![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 months ago
Closed 3 months ago
#18273 closed defect (duplicate)
Crash in NSAccessibilityEntryPointIsAccessibilityElement on Mac
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.5-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 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 0x0000000206a6df00 (most recent call first):
File "/Applications/ChimeraX-1.10.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.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, psutil._psutil_osx, psutil._psutil_posix, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, PIL._imaging, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath (total: 56)
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{
"uptime" : 950000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac16,7",
"coalitionID" : 17259,
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"build" : "24F74",
"releaseType" : "User"
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"captureTime" : "2025-07-25 09:34:40.8117 +0800",
"codeSigningMonitor" : 2,
"incident" : "7EDE3C7A-4C21-4980-B3E4-5D91F272E768",
"pid" : 7475,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-07-25 09:33:03.1753 +0800",
"procStartAbsTime" : 22813377975158,
"procExitAbsTime" : 22815720877446,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.0","CFBundleVersion":"1.10.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"D2FA6C1C-2B2C-5740-9937-6EC3F9465668","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "BC93AEFE-3A5C-97CB-D200-841D4D491F7A",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["regionIneligible","countryBillingIneligible","countryLocationIneligible"]},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"wakeTime" : 4959,
"sleepWakeUUID" : "3F3675C8-1945-47DA-80E1-87F28FDEA484",
"sip" : "enabled",
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"exception" : {"codes":"0x0000000000000001, 0x000000010000001e","rawCodes":[1,4294967326],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000000010000001e"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":7475},
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"path" : "\/Applications\/ChimeraX-1.10.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/pdb\/_pdbio.cpython-311-darwin.so",
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"path" : "\/Applications\/ChimeraX-1.10.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/etree.cpython-311-darwin.so",
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"path" : "\/Applications\/ChimeraX-1.10.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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"path" : "\/Applications\/ChimeraX-1.10.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"
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"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
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"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
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"name" : "AppKit",
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===== Log before crash start =====
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> /Users/hp/data/map_L/figure/figure_zjl_20250724/Upa_GC_density_20250725.cxs
Opened Upa_ECD_sharpened_map.ccp4 as #3, grid size 400,400,400, pixel 0.93,
shown at level 8.16, step 1, values float32
Log from Fri Jul 25 09:21:27 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/hp/data/map_L/figure/Chimera X Data from L/UP ECD 25.7.11/UP
> ECD 25.7.8.cxs"
Log from Thu Jul 10 16:42:08 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "C:/Users/hongn/Desktop/Chimera X Data/UP ECD 25.7.8.cxs"
Log from Tue Jul 8 10:28:52 2025 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 C:/Users/hongn/Desktop/CaSR/map/Upa_ECD-model-
> coot-2_real_space_refined_010.pdb
Chain information for Upa_ECD-model-coot-2_real_space_refined_010.pdb #1
---
Chain | Description
A | No description available
B | No description available
> select /B:545@CG
1 atom, 1 residue, 1 model selected
> select clear
> select /E:2@C6
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
28 atoms, 29 bonds, 2 residues, 1 model selected
> select up
8689 atoms, 8906 bonds, 1096 residues, 1 model selected
> select down
