/Figure 3_A closer look_2.cxs"" format session

Opened Composite Map.mrc as #2, grid size 512,512,512, pixel 0.73, shown at
level 0.0208, step 1, values float32  
Opened Composite Map.mrc 0 as #3.1, grid size 512,512,512, pixel 0.73, shown
at level 0.0208, step 1, values float32  
Opened Composite Map.mrc 1 as #3.2, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 2 as #3.3, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 3 as #3.4, grid size 512,512,512, pixel 0.73, shown
at level 0.04, step 1, values float32  
Opened Composite Map.mrc 4 as #3.5, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 5 as #3.6, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 6 as #3.7, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 7 as #3.8, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 8 as #3.9, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 9 as #3.10, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 10 as #3.11, grid size 512,512,512, pixel 0.73, shown
at level 0.04, step 1, values float32  
Opened Composite Map.mrc 11 as #3.12, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 12 as #3.13, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 13 as #3.14, grid size 512,512,512, pixel 0.73, shown
at level 0.03, step 1, values float32  
Opened Composite Map.mrc 14 as #3.15, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  

> view name session-start

opened ChimeraX session  

> hide #!3 models

> ui tool show ""Side View""

> select #1/F:81@CA

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select #1/F:81

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

> hide sel atoms

> select #1/F:74@CA

1 atom, 1 residue, 1 model selected  

> select #1/F:74@CB

1 atom, 1 residue, 1 model selected  

> select add #1

31580 atoms, 32552 bonds, 2 pseudobonds, 4091 residues, 2 models selected  

> select subtract #1

Nothing selected  

> select #1/F:74

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

> hide sel atoms

> select add #1

31580 atoms, 32552 bonds, 2 pseudobonds, 4091 residues, 2 models selected  

> select subtract #1

Nothing selected  

> save /Users/gyanaprakashmahapatra/Desktop/image45.png supersample 3

> save
> ""/Users/gyanaprakashmahapatra/OneDrive/SYNMIKRO/Ph.D/Projects/Supercomplex/Chlamydomonas/Manuscript/Final
> Figures/Figure 3/Figure 3_A closer look_2_New.cxs"" includeMaps true

> close #1-4

> open ""/Users/gyanaprakashmahapatra/Library/CloudStorage/OneDrive-
> Personal/SYNMIKRO/Ph.D/Projects/Supercomplex/Chlamydomonas/Manuscript/Final
> Figures/Figure 3/Figure 3_A closer look_3.cxs""

Opened Composite Map.mrc as #2, grid size 512,512,512, pixel 0.73, shown at
level 0.0208, step 1, values float32  
Opened Composite Map.mrc 0 as #3.1, grid size 512,512,512, pixel 0.73, shown
at level 0.0208, step 1, values float32  
Opened Composite Map.mrc 1 as #3.2, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 2 as #3.3, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 3 as #3.4, grid size 512,512,512, pixel 0.73, shown
at level 0.04, step 1, values float32  
Opened Composite Map.mrc 4 as #3.5, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 5 as #3.6, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 6 as #3.7, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 7 as #3.8, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 8 as #3.9, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 9 as #3.10, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 10 as #3.11, grid size 512,512,512, pixel 0.73, shown
at level 0.04, step 1, values float32  
Opened Composite Map.mrc 11 as #3.12, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 12 as #3.13, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 13 as #3.14, grid size 512,512,512, pixel 0.73, shown
at level 0.03, step 1, values float32  
Opened Composite Map.mrc 14 as #3.15, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  

