![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 weeks ago
Closed 6 weeks ago
#18890 closed defect (can't reproduce)
Crash in event loop
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.6.1-arm64-arm-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: Segmentation fault
Current thread 0x000000020bb860c0 (most recent call first):
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb_lib._load_libs, 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, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imaging, PIL._imagingmath, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PIL._webp (total: 53)
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"procRole" : "Foreground",
"version" : 2,
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"codeSigningMonitor" : 1,
"incident" : "62391ECA-3E4D-4079-A5CE-74D6FC90884A",
"pid" : 55843,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-09-27 18:09:39.8242 +0800",
"procStartAbsTime" : 9259864624802,
"procExitAbsTime" : 9326180818585,
"procName" : "ChimeraX",
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "A08A8810-33E4-B3B2-BD1A-6A4DFA917FA9",
"appleIntelligenceStatus" : {"reasons":["selectedLanguageDoesNotMatchSelectedSiriLanguage","countryLocationIneligible","countryBillingIneligible","regionIneligible"],"state":"unavailable"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
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"sleepWakeUUID" : "C7FF7753-74A4-4C7C-BF1C-046E22A86F1B",
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===== 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 /Users/muzi/Desktop/center_49ns.pdb
Summary of feedback from opening /Users/muzi/Desktop/center_49ns.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK THIS IS A SIMULATION BOX
center_49ns.pdb title:
Title in water t= 49000.00000 step= 2450 [more info...]
Chain information for center_49ns.pdb #1
---
Chain | Description
? | No description available
Non-standard residues in center_49ns.pdb #1
---
HSP — (HSP)
LIG — (LIG)
Computing secondary structure
> ui mousemode right select
> select clear
> select protein
8188 atoms, 8270 bonds, 526 residues, 1 model selected
> rainbow sel
> select ~sel & ##selected
9600 atoms, 9400 bonds, 200 residues, 1 model selected
> hide sel atoms
> select main
8188 atoms, 8270 bonds, 526 residues, 1 model selected
> hide sel atoms
> select clear
> select ligand
9600 atoms, 9400 bonds, 200 residues, 1 model selected
> show sel atoms
> color sel byelement
> select clear
Drag select of 1 residues
Drag select of 1152 atoms, 18 residues, 1131 bonds
> color sel red
> color sel byelement
> color sel orange red
> color sel byhetero
> select ligand
9600 atoms, 9400 bonds, 200 residues, 1 model selected
> color sel red
> color sel byhetero
> color sel byelement
> select H
9974 atoms, 726 residues, 1 model selected
> hide sel atoms
> select clear
> select add /?:120
28 atoms, 28 bonds, 2 residues, 1 model selected
> select add /?:121
66 atoms, 64 bonds, 4 residues, 1 model selected
> select add /?:122
86 atoms, 82 bonds, 6 residues, 1 model selected
> select up
914 atoms, 920 bonds, 58 residues, 1 model selected
> select add /?:90
948 atoms, 952 bonds, 60 residues, 1 model selected
> select up
1324 atoms, 1330 bonds, 83 residues, 1 model selected
> select clear
> select ligand
9600 atoms, 9400 bonds, 200 residues, 1 model selected
> hide sel atoms
Drag select of 261 residues
Drag select of 20 residues
Drag select of 19 residues
> select up
4123 atoms, 4163 bonds, 265 residues, 1 model selected
> select down
4048 atoms, 260 residues, 1 model selected
> select up
4123 atoms, 4163 bonds, 265 residues, 1 model selected
> select down
4048 atoms, 260 residues, 1 model selected
> select up
4123 atoms, 4163 bonds, 265 residues, 1 model selected
> select down
4048 atoms, 260 residues, 1 model selected
> select up
4123 atoms, 4163 bonds, 265 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #ededecff
> select clear
> undo
> select up
8188 atoms, 8270 bonds, 526 residues, 1 model selected
> select down
4123 atoms, 4163 bonds, 265 residues, 1 model selected
> select down
4123 atoms, 4163 bonds, 265 residues, 1 model selected
> select down
4123 atoms, 4163 bonds, 265 residues, 1 model selected
> select down
4123 atoms, 4163 bonds, 265 residues, 1 model selected
> select down
4123 atoms, 4163 bonds, 265 residues, 1 model selected
> select clear
Drag select of 263 residues
> ui tool show "Color Actions"
> color sel #7aa4a4ff
> color sel #aeececff
> color sel #aeededff
> color sel #afeeeeff
> color sel #b0efefff
> color sel #b0f0f0ff
> color sel #b1f0f0ff
> color sel #b1f1f1ff
> color sel #b2f2f2ff
> select clear
Drag select of 15 residues
Drag select of 263 residues
