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Opened 94 minutes ago
#19500 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-13.7.8-x86_64-i386-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x00007ff84d225a00 (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/graphics/opengl.py", line 248 in swap_buffers
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 561 in swap_buffers
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 202 in draw
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84 in draw_new_frame
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
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.map._map, psutil._psutil_osx, psutil._psutil_posix, chimerax.surface._surface, chimerax.pdb_lib._load_libs, 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, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imaging, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 54)
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{
"uptime" : 780000,
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro14,3",
"coalitionID" : 651,
"osVersion" : {
"train" : "macOS 13.7.8",
"build" : "22H730",
"releaseType" : "User"
},
"captureTime" : "2025-12-09 15:54:49.1009 +0900",
"incident" : "CB525A16-0585-47D7-B864-47568E209E5C",
"pid" : 25601,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-12-09 11:05:51.0898 +0900",
"procStartAbsTime" : 768953201977804,
"procExitAbsTime" : 786290382528450,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.1","CFBundleVersion":"1.10.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"1C1BA882-85C6-57E2-92CE-D90DBE8C3BC6","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "3784FD91-D5BB-1D78-C091-43F051F69DD9",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 101975,
"bridgeVersion" : {"build":"14Y910","train":"3.0"},
"sleepWakeUUID" : "40FB301B-00AB-4991-BE4C-3934190B0F2C",
"sip" : "enabled",
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"termination" : {"flags":0,"code":6,"namespace":"SIGNAL","indicator":"Abort trap: 6","byProc":"ChimeraX","byPid":25601},
"asi" : {"libsystem_c.dylib":["abort() called"]},
"asiSignatures" : ["Graphics kernel error: 0x1ba285f9\n"],
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
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"uuid" : "7d784f30-bee3-30c1-8247-a01d90a9bd8e",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "1979.104.902"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703454195712,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3112954,
"uuid" : "a798e4be-2bf2-35dc-9d38-1d4521cf926e",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703287902208,
"size" : 624176,
"uuid" : "30314c55-d8f5-398e-b837-1b1760596c7f",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703307210752,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.Foundation",
"size" : 9998322,
"uuid" : "f962eed3-9d18-3e45-9da2-b1e3529053e1",
"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
"name" : "Foundation",
"CFBundleVersion" : "1979.104.902"
}
],
"sharedCache" : {
"base" : 140703287279616,
"size" : 21474836480,
"uuid" : "8eee6686-4d40-33a3-b07b-b334fd3e3ecc"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)\nWritable regions: Total=19.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=19.4G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 512K 4 \nActivity Tracing 256K 1 \nCG backing stores 3248K 8 \nCG image 2388K 86 \nColorSync 272K 31 \nCoreAnimation 7804K 129 \nCoreGraphics 16K 3 \nCoreImage 48K 4 \nCoreServices 840K 3 \nCoreUI image data 5604K 44 \nFoundation 40K 2 \nIOKit 23.3M 3 \nKernel Alloc Once 8K 1 \nMALLOC 12.0G 654 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMach message 16K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 112K 28 \nStack 194.7M 29 \nStack Guard 56.0M 1 \nVM_ALLOCATE 7.2G 322 \n__CTF 824 1 \n__DATA 45.0M 803 \n__DATA_CONST 63.2M 499 \n__DATA_DIRTY 1868K 243 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 201.0M 144 \n__OBJC_RO 66.3M 1 \n__OBJC_RW 2013K 2 \n__TEXT 1.0G 806 \ndyld private memory 324K 4 \nmapped file 606.2M 112 \nshared memory 3580K 34 \n=========== ======= ======= \nTOTAL 21.5G 4020 \nTOTAL, minus reserved VM space 21.5G 4020 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "f36146c1247f34c0abc869b08c947863835f819f",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "60356660bbe37970735c5624",
"factorPackIds" : {
},
"deploymentId" : 240000027
},
{
"rolloutId" : "64628732bf2f5257dedc8988",
"factorPackIds" : {
},
"deploymentId" : 240000001
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
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
> /Volumes/内藤USB/chimerasin/GH挿入/map/cryosparc_P77_J247_010_volume_map_sharp_fliped.mrc
Opened cryosparc_P77_J247_010_volume_map_sharp_fliped.mrc as #1, grid size
288,288,288, pixel 0.806, shown at level 0.0665, step 2, values float32
> open
> /Volumes/内藤USB/chimerasin/GH挿入/model/GH_mutant_C7new_real_space_refined-
> coot-0.pdb
Chain information for GH_mutant_C7new_real_space_refined-coot-0.pdb #2
---
Chain | Description
A B C D E F G | No description available
> set bgColor white
> show cartoons
> style stick
Changed 16597 atom styles
> show atoms
> volume #1 step 1
> surface dust #1 size 8.06
> transparency 50
> view orient
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> turn x 90
> save /Users/labmos/Desktop/image12.png supersample 3
> lighting full
> lighting shadows false
> lighting shadows true
> lighting full
> lighting soft
> lighting full
> lighting simple
> lighting full
> view orient
> turn x 90
> save /Users/labmos/Desktop/image13.png supersample 3
> color #2 white
> select /F:126@CZ
1 atom, 1 residue, 1 model selected
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
1420 atoms, 1456 bonds, 174 residues, 1 model selected
> ui tool show "Surface Zone"
> surface zone #1 nearAtoms #2 distance 4.84
> select add #2
16597 atoms, 16975 bonds, 2065 residues, 1 model selected
> select subtract #2
Nothing selected
> select #1
2 models selected
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select down
2 models selected
> select down
2 models selected
> select down
2 models selected
> select down
2 models selected
> select down
2 models selected
> select down
2 models selected
> select subtract #1
Nothing selected
> select add #2
16597 atoms, 16975 bonds, 2065 residues, 1 model selected
> select add #1
16597 atoms, 16975 bonds, 2065 residues, 3 models selected
> select down
16597 atoms, 16975 bonds, 2065 residues, 3 models selected
> select down
16597 atoms, 16975 bonds, 2065 residues, 3 models selected
> select down
16597 atoms, 16975 bonds, 2065 residues, 3 models selected
> select clear
> surface dust #1 size 8.06
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
1420 atoms, 1456 bonds, 174 residues, 1 model selected
> surface zone #1 nearAtoms sel distance 4.84
> surface dust #1 size 8.06
> surface zone #1 nearAtoms sel distance 4.84
> surface zone #1 nearAtoms sel distance 4.75
> surface zone #1 nearAtoms sel distance 3.8
> surface zone #1 nearAtoms sel distance 3.73
> surface zone #1 nearAtoms sel distance 5.2
> surface unzone #1
> surface zone #1 nearAtoms sel distance 5.2
> select add #2
16597 atoms, 16975 bonds, 2065 residues, 1 model selected
> select add #1
16597 atoms, 16975 bonds, 2065 residues, 3 models selected
> surface dust #1 size 8.06
> show (#2 & sel) target ab
> hide #2 target m
> select clear
> select /A
2371 atoms, 2425 bonds, 295 residues, 1 model selected
> cartoon #1
> show #1 target ab
> select /A
2371 atoms, 2425 bonds, 295 residues, 1 model selected
> surface #1
No atoms specified by #1
