id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
16591	Crash on Mac waking from sleep	martik39@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-15.1.1-x86_64-i386-64bit
ChimeraX Version: 1.8rc202405230136 (2024-05-23 01:36:41 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 0x00007ff852289b40 (most recent call first):
  File ""/Applications/ChimeraX-1.8-rc2024.05.23.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 302 in event_loop
  File ""/Applications/ChimeraX-1.8-rc2024.05.23.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-rc2024.05.23.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.map._map, 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, chimerax.surface._surface, chimerax.pdb_lib._load_libs, 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, lxml._elementpath, lxml.etree, PIL._imagingmath (total: 59)


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    ""path"" : ""\/Applications\/ChimeraX-1.8-rc2024.05.23.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/_elementpath.cpython-311-darwin.so"",
    ""name"" : ""_elementpath.cpython-311-darwin.so""
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    ""base"" : 5587546112,
    ""size"" : 32768,
    ""uuid"" : ""4cafbf15-47c9-3e93-abf0-7f8f01ea6b1d"",
    ""path"" : ""\/Applications\/ChimeraX-1.8-rc2024.05.23.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/_imagingmath.cpython-311-darwin.so"",
    ""name"" : ""_imagingmath.cpython-311-darwin.so""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 140703385726976,
    ""size"" : 245760,
    ""uuid"" : ""1b806694-216b-3869-9a82-0094a1ad6ba0"",
    ""path"" : ""\/usr\/lib\/system\/libsystem_kernel.dylib"",
    ""name"" : ""libsystem_kernel.dylib""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 140703385972736,
    ""size"" : 49152,
    ""uuid"" : ""ba536cd2-1b67-33bb-ab33-73949260c730"",
    ""path"" : ""\/usr\/lib\/system\/libsystem_pthread.dylib"",
    ""name"" : ""libsystem_pthread.dylib""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 140703384555520,
    ""size"" : 561144,
    ""uuid"" : ""f1ddf520-c61e-33b8-9512-c3305004e4df"",
    ""path"" : ""\/usr\/lib\/system\/libsystem_c.dylib"",
    ""name"" : ""libsystem_c.dylib""
  },
  {
    ""source"" : ""P"",
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    ""base"" : 140703386198016,
    ""size"" : 40960,
    ""uuid"" : ""99ed579c-5be6-3fbd-85d3-fe4dd2121de0"",
    ""path"" : ""\/usr\/lib\/system\/libsystem_platform.dylib"",
    ""name"" : ""libsystem_platform.dylib""
  },
  {
    ""size"" : 0,
    ""source"" : ""A"",
    ""base"" : 0,
    ""uuid"" : ""00000000-0000-0000-0000-000000000000""
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    ""CFBundleShortVersionString"" : ""1.600.0"",
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    ""size"" : 4976630,
    ""uuid"" : ""8609cb34-bab0-3736-a774-fdf7fbe44b8f"",
    ""path"" : ""\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight"",
    ""name"" : ""SkyLight""
  },
  {
    ""source"" : ""P"",
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    ""base"" : 140703384248320,
    ""size"" : 294906,
    ""uuid"" : ""b9d99f1b-62d1-357d-89a8-5ab5871d9e33"",
    ""path"" : ""\/usr\/lib\/system\/libdispatch.dylib"",
    ""name"" : ""libdispatch.dylib""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64h"",
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    ""size"" : 4841459,
    ""uuid"" : ""59040703-0ba6-3fe8-a7fd-04edf3bb0b03"",
    ""path"" : ""\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation"",
    ""name"" : ""CoreFoundation"",
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    ""size"" : 3002356,
    ""uuid"" : ""f01dcd65-0a63-39f5-b7a1-f4c790a6ce5c"",
    ""path"" : ""\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox"",