> ui tool show "Color Actions"
> color sel #b6f48aff
> select clear
> select ligand
9600 atoms, 9400 bonds, 200 residues, 1 model selected
> show sel atoms
> select clear
Drag select of 7 atoms, 6 bonds
> select H
9974 atoms, 726 residues, 1 model selected
> hide sel atoms
> select clear
> set bgColor white
> lighting soft
> lighting flat
> lighting soft
> lighting full
> lighting simple
> lighting soft
> graphics silhouettes false
> lighting full
> graphics silhouettes true
> graphics silhouettes false
> lighting soft
> graphics silhouettes true
> lighting flat
> lighting full
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> camera ortho
> select clear
> camera ortho
> view
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
Drag select of 120 atoms, 120 bonds
> select up
140 atoms, 121 bonds, 17 residues, 1 model selected
> select clear
> select /?:58
34 atoms, 32 bonds, 2 residues, 1 model selected
> select up
618 atoms, 620 bonds, 40 residues, 1 model selected
> select up
8188 atoms, 8270 bonds, 526 residues, 1 model selected
> graphics silhouettes true
> graphics silhouettes false
> lighting full
> lighting flat
> lighting full
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> select clear
> select /?:152
32 atoms, 30 bonds, 2 residues, 1 model selected
> select up
273 atoms, 275 bonds, 17 residues, 1 model selected
> select up
8188 atoms, 8270 bonds, 526 residues, 1 model selected
> graphics silhouettes true
> graphics silhouettes false
> lighting soft
> lighting full
> lighting soft
> lighting full
> select clear
> lighting full
> graphics silhouettes true
> lighting full
> lighting soft
> lighting full
> graphics silhouettes false
> lighting full
> camera
Camera parameters:
type: orthographic
position: -100.06 104.54 97.943
view direction: 0.97574 -0.17415 -0.13269
field width: 157.14
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting simple
> lighting full
> graphics silhouettes true
> lighting soft
> select clear
Drag select of 1 atoms, 2 bonds
> select clear
> select /?:270@C9
1 atom, 1 residue, 1 model selected
> select clear
Drag select of 165 atoms, 155 bonds
> select up
182 atoms, 156 bonds, 22 residues, 1 model selected
> select up
1056 atoms, 1034 bonds, 22 residues, 1 model selected
> select up
17788 atoms, 17670 bonds, 726 residues, 1 model selected
> select down
1056 atoms, 1034 bonds, 22 residues, 1 model selected
> select up
17788 atoms, 17670 bonds, 726 residues, 1 model selected
> select down
1056 atoms, 1034 bonds, 22 residues, 1 model selected
> select clear
> select C
5596 atoms, 4484 bonds, 726 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark gray
> color sel light gray
> undo
> select clear
> select ligand
9600 atoms, 9400 bonds, 200 residues, 1 model selected
> select C
5596 atoms, 4484 bonds, 726 residues, 1 model selected
> select clear
> select ligand
9600 atoms, 9400 bonds, 200 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light gray
> color sel byhetero
> select clear
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> select ligand
9600 atoms, 9400 bonds, 200 residues, 1 model selected
> ui tool show "Color Actions"
> color sel gainsboro
> color sel byhetero
> select clear
> lighting soft
> lighting full
> lighting soft
Drag select of 18 atoms, 19 bonds
> select clear
> select ligand
9600 atoms, 9400 bonds, 200 residues, 1 model selected
> select clear
> graphics silhouettes false
> lighting soft
> lighting full
> transparency 50 target a
> transparency 30 target a
> lighting full
> lighting soft
> lighting full
> transparency 10 target a
> select /?:136
34 atoms, 32 bonds, 2 residues, 1 model selected
> select up
914 atoms, 920 bonds, 58 residues, 1 model selected
> select up
8188 atoms, 8270 bonds, 526 residues, 1 model selected
> select clear
> select ligand
9600 atoms, 9400 bonds, 200 residues, 1 model selected
> hide sel atoms
Drag select of 262 residues
Drag select of 3 residues
> select up
4123 atoms, 4163 bonds, 265 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light sky blue
> color sel cornflower blue
Drag select of 5 residues
Drag select of 266 residues
> select down
4136 atoms, 266 residues, 1 model selected
Drag select of 5 residues
Drag select of 218 residues
> select clear
Drag select of 50 residues
> select up
1205 atoms, 1213 bonds, 77 residues, 1 model selected
> select up
4094 atoms, 4135 bonds, 263 residues, 1 model selected
> ui tool show "Color Actions"
> color sel forest green
> color sel medium sea green
> color sel dark sea green
> color sel yellow green
> color sel lime
> color sel green
> color sel chartreuse
> color sel lawn green
> color sel spring green
> color sel lime green
> color sel forest green
> color sel sea green
> color sel medium sea green
> select clear
