id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
16397	Crash on Mac waking from sleep	chimerax-bug-report@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-15.1.1-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.
Fatal Python error: Segmentation fault

Current thread 0x00000001e698f840 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 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.surface._surface, chimerax.map._map, chimerax.pdb_lib._load_libs, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, openmm._openmm, openmm.app.internal.compiled, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, PIL._imagingmath (total: 63)


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  ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.7G resident=0K(0%) swapped_out_or_unallocated=1.7G(100%)\nWritable regions: Total=5.6G written=2682K(0%) resident=2682K(0%) swapped_out=0K(0%) unallocated=5.6G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               256K        2 \nActivity Tracing                   256K        1 \nCG image                           768K       40 \nColorSync                          592K       31 \nCoreAnimation                     2752K      160 \nCoreGraphics                        48K        3 \nCoreServices                       624K        2 \nCoreUI image data                 5424K       41 \nFoundation                          48K        2 \nKernel Alloc Once                   32K        1 \nMALLOC                             4.5G      207 \nMALLOC guard page                  288K       18 \nMach message                        64K        2 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                       1168K       73 \nStack                            174.0M       74 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      322.0M      224 \nVM_ALLOCATE (reserved)           608.0M        4         reserved VM address space (unallocated)\n__AUTH                            3684K      489 \n__AUTH_CONST                      53.6M      704 \n__CTF                               824        1 \n__DATA                            27.6M      879 \n__DATA_CONST                      30.8M      893 \n__DATA_DIRTY                      2000K      254 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__LINKEDIT                       622.8M      185 \n__OBJC_RW                         2354K        1 \n__TEXT                             1.0G      910 \n__TPRO_CONST                       272K        2 \ndyld private memory                 48K        2 \nmapped file                      592.2M      112 \nowned unmapped memory             82.8M        1 \npage table in kernel              2682K        1 \nshared memory                     3744K       25 \n===========                     =======  ======= \nTOTAL                              8.0G     5351 \nTOTAL, minus reserved VM space     7.4G     5351 \n"",
  ""legacyInfo"" : {
  ""threadTriggered"" : {
    ""name"" : ""CrBrowserMain"",
    ""queue"" : ""com.apple.main-thread""
  }
},
  ""logWritingSignature"" : ""f0d2c1f9447108e388dab579e48f4e613728ce18"",
  ""trialInfo"" : {
  ""rollouts"" : [
    {
      ""rolloutId"" : ""6297d96be2c9387df974efa4"",
      ""factorPackIds"" : {

      },
      ""deploymentId"" : 240000032
    },
    {
      ""rolloutId"" : ""64c17a9925d75a7281053d4c"",
      ""factorPackIds"" : {
        ""SIRI_AUDIO_DISABLE_MEDIA_ENTITY_SYNC"" : ""64d29746ad29a465b3bbeace""
      },
      ""deploymentId"" : 240000001
    }
  ],
  ""experiments"" : [
    {
      ""treatmentId"" : ""45f4e2a5-551b-4bc2-a2dc-19c244dda8f8"",
      ""experimentId"" : ""6643969b3099cf28e049862f"",
      ""deploymentId"" : 400000007
    }
  ]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/menmt0930/Downloads/aMSA_new_model.cxs

Opened postprocess_masked_sharpened.ccp4 as #2, grid size 320,320,320, pixel
1.03, shown at level 0.0117, step 1, values float32  
Log from Sun Dec 1 18:10:16 2024 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
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/menmt0930/Downloads/8-layers_strand.pdb

Chain information for 8-layers_strand.pdb #1  
---  
Chain | Description  
A1 A2 A3 A4 A5 A6 A7 A8 | No description available  
B1 B2 B3 B4 B5 B6 B7 B8 | No description available  
C1 C2 C3 | No description available  
C4 | No description available  
C5 C6 C7 | No description available  
C8 | No description available  
  

> style stick

Changed 8396 atom styles  

> hide cartoons

> show cartoons

> hide atoms

> argument: setattr res ss_type 0

Unknown command: argument: setattr res ss_type 0  

> setattr res ss_type 0

Assigning ss_type attribute to 1245 items  

> setattr /B1-B8:38-42, 44-46, 48-50, 52-55, 60-63, 69-71, 75-82, 90-92, 94-99
> res ss_type 2