    ""name"" : ""HIToolbox""
  },
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    ""CFBundleShortVersionString"" : ""6.9"",
    ""CFBundleIdentifier"" : ""com.apple.AppKit"",
    ""size"" : 21753843,
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    ""path"" : ""\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit"",
    ""name"" : ""AppKit"",
    ""CFBundleVersion"" : ""2575.20.21""
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    ""size"" : 574280,
    ""uuid"" : ""4d52bd1e-6a0e-31db-b564-9e2029fdcd6f"",
    ""path"" : ""\/usr\/lib\/dyld"",
    ""name"" : ""dyld""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 140703383969792,
    ""size"" : 278528,
    ""uuid"" : ""3019c6df-ff8c-3f17-b57e-fc68f4626dc4"",
    ""path"" : ""\/usr\/lib\/system\/libsystem_malloc.dylib"",
    ""name"" : ""libsystem_malloc.dylib""
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  {
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    ""size"" : 511996,
    ""uuid"" : ""d09eb0d4-5624-30a0-9b5a-745d78ce3591"",
    ""path"" : ""\/usr\/lib\/libc++.1.dylib"",
    ""name"" : ""libc++.1.dylib""
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},
  ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.3G resident=0K(0%) swapped_out_or_unallocated=1.3G(100%)\nWritable regions: Total=1.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.3G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               384K        3 \nActivity Tracing                   256K        1 \nCG image                          1916K       47 \nCG raster data                       8K        1 \nColorSync                          256K       34 \nCoreAnimation                     1868K      159 \nCoreGraphics                        12K        3 \nCoreImage                           60K        3 \nCoreUI image data                 5176K       40 \nFoundation                          40K        2 \nIOKit                             23.3M        3 \nKernel Alloc Once                    8K        1 \nMALLOC                           867.9M      678 \nMALLOC guard page                   48K       12 \nMALLOC_LARGE (reserved)            384K        1         reserved VM address space (unallocated)\nMach message                        16K        2 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        176K       44 \nStack                            180.3M       45 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      208.2M      201 \nVM_ALLOCATE (reserved)            64.0M        1         reserved VM address space (unallocated)\n__CTF                               824        1 \n__DATA                            33.0M      865 \n__DATA_CONST                      93.6M      759 \n__DATA_DIRTY                      1808K      252 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__LINKEDIT                       214.3M      155 \n__OBJC_RO                         76.3M        1 \n__OBJC_RW                         2355K        2 \n__TEXT                             1.1G      883 \n__TPRO_CONST                       272K        2 \ndyld private memory                 20K        2 \nmapped file                      296.7M       86 \nowned unmapped memory             5356K        1 \nshared memory                     3512K       29 \n===========                     =======  ======= \nTOTAL                              3.2G     4326 \nTOTAL, minus reserved VM space     3.2G     4326 \n"",
  ""legacyInfo"" : {
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},
  ""logWritingSignature"" : ""2e26fe47b466d3c2c2a69859e32e9f36d4716104"",
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===== Log before crash start =====
Startup Messages  
---  
notes | available bundle cache has not been initialized yet  
Database-fetch provider 'redo' in bundle Map specified unknown data format
'MTZ'  
  