> select ligand
9600 atoms, 9400 bonds, 200 residues, 1 model selected
> show sel atoms
> select clear
> select H
9974 atoms, 726 residues, 1 model selected
> hide sel atoms
> select clear
> transparency 30 target a
> transparency 50 target a
> transparency 5 target a
Drag select of 1 atoms, 3 residues
> select clear
> lighting soft
> lighting full
> lighting soft
> lighting full
> ui tool show "Color Actions"
> color #b6f48aff
> color #aee984ff
> color #abe682ff
> color #abe582ff
> color #aae481ff
> color #a9e380ff
> color #a9e280ff
> color #a7e07fff
> color #a5dd7dff
> color #a4dc7dff
> color #a3da7cff
> color #a2d97bff
> color #a1d87bff
> color #a0d679ff
> color #9fd579ff
> color #9fd578ff
> color #9ed478ff
> color #9ed378ff
> color #9dd377ff
> color #9cd277ff
> color #9bcf76ff
> color #9acf75ff
> color #9ace75ff
> color #98cb73ff
> color #97cb73ff
> color #97ca73ff
> color #97ca72ff
> color #95c871ff
> color #95c771ff
> undo
> select ligand
9600 atoms, 9400 bonds, 200 residues, 1 model selected
> hide sel atoms
Drag select of 90 residues
> select up
1879 atoms, 1894 bonds, 120 residues, 1 model selected
> select up
4094 atoms, 4135 bonds, 263 residues, 1 model selected
> select clear
> show atoms
> hide atoms
> lighting full
> lighting soft
> lighting full
> lighting soft
> select ligand
9600 atoms, 9400 bonds, 200 residues, 1 model selected
> show sel atoms
> select clear
> lighting full
> lighting soft
Drag select of 37 atoms, 37 bonds
> select clear
> lighting flat
> lighting full
> graphics silhouettes false
> lighting soft
> lighting full
> graphics silhouettes true
> graphics silhouettes false
> select ligand
9600 atoms, 9400 bonds, 200 residues, 1 model selected
> hide sel atoms
Drag select of 90 residues
> select up
1916 atoms, 1931 bonds, 122 residues, 1 model selected
> select up
4094 atoms, 4135 bonds, 263 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #b2f2f2ff
> color sel #aff2f2ff
> color sel #aff1f1ff
> color sel #aef1f1ff
> color sel #aef0f0ff
> color sel #aeefefff
> color sel #adeeeeff
> color sel #abececff
> color sel #abebebff
> color sel #aaeaeaff
> color sel #a9e9e9ff
> color sel #a8e8e8ff
> color sel #a8e7e7ff
> color sel #a7e7e7ff
> color sel #a7e6e6ff
> color sel #a6e5e5ff
> color sel #a5e4e4ff
> color sel #a5e3e3ff
> color sel #a4e2e2ff
> color sel #a2e0e0ff
> color sel #9fdbdbff
> color sel #9edadaff
> color sel #9ed9d9ff
> color sel #9dd8d8ff
> color sel #9cd8d8ff
> color sel #9cd7d7ff
> color sel #9bd6d6ff
> color sel #9cd7d7ff
> color sel #9dd8d8ff
> color sel #9dd9d9ff
> color sel #9fdbdbff
> color sel #9fdcdcff
> color sel #a0dcdcff
> color sel #a0ddddff
> color sel #a1ddddff
> color sel #a1dedeff
> color sel #a2dfdfff
> color sel #a1dedeff
> color sel #a1ddddff
> color sel #a0ddddff
> color sel #9fdbdbff
> color sel #9dd9d9ff
> color sel #9dd8d8ff
> color sel #9bd5d5ff
> color sel #9ad5d5ff
> color sel #9ad4d4ff
> color sel #98d2d2ff
> color sel #98d1d1ff
> color sel #97d1d1ff
> color sel #97d0d0ff
> color sel #96cfcfff
> color sel #94cdcdff
> color sel #93cbcbff
> color sel #93cacaff
> color sel #92cacaff
> color sel #91c8c8ff
> color sel #90c6c6ff
> color sel #8fc6c6ff
> color sel #8fc5c5ff
> color sel #8ec3c3ff
> color sel #7cababff
> color sel #5c7e7eff
> color sel #5b7e7eff
> color sel #5a7c7cff
> color sel #638888ff
> color sel #6f9999ff
> color sel #77a4a4ff
> color sel #79a7a7ff
> color sel #7ba9a9ff
> color sel #7cababff
> color sel #7dadadff
> color sel #7faeaeff
> color sel #7fafafff
> color sel #7fb0b0ff
> color sel #84b6b6ff
> color sel #87babaff
> color sel #8abebeff
> color sel #8abfbfff
> color sel #8abebeff
> color sel #88bbbbff
> color sel #87babaff
> color sel #86b8b8ff
> color sel #85b8b8ff
> color sel #85b7b7ff
> color sel #83b5b5ff
> color sel #82b4b4ff
> color sel #82b3b3ff
> color sel #83b4b4ff
> color sel #8abebeff
> color sel #97d0d0ff
> color sel #9ad4d4ff
> color sel #9bd6d6ff
> color sel #9cd7d7ff
> color sel #9edadaff
> color sel #a1ddddff
> color sel #a7e6e6ff
> color sel #aaebebff
> color sel #b1f4f4ff
> color sel #b3f7f7ff
> color sel #b4f8f8ff
> color sel #b5f9f9ff
> color sel #b4f9f9ff
> color sel #b2f5f5ff
> color sel #adefefff
> color sel #a5e4e4ff
> color sel #a4e2e2ff
> color sel #a1dedeff
> color sel #9fdcdcff
> color sel #9edadaff
> color sel #9ed9d9ff
> color sel #9bd6d6ff
> color sel #9ad4d4ff
> color sel #99d3d3ff
> color sel #97d1d1ff
> color sel #95ceceff
> color sel #91c8c8ff
> color sel #91c7c7ff
> color sel #8fc6c6ff
> color sel #8ec4c4ff
> color sel #8dc2c2ff
> color sel #8bc0c0ff
> color sel #8bbfbfff
> color sel #89bdbdff
> color sel #88bbbbff
> color sel #87babaff
> color sel #85b8b8ff
> color sel #83b5b5ff
> color sel #83b4b4ff
> color sel #81b2b2ff
> color sel #80b0b0ff