Assigning ss_type attribute to 312 items  

> setattr /A1-A8:15-17, 25-57, 32-34, 37-40, 43-45, 54-58, 62-65, 69-71,
> 76-79, 81-82, 87-92, 94-99 res ss_type 2

Assigning ss_type attribute to 496 items  

> setattr /A1-A8 res ss_type 0

Assigning ss_type attribute to 696 items  

> setattr /A1-A8:15-17, 25-27, 32-34, 37-40, 43-45, 54-58, 62-65, 69-71,
> 76-79, 81-82, 87-92, 94-99 res ss_type 2

Assigning ss_type attribute to 368 items  

OpenType support missing for "".AppleSystemUIFont"", script 10  

> save /Users/menmt0930/Downloads/8-layers_strand.pdb relModel #1

> select /A1-A8

4664 atoms, 4680 bonds, 696 residues, 1 model selected  

> color sel light sea green

> set bgColor white

> select clear

> select /B1-B8

3504 atoms, 3520 bonds, 504 residues, 1 model selected  

> color sel hot pink

> select clear

> select /C1-C8

228 atoms, 220 bonds, 45 residues, 1 model selected  

> color sel dim gray

> select clear

> save /Users/menmt0930/Downloads/8-layers_strand.pdb relModel #1

> close

> open /Users/menmt0930/Downloads/8-layers_strand.pdb format pdb

Chain information for 8-layers_strand.pdb #1  
---  
Chain | Description  
A1 A2 A3 A4 A5 A6 A7 A8 | No description available  
B1 B2 B3 B4 B5 B6 B7 B8 | No description available  
C1 C2 C3 | No description available  
C4 | No description available  
C5 C6 C7 | No description available  
C8 | No description available  
  

> close

> open /Users/menmt0930/Downloads/8-layers_strand.pdb

Chain information for 8-layers_strand.pdb #1  
---  
Chain | Description  
A1 A2 A3 A4 A5 A6 A7 A8 | No description available  
B1 B2 B3 B4 B5 B6 B7 B8 | No description available  
C1 C2 C3 | No description available  
C4 | No description available  
C5 C6 C7 | No description available  
C8 | No description available  
  

> style stick

Changed 8396 atom styles  

> show cartoons

> hide atoms

> open
> /Volumes/masa6tb/phenix_Gabor/2/LocalAnisoSharpen_2/postprocess_masked_sharpened.ccp4
> format ccp4

Opened postprocess_masked_sharpened.ccp4 as #2, grid size 320,320,320, pixel
1.03, shown at level 0.000294, step 2, values float32  

> volume #2 step 1

> volume #2 color #ffd479

> volume #2 color #ffd4791b

> volume #2 level 0.01368

> volume #2 color #ffd4794c

> volume #2 level 0.01166

> select /C1-C8

228 atoms, 220 bonds, 45 residues, 1 model selected  

> color sel dim gray

> select /B1-B8

3504 atoms, 3520 bonds, 504 residues, 1 model selected  

> color sel hot pink

> select /C1-C8

228 atoms, 220 bonds, 45 residues, 1 model selected  

> select /C1-C8

228 atoms, 220 bonds, 45 residues, 1 model selected  

> select /B1-B8

3504 atoms, 3520 bonds, 504 residues, 1 model selected  

> select /A1-A8

4664 atoms, 4680 bonds, 696 residues, 1 model selected  

> color sel cornflower blue

> select clear

> save /Users/menmt0930/Downloads/aMSA_new_model.cxs

——— End of log from Sun Dec 1 18:10:16 2024 ———

opened ChimeraX session  

> hide #1 models

> set bgColor black

> view orient

> volume #2 style image region all imageMode ""tilted slab"" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 164.8 tiltedSlabSpacing 1.03 tiltedSlabPlaneCount 10

> mousemode rightMode ""rotate slab""

> volume #2 level -1.231e-05,0 level 0.0002941,0.8 level 0.06391,1

> volume #2 level -1.231e-05,0 level 0.01349,0.7559 level 0.06391,1

> volume #2 style surface

> volume #2 level 0.05

> volume #2 level 0.02

> volume #2 level 0.005

> volume #2 level 0.008

> volume #2 level 0.01

> volume #2 style image colorMode opaque8 orthoplanes xyz positionPlanes
> 159,159,159 imageMode orthoplanes