UCSF ChimeraX version: 1.8rc202405230136 (2024-05-23)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open ""/Users/olgakarlita2012/Desktop/PKG/PKG Manuscript Final Figures/PKG
> Chimera figures.cxs""

opened ChimeraX session  

> set bgColor white

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting simple

> lighting full

> lighting flat

> color #1 #acacacff

> color #1 #cdcdcdff

> color #1 #e9e9e9ff

> color #1 #dededeff

> color #1 #cdcdcdff

> color #1 gainsboro

> color #1 #bfdaf1ff

> color #1 #a4bcd0ff

> color #1 #c9e6ffff

> color #1 #c9e6ff8c

> color #1 #c9e6ff1c

> color #1 #c9e6ff00

> color #1 #ebebebff

> color #1 #d6d6d6ff

> color #1 #ebebebff

> color #1 #d6d6d6ff

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> select /a: 226, 227, 234, 240, 243, 244, 246, 247, 248, 250, 252, 265, 268,
> 276, 278, 280, 296, 298, 302, 303, 311, 319, 321, 327,338, 341, 342, 347,
> 360, 366

238 atoms, 218 bonds, 30 residues, 1 model selected  

> color sel cornflower blue

> color sel #bed9f0ff

> color sel #bdd9f0ff

> color sel #bdd8efff

> color sel #8ca0b1ff

> color sel #788998ff

> color sel #728290ff

> color sel #70808dff

> color sel #6e7e8bff

> color sel #6e7d8bff

> color sel #6d7d8aff

> color sel #6d7c8aff

> color sel #6c7c89ff

> color sel #6c7b89ff

> color sel #6b7b88ff

> color sel #6a7986ff

> color sel #697885ff

> color sel #697884ff

> color sel #687784ff

> color sel #677683ff

> color sel #677682ff

> color sel #677582ff

> color sel #667582ff

> color sel #667581ff

> color sel #667481ff

> color sel #697885ff

> color sel #6f7f8dff

> color sel #728290ff

> color sel #768695ff

> color sel #788998ff

> color sel #798a99ff

> color sel #7b8d9cff

> color sel #7e909fff

> color sel #8396a6ff

> color sel #889bacff

> color sel #8b9fb0ff

> color sel #8ea2b4ff

> color sel #8fa4b5ff

> color sel #91a6b8ff

> color sel #92a7b9ff

> color sel #93a8baff

> color sel #95aabdff

> color sel #96abbdff

> color sel #96abbeff

> color sel #96acbeff

> color sel #97adbfff

> color sel #99afc1ff

> color sel #9bb1c4ff

> color sel #9bb2c5ff

> color sel #9eb4c8ff

> color sel #a0b7cbff

> color sel #a1b8ccff

> color sel #a3bacfff

> color sel #a6bdd2ff

> color sel #a7bfd4ff

> color sel #a9c1d6ff

> color sel #aac2d7ff

> color sel #abc4d9ff

> color sel #abc3d8ff

> color sel #aac2d7ff

> color sel #a8c0d5ff

> color sel #a6bed2ff

> color sel #a3bbcfff

> color sel #a2b9cdff

> color sel #a1b8ccff

> color sel #a0b7cbff

> color sel #9fb6caff

> color sel #9fb5c9ff

> color sel #9eb5c9ff

> color sel #9eb4c8ff

> color sel #9eb4c8fa

> color sel #9eb4c8ed

> color sel #9eb4c8bd

> color sel #9eb4c8b6

> color sel #9eb4c8ad

> color sel #9eb4c8a7

> color sel #9eb4c8a3

> color sel #9eb4c8a0