> color sel #7fb0b0ff
> color sel #80b0b0ff
> color sel #80b1b1ff
> color sel #81b2b2ff
> color sel #82b3b3ff
> color sel #82b4b4ff
> color sel #83b4b4ff
> color sel #84b5b5ff
> color sel #84b6b6ff
> color sel #85b8b8ff
> color sel #86b8b8ff
> color sel #87babaff
> color sel #88bbbbff
> color sel #88bcbcff
> color sel #88bbbbff
> color sel #87babaff
> color sel #86b9b9ff
> color sel #86b8b8ff
> color sel #85b8b8ff
> color sel #84b7b7ff
> color sel #84b6b6ff
> color sel #84b5b5ff
> color sel #83b5b5ff
> color sel #82b4b4ff
> color sel #82b3b3ff
Drag select of 92 residues
> select up
2162 atoms, 2182 bonds, 138 residues, 1 model selected
> select up
4094 atoms, 4135 bonds, 263 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #b6f48aff
> color sel #b3f088ff
> color sel #a9e280ff
> color sel #a8e180ff
> color sel #a8e17fff
> color sel #a5dd7dff
> color sel #a4dc7dff
> color sel #a3db7cff
> color sel #a1d87aff
> color sel #a0d67aff
> color sel #9ed478ff
> color sel #9dd377ff
> color sel #9cd277ff
> color sel #9cd176ff
> color sel #9acf75ff
> color sel #9ace75ff
> color sel #98cc74ff
> color sel #97ca72ff
> color sel #95c871ff
> color sel #94c771ff
> color sel #94c670ff
> color sel #93c670ff
> color sel #92c46fff
> color sel #92c36fff
> color sel #91c36eff
> color sel #91c26eff
> color sel #90c26eff
> color sel #90c16eff
> color sel #90c16dff
> color sel #8fc06dff
> color sel #8fbf6cff
> color sel #8ebe6cff
> color sel #8cbc6bff
> color sel #8cbb6aff
> color sel #8bbb6aff
> color sel #8bba6aff
> color sel #8bba69ff
> color sel #8ab969ff
> color sel #89b868ff
> color sel #89b768ff
> color sel #88b667ff
> color sel #87b567ff
> color sel #87b566ff
> color sel #86b466ff
> color sel #85b265ff
> color sel #84b164ff
> color sel #83b064ff
> color sel #82af63ff
> color sel #82ae63ff
> color sel #82ae62ff
> color sel #81ad62ff
> color sel #81ac62ff
> color sel #80ac62ff
> color sel #80ac61ff
> color sel #80ab61ff
> color sel #7fab61ff
> color sel #7aa45dff
> color sel #79a25cff
> color sel #78a15bff
> color sel #769f5aff
> color sel #769e5aff
> color sel #759d59ff
> color sel #749b58ff
> color sel #739a57ff
> color sel #749b58ff
> color sel #77a05bff
> color sel #7aa35cff
> color sel #7ea960ff
> color sel #81ad62ff
> color sel #82af63ff
> color sel #83b064ff
> color sel #84b265ff
> color sel #87b466ff
> color sel #87b567ff
> color sel #88b667ff
> color sel #89b768ff
> color sel #8ab969ff
> color sel #8bba69ff
> color sel #8bba6aff
> color sel #8cbc6aff
> color sel #8dbc6bff
> color sel #8dbd6bff
> color sel #8dbe6bff
> color sel #8fc06dff
> color sel #90c16dff
> color sel #90c16eff
> color sel #90c26eff
> color sel #91c26eff
> color sel #92c46fff
> color sel #93c570ff
> color sel #92c36fff
> color sel #91c26eff
> color sel #90c26eff
> color sel #90c16eff
> color sel #8ebe6cff
> color sel #8cbc6bff
> color sel #8cbc6aff
> color sel #8cbb6aff
> color sel #8bba6aff
> color sel #8bba69ff
> color sel #8ab969ff
> color sel #89b868ff
> select clear
> select ligand
9600 atoms, 9400 bonds, 200 residues, 1 model selected
> show sel atoms
> select H
9974 atoms, 726 residues, 1 model selected
> hide sel atoms
> color sel byelement
> select clear
Drag select of 43 atoms, 41 bonds
> select up
50 atoms, 41 bonds, 8 residues, 1 model selected
> select up
384 atoms, 376 bonds, 8 residues, 1 model selected
> select up
17788 atoms, 17670 bonds, 726 residues, 1 model selected
> select down
384 atoms, 376 bonds, 8 residues, 1 model selected
> select ligand
9600 atoms, 9400 bonds, 200 residues, 1 model selected
> color sel byelement
> ui tool show "Color Actions"
> color sel white smoke
> color sel byhetero
> select clear
> transparency 0 target a
> camera mono
> save /Users/muzi/Desktop/zein/ph=2/double_zein/double_zein_ph2.cxs
No map chosen to save
> select add #1
17788 atoms, 17670 bonds, 726 residues, 1 model selected
No map chosen to save
> save /Users/muzi/Desktop/image1.png supersample 3
> select clear
> save /Users/muzi/Desktop/image2.png supersample 3
> select add #1
17788 atoms, 17670 bonds, 726 residues, 1 model selected
> select clear
> select #1
17788 atoms, 17670 bonds, 726 residues, 1 model selected
> save /Users/muzi/Desktop/zein/ph=2/double_zein/double_zein_ph2.tif width 936
> height 768 supersample 3
===== 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.
> open /Users/muzi/Desktop/zein/ph=2/double_zein/double_zein_ph2.cxs
Log from Sat Sep 27 18:52:14 2025UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/muzi/Desktop/center_49ns.pdb
Summary of feedback from opening /Users/muzi/Desktop/center_49ns.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK THIS IS A SIMULATION BOX
center_49ns.pdb title:
Title in water t= 49000.00000 step= 2450 [more info...]