> volume #2 region 0,0,159,319,319,159 step 1 colorMode auto8 imageMode ""full
> region""

> view orient

> volume #2 style image region all imageMode ""tilted slab"" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 164.8 tiltedSlabSpacing 1.03 tiltedSlabPlaneCount 10

> mousemode rightMode ""rotate slab""

> volume planes z style image imageMode ""full region""

> mousemode rightMode ""move planes""

> volume showOutlineBox false

> volume #2 style image region all imageMode ""tilted slab"" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 164.8 tiltedSlabSpacing 1.03 tiltedSlabPlaneCount 10

> mousemode rightMode ""rotate slab""

> ui mousemode right ""move planes""

> volume #2 tiltedSlabOffset 139 tiltedSlabPlaneCount 10

> volume #2 tiltedSlabOffset 131.8 tiltedSlabPlaneCount 10

> volume #2 tiltedSlabOffset 140.1 tiltedSlabPlaneCount 10

> volume #2 tiltedSlabOffset 123.6 tiltedSlabPlaneCount 10

> volume #2 tiltedSlabOffset 152.4 tiltedSlabPlaneCount 10

> volume #2 level 0.002738,0.01471 level 0.01349,0.7559 level 0.06391,1

> volume #2 level 0.004,0.01471 level 0.01349,0.7559 level 0.06391,1

> volume #2 level 0.005,0.01471 level 0.01349,0.7559 level 0.06391,1

> volume #2 level 0.005,0.01471 level 0.01111,0.7706 level 0.06391,1

> volume #2 level 0.005,0.01471 level 0.05,0.7706 level 0.06391,1

> volume #2 style surface

> volume #2 style image tiltedSlabOffset 131.3 tiltedSlabSpacing 1.03
> tiltedSlabPlaneCount 64

> volume #2 style image region all imageMode ""tilted slab"" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 164.8 tiltedSlabSpacing 1.03 tiltedSlabPlaneCount 10

> mousemode rightMode ""rotate slab""

> ui mousemode right ""move planes""

> volume planes z style image imageMode ""full region""

> mousemode rightMode ""move planes""

> volume #2 style image region all imageMode ""tilted slab"" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 164.8 tiltedSlabSpacing 1.03 tiltedSlabPlaneCount 10

> mousemode rightMode ""rotate slab""

> ui mousemode right ""move planes""

> volume #2 tiltedSlabOffset 164.8 tiltedSlabPlaneCount 10

> volume #2 tiltedSlabOffset 150.4 tiltedSlabPlaneCount 10

> volume #2 level 0.005,0.01471 level 0.004,0.7706 level 0.06391,1

> volume #2 level 0.005,0.01471 level 0.003633,0.3882 level 0.06391,1

> volume #2 level 0.007383,0.8971 level 0.003633,0.3882 level 0.06391,1

> volume #2 level 0.007383,0.8971 level 0.00235,0.06471 level 0.06391,1

> volume #2 level 0.007383,0.8971 level 0.004,0.06471 level 0.06391,1

> volume #2 level 0.01,0.8971 level 0.004,0.06471 level 0.06391,1

> volume #2 level 0.015,0.8971 level 0.004,0.06471 level 0.06391,1

> volume #2 level 0.013,0.8971 level 0.004,0.06471 level 0.06391,1

> volume #2 level 0.012,0.8971 level 0.004,0.06471 level 0.06391,1

> volume #2 level 0.012,0.8971 level 0.003,0.06471 level 0.06391,1

> volume #2 level 0.012,0.8971 level 0.002,0.06471 level 0.06391,1

> volume #2 level 0.012,0.8971 level 0.004,0.06471 level 0.06391,1

> volume #2 level 0.012,0.8971 level 0.005,0.06471 level 0.06391,1

> turn x 90

> volume #2 tiltedSlabOffset 150.4 tiltedSlabPlaneCount 10

> ui mousemode right ""move planes""