> color sel #9eb4c89e

> color sel #9eb4c89d

> color sel #9eb4c89c

> color sel #9eb4c89b

> color sel #9eb4c89a

> color sel #9eb4c898

> color sel #9eb4c895

> color sel #9eb4c88f

> color sel #9eb4c88c

> color sel #9eb4c889

> color sel #9eb4c883

> color sel #9eb4c880

> color sel #9eb4c88a

> color sel #9eb4c88d

> color sel #9eb4c893

> color sel #9eb4c89c

> color sel #9eb4c8a0

> color sel #9eb4c8af

> color sel #9eb4c8ba

> color sel #9eb4c8bd

> color sel #9eb4c8c0

> color sel #9eb4c8c6

> color sel #9eb4c8cb

> color sel #9eb4c8ce

> color sel #9eb4c8d0

> color sel #9eb4c8d2

> color sel #9eb4c8d3

> color sel #9eb4c8d6

> color sel #9eb4c8d9

> color sel #9eb4c8dc

> color sel #9eb4c8de

> color sel #9eb4c8e1

> color sel #9eb4c8e3

> color sel #9eb4c8e8

> color sel #9eb4c8ea

> color sel #9eb4c8ec

> color sel #9eb4c8ed

> color sel #9eb4c8ef

> color sel #9eb4c8f0

> color sel #9eb4c8f1

> color sel #9eb4c8f2

> color sel #9eb4c8f3

> color sel #9eb4c8f6

> color sel #9eb4c8fa

> color sel #9eb4c8fb

> color sel #9eb4c8fc

> color sel #9eb4c8fe

> color sel #9eb4c8ff

> color sel #bcd7eeff

> color sel #bbd4eeff

> color sel #bad4edff

> color sel #b9d3ecff

> color sel #b8d2ebff

> color sel #b8d1ebff

> color sel #b8d1eaff

> color sel #b6cfe8ff

> color sel #b5cee7ff

> color sel #b4cde6ff

> color sel #b3cbe4ff

> color sel #b2cae2ff

> color sel #b1c9e1ff

> color sel #b0c8e1ff

> color sel #b0c8e0ff

> color sel #afc7dfff

> color sel #aec6deff

> color sel #aec5ddff

> color sel #adc5ddff

> color sel #adc4dcff

> color sel #acc3dbff

> color sel #abc3daff

> color sel #abc2daff

> color sel #abc2d9ff

> color sel #aac1d8ff

> color sel #a9c0d8ff

> color sel #a9c0d7ff

> color sel #a8bfd6ff

> color sel #a7bed5ff

> color sel #a7bed4ff

> color sel #a6bdd4ff

> color sel #a6bdd3ff

> color sel #a6bcd3ff

> color sel #a5bcd3ff

> color sel #a5bcd2ff

> color sel #6e87acff

> color sel #6e87acfa

> color sel #6e87aced

> color sel #6e87ace3

> color sel #6e87acdc

> color sel #6e87acd5

> color sel #6e87accb

> color sel #6e87acc7

> color sel #6e87acc4

> color sel #6e87acc1

> color sel #6e87acbe

> color sel #6e87acbc

> color sel #6e87acb9

> color sel #6e87acb3

> color sel #6e87acb2

> color sel #6e87acb0

> color sel #6e87acaf

> color sel #6e87acb0

> color sel #6e87acb2

> color sel #6e87acb3

> select clear

> select /a:234

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

> hide sel cartoons

> hide sel atoms

> show sel atoms

> hide sel target a

> cartoon sel

> select clear

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting flat

> select /a: 226, 227, 234, 240, 243, 244, 246, 247, 248, 250, 252, 265, 268,
> 276, 278, 280, 296, 298, 302, 303, 311, 319, 321, 327,338, 341, 342, 347,
> 360, 366