28 atoms, 29 bonds, 2 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
28 atoms, 29 bonds, 2 residues, 1 model selected
> select up
8661 atoms, 8876 bonds, 1094 residues, 1 model selected
> select down
28 atoms, 29 bonds, 2 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /B:901@O4
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
3417 atoms, 3508 bonds, 431 residues, 1 model selected
> select down
14 atoms, 14 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
28 atoms, 29 bonds, 2 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select /A:901@O6
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
3427 atoms, 3516 bonds, 437 residues, 1 model selected
> select down
14 atoms, 14 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
3403 atoms, 3493 bonds, 430 residues, 1 model selected
> select down
14 atoms, 14 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
3413 atoms, 3501 bonds, 436 residues, 1 model selected
> select down
14 atoms, 14 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select /B:902@O6
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
3389 atoms, 3478 bonds, 429 residues, 1 model selected
> select down
14 atoms, 14 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select /B:904@O4
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
3375 atoms, 3463 bonds, 428 residues, 1 model selected
> select down
14 atoms, 14 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> delete pbonds
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> select /A:909@CA
1 atom, 1 residue, 1 model selected
> color sel yellow
> select clear
> select /A:908@CA
1 atom, 1 residue, 1 model selected
> color sel yellow
> select clear
> select /A:907@CA
1 atom, 1 residue, 1 model selected
> color sel yellow
> select clear
> select /B:908@CA
1 atom, 1 residue, 1 model selected
> color sel yellow
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 1 model selected
> style sel ball
Changed 5 atom styles
> select /A:910@O2
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 1 model selected
> style sel ball
Changed 5 atom styles
> select /F:1@O05
1 atom, 1 residue, 1 model selected
> select up
34 atoms, 34 bonds, 1 residue, 1 model selected
> select up
8507 atoms, 8711 bonds, 1083 residues, 1 model selected
> select down
34 atoms, 34 bonds, 1 residue, 1 model selected
> style sel stick
Changed 34 atom styles
> show sel atoms
> hide sel atoms
> undo
[Repeated 1 time(s)]
> style sel ball
Changed 34 atom styles
> undo
> color sel byelement
> color sel byhetero
> color sel cornflower blue
> undo
> lighting simple
> lighting soft
> lighting full
> undo
[Repeated 4 time(s)]
> ui tool show "Color Actions"
> color sel byhetero
> color sel purple
> color sel bychain target acsp
> color sel bypolymer target acsp
> color sel byhetero target acsp
> color sel byelement target acsp
> color sel bynucleotide target acsp
> color sel cyan target acsp
> color sel cyan
> color sel byhetero
> color sel light sea green
> color sel light sea green target f
> color sel orange target f
> color sel orange target af
> color sel byhetero
> color sel medium blue
> color sel byhetero
> color sel cornflower blue
> color sel byhetero
> select clear
[Repeated 2 time(s)]
> select /A:598
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
182 atoms, 185 bonds, 26 residues, 1 model selected
> select up
3399 atoms, 3486 bonds, 435 residues, 1 model selected
> select up
3412 atoms, 3498 bonds, 437 residues, 1 model selected
> select up
4222 atoms, 4327 bonds, 541 residues, 1 model selected
> select up
4230 atoms, 4331 bonds, 545 residues, 1 model selected
> select up
8507 atoms, 8711 bonds, 1083 residues, 1 model selected
> select down
4230 atoms, 4331 bonds, 545 residues, 1 model selected
> select down
4222 atoms, 4327 bonds, 541 residues, 1 model selected
> select down
3412 atoms, 3498 bonds, 437 residues, 1 model selected
> select down
3399 atoms, 3486 bonds, 435 residues, 1 model selected
> select up
3412 atoms, 3498 bonds, 437 residues, 1 model selected
> select up
4222 atoms, 4327 bonds, 541 residues, 1 model selected
> select up
4230 atoms, 4331 bonds, 545 residues, 1 model selected
> select up
8507 atoms, 8711 bonds, 1083 residues, 1 model selected
> select down
4230 atoms, 4331 bonds, 545 residues, 1 model selected
> select /A:908@CA