Chain information for center_49ns.pdb #1
---
Chain | Description
? | No description available
Non-standard residues in center_49ns.pdb #1
---
HSP — (HSP)
LIG — (LIG)
Computing secondary structure
> ui mousemode right select
> select clear
> select protein
8188 atoms, 8270 bonds, 526 residues, 1 model selected
> rainbow sel
> select ~sel & ##selected
9600 atoms, 9400 bonds, 200 residues, 1 model selected
> hide sel atoms
> select main
8188 atoms, 8270 bonds, 526 residues, 1 model selected
> hide sel atoms
> select clear
> select ligand
9600 atoms, 9400 bonds, 200 residues, 1 model selected
> show sel atoms
> color sel byelement
> select clear
Drag select of 1 residues
Drag select of 1152 atoms, 18 residues, 1131 bonds
> color sel red
> color sel byelement
> color sel orange red
> color sel byhetero
> select ligand
9600 atoms, 9400 bonds, 200 residues, 1 model selected
> color sel red
> color sel byhetero
> color sel byelement
> select H
9974 atoms, 726 residues, 1 model selected
> hide sel atoms
> select clear
> select add /?:120
28 atoms, 28 bonds, 2 residues, 1 model selected
> select add /?:121
66 atoms, 64 bonds, 4 residues, 1 model selected
> select add /?:122
86 atoms, 82 bonds, 6 residues, 1 model selected
> select up
914 atoms, 920 bonds, 58 residues, 1 model selected
> select add /?:90
948 atoms, 952 bonds, 60 residues, 1 model selected
> select up
1324 atoms, 1330 bonds, 83 residues, 1 model selected
> select clear
> select ligand
9600 atoms, 9400 bonds, 200 residues, 1 model selected
> hide sel atoms
Drag select of 261 residues
Drag select of 20 residues
Drag select of 19 residues
> select up
4123 atoms, 4163 bonds, 265 residues, 1 model selected
> select down
4048 atoms, 260 residues, 1 model selected
> select up
4123 atoms, 4163 bonds, 265 residues, 1 model selected
> select down
4048 atoms, 260 residues, 1 model selected
> select up
4123 atoms, 4163 bonds, 265 residues, 1 model selected
> select down
4048 atoms, 260 residues, 1 model selected
> select up
4123 atoms, 4163 bonds, 265 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #ededecff
> select clear
[Repeated 1 time(s)]
> undo
[Repeated 3 time(s)]
> select up
8188 atoms, 8270 bonds, 526 residues, 1 model selected
> select down
4123 atoms, 4163 bonds, 265 residues, 1 model selected
> select down
4123 atoms, 4163 bonds, 265 residues, 1 model selected
> select down
4123 atoms, 4163 bonds, 265 residues, 1 model selected
> select down
4123 atoms, 4163 bonds, 265 residues, 1 model selected
> select down
4123 atoms, 4163 bonds, 265 residues, 1 model selected
> select clear
Drag select of 263 residues
> ui tool show "Color Actions"
> color sel #7aa4a4ff
> color sel #aeececff
> color sel #aeededff
[Repeated 1 time(s)]
> color sel #afeeeeff
> color sel #b0efefff
[Repeated 1 time(s)]
> color sel #b0f0f0ff
> color sel #b1f0f0ff
> color sel #b1f1f1ff
[Repeated 1 time(s)]
> color sel #b2f2f2ff
[Repeated 1 time(s)]
> select clear
Drag select of 15 residues
Drag select of 263 residues
> ui tool show "Color Actions"
> color sel #b6f48aff
> select clear
> select ligand
9600 atoms, 9400 bonds, 200 residues, 1 model selected
> show sel atoms
> select clear
Drag select of 7 atoms, 6 bonds
> select H
9974 atoms, 726 residues, 1 model selected
> hide sel atoms
> select clear
> set bgColor white
> lighting soft
> lighting flat
> lighting soft
> lighting full
> lighting simple
> lighting soft
> graphics silhouettes false
> lighting full
> graphics silhouettes true
> graphics silhouettes false
> lighting soft
> graphics silhouettes true
> lighting flat
> lighting full
> lighting soft
[Repeated 1 time(s)]
> graphics silhouettes false
> graphics silhouettes true
> camera ortho
> select clear
> camera ortho
> view
[Repeated 1 time(s)]
> lighting soft
[Repeated 1 time(s)]
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
Drag select of 120 atoms, 120 bonds
> select up
140 atoms, 121 bonds, 17 residues, 1 model selected
> select clear
> select /?:58
34 atoms, 32 bonds, 2 residues, 1 model selected
> select up
618 atoms, 620 bonds, 40 residues, 1 model selected
> select up
8188 atoms, 8270 bonds, 526 residues, 1 model selected
> graphics silhouettes true
> graphics silhouettes false
> lighting full
> lighting flat
> lighting full
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> select clear
> select /?:152
32 atoms, 30 bonds, 2 residues, 1 model selected
> select up
273 atoms, 275 bonds, 17 residues, 1 model selected
> select up
8188 atoms, 8270 bonds, 526 residues, 1 model selected
> graphics silhouettes true