238 atoms, 218 bonds, 30 residues, 1 model selected  

> color sel #6e87acb3

> color sel #6e87acb4

> color sel #6e87acb8

> color sel #6e87acbf

> color sel #6e87acc9

> color sel #6e87accf

> color sel #6e87acd9

> color sel #6e87ace2

> color sel #6e87ace8

> color sel #6e87aceb

> color sel #6e87acf0

> color sel #6e87acff

> color sel #6e87acf5

> color sel #6e87ace9

> color sel #6e87acbb

> color sel #6e87aca4

> color sel #6e87ac99

> color sel #6e87ac95

> color sel #6e87ac92

> color sel #6e87ac8d

> color sel #6e87ac87

> color sel #6e87ac82

> color sel #6e87ac80

> color sel #6e87ac76

> color sel #6e87ac74

> color sel #6e87ac72

> color sel #6e87ac71

> color sel #6e87ac70

> color sel #6e87ac6e

> color sel #6e87ac6d

> color sel #6e87ac6c

> color sel #6e87ac6b

> color sel #6e87ac6a

> color sel #6e87ac69

> color sel #6e87ac68

> color sel #6e87ac67

> color sel #6e87ac68

> color sel #6e87ac77

> color sel #6e87ac80

> color sel #6e87ac8a

> color sel #6e87aca7

> color sel #6e87acc6

> color sel #6e87acea

> color sel #6e87acf8

> color sel #6e87acf9

> color sel #6e87acfb

> color sel #6e87acfe

> color sel #6e87acff

> color sel #6d86acff

> color sel #6f88afff

> color sel #7089b0ff

> color sel #728bb3ff

> color sel #738db5ff

> color sel #748eb6ff

> color sel #748fb7ff

> color sel #758fb8ff

> color sel #7690b9ff

> color sel #7691baff

> color sel #7792bbff

> color sel #7893bcff

> color sel #7894bdff

> color sel #7995bfff

> color sel #7a95c0ff

> color sel #7b96c1ff

> color sel #7b97c2ff

> color sel #7c98c2ff

> color sel #7d99c5ff

> color sel #7d9ac5ff

> color sel #7e9bc7ff

> color sel #7f9cc8ff

> color sel #829fccff

> color sel #84a2d0ff

> color sel #87a6d5ff

> color sel #89a9d8ff

> color sel #8aa9d9ff

> color sel #8aa9d8ff

> color sel #89a8d7ff

> color sel #88a7d6ff

> color sel #87a5d4ff

> color sel #85a4d2ff

> color sel #84a2d0ff

> color sel #82a0cdff

> color sel #829fcdff

> color sel #829fccff

> color sel #819fccff

> color sel #819fcbff

> color sel #819fccff

> color sel #82a0cdff

> color sel #84a2cfff

> color sel #85a3d1ff

> color sel #87a6d5ff

> color sel #88a6d6ff

> color sel #88a7d6ff

> color sel #88a8d7ff

> select clear

> save ""/Users/olgakarlita2012/Desktop/PKG/PKG Manuscript Final Figures/T and
> Class CHESCA/T-CHESCA map chimera.png"" width 713 height 715 supersample 3

> save ""/Users/olgakarlita2012/Desktop/PKG/PKG Manuscript Final Figures/T and
> Class CHESCA/T-CHESCA map chimera.png"" width 1600 height 1604 supersample 3

> color #1 #dededfff

> select /a: 227, 229, 233, 234, 243, 246, 247, 250, 251, 252, 265, 266, 276,
> 304, 337, 338, 339, 341, 345, 350, 360, 366