1 atom, 1 residue, 1 model selected
> select /A:908@CA
1 atom, 1 residue, 1 model selected
> select /A:908@CA
1 atom, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select /A:591
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
182 atoms, 185 bonds, 26 residues, 1 model selected
> select up
3399 atoms, 3486 bonds, 435 residues, 1 model selected
> select up
3412 atoms, 3498 bonds, 437 residues, 1 model selected
> select up
4222 atoms, 4327 bonds, 541 residues, 1 model selected
> select up
4230 atoms, 4331 bonds, 545 residues, 1 model selected
> select up
8507 atoms, 8711 bonds, 1083 residues, 1 model selected
> select down
4230 atoms, 4331 bonds, 545 residues, 1 model selected
> color sel #6fffbcff
> color sel #70ffbcff
> color sel #72ffb4ff
> color sel #73ffb4ff
> color sel #75ffb5ff
> color sel #78ffb7ff
> color sel #7cffb9ff
> color sel #86ffbcff
> color sel #8cffc0ff
> color sel #94ffc4ff
> color sel #98ffc6ff
> color sel #9bffc8ff
> color sel #9cffc9ff
> color sel #a0ffcbff
> color sel #a0ffc3ff
> color sel #9effbeff
> color sel #9cffa8ff
> color sel #9eff9cff
> color sel #a3ff99ff
> color sel #b1ff99ff
> color sel #c1ff98ff
> color sel #caff98ff
> color sel #cdff98ff
> color sel #d5ff97ff
> color sel #dfff94ff
> color sel #e2ff93ff
> color sel #dcff7dff
> color sel #daff73ff
> color sel #d9ff70ff
> color sel #d0ff69ff
> color sel #c1ff5dff
> color sel #b7ff58ff
> color sel #b1ff57ff
> color sel #acff53ff
> color sel #abff52ff
> color sel #9eff4fff
> color sel #9bff4fff
> color sel #95ff4fff
> color sel #8dff4fff
> color sel #8cff4eff
> color sel #8aff4bff
> color sel #84ff4bff
> color sel #81ff4bff
> color sel #75ff4bff
> color sel #72ff4bff
> color sel #6cff4bff
> color sel #63ff4bff
> color sel #5dff4bff
> color sel #57ff4bff
> color sel #4eff4bff
> color sel #4bff57ff
> color sel #4bff66ff
> color sel #4bff6fff
> color sel #4bff7eff
> color sel #4bff84ff
> color sel #4bff8dff
> color sel #4bff93ff
> color sel #4bff96ff
> color sel #4bff9cff
> color sel #4bffabff
> color sel #4bffaeff
> color sel #4cffaeff
> color sel #4fffb0ff
> color sel #50ffb0ff
> color sel #50ffa2ff
> color sel #50ff87ff
> color sel #4eff54ff
> color sel #5eff4cff
> color sel #64ff4cff
> color sel #6dff4cff
> color sel #76ff4cff
> color sel #82ff4cff
> color sel #84ff4fff
> color sel #97ff52ff
> color sel #a7ff54ff
> color sel #acff54ff
> color sel #b8ff5aff
> color sel #bbff61ff
> color sel #c2ff61ff
> color sel #c3ff62ff
> color sel #bbff62ff
> color sel #b6ff62ff
> color sel #aeff62ff
> color sel #a9ff62ff
> color sel #99ff62ff
> color sel #9aff63ff
> color sel #9cff67ff
> color sel #9fff6bff
> color sel #9fff6cff
> color sel #a1ff6eff
> color sel #a1ff6fff
> color sel #a2ff70ff
> color sel #a5ff75ff
> color sel #a7ff78ff
> color sel #a8ff79ff
> color sel #a9ff7bff
> color sel #abff7dff
> color sel #abff7eff
> color sel #acff80ff
> color sel #aeff83ff
> color sel #b0ff85ff
> color sel #b0ff86ff
> color sel #b1ff87ff
> color sel #b4ff8bff
> color sel #afff8cff
> color sel #b1ff8fff
> color sel #a9ff8fff
> color sel #adff8fff
> color sel #b1ff8fff
> color sel #b6ff8fff
> color sel #baff8fff
> color sel #bcff8fff
> color sel #c1ff8fff
> color sel #c0ff8fff
> color sel #bcff8fff
> color sel #b6ff8fff
> color sel #b2ff8fff
> color sel #b6ff8fff
> color sel #c4ff8cff
> color sel #d1ff8bff
> color sel #d3ff8bff
> color sel #cdff8bff
> color sel #c7ff8bff
> color sel #bfff8bff
> color sel #bdff8bff
> color sel #b4ff8bff
> color sel #aeff8bff
> color sel #aaff8bff
> select clear
> select /B:570
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
129 atoms, 131 bonds, 18 residues, 1 model selected
> select up
3361 atoms, 3448 bonds, 427 residues, 1 model selected
> select up
3382 atoms, 3468 bonds, 430 residues, 1 model selected
> select up
4203 atoms, 4308 bonds, 534 residues, 1 model selected
> select up
4209 atoms, 4312 bonds, 536 residues, 1 model selected
> color sel #3cffefff
> select clear
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> lighting simple
> lighting soft
> lighting full
> lighting shadows false
> lighting flat
[Repeated 1 time(s)]
> undo
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> lighting flat
> lighting shadows true intensity 0.5
> lighting flat
> undo
[Repeated 6 time(s)]
> lighting simple