> show #2 models
> cartoon sel
> select up
16597 atoms, 16975 bonds, 2065 residues, 1 model selected
> select up
16597 atoms, 16975 bonds, 2065 residues, 3 models selected
> select up
16597 atoms, 16975 bonds, 2065 residues, 3 models selected
> select up
16597 atoms, 16975 bonds, 2065 residues, 3 models selected
> select up
16597 atoms, 16975 bonds, 2065 residues, 3 models selected
> select up
16597 atoms, 16975 bonds, 2065 residues, 3 models selected
> select down
16597 atoms, 16975 bonds, 2065 residues, 1 model selected
> hide sel target a
> cartoon hide sel
> select /A
2371 atoms, 2425 bonds, 295 residues, 1 model selected
> hide #* target a
> show sel target ab
> cartoon sel
> ui mousemode right "map eraser"
> volume erase #1 center 125.64,97.17,71.132 radius 17.251
Opened cryosparc_P77_J247_010_volume_map_sharp_fliped.mrc copy as #4, grid
size 288,288,288, pixel 0.806, shown at step 1, values float32
> volume erase #4 center 125.64,97.17,71.132 radius 17.177
> surface dust #4 size 8.06
> volume erase #4 center 123.67,122.91,72.094 radius 25.418 outside true
> volume erase #4 center 128.3,114.34,91.303 radius 10.794
> volume erase #4 center 132.98,113.9,88.585 radius 17.061
> volume erase #4 center 135.03,111.11,99.629 radius 25.418
> volume erase #4 center 135.03,111.11,99.629 radius 24.838
> volume erase #4 center 101.82,107.2,66.042 radius 24.838
> volume erase #4 center 103.08,129.92,46.903 radius 24.838
> volume erase #4 center 97.422,130.49,55.822 radius 24.838
> volume erase #4 center 92.146,129.29,65.789 radius 24.838
> volume erase #4 center 133.81,112.69,106.41 radius 24.838
> volume erase #4 center 140.98,114.65,101.44 radius 29.016
> volume erase #4 center 141.77,93.326,81.335 radius 29.016
> volume erase #4 center 141.61,93.78,81.021 radius 29.016
> volume erase #4 center 141.37,94.559,80.716 radius 29.016
> volume #4 level 0.05016
> volume #4 level 0.05949
> volume #4 level 0.06765
> undo
> ui mousemode right "map eraser"
> volume copy #4 subregion 141,147,86,155,161,100
Opened cryosparc_P77_J247_010_volume_map_sharp_fliped.mrc copy as #5, grid
size 15,15,15, pixel 0.806, shown at step 1, values float32
> undo
> hide #3 models
> show #!1 models
> ui mousemode right "map eraser"
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> hide #!1 models
> hide #!4 models
> show #!5 models
> close #5
> show #!1 models
> hide (#2 & sel) target a
> cartoon hide (#2 & sel)
> select /A
2371 atoms, 2425 bonds, 295 residues, 1 model selected
> cartoon sel
> show #3 models
> volume erase #1 center 119.89,119.11,147.58 radius 38.185
Opened cryosparc_P77_J247_010_volume_map_sharp_fliped.mrc copy as #5, grid
size 288,288,288, pixel 0.806, shown at step 1, values float32
> surface dust #5 size 8.06
> volume erase #5 center 116.37,69.584,68.758 radius 38.185
> volume erase #5 center 157.59,148.59,111.93 radius 38.185
> volume erase #5 center 152.8,145.47,138.14 radius 42.479
> volume erase #5 center 149.41,141.95,139.09 radius 42.479
> volume erase #5 center 170.63,126.9,114.53 radius 42.479
> volume erase #5 center 143.4,82.757,120.37 radius 42.479
> volume erase #5 center 144.9,84.882,100.31 radius 42.479
> volume erase #5 center 107.02,53.186,142.96 radius 42.479
> volume erase #5 center 93.639,63.333,90.34 radius 42.479
> volume erase #5 center 75.169,76.497,137.95 radius 42.479
> volume erase #5 center 122.89,176.1,122.27 radius 47.47
> volume erase #5 center 83.596,171.62,141.09 radius 47.47
> volume erase #5 center 88.983,188.33,96.741 radius 47.47
> volume erase #5 center 85.868,180.37,98.343 radius 47.47
> volume erase #5 center 60.268,159.86,96.83 radius 47.47
> volume erase #5 center 58.98,155.94,99.58 radius 47.47
> volume erase #5 center 167.99,87.297,121.75 radius 68.594
> volume erase #5 center 166.63,87.606,119.49 radius 68.594