186 atoms, 177 bonds, 22 residues, 1 model selected  

> color sel #cbdac9ff

> color sel #6b895bff

> color sel #6a895bff

> color sel #6b8a5bff

> color sel #6b8b5cff

> color sel #6d8d5dff

> color sel #6e8e5eff

> color sel #709160ff

> color sel #719160ff

> color sel #739462ff

> color sel #749663ff

> color sel #759764ff

> color sel #769965ff

> color sel #779965ff

> color sel #779a66ff

> color sel #789b67ff

> color sel #799c67ff

> color sel #7a9e68ff

> color sel #7b9f69ff

> color sel #7ca16aff

> color sel #7fa46dff

> color sel #80a56dff

> color sel #80a66eff

> color sel #81a66eff

> color sel #82a76fff

> color sel #82a86fff

> color sel #83aa70ff

> color sel #84aa70ff

> color sel #84aa71ff

> color sel #85ac72ff

> color sel #86ad73ff

> color sel #87af74ff

> color sel #88b075ff

> color sel #8ab276ff

> color sel #8bb376ff

> color sel #8cb578ff

> color sel #8db678ff

> color sel #8db678fe

> color sel #8db678fb

> color sel #8db678f6

> color sel #8db678f3

> color sel #8db678ef

> color sel #8db678ea

> color sel #8db678e8

> color sel #8db678e6

> color sel #8db678e5

> color sel #8db678e4

> color sel #8db678e1

> color sel #8db678e0

> color sel #8db678de

> color sel #8db678dc

> color sel #8db678db

> color sel #8db678d8

> color sel #8db678d2

> color sel #8db678d1

> color sel #8db678d2

> color sel #8db678d3

> color sel #8db678d5

> color sel #8db678d7

> color sel #8db678d8

> color sel #8db678d9

> color sel #8db678da

> color sel #8db678dc

> color sel #8db678dd

> color sel #8db678df

> color sel #8db678e0

> color sel #8db678e2

> color sel #8db678e4

> color sel #8db678e5

> color sel #8db678e6

> color sel #8db678e7

> color sel #8db678e9

> color sel #8db678ea

> color sel #8db678eb

> color sel #8db678ec

> color sel #8db678ed

> color sel #8db678ee

> color sel #8db678ef

> color sel #8db679ef

> color sel #8eb779ef

> color sel #8fb97aef

> color sel #8fb97bef

> color sel #90ba7bef

> color sel #90bb7bef

> color sel #91bb7cef

> color sel #91bb7cf0

> select clear

> select /a: 227, 229, 233, 234, 243, 246, 247, 250, 251, 252, 265, 266, 276,
> 304, 337, 338, 339, 341, 345, 350, 360, 366

186 atoms, 177 bonds, 22 residues, 1 model selected  

> color sel #91bb7cf0

> color sel #8cb578f0

> color sel #81a76ef0

> color sel #7ea36cf0

> color sel #7ea26bf0

> color sel #7da26bf0

> color sel #7ea36cf0

> color sel #7fa46df0

> color sel #80a66ef0

> color sel #81a66ef0

> color sel #81a76ef0

> color sel #82a86ff0

> color sel #83a970f0

> color sel #83aa70f0

> color sel #84aa71f0

> color sel #85ac72f0

> color sel #86ad72f0

> color sel #86ad73f0

> color sel #86ae73f0

> color sel #87af74f0

> color sel #88b074f0

> color sel #89b175f0

> color sel #8ab376f0

> color sel #92bc7cf0

> color sel #97c481f0

> color sel #99c582f0

> color sel #9cca85f0

> color sel #9ecc87f0

> color sel #a0cf89f0

> color sel #a4d38cf0

> color sel #a5d68df0

> color sel #a3d38cf0

> color sel #a0cf89f0

> color sel #9dcb86f0

> color sel #9bc985f0

> color sel #9ac683f0

> color sel #98c482f0

> color sel #96c280f0

> color sel #96c180f0

> color sel #95c07ff0

> color sel #94bf7ff0

> color sel #93be7ef0

> color sel #92bd7df0

> color sel #92bc7cf0

> color sel #91bb7cf0

> color sel #90ba7bf0

> color sel #90b97bf0

> color sel #8fb97af0

> color sel #8fb87af0

> color sel #8eb87af0

> color sel #8eb879f0

> color sel #8eb779f0

> color sel #8db679f0

> color sel #8db678f0

> color sel #8db578f0

> color sel #8cb578f0

> color sel #8cb477f0

> color sel #8bb477f0

> color sel #8bb376f0

> color sel #8ab276f0

> color sel #89b175f0

> color sel #88b074f0

> color sel #87af73f0

> color sel #87ae73f0

> select clear

> save ""/Users/olgakarlita2012/Desktop/PKG/PKG Manuscript Final Figures/T and
> Class CHESCA/Class-CHESCA/Class C map chimera.png"" width 1600 height 1836
> supersample 3