> graphics silhouettes false
> lighting soft
> lighting full
> lighting soft
> lighting full
> select clear
> lighting full
> graphics silhouettes true
> lighting full
> lighting soft
> lighting full
> graphics silhouettes false
> lighting full
> camera
Camera parameters:
type: orthographic
position: -100.06 104.54 97.943
view direction: 0.97574 -0.17415 -0.13269
field width: 157.14
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting simple
[Repeated 1 time(s)]
> lighting full
> graphics silhouettes true
> lighting soft
> select clear
Drag select of 1 atoms, 2 bonds
> select clear
> select /?:270@C9
1 atom, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]Drag select of 165 atoms, 155 bonds
> select up
182 atoms, 156 bonds, 22 residues, 1 model selected
> select up
1056 atoms, 1034 bonds, 22 residues, 1 model selected
> select up
17788 atoms, 17670 bonds, 726 residues, 1 model selected
> select down
1056 atoms, 1034 bonds, 22 residues, 1 model selected
> select up
17788 atoms, 17670 bonds, 726 residues, 1 model selected
> select down
1056 atoms, 1034 bonds, 22 residues, 1 model selected
> select clear
> select C
5596 atoms, 4484 bonds, 726 residues, 1 model selected
> ui tool show "Color Actions"
[Repeated 1 time(s)]
> color sel dark gray
> color sel light gray
> undo
[Repeated 1 time(s)]
> select clear
> select ligand
9600 atoms, 9400 bonds, 200 residues, 1 model selected
> select C
5596 atoms, 4484 bonds, 726 residues, 1 model selected
> select clear
> select ligand
9600 atoms, 9400 bonds, 200 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light gray
> color sel byhetero
> select clear
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> select ligand
9600 atoms, 9400 bonds, 200 residues, 1 model selected
> ui tool show "Color Actions"
> color sel gainsboro
> color sel byhetero
> select clear
> lighting soft
> lighting full
> lighting soft
Drag select of 18 atoms, 19 bonds
> select clear
> select ligand
9600 atoms, 9400 bonds, 200 residues, 1 model selected
> select clear
> graphics silhouettes false
> lighting soft
> lighting full
> transparency 50 target a
> transparency 30 target a
> lighting full
> lighting soft
> lighting full
> transparency 10 target a
> select /?:136
34 atoms, 32 bonds, 2 residues, 1 model selected
> select up
914 atoms, 920 bonds, 58 residues, 1 model selected
> select up
8188 atoms, 8270 bonds, 526 residues, 1 model selected
> select clear
> select ligand
9600 atoms, 9400 bonds, 200 residues, 1 model selected
> hide sel atoms
Drag select of 262 residues
Drag select of 3 residues
> select up
4123 atoms, 4163 bonds, 265 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light sky blue
> color sel cornflower blue
Drag select of 5 residues
[Repeated 1 time(s)]Drag select of 266 residues
> select down
4136 atoms, 266 residues, 1 model selected
Drag select of 5 residues
Drag select of 218 residues
> select clear
Drag select of 50 residues
> select up
1205 atoms, 1213 bonds, 77 residues, 1 model selected
> select up
4094 atoms, 4135 bonds, 263 residues, 1 model selected
> ui tool show "Color Actions"
> color sel forest green
> color sel medium sea green
> color sel dark sea green
[Repeated 1 time(s)]
> color sel yellow green
> color sel lime
> color sel green
> color sel chartreuse
> color sel lawn green
> color sel spring green
> color sel lime green
> color sel forest green
> color sel sea green
> color sel medium sea green
> select clear
> select ligand
9600 atoms, 9400 bonds, 200 residues, 1 model selected
> show sel atoms
> select clear
[Repeated 1 time(s)]
> select H
9974 atoms, 726 residues, 1 model selected
> hide sel atoms
> select clear
> transparency 30 target a
> transparency 50 target a
> transparency 5 target a
Drag select of 1 atoms, 3 residues
> select clear
> lighting soft
> lighting full
> lighting soft
> lighting full
> ui tool show "Color Actions"
> color #b6f48aff
[Repeated 1 time(s)]
> color #aee984ff
> color #abe682ff
> color #abe582ff
> color #aae481ff
> color #a9e380ff
> color #a9e280ff
> color #a7e07fff
> color #a5dd7dff
> color #a4dc7dff
> color #a3da7cff
> color #a2d97bff
> color #a1d87bff
> color #a0d679ff
> color #9fd579ff
[Repeated 1 time(s)]
> color #9fd578ff
> color #9ed478ff
> color #9ed378ff
> color #9dd377ff
> color #9cd277ff
> color #9bcf76ff
> color #9acf75ff
> color #9ace75ff
> color #98cb73ff
> color #97cb73ff
> color #97ca73ff
> color #97ca72ff
> color #95c871ff
> color #95c771ff
> undo
[Repeated 9 time(s)]
> select ligand
9600 atoms, 9400 bonds, 200 residues, 1 model selected