> view name session-start

opened ChimeraX session  

> hide #!3 models

> select #1/A:653

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

> hide sel cartoons

> select #1/A:749

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

> select #1/A:750

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

> select add #1/A:749

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

> select add #1/A:748

21 atoms, 18 bonds, 3 residues, 1 model selected  

> select add #1/A:745

26 atoms, 22 bonds, 4 residues, 1 model selected  

> select add #1/A:746

37 atoms, 32 bonds, 5 residues, 1 model selected  

> select add #1/A:742

48 atoms, 43 bonds, 6 residues, 1 model selected  

> select add #1/A:741

54 atoms, 48 bonds, 7 residues, 1 model selected  

> select add #1/A:671

62 atoms, 55 bonds, 8 residues, 1 model selected  

> select add #1/A:139

71 atoms, 63 bonds, 9 residues, 1 model selected  

> select add #1/A:138

79 atoms, 70 bonds, 10 residues, 1 model selected  

> select add #1/A:137

83 atoms, 73 bonds, 11 residues, 1 model selected  

> select add #1/A:136

92 atoms, 81 bonds, 12 residues, 1 model selected  

> select add #1/A:135

103 atoms, 92 bonds, 13 residues, 1 model selected  

> select add #1/A:134

107 atoms, 95 bonds, 14 residues, 1 model selected  

> select add #1/A:132

111 atoms, 98 bonds, 15 residues, 1 model selected  

> select add #1/A:131

118 atoms, 104 bonds, 16 residues, 1 model selected  

> select add #1/A:133

122 atoms, 107 bonds, 17 residues, 1 model selected  

> select add #1/A:130

130 atoms, 114 bonds, 18 residues, 1 model selected  

> select add #1/A:129

134 atoms, 117 bonds, 19 residues, 1 model selected  

> select add #1/A:128

142 atoms, 124 bonds, 20 residues, 1 model selected  

> hide sel cartoons

> select #1/A:744

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

> hide sel cartoons

> save /Users/gyanaprakashmahapatra/Desktop/image46.png supersample 3

> select #1/A:738

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

> hide sel cartoons

> save /Users/gyanaprakashmahapatra/Desktop/image47.png supersample 3

> save
> ""/Users/gyanaprakashmahapatra/OneDrive/SYNMIKRO/Ph.D/Projects/Supercomplex/Chlamydomonas/Manuscript/Final
> Figures/Figure 3/Figure 3_A closer look_3_New.cxs"" includeMaps true

> close #1-4

> open
> ""/Users/gyanaprakashmahapatra/OneDrive/SYNMIKRO/Ph.D/Projects/Supercomplex/Chlamydomonas/Manuscript/Final
> Figures/Figure 3/Figure 3_A closer look_2_New.cxs"" format session

Opened Composite Map.mrc as #2, grid size 512,512,512, pixel 0.73, shown at
level 0.0208, step 1, values float32  
Opened Composite Map.mrc 0 as #3.1, grid size 512,512,512, pixel 0.73, shown
at level 0.0208, step 1, values float32  
Opened Composite Map.mrc 1 as #3.2, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 2 as #3.3, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 3 as #3.4, grid size 512,512,512, pixel 0.73, shown
at level 0.04, step 1, values float32  
Opened Composite Map.mrc 4 as #3.5, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 5 as #3.6, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 6 as #3.7, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 7 as #3.8, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 8 as #3.9, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 9 as #3.10, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 10 as #3.11, grid size 512,512,512, pixel 0.73, shown
at level 0.04, step 1, values float32  
Opened Composite Map.mrc 11 as #3.12, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 12 as #3.13, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 13 as #3.14, grid size 512,512,512, pixel 0.73, shown
at level 0.03, step 1, values float32  
Opened Composite Map.mrc 14 as #3.15, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  

> view name session-start

opened ChimeraX session  

> close #1-4

> open ""/Users/gyanaprakashmahapatra/Library/CloudStorage/OneDrive-
> Personal/SYNMIKRO/Ph.D/Projects/Supercomplex/Chlamydomonas/Manuscript/Final
> Figures/Figure 3/Figure 3_A closer look_3_New.cxs""

Opened Composite Map.mrc as #2, grid size 512,512,512, pixel 0.73, shown at
level 0.0208, step 1, values float32  
Opened Composite Map.mrc 0 as #3.1, grid size 512,512,512, pixel 0.73, shown
at level 0.0208, step 1, values float32  
Opened Composite Map.mrc 1 as #3.2, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 2 as #3.3, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 3 as #3.4, grid size 512,512,512, pixel 0.73, shown
at level 0.04, step 1, values float32  
Opened Composite Map.mrc 4 as #3.5, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 5 as #3.6, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 6 as #3.7, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 7 as #3.8, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 8 as #3.9, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 9 as #3.10, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 10 as #3.11, grid size 512,512,512, pixel 0.73, shown
at level 0.04, step 1, values float32  
Opened Composite Map.mrc 11 as #3.12, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 12 as #3.13, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  
Opened Composite Map.mrc 13 as #3.14, grid size 512,512,512, pixel 0.73, shown
at level 0.03, step 1, values float32  
Opened Composite Map.mrc 14 as #3.15, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32  