> volume erase #5 center 176.73,86.184,107.41 radius 68.594
> volume erase #5 center 176.27,86.408,107.18 radius 68.594
> volume erase #5 center 51.357,103.3,39.818 radius 68.594
> volume erase #5 center 58.934,104.68,42.792 radius 68.594
> volume erase #5 center 102.32,135.12,56.79 radius 17.061
> volume erase #5 center 104.44,133.4,52.478 radius 22.284
> volume erase #5 center 125.24,94.713,72.567 radius 22.284
> volume erase #5 center 133.1,124.63,106.75 radius 22.284
> volume erase #5 center 97.322,148.95,109.35 radius 22.284
> volume erase #5 center 112.62,141.56,121.54 radius 22.284
> volume erase #5 center 119.13,140.5,117.26 radius 22.284
> volume erase #5 center 99.324,101.72,81.933 radius 22.284
> volume erase #5 center 98.26,100.87,85.097 radius 22.284
> volume erase #5 center 70.527,113.11,163.48 radius 22.284
> volume erase #5 center 81.449,114.62,149.14 radius 22.284
> show sel target ab
> cartoon hide sel
> select ::name="SER"
1260 atoms, 1071 bonds, 210 residues, 1 model selected
> color sel blue
> select ::name="TYR"
1428 atoms, 1435 bonds, 119 residues, 1 model selected
> color sel red
> select ::name="VAL"
1029 atoms, 882 bonds, 147 residues, 1 model selected
> select ::name="VAL"
1029 atoms, 882 bonds, 147 residues, 1 model selected
> color sel hot pink
> select ::name="ASP"
1400 atoms, 1239 bonds, 175 residues, 1 model selected
> color sel light sea green
> color sel lime
> select clear
> select ::name="ASP"
1400 atoms, 1239 bonds, 175 residues, 1 model selected
> color sel forest green
> select clear
> select ::name="ASP"
1400 atoms, 1239 bonds, 175 residues, 1 model selected
> color sel cyan
> color sel light sea green
> color sel forest green
> select clear
> select ::name="ARG"
924 atoms, 840 bonds, 84 residues, 1 model selected
> color sel yellow
> select ::name="HIS"
280 atoms, 280 bonds, 28 residues, 1 model selected
> color sel cornflower blue
> select clear
> hide #!5 models
> show #!5 models
> color #5 #b2b2b245 models
> color #5 #b2b2b23b models
> volume #!5 style mesh
> volume #!5 style surface
> volume #!5 style mesh
> volume #5 level 0.07158
> volume #5 level 0.06819
> volume #5 level 0.06139
> volume #5 level 0.06819
> volume #5 color #b2b2b27e
> volume #5 color #b2b2b2
> volume #5 color #b2b2b2e5
> lighting full
> lighting shadows false
> lighting shadows true
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting shadows true
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting full
> lighting soft
> lighting simple
> lighting full
> lighting simple
> lighting full
> lighting simple
> lighting full
> lighting simple
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 2/A
> select /A:115-116
15 atoms, 14 bonds, 2 residues, 1 model selected
> select /A:115-144
216 atoms, 220 bonds, 30 residues, 1 model selected
> hide #* target a
> show sel target ab
> select clear
> select /A:21-29,34-43,50-61,66-69,75-89,97-102,109-121
565 atoms, 572 bonds, 69 residues, 1 model selected
> select /A:21-29,34-43,50-61,66-69,75-89,97-102,109-121
565 atoms, 572 bonds, 69 residues, 1 model selected
> select /A:111-165
423 atoms, 432 bonds, 55 residues, 1 model selected
> select /A:111-165
423 atoms, 432 bonds, 55 residues, 1 model selected
> select /A:111
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:111-113
29 atoms, 29 bonds, 3 residues, 1 model selected
> show sel target ab
> select /A:21-29,34-43,50-61,66-69,75-89,97-102,109-121
565 atoms, 572 bonds, 69 residues, 1 model selected
> select /A:114
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:114
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel target ab
> select clear
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting full
> lighting simple
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> lighting full
> lighting soft