> hide sel atoms
Drag select of 90 residues
> select up
1879 atoms, 1894 bonds, 120 residues, 1 model selected
> select up
4094 atoms, 4135 bonds, 263 residues, 1 model selected
> select clear
> show atoms
> hide atoms
> lighting full
> lighting soft
> lighting full
> lighting soft
> select ligand
9600 atoms, 9400 bonds, 200 residues, 1 model selected
> show sel atoms
> select clear
> lighting full
> lighting soft
Drag select of 37 atoms, 37 bonds
> select clear
> lighting flat
> lighting full
> graphics silhouettes false
> lighting soft
> lighting full
> graphics silhouettes true
> graphics silhouettes false
> select ligand
9600 atoms, 9400 bonds, 200 residues, 1 model selected
> hide sel atoms
Drag select of 90 residues
> select up
1916 atoms, 1931 bonds, 122 residues, 1 model selected
> select up
4094 atoms, 4135 bonds, 263 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #b2f2f2ff
> color sel #aff2f2ff
> color sel #aff1f1ff
> color sel #aef1f1ff
> color sel #aef0f0ff
[Repeated 1 time(s)]
> color sel #aeefefff
> color sel #adeeeeff
> color sel #abececff
[Repeated 1 time(s)]
> color sel #abebebff
> color sel #aaeaeaff
> color sel #a9e9e9ff
[Repeated 2 time(s)]
> color sel #a8e8e8ff
[Repeated 1 time(s)]
> color sel #a8e7e7ff
> color sel #a7e7e7ff
> color sel #a7e6e6ff
[Repeated 1 time(s)]
> color sel #a6e5e5ff
> color sel #a5e4e4ff
> color sel #a5e3e3ff
[Repeated 1 time(s)]
> color sel #a4e2e2ff
> color sel #a2e0e0ff
> color sel #9fdbdbff
> color sel #9edadaff
> color sel #9ed9d9ff
> color sel #9dd8d8ff
> color sel #9cd8d8ff
> color sel #9cd7d7ff
[Repeated 2 time(s)]
> color sel #9bd6d6ff
> color sel #9cd7d7ff
[Repeated 1 time(s)]
> color sel #9dd8d8ff
> color sel #9dd9d9ff
> color sel #9fdbdbff
> color sel #9fdcdcff
> color sel #a0dcdcff
[Repeated 1 time(s)]
> color sel #a0ddddff
> color sel #a1ddddff
> color sel #a1dedeff
[Repeated 2 time(s)]
> color sel #a2dfdfff
> color sel #a1dedeff
[Repeated 2 time(s)]
> color sel #a1ddddff
> color sel #a0ddddff
> color sel #9fdbdbff
[Repeated 1 time(s)]
> color sel #9dd9d9ff
> color sel #9dd8d8ff
> color sel #9bd5d5ff
> color sel #9ad5d5ff
> color sel #9ad4d4ff
> color sel #98d2d2ff
> color sel #98d1d1ff
[Repeated 1 time(s)]
> color sel #97d1d1ff
> color sel #97d0d0ff
[Repeated 1 time(s)]
> color sel #96cfcfff
> color sel #94cdcdff
> color sel #93cbcbff
> color sel #93cacaff
> color sel #92cacaff
> color sel #91c8c8ff
> color sel #90c6c6ff
> color sel #8fc6c6ff
> color sel #8fc5c5ff
> color sel #8ec3c3ff
> color sel #7cababff
> color sel #5c7e7eff
> color sel #5b7e7eff
> color sel #5a7c7cff
[Repeated 2 time(s)]
> color sel #638888ff
> color sel #6f9999ff
> color sel #77a4a4ff
> color sel #79a7a7ff
> color sel #7ba9a9ff
> color sel #7cababff
> color sel #7dadadff
> color sel #7faeaeff
> color sel #7fafafff
[Repeated 1 time(s)]
> color sel #7fb0b0ff
> color sel #84b6b6ff
> color sel #87babaff
> color sel #8abebeff
> color sel #8abfbfff
> color sel #8abebeff
> color sel #88bbbbff
> color sel #87babaff
[Repeated 1 time(s)]
> color sel #86b8b8ff
> color sel #85b8b8ff
> color sel #85b7b7ff
> color sel #83b5b5ff
> color sel #82b4b4ff
> color sel #82b3b3ff
> color sel #83b4b4ff
> color sel #8abebeff
> color sel #97d0d0ff
> color sel #9ad4d4ff
> color sel #9bd6d6ff
> color sel #9cd7d7ff
> color sel #9edadaff
> color sel #a1ddddff
> color sel #a7e6e6ff
> color sel #aaebebff
> color sel #b1f4f4ff
> color sel #b3f7f7ff
[Repeated 1 time(s)]
> color sel #b4f8f8ff
[Repeated 1 time(s)]
> color sel #b5f9f9ff
> color sel #b4f9f9ff
> color sel #b2f5f5ff
> color sel #adefefff
> color sel #a5e4e4ff
> color sel #a4e2e2ff
> color sel #a1dedeff
> color sel #9fdcdcff
> color sel #9edadaff
> color sel #9ed9d9ff
> color sel #9bd6d6ff
> color sel #9ad4d4ff
> color sel #99d3d3ff
> color sel #97d1d1ff
> color sel #95ceceff
> color sel #91c8c8ff
> color sel #91c7c7ff
> color sel #8fc6c6ff
> color sel #8ec4c4ff
> color sel #8dc2c2ff
> color sel #8bc0c0ff
> color sel #8bbfbfff
> color sel #89bdbdff
> color sel #88bbbbff
> color sel #87babaff
> color sel #85b8b8ff
> color sel #83b5b5ff
> color sel #83b4b4ff
[Repeated 1 time(s)]
> color sel #81b2b2ff
> color sel #80b0b0ff
> color sel #7fb0b0ff
> color sel #80b0b0ff
> color sel #80b1b1ff
> color sel #81b2b2ff
[Repeated 1 time(s)]
> color sel #82b3b3ff
> color sel #82b4b4ff
> color sel #83b4b4ff
> color sel #84b5b5ff
> color sel #84b6b6ff
> color sel #85b8b8ff
> color sel #86b8b8ff
> color sel #87babaff
[Repeated 1 time(s)]
> color sel #88bbbbff
[Repeated 1 time(s)]