> color #1 #e5e4e5ff

> select /a227, 234, 243, 246, 250, 252, 327, 360

Nothing selected  

> select /a227, 234, 243, 246, 250, 252, 327, 360

Nothing selected  

> select /a: 227, 234, 243, 246, 250, 252, 327, 360

69 atoms, 63 bonds, 8 residues, 1 model selected  

> color sel #7c5da1ff

> color sel #7c5da1fb

> color sel #7c5da1f8

> color sel #7c5da1ef

> color sel #7c5da1eb

> color sel #7c5da1e7

> color sel #7c5da1e4

> color sel #7c5da1da

> color sel #7c5da1d5

> color sel #7c5da1d2

> color sel #7c5da1ce

> color sel #7c5da1c8

> color sel #7c5da1c5

> color sel #7c5da1c3

> color sel #7c5da1c1

> color sel #7c5da1c0

> color sel #7c5da1bf

> color sel #7c5da1be

> color sel #7c5da1bd

> color sel #7b5ba1bd

> color sel #7b5ca1bd

> color sel #7c5ca3bd

> color sel #7f5ea5bd

> color sel #8160a8bd

> color sel #8260aabd

> color sel #8462acbd

> color sel #8563aebd

> color sel #8664b0bd

> color sel #8865b1bd

> color sel #8966b3bd

> color sel #8a67b5bd

> color sel #8c68b7bd

> color sel #8d68b8bd

> color sel #8d69b8bd

> color sel #8e6ababd

> color sel #906bbcbd

> color sel #906bbdbd

> color sel #916bbdbd

> color sel #926cbebd

> color sel #936dc0bd

> color sel #946ec1bd

> color sel #946ec1bc

> color sel #946ec1bb

> color sel #946ec1b1

> color sel #946ec1aa

> color sel #946ec1a3

> color sel #946ec1a1

> color sel #946ec19f

> color sel #946ec19b

> color sel #946ec199

> color sel #946ec198

> color sel #946ec197

> color sel #946ec196

> color sel #946ec197

> color sel #946ec199

> color sel #946ec19a

> color sel #946ec19b

> color sel #946ec19c

> color sel #946ec19d

> color sel #946ec19f

> color sel #946ec19e

> select clear

> save ""/Users/olgakarlita2012/Desktop/PKG/PKG Manuscript Final Figures/T C
> and DRMs map common DRMs.png"" width 473 height 730 supersample 3

> select /a: 227, 234, 243, 246, 250, 252, 327, 360

69 atoms, 63 bonds, 8 residues, 1 model selected  

> style sel stick

Changed 69 atom styles  

> show sel atoms

> hide sel atoms

> show sel atoms

> select clear

> lighting flat

> lighting shadows true intensity 0.5

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows false

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting flat

> lighting soft

> lighting flat

> save ""/Users/olgakarlita2012/Desktop/PKG/PKG Manuscript Final Figures/T C
> and DRMs map common DRMs.png"" width 1600 height 1589 supersample 3


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

Log:
Startup Messages  
---  
notes | available bundle cache has not been initialized yet  
Database-fetch provider 'redo' in bundle Map specified unknown data format
'MTZ'  
  
UCSF ChimeraX version: 1.8rc202405230136 (2024-05-23)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 ATI-6.1.13
OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

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: MacBookPro16,1
      Processor Name: 6-Core Intel Core i7
      Processor Speed: 2.6 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 12 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 2069.40.2.0.0 (iBridge: 22.16.11072.0.0,0)
      OS Loader Version: 582~2132

Software:

    System Software Overview:

      System Version: macOS 15.1.1 (24B91)
      Kernel Version: Darwin 24.1.0
      Time since boot: 3 days, 51 minutes

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0000
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3

    AMD Radeon Pro 5300M:

      Chipset Model: AMD Radeon Pro 5300M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0043
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32207P1-019
      Option ROM Version: 113-D32207P1-019
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        LG IPS FULLHD:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number:             
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 0.00


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: 1.6.3
    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
    ChimeraX-AtomicLibrary: 14.0.5
    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: 1.2.4
    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-ColorActions: 1.0.4
    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: 1.8rc202405230136
    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: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.16
    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: 1.13.4
    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: 3.0.10
    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: 1.4.2
    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: 4.51.0
    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: 8.1.2
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.10
    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: 3.0.43
    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
    traitlets: 5.14.2
    typing-extensions: 4.11.0
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10
}}}
"	defect	closed	normal		Window Toolkit		duplicate						all	ChimeraX