> lighting simple
> graphics silhouettes false
> lighting soft
> lighting simple
> graphics silhouettes true
> lighting full
> lighting simple
> lighting soft
> lighting full
> lighting flat
> graphics silhouettes false
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting shadows false
> lighting shadows true
> lighting full
> lighting soft
> lighting simple
> ui tool show H-Bonds
> hbonds reveal true
2069 hydrogen bonds found
> ui tool show H-Bonds
> hbonds intraModel false intraMol false intraRes false reveal true
0 hydrogen bonds found
> ui tool show H-Bonds
> hbonds intraMol false intraRes false reveal true
371 hydrogen bonds found
> ui tool show H-Bonds
> hbonds intraModel false reveal true
0 hydrogen bonds found
> ui tool show H-Bonds
> hbonds reveal true
2069 hydrogen bonds found
> ui tool show H-Bonds
> hbonds :A
Atom specifier selects no atoms
> hbonds :A
Atom specifier selects no atoms
> hbonds
2069 hydrogen bonds found
> hide #!2 models
> show #!2 models
> select /A:21-29,34-43,50-61,66-69,75-89,97-102,109-121
565 atoms, 572 bonds, 25 pseudobonds, 69 residues, 2 models selected
> select /A:111
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:111-144
251 atoms, 256 bonds, 19 pseudobonds, 34 residues, 2 models selected
> hide #* target a
> show (#!2 & sel) target ab
> select clear
> graphics silhouettes true
> lighting soft
> lighting simple
> lighting full
> lighting shadows false
> graphics silhouettes false
> lighting full
> lighting simple
> lighting full
> lighting simple
> lighting full
> lighting simple
> set bgColor white
> transparency #3#5.1 0
> transparency #3#5.1 50
> volume #!5 style mesh
> transparency #3#5.1 0
> lighting simple
> lighting soft
> lighting full
> lighting simple
> save /Users/labmos/Desktop/image14.png supersample 3
> volume #5 color black
> lighting full
> lighting simple
> lighting full
> lighting shadows false
> lighting shadows true
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting soft
> lighting flat
> graphics silhouettes false
> lighting simple
> lighting full
> ui tool show H-Bonds
> hbonds color #2723af radius 0.135 dashes 9 reveal true
2069 hydrogen bonds found
> select /A:111-144
251 atoms, 256 bonds, 19 pseudobonds, 34 residues, 2 models selected
> select /A:111
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:111-144
251 atoms, 256 bonds, 19 pseudobonds, 34 residues, 2 models selected
> hide #* target a
> show (#!2 & sel) target ab
> select clear
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> volume #5 color #000000b2
> ui tool show H-Bonds
> hbonds color #2723af radius 0.205 dashes 9 reveal true
2069 hydrogen bonds found
> hide #* target a
> show #2-3,5 target ab
> select /A:144-145
17 atoms, 17 bonds, 2 residues, 1 model selected
> select /A:111-145
258 atoms, 263 bonds, 21 pseudobonds, 35 residues, 2 models selected
> hide #* target a
> show (#!2 & sel) target ab
> select clear
> ui tool show H-Bonds
> hbonds color #2723af radius 0.205 dashes 14 reveal true
2069 hydrogen bonds found
Mismatch between Cocoa '\x0' and Carbon 'u' for virtual key 32 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'U' for virtual key 32 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'u' for virtual key 32 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'u' for virtual key 32 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00a8' for virtual key 32 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00a8' for virtual key 32 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00a8' for virtual key 32 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00a8' for virtual key 32 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> undo
Undo failed, probably because structures have been modified.
> undo
Undo failed, probably because structures have been modified.