> view orient

> volume #2 tiltedSlabOffset 155.5 tiltedSlabPlaneCount 10

OpenType support missing for "".AppleSystemUIFont"", script 10  

> turn x 90

> volume #2 level 0.01,0.8971 level 0.005,0.06471 level 0.06391,1

> volume #2 level 0.015,0.8971 level 0.005,0.06471 level 0.06391,1

> volume #2 level 0.014,0.8971 level 0.005,0.06471 level 0.06391,1

> volume #2 level 0.013,0.8971 level 0.005,0.06471 level 0.06391,1

> volume #2 level 0.012,0.8971 level 0.005,0.06471 level 0.06391,1

> volume #2 level 0.01,0.8971 level 0.005,0.06471 level 0.06391,1

> volume #2 level 0.0125,0.8971 level 0.005,0.06471 level 0.06391,1

> save /Users/menmt0930/Downloads/cross-section.png width 1032 height 898
> supersample 3

> hide #!2 models

> show #1 models

> hide #1 models

> show #!2 models

> volume #2 style surface

> close #2

> open /Users/menmt0930/Downloads/3-2.mrc

Opened 3-2.mrc as #2, grid size 320,320,320, pixel 1.03, shown at level
6.71e-06, step 2, values float32  

> volume #2 step 1

> volume #2 level 0.005908

> volume #2 level 0.006374

> show #1 models

> select /A3, B3, C3

1057 atoms, 1060 bonds, 157 residues, 1 model selected  

> select ~sel & ##selected

7339 atoms, 7360 bonds, 1088 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> close #1

> open /Users/menmt0930/Downloads/8-layers_strand.pdb

Chain information for 8-layers_strand.pdb #1  
---  
Chain | Description  
A1 A2 A3 A4 A5 A6 A7 A8 | No description available  
B1 B2 B3 B4 B5 B6 B7 B8 | No description available  
C1 C2 C3 | No description available  
C4 | No description available  
C5 C6 C7 | No description available  
C8 | No description available  
  

> select /A4, B4, C4

1051 atoms, 1054 bonds, 156 residues, 1 model selected  

> select ~sel & ##selected

7345 atoms, 7366 bonds, 1089 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> style stick

Changed 1051 atom styles  

> show atoms

> volume #2 color #b2b2b24f

> volume #2 level 0.005442

> volume #2 level 0.00715

> volume #2 level 0.005753

> close #2

> open /Users/menmt0930/Downloads/aMSA_new_model.cxs

Opened postprocess_masked_sharpened.ccp4 as #2, grid size 320,320,320, pixel
1.03, shown at level 0.0117, step 1, values float32  
opened ChimeraX session  

> ui tool show ""Side View""

> hide #1 models

> volume #2 level 0.01038

> volume #2 level 0.01

> volume #2 level 0.01128

> open
> /Users/menmt0930/mnt/masa20tb4/Relion/atypical_msa_tcortex/LocalRes/job1225/relion_locres.mrc
> format mrc

Opened relion_locres.mrc as #3, grid size 320,320,320, pixel 1.03, shown at
level 23.5, step 2, values float32  

> ui tool show ""Surface Color""

> key red-white-blue :0.0 :0.5 :1.0 showTool true

> ui mousemode right ""color key""

> key red-white-blue :0.0 :0.5 :1.0 white:

> key red:0.0 white:0.5 blue:1.0 white: white:

> key white: white: blue:1.0 white:0.5 red:0.0

> key red:0.0 white:0.5 blue:1.0 white: white:

> ui mousemode right ""move planes""

> color sample #2.1 map #3 palette
> 3,#0000ff:3.2,#00ffff:3.4,#00ff00:3.6,#ffff00:3.8,#ff0000

Map values for surface ""surface"": minimum 3.082, mean 3.333, maximum 5.28  
Map values for surface ""cap far"": minimum 3.133, mean 3.36, maximum 4.736  
Map values for surface ""cap near"": minimum 3.133, mean 3.362, maximum 5.121  

> color sample #2.1 map #3 palette
> 3,#0000ff:3.2,#00ffff:3.4,#00ff00:3.6,#ffff00:3.8,#ff0000

Map values for surface ""surface"": minimum 3.082, mean 3.333, maximum 5.28  
Map values for surface ""cap far"": minimum 3.133, mean 3.36, maximum 4.736  
Map values for surface ""cap near"": minimum 3.133, mean 3.362, maximum 5.121  

> key rainbow :3.0 :3.2 :3.4 :3.6 :3.8 showTool true

> ui mousemode right ""color key""

> ui mousemode right ""move planes""

> color sample #2.1 map #3 palette
> 3.1,#0000ff:3.2,#00ffff:3.4,#00ff00:3.6,#ffff00:3.8,#ff0000