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> select clear
> select /B:570
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
129 atoms, 131 bonds, 18 residues, 1 model selected
> select up
3361 atoms, 3448 bonds, 427 residues, 1 model selected
> select up
3382 atoms, 3468 bonds, 430 residues, 1 model selected
> select up
4203 atoms, 4308 bonds, 534 residues, 1 model selected
> color #1 #3cffefff
> color #1 #aaff8bff
> select clear
> select /B:585
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
129 atoms, 131 bonds, 18 residues, 1 model selected
> select up
3361 atoms, 3448 bonds, 427 residues, 1 model selected
> select up
3382 atoms, 3468 bonds, 430 residues, 1 model selected
> select up
4203 atoms, 4308 bonds, 534 residues, 1 model selected
> select up
4209 atoms, 4312 bonds, 536 residues, 1 model selected
> select up
8507 atoms, 8711 bonds, 1083 residues, 1 model selected
> select down
4209 atoms, 4312 bonds, 536 residues, 1 model selected
> color sel byelement
> color sel #d7e9f8ff
> color sel #f9f9f9ff
> color sel #f0f0f0ff
> color sel #aaff8bff
> color sel #828790ff
> color sel #f0f0f0ff
> color sel #3cffefff
> select clear
> select /A:909@CA
1 atom, 1 residue, 1 model selected
> color sel yellow
> select /A:908@CA
1 atom, 1 residue, 1 model selected
> color sel yellow
Drag select of 2 residues
> select clear
> select /A:907@CA
1 atom, 1 residue, 1 model selected
> color sel yellow
> select clear
> select /B:908@CA
1 atom, 1 residue, 1 model selected
> color sel yellow
> select clear
> select /A:910@O1
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 1 model selected
> color sel byelement
> select clear
> select /B:909@O2
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
4209 atoms, 4312 bonds, 536 residues, 1 model selected
> select down
5 atoms, 4 bonds, 1 residue, 1 model selected
> color sel byelement
> select clear
> select /G:1@O05
1 atom, 1 residue, 1 model selected
> select up
34 atoms, 34 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel forest green
> color sel purple
> color sel byhetero
> select clear
> select /F:1@S02
1 atom, 1 residue, 1 model selected
Drag select of 1 atoms, 2 residues
> select clear
> select /F:1@O05
1 atom, 1 residue, 1 model selected
> select up
34 atoms, 34 bonds, 1 residue, 1 model selected
> select up
8507 atoms, 8711 bonds, 1083 residues, 1 model selected
> select down
34 atoms, 34 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel purple
> color sel byhetero
> select clear
> set bgColor white
> set bgColor #ffffff00
> select /A
4230 atoms, 4331 bonds, 545 residues, 1 model selected
> color sel #885599ff
> color sel #859ed7ff
> select clear
> transparency 30
> select clear
> select /A
4230 atoms, 4331 bonds, 545 residues, 1 model selected
> transparency sel 50
> select clear
> select /A
4230 atoms, 4331 bonds, 545 residues, 1 model selected
> lighting simple
> lighting soft
> lighting simple
> select clear
> select /B
4209 atoms, 4312 bonds, 536 residues, 1 model selected
> color sel #7722ddff
> color sel #72d3d4ff
> color sel #000099ff
> color sel #009e75ff
> color sel #009e74ff
> select clear
> select /A:570
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
182 atoms, 185 bonds, 26 residues, 1 model selected
> select up
3399 atoms, 3486 bonds, 435 residues, 1 model selected
> select up
3412 atoms, 3498 bonds, 437 residues, 1 model selected
> select up
4222 atoms, 4327 bonds, 541 residues, 1 model selected
> select clear
> select /A
4230 atoms, 4331 bonds, 545 residues, 1 model selected
> color sel #cc00eeff
> color sel #c0e7daff
> select clear
> color #998899ff
> color #989cc8ff
> select /A
4230 atoms, 4331 bonds, 545 residues, 1 model selected
> color sel #ee5599ff
> color sel #e59693ff
> select clear
> select /A:908@CA
1 atom, 1 residue, 1 model selected
> transparency sel 50
> select /A
4230 atoms, 4331 bonds, 545 residues, 1 model selected
> transparency sel 100
> select clear
> select /A
4230 atoms, 4331 bonds, 545 residues, 1 model selected
> cartoon style sel xsection oval modeHelix default
> cartoon style sel xsection rectangle modeHelix default
> cartoon style (sel & coil) xsection oval
> cartoon style sel xsection barbell modeHelix default
> cartoon style sel modeHelix tube sides 20
> undo
> select clear
> select /A
4230 atoms, 4331 bonds, 545 residues, 1 model selected