> ui tool show H-Bonds
> hbonds color #2723af radius 0.205 dashes 7 reveal true
2069 hydrogen bonds found
> hbonds color #2723af radius 0.205 reveal true
2069 hydrogen bonds found
> hbonds color #2723af radius 0.205 dashes 5 reveal true
2069 hydrogen bonds found
> hbonds color #2723af radius 0.205 dashes 5 reveal true
2069 hydrogen bonds found
> hbonds color #2723af radius 0.305 dashes 7 reveal true
2069 hydrogen bonds found
> hbonds color #2723af radius 0.305 reveal true
2069 hydrogen bonds found
> hbonds color #2723af radius 0.305 reveal true
2069 hydrogen bonds found
> hbonds color #2723af radius 0.305 reveal true
2069 hydrogen bonds found
> hbonds color #2723af radius 0.305 reveal true
2069 hydrogen bonds found
> hbonds color #2723af radius 0.305 reveal true
2069 hydrogen bonds found
> hbonds color #2723af radius 0.305 reveal true
2069 hydrogen bonds found
> hbonds color #2723af radius 0.305 reveal true
2069 hydrogen bonds found
> hbonds color #2723af radius 0.305 reveal true
2069 hydrogen bonds found
> select /A:145
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:145
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:144-146
25 atoms, 25 bonds, 3 residues, 1 model selected
> select /A:111-146
266 atoms, 271 bonds, 21 pseudobonds, 36 residues, 2 models selected
> hide #* target a
> show (#!2 & sel) target ab
> hbonds color #2723af radius 0.305 reveal true
2069 hydrogen bonds found
> hide #* target a
> show sel target ab
> select clear
> wobble aspect 5
> ~wobble
Unknown command: ~wobble
> stop
> hide #3 models
Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'V' for virtual key 9 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u221a' for virtual key 9 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u25ca' for virtual key 9 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u221a' for virtual key 9 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u25ca' for virtual key 9 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> view name p1
> view name p2
> movie record
> fly p1 p2
> fly p2 p1
> movie encode
Movie saved to /Users/labmos/Desktop/movie.mp4
Mismatch between Cocoa '\x0' and Carbon '\x9' for virtual key 48 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x9' for virtual key 48 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x9' for virtual key 48 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x9' for virtual key 48 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x9' for virtual key 48 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x9' for virtual key 48 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x9' for virtual key 48 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x9' for virtual key 48 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x9' for virtual key 48 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x9' for virtual key 48 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x9' for virtual key 48 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x9' for virtual key 48 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x9' for virtual key 48 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x9' for virtual key 48 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x9' for virtual key 48 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x9' for virtual key 48 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> movie encode C:/Desktop/1beta_heapin_shake.mp4
No frames have been recorded
> save /Users/labmos/Downloads/chimerasinGH_1βhairpin_colored.cxs includeMaps
> true
> save /Users/labmos/Desktop/image15.png supersample 3
> ui tool show H-Bonds
> hbonds color #000000 radius 0.305 reveal true
2069 hydrogen bonds found
> hbonds color #000000 radius 0.305 dashes 10000000 reveal true
2069 hydrogen bonds found
===== Log before crash end =====
Log:
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 ATI-4.14.4
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: 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: MacBookPro14,3
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2.9 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 529.140.2.0.0
OS Loader Version: 577.140.2~30
SMC Version (system): 2.45f5
Software:
System Software Overview:
System Version: macOS 13.7.8 (22H730)
Kernel Version: Darwin 22.6.0
Time since boot: 12日 23時間 23分
Graphics/Displays:
Intel HD Graphics 630:
Chipset Model: Intel HD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x591b
Revision ID: 0x0004
Automatic Graphics Switching: Supported
gMux Version: 4.0.29 [3.2.8]
Metal Support: Metal 3
Radeon Pro 560:
Chipset Model: Radeon Pro 560
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x67ef
Revision ID: 0x00c0
ROM Revision: 113-C980AJ-927
VBIOS Version: 113-C9801AU-A02
EFI Driver Version: 01.A0.927
Automatic Graphics Switching: Supported
gMux Version: 4.0.29 [3.2.8]
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2880 x 1800 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
VZ249:
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: M8LMRS026927
Mirror: Off
Online: Yes
Rotation: Supported
Adapter Type: Thunderbolt/DisplayPort
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
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