Map values for surface ""surface"": minimum 3.082, mean 3.333, maximum 5.28  
Map values for surface ""cap far"": minimum 3.133, mean 3.36, maximum 4.736  
Map values for surface ""cap near"": minimum 3.133, mean 3.362, maximum 5.121  

> color sample #2.1 map #3 palette
> 3.1,#0000ff:3.2,#00ffff:3.4,#00ff00:3.6,#ffff00:3.9,#ff0000

Map values for surface ""surface"": minimum 3.082, mean 3.333, maximum 5.28  
Map values for surface ""cap far"": minimum 3.133, mean 3.36, maximum 4.736  
Map values for surface ""cap near"": minimum 3.133, mean 3.362, maximum 5.121  

> color sample #2.1 map #3 palette
> 3.1,#0000ff:3.2,#00ffff:3.3,#00ff00:3.4,#ffff00:3.5,#ff0000

Map values for surface ""surface"": minimum 3.082, mean 3.333, maximum 5.28  
Map values for surface ""cap far"": minimum 3.133, mean 3.36, maximum 4.736  
Map values for surface ""cap near"": minimum 3.133, mean 3.362, maximum 5.121  

> volume #2 level 0.01223

> volume #2 level 0.009396

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> volume #2 level 0.008829

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> color sample #2.1 map #3 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000

Map values for surface ""surface"": minimum 3.081, mean 3.384, maximum 5.797  
Map values for surface ""cap far"": minimum 3.133, mean 3.416, maximum 5.035  
Map values for surface ""cap near"": minimum 3.133, mean 3.416, maximum 5.278  

> color sample #2.1 map #3 palette
> 3.1,#0000ff:3.3,#00ffff:3.5,#00ff00:3.7,#ffff00:3.9,#ff0000

Map values for surface ""surface"": minimum 3.081, mean 3.384, maximum 5.797  
Map values for surface ""cap far"": minimum 3.133, mean 3.416, maximum 5.035  
Map values for surface ""cap near"": minimum 3.133, mean 3.416, maximum 5.278  

> key rainbow :3.1 :3.3 :3.5 :3.7 :3.9 showTool true

> ui mousemode right ""color key""

> volume #2 level 0.009585

> view orient

> turn x 90

> color sample #2.1 map #3 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000

Map values for surface ""surface"": minimum 3.082, mean 3.365, maximum 5.762  

> hide #1 models

> color sample #2.1 map #3 palette
> 3.1,#0000ff:3.3,#00ffff:3.5,#00ff00:3.7,#ffff00:3.9,#ff0000

Map values for surface ""surface"": minimum 3.082, mean 3.365, maximum 5.762  

> key rainbow :3.1 :3.3 :3.5 :3.7 :3.9 showTool true

> view orient

> turn x 90

> color sample #2.1 map #3 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000

Map values for surface ""surface"": minimum 3.082, mean 3.365, maximum 5.762  

> color sample #2.1 map #3 palette
> 3.1,#0000ff:3.3,#00ffff:3.5,#00ff00:3.7,#ffff00:3.9,#ff0000

Map values for surface ""surface"": minimum 3.082, mean 3.365, maximum 5.762  

> hide #!3 models

> ui tool show ""Side View""

> hide #!2 models

> show #!2 models

> hide #4 models

> show #4 models

> ui tool show ""Side View""

> view

> ui tool show ""Side View""

> lighting soft

> lighting simple

> lighting soft

> lighting full

> lighting soft

> lighting simple

> lighting soft

> lighting simple

> turn x 90

> ui tool show ""Side View""

> view orient

> turn x 90

> color sample #2.1 map #3 palette
> 3.1,#0000ff:3.3,#00ffff:3.5,#00ff00:3.7,#ffff00:3.9,#ff0000

Map values for surface ""surface"": minimum 3.082, mean 3.365, maximum 5.762  
Map values for surface ""cap far"": minimum 3.13, mean 3.353, maximum 4.166  
Map values for surface ""cap near"": minimum 3.133, mean 3.34, maximum 4.438  