> color sel #88bcbcff
> color sel #88bbbbff
[Repeated 1 time(s)]
> color sel #87babaff
[Repeated 1 time(s)]
> color sel #86b9b9ff
[Repeated 1 time(s)]
> color sel #86b8b8ff
> color sel #85b8b8ff
> color sel #84b7b7ff
> color sel #84b6b6ff
[Repeated 1 time(s)]
> color sel #84b5b5ff
> color sel #83b5b5ff
[Repeated 1 time(s)]
> color sel #82b4b4ff
> color sel #82b3b3ff
Drag select of 92 residues
> select up
2162 atoms, 2182 bonds, 138 residues, 1 model selected
> select up
4094 atoms, 4135 bonds, 263 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #b6f48aff
[Repeated 2 time(s)]
> color sel #b3f088ff
> color sel #a9e280ff
> color sel #a8e180ff
> color sel #a8e17fff
> color sel #a5dd7dff
> color sel #a4dc7dff
> color sel #a3db7cff
[Repeated 1 time(s)]
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> color sel #a0d67aff
> color sel #9ed478ff
> color sel #9dd377ff
> color sel #9cd277ff
> color sel #9cd176ff
> color sel #9acf75ff
> color sel #9ace75ff
> color sel #98cc74ff
> color sel #97ca72ff
> color sel #95c871ff
> color sel #94c771ff
> color sel #94c670ff
> color sel #93c670ff
> color sel #92c46fff
[Repeated 1 time(s)]
> color sel #92c36fff
> color sel #91c36eff
> color sel #91c26eff
> color sel #90c26eff
> color sel #90c16eff
> color sel #90c16dff
> color sel #8fc06dff
> color sel #8fbf6cff
> color sel #8ebe6cff
> color sel #8cbc6bff
> color sel #8cbb6aff
> color sel #8bbb6aff
> color sel #8bba6aff
> color sel #8bba69ff
> color sel #8ab969ff
[Repeated 2 time(s)]
> color sel #89b868ff
[Repeated 1 time(s)]
> color sel #89b768ff
> color sel #88b667ff
> color sel #87b567ff
> color sel #87b566ff
> color sel #86b466ff
> color sel #85b265ff
> color sel #84b164ff
> color sel #83b064ff
> color sel #82af63ff
> color sel #82ae63ff
> color sel #82ae62ff
> color sel #81ad62ff
> color sel #81ac62ff
> color sel #80ac62ff
> color sel #80ac61ff
> color sel #80ab61ff
> color sel #7fab61ff
> color sel #7aa45dff
> color sel #79a25cff
> color sel #78a15bff
> color sel #769f5aff
> color sel #769e5aff
> color sel #759d59ff
> color sel #749b58ff
> color sel #739a57ff
> color sel #749b58ff
> color sel #77a05bff
> color sel #7aa35cff
> color sel #7ea960ff
> color sel #81ad62ff
> color sel #82af63ff
> color sel #83b064ff
> color sel #84b265ff
> color sel #87b466ff
> color sel #87b567ff
> color sel #88b667ff
[Repeated 1 time(s)]
> color sel #89b768ff
> color sel #8ab969ff
[Repeated 1 time(s)]
> color sel #8bba69ff
> color sel #8bba6aff
> color sel #8cbc6aff
> color sel #8dbc6bff
> color sel #8dbd6bff
> color sel #8dbe6bff
> color sel #8fc06dff
> color sel #90c16dff
> color sel #90c16eff
> color sel #90c26eff
> color sel #91c26eff
> color sel #92c46fff
> color sel #93c570ff
[Repeated 1 time(s)]
> color sel #92c36fff
> color sel #91c26eff
> color sel #90c26eff
> color sel #90c16eff
> color sel #8ebe6cff
> color sel #8cbc6bff
> color sel #8cbc6aff
> color sel #8cbb6aff
> color sel #8bba6aff
> color sel #8bba69ff
> color sel #8ab969ff
[Repeated 1 time(s)]
> color sel #89b868ff
> select clear
> select ligand
9600 atoms, 9400 bonds, 200 residues, 1 model selected
> show sel atoms
> select H
9974 atoms, 726 residues, 1 model selected
> hide sel atoms
> color sel byelement
> select clear
Drag select of 43 atoms, 41 bonds
> select up
50 atoms, 41 bonds, 8 residues, 1 model selected
> select up
384 atoms, 376 bonds, 8 residues, 1 model selected
> select up
17788 atoms, 17670 bonds, 726 residues, 1 model selected
> select down
384 atoms, 376 bonds, 8 residues, 1 model selected
> select ligand
9600 atoms, 9400 bonds, 200 residues, 1 model selected
> color sel byelement
> ui tool show "Color Actions"
> color sel white smoke
> color sel byhetero
> select clear
> transparency 0 target a
> camera mono
> save /Users/muzi/Desktop/zein/ph=2/double_zein/double_zein_ph2.cxs
——— End of log from Sat Sep 27 18:52:14 2025 ———
> view name session-start
opened ChimeraX session
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: MKGR3CH/A
Chip: Apple M1 Pro
Total Number of Cores: 8 (6 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6.1 (24G90)
Kernel Version: Darwin 24.6.0
Time since boot: 13天12分钟
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 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
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
Change History (2)
comment:1 by , 6 weeks ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in event loop |
comment:2 by , 6 weeks ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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