> cartoon style sel modeHelix tube sides 20
> select clear
> lighting simple
> lighting soft
> lighting full
> lighting shadows false
> lighting simple
> lighting soft
[Repeated 2 time(s)]
> lighting shadows true intensity 0.5
> lighting soft
> select /A:909@CA
1 atom, 1 residue, 1 model selected
> color sel yellow
> select clear
> select /A:909@CA
1 atom, 1 residue, 1 model selected
> color sel yellow
> select clear
> select /A:233
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select /A:908@CA
1 atom, 1 residue, 1 model selected
> color sel yellow
> select clear
> select /A:907@CA
1 atom, 1 residue, 1 model selected
> color sel yellow
> select clear
> select /B:908@CA
1 atom, 1 residue, 1 model selected
> color sel yellow
> select clear
> select /F:1@S02
1 atom, 1 residue, 1 model selected
> select clear
> select /F:1@O05
1 atom, 1 residue, 1 model selected
> select up
34 atoms, 34 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel orange red
> color sel byhetero
> color sel forest green
> color sel byhetero
> select clear
> select /G:1@O05
1 atom, 1 residue, 1 model selected
> select up
34 atoms, 34 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel forest green
> color sel byhetero
> select clear
> select /B:909@O4
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 1 model selected
> style sel ball
Changed 5 atom styles
> style sel ball
Changed 5 atom styles
> color sel byelement
> select clear
> select /A:910@O2
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 1 model selected
> color sel byelement
> select clear
[Repeated 1 time(s)]
> select /A:592
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A
4230 atoms, 4331 bonds, 545 residues, 1 model selected
> lighting flat
> select clear
> undo
[Repeated 1 time(s)]
> select clear
> lighting simple
> lighting soft
> lighting full
> lighting shadows false
> lighting shadows true
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
No Surface models open
> graphics silhouettes false
> lighting shadows false
> lighting full
> lighting soft
> lighting full
> lighting shadows false
> undo
[Repeated 6 time(s)]
> lighting simple
> lighting soft
> lighting full
> lighting shadows false
> graphics silhouettes true
> lighting flat
> graphics silhouettes false
> lighting simple
> lighting soft
> lighting full
> lighting shadows false
> graphics silhouettes true
> lighting shadows true
> lighting soft
> lighting full
> lighting shadows false
> save "C:/Users/hongn/Desktop/Up ECD 25.7.8.cxs"
> style ringFill thick
Changed 1083 residue ring styles
> style ringFill thin
Changed 1083 residue ring styles
> style ringFill off
Changed 1083 residue ring styles
> select clear
> select /A:591
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
182 atoms, 185 bonds, 26 residues, 1 model selected
> select down
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> select /A:585
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> distance #1/A:585@CA #1/B:585@CA
Distance between /A CYS 585 CA and /B CYS 585 CA: 24.395Å
> color #2.1 black models
> color #2.1 white models
> color #2.1 black models
> select clear
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 target m
> hide #2.1 models
> log metadata #1
No models had metadata
> log chains #1
Chain information for Upa_ECD-model-coot-2_real_space_refined_010.pdb #1
---
Chain | Description
A | No description available
B | No description available
> show #2.1 models
> hide #2.1 models
> color #2 black models
> color #2 #9f9f9fff models
> color #2 #d9d9d9ff models
> color #2 #dededeff models
> color #2 #969696ff models
> color #2 #909090ff models
> select /A:591
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:591
6 atoms, 5 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select /A:598
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
176 atoms, 179 bonds, 25 residues, 1 model selected
> select down
6 atoms, 5 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select /A:597
6 atoms, 5 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select /A:596
7 atoms, 6 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select /A:595
10 atoms, 10 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select /A:594
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> save "C:/Users/hongn/Desktop/UP ECD 25.7.8.jpg" width 1981 height 1051