> volume #2 level 0.01147

> volume #2 level 0.01223

> volume #2 level 0.009962

> volume #2 level 0.01

> volume #2 level 0.011

> volume #2 level 0.01

> key rainbow :3.1 :3.3 :3.5 :3.7 :3.9 showTool true

> key size 0.2,0.05000

> key size 0.0000,0.05000

> key size 0.00000,0.05000

> key size 0.00000,0.5000

> key size 0.00000,0.0000

> key size 0.00000,0.2

> key size 0.00000,0.21000

> key size 0.00000,0.22000

> key size 0.00000,0.23000

> key size 0.00000,0.24000

> key size 0.00000,0.25000

> key size 0.01000,0.25000

> key size 0.02000,0.25000

> key size 0.03000,0.25000

> key size 0.04000,0.25000

> key size 0.05000,0.25000

> key pos 0.71000,0.08000

> key pos 0.72000,0.08000

> key pos 0.73000,0.08000

> key pos 0.74000,0.08000

> key pos 0.75000,0.08000

> key pos 0.76000,0.08000

> key pos 0.77000,0.08000

> key pos 0.78000,0.08000

> key pos 0.79000,0.08000

> key pos 0.80000,0.08000

> key pos 0.81000,0.08000

> key pos 0.82000,0.08000

> key pos 0.83000,0.08000

> key pos 0.84000,0.08000

> key pos 0.83000,0.08000

> key pos 0.83000,0.07000

> key pos 0.83000,0.08000

> key pos 0.83000,0.09000

> key pos 0.83000,0.10000

> key pos 0.83000,0.11000

> key pos 0.83000,0.12000

> key pos 0.83000,0.13000

> key pos 0.83000,0.14000

> key pos 0.83000,0.15000

> key pos 0.83000,0.16000

> key pos 0.83000,0.17000

> key pos 0.83000,0.18000

> key pos 0.83000,0.19000

> key pos 0.83000,0.20000

> key pos 0.83000,0.21000

> key pos 0.83000,0.22000

> key pos 0.83000,0.23000

> key pos 0.83000,0.24000

> key pos 0.83000,0.25000

> key pos 0.83000,0.26000

> save ""/Users/menmt0930/Downloads/local resolution.cxs""

> save ""/Users/menmt0930/Downloads/local resolution.png"" width 897 height 782
> supersample 3 transparentBackground true

> key rainbow :3.1 :3.3 :3.5 :3.7 :3.9 showTool true

> key size 0.05000,0.24000

> key size 0.05000,0.25000

> key size 0.04000,0.25000

> key size 0.03000,0.25000

> key size 0.02000,0.25000

> key size 0.03000,0.25000

> key fontSize 23

> key fontSize 22

> key fontSize 21

> key fontSize 20

> key fontSize 19

> key fontSize 18

> key fontSize 17

> key fontSize 16

> key fontSize 15

> key fontSize 14

> key fontSize 15

> key fontSize 16

> save ""/Users/menmt0930/Downloads/local resolution.png"" width 897 height 782
> supersample 3

> save ""/Users/menmt0930/Downloads/local resolution.cxs""

> save ""/Users/menmt0930/Downloads/local resolution.png"" width 897 height 782
> supersample 3 transparentBackground true


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

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
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/menmt0930/Downloads/8-layers_strand_copy.pdb

Chain information for 8-layers_strand_copy.pdb #1  
---  
Chain | Description  
A1 A2 A3 A4 A5 A6 A7 A8 | No description available  
B1 B2 B3 B4 B5 B6 B7 B8 | No description available  
C1 C2 C3 | No description available  
C4 | No description available  
C5 C6 C7 | No description available  
C8 | No description available  
  




OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M2 Ultra
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: Mac Studio
      Model Identifier: Mac14,14
      Model Number: Z18000049VC/A
      Chip: Apple M2 Ultra
      Total Number of Cores: 24 (16 performance and 8 efficiency)
      Memory: 128 GB
      System Firmware Version: 11881.41.5
      OS Loader Version: 11881.41.5

Software:

    System Software Overview:

      System Version: macOS 15.1.1 (24B91)
      Kernel Version: Darwin 24.1.0
      Time since boot: 1 day, 23 hours, 48 minutes

Graphics/Displays:

    Apple M2 Ultra:

      Chipset Model: Apple M2 Ultra
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 76
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        DELL S2721QS:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        DELL S2721QS:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 30.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


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-Clipper: 0.23.1
    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-ISOLDE: 1.8
    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