> view name session-start

opened ChimeraX session  

> close #1-4

> open
> /Users/gyanaprakashmahapatra/Downloads/cryosparc_P173_J671_map_locres.mrc

Opened cryosparc_P173_J671_map_locres.mrc as #1, grid size 512,512,512, pixel
0.73, shown at level 2.96, step 1, values float32  

> volume #1 level 3.814

> close #1

> open
> /Users/gyanaprakashmahapatra/Downloads/cryosparc_P173_J671_map_locres.mrc
> format mrc

Opened cryosparc_P173_J671_map_locres.mrc as #1, grid size 512,512,512, pixel
0.73, shown at level 2.96, step 1, values float32  

> open ""/Users/gyanaprakashmahapatra/Library/CloudStorage/OneDrive-
> Personal/SYNMIKRO/Ph.D/Projects/Supercomplex/Chlamydomonas/CS_PSI-
> CytC6/Jobs/J575_NU-refine_1.8Å str_Same as J458/J575_sharp map.mrc""

Opened J575_sharp map.mrc as #2, grid size 512,512,512, pixel 0.73, shown at
level 0.0459, step 1, values float32  

> volume #2 level 0.09183

> ui tool show ""Surface Color""

> color sample #2.1 map #1 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080

Map values for surface ""surface"": minimum 0, mean 1.758, maximum 21.77  

> volume #1 level 6.738

> hide #!1 models

> color sample #2.1 map #1 palette 1.5,#0000ff:2,#ffffff:2.5,#ff0000
> outsideColor #808080

Map values for surface ""surface"": minimum 0, mean 1.758, maximum 21.77  

> volume #2 level 0.08237

> color sample #2.1 map #1 palette 1.5,#0000ff:2,#00f900:2.5,#ff0000
> outsideColor #808080

Map values for surface ""surface"": minimum 0, mean 1.759, maximum 23.84  


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

Log:
> buttonpanel Volume_series rows 3 columns 4

> buttonpanel Volume_series add Open_series command ""open browse vseries true""

> buttonpanel Volume_series add Play_1 command ""vseries play #1 direction
> oscillate loop true cacheFrames 20 maxFrameRate 20 normalize true""

> buttonpanel Volume_series add Stop_1 command ""vseries stop #1""

> buttonpanel Volume_series add Play_2 command ""vseries play #2 direction
> oscillate loop true cacheFrames 20 maxFrameRate 20 normalize true""

> buttonpanel Volume_series add Stop_2 command ""vseries stop #2""

> buttonpanel Volume_series add Play_3 command ""vseries play #3 direction
> oscillate loop true cacheFrames 20 maxFrameRate 20 normalize true""

> buttonpanel Volume_series add Stop_3 command ""vseries stop #3""

> buttonpanel Volume_series add Play_4 command ""vseries play #4 direction
> oscillate loop true cacheFrames 20 maxFrameRate 20 normalize true""

> buttonpanel Volume_series add Stop_4 command ""vseries stop #4""

> buttonpanel Volume_series add Play_5 command ""vseries play #5 direction
> oscillate loop true cacheFrames 20 maxFrameRate 20 normalize true""

> buttonpanel Volume_series add Stop_5 command ""vseries stop #5""

> buttonpanel Volume_series add Play_6 command ""vseries play #6 direction
> oscillate loop true cacheFrames 20 maxFrameRate 20 normalize true""

> buttonpanel Volume_series add Stop_6 command ""vseries stop #6""

> buttonpanel Volume_series add Record command ""movie record""

> buttonpanel Volume_series add Encode command ""movie encode output browse""

UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,1
      Model Number: MK193LL/A
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.121.1
      OS Loader Version: 11881.121.1

Software:

    System Software Overview:

      System Version: macOS 15.5 (24F74)
      Kernel Version: Darwin 24.5.0
      Time since boot: 10 days, 6 hours, 44 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        BE24W:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported
        PA278QV:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 75.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.6.1
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.19
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    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-MutationScores: 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: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    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: 1.1.3
    ChimeraX-ProfileGrids: 1.1.3
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    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: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.45.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.10.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.15
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.59.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.3.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.1
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
}}}
"	defect	closed	normal		Window Toolkit		can't reproduce						all	ChimeraX