> supersample 3
> save "C:/Users/hongn/Desktop/UP ECD 25.7.8.cxs"
——— End of log from Tue Jul 8 10:28:52 2025 ———
opened ChimeraX session
> select /A:592
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> hide #!2 models
> select /G:1@O05
1 atom, 1 residue, 1 model selected
> select up
34 atoms, 34 bonds, 1 residue, 1 model selected
> style sel ball
Changed 34 atom styles
> ui tool show "Color Actions"
> color sel light sea green
> color sel byhetero
> select clear
> select /F:1@CL01
1 atom, 1 residue, 1 model selected
> select up
34 atoms, 34 bonds, 1 residue, 1 model selected
> select up
8464 atoms, 8666 bonds, 1077 residues, 1 model selected
> select down
34 atoms, 34 bonds, 1 residue, 1 model selected
> style sel ball
Changed 34 atom styles
> ui tool show "Color Actions"
> color sel light sea green
> color sel byhetero
> select clear
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> save C:\Users\hongn/Desktop\image3.png supersample 3
> save "C:/Users/hongn/Desktop/Chimera X Data/UP ECD 25.7.8.cxs"
——— End of log from Thu Jul 10 16:42:08 2025 ———
> view name session-start
opened ChimeraX session
> open
> /Users/hp/data/map_L/phenix_upa/Autosharpen_19/Upa_ECD_sharpened_map.ccp4
Opened Upa_ECD_sharpened_map.ccp4 as #3, grid size 400,400,400, pixel 0.93,
shown at level 2.9, step 2, values float32
> volume #3 step 1
> volume #3 level 8.161
> open /Users/hp/data/map_L/model_coot/Upa_ECD-model-
> coot-2_real_space_refined_010.pdb
Chain information for Upa_ECD-model-coot-2_real_space_refined_010.pdb #4
---
Chain | Description
A | No description available
B | No description available
> hide #!3 models
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> hide #!4 models
> show #!4 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
34 atoms, 34 bonds, 1 residue, 1 model selected
> select ~sel & ##selected
8655 atoms, 8872 bonds, 5 pseudobonds, 1095 residues, 2 models selected
> delete atoms (#!4 & sel)
> delete bonds (#!4 & sel)
> volume zone #3 nearAtoms sel & #4 range 3.0
no atoms specified for zone
> hide #!4 models
> show #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> select add #4
34 atoms, 34 bonds, 1 residue, 1 model selected
> volume zone #3 nearAtoms sel & #4 range 3.0
> show #!3 models
> volume zone #3 nearAtoms sel & #4 range 2.5
> transparency #3 50
> show #!1 models
> hide #!4 models
> volume zone #3 nearAtoms sel & #4 range 2.2
> volume zone #3 nearAtoms sel & #4 range 2.0
> save /Users/hp/Desktop/image3.png supersample 3
> save
> /Users/hp/data/map_L/figure/figure_zjl_20250724/Upa_GC_density_20250725.cxs
——— End of log from Fri Jul 25 09:21:27 2025 ———
> view name session-start
opened ChimeraX session
> open "/Users/hp/data/map_L/figure/Chimera X Data from L/Neo CRD
> 25.7.11/Neo_ECD_model-coot-6(1).pdb"
Chain information for Neo_ECD_model-coot-6(1).pdb #5
---
Chain | Description
A | No description available
B | No description available
> hide #!1 models
> hide #!3 models
> show #!3 models
> hide #!5 models
> show #!5 models
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac16,7
Model Number: Z1FT0008MCH/A
Chip: Apple M4 Pro
Total Number of Cores: 14 (10 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 11881.121.1
OS Loader Version: 11881.121.1
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 14天16小时23分钟
Graphics/Displays:
Apple M4 Pro:
Chipset Model: Apple M4 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 20
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.5.0
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: 14.1.18
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
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: 1.1.2
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: 7.9.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.4
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: 4.4.4
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
pyelftools: 0.32
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: 4.14.0
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
Change History (2)
comment:1 by , 3 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in NSAccessibilityEntryPointIsAccessibilityElement on Mac |
comment:2 by , 3 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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