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Opened 8 hours ago
#19485 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-15.5-arm64-arm-64bit
ChimeraX Version: 1.8rc202405282004 (2024-05-28 20:04:22 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 0x0000000208bf9f00 (most recent call first):
File "/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 52 in
File "/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 61 in
File "/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 61 in python_instances_of_class
File "/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 2642 in
File "/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py", line 290 in
File "/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py", line 290 in include_state
File "/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 260 in discovery
File "/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 646 in save
File "/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 922 in save
File "/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 95 in save
File "/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 101 in provider_save
File "/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213 in run
File "/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 86 in cmd_save
File "/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213 in run
File "/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 62 in display
File "/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 138 in show_save_file_dialog
File "/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 127 in
File "/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 307 in event_loop
File "/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.pdb_lib._load_libs, chimerax.surface._surface, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, PIL._imagingmath, 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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 55)
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"procLaunch" : "2025-12-06 12:28:47.7049 -0600",
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"procExitAbsTime" : 52971545879837,
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"name" : "_cmsgpack.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6889832448,
"size" : 243284,
"uuid" : "60485b6f-67e5-38c1-aec9-efd6031ff166",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6890078208,
"size" : 51784,
"uuid" : "647b91fc-96d3-3bbb-af08-970df45257c8",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6888599552,
"size" : 529520,
"uuid" : "f4529d5e-24f3-3bbb-bd3c-984856875fc8",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6890328064,
"size" : 31568,
"uuid" : "519f3220-7499-334a-96d6-ccf3dc28f986",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6890557440,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 5500928,
"uuid" : "df489a59-b4f6-32b8-9bb4-9b832960aa52",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "3502.1.401"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 7085903872,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3174368,
"uuid" : "9286e29f-fcee-31d0-acea-2842ea23bedf",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6957043712,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 21568640,
"uuid" : "5d0da1bd-412c-3ed8-84e9-40ca62fe7b42",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2575.60.5"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6886277120,
"size" : 636112,
"uuid" : "9cf0401a-a938-389e-a77d-9e9608076ccf",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6889132032,
"size" : 577528,
"uuid" : "875203a1-087b-33a6-93a5-928bb7e9114c",
"path" : "\/usr\/lib\/libc++.1.dylib",
"name" : "libc++.1.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6913560576,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.Foundation",
"size" : 14586624,
"uuid" : "e8f6a451-0acc-3e05-b18f-fec6618ce44a",
"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
"name" : "Foundation",
"CFBundleVersion" : "3502.1.401"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6888296448,
"size" : 288576,
"uuid" : "8bf83cda-8db1-3d46-94b0-d811bd77e078",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
}
],
"sharedCache" : {
"base" : 6885441536,
"size" : 5047205888,
"uuid" : "d7397d7f-8df9-3920-81a7-c0a144be9c51"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=4.4G written=14.9M(0%) resident=2570K(0%) swapped_out=12.4M(0%) unallocated=4.4G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 896K 7 \nActivity Tracing 256K 1 \nCG image 2224K 43 \nColorSync 736K 38 \nCoreAnimation 18.6M 164 \nCoreGraphics 64K 4 \nCoreGraphics (reserved) 16K 1 reserved VM address space (unallocated)\nCoreImage 64K 2 \nCoreUI image data 3120K 23 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 3.9G 115 \nMALLOC guard page 288K 18 \nMach message 96K 4 \nOpenGL GLSL 384K 4 \nSTACK GUARD 736K 46 \nStack 182.1M 47 \nStack Guard 56.0M 1 \nVM_ALLOCATE 180.3M 222 \nVM_ALLOCATE (reserved) 160.0M 3 reserved VM address space (unallocated)\n__AUTH 5521K 698 \n__AUTH_CONST 77.4M 945 \n__CTF 824 1 \n__DATA 34.1M 1084 \n__DATA_CONST 36.8M 1101 \n__DATA_DIRTY 2778K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 645.8M 150 \n__OBJC_RO 61.4M 1 \n__OBJC_RW 2396K 1 \n__TEXT 1.3G 1117 \n__TEXT (graphics) 4064K 4 \n__TPRO_CONST 128K 2 \ndyld private memory 1536K 13 \nmapped file 312.6M 89 \npage table in kernel 2570K 1 \nshared memory 3296K 24 \n=========== ======= ======= \nTOTAL 6.9G 6322 \nTOTAL, minus reserved VM space 6.8G 6322 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "c1a73ca72bceae2ab2eb978a41f5b091cc7eafd2",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "63508950b3714d3622fc77f7",
"factorPackIds" : {
"SIRI_MEMORY_SYNC_CONFIG" : "6526e111d0c9ce2f459b54a8"
},
"deploymentId" : 240000015
},
{
"rolloutId" : "6761d0c9df60af01adb250fb",
"factorPackIds" : {
},
"deploymentId" : 240000009
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
Startup Errors
---
error | Bundle 'ChimeraX-Clipper' custom initialization failed
warning | Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 501, in get_module
m = importlib.import_module(self.package_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/importlib/__init__.py",
line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "", line 1204, in _gcd_import
File "", line 1176, in _find_and_load
File "", line 1147, in _find_and_load_unlocked
File "", line 690, in _load_unlocked
File "", line 940, in exec_module
File "", line 241, in _call_with_frames_removed
File "/Users/h.b/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/clipper/__init__.py", line 32, in
__version__ = _version()
^^^^^^^^^^
File "/Users/h.b/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/clipper/__init__.py", line 30, in _version
return pkg_resources.require('ChimeraX-Clipper')[0].version
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/pkg_resources/__init__.py", line 937, in require
needed = self.resolve(parse_requirements(requirements))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/pkg_resources/__init__.py", line 798, in resolve
dist = self._resolve_dist(
^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/pkg_resources/__init__.py", line 844, in _resolve_dist
raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (ChimeraX-Core 1.8rc202405282004
(/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages), Requirement.parse('ChimeraX-Core~=1.8.0'), {'ChimeraX-Clipper'})
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 375, in initialize
api = self._get_api(session.logger)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 520, in _get_api
m = self.get_module()
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 503, in get_module
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-
Clipper's module: (ChimeraX-Core 1.8rc202405282004
(/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages), Requirement.parse('ChimeraX-Core~=1.8.0'), {'ChimeraX-Clipper'})
UCSF ChimeraX version: 1.8rc202405282004 (2024-05-28)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/h.b/Downloads/sfgfpnB15_refine_042.pdb format pdb
Chain information for sfgfpnB15_refine_042.pdb #1
---
Chain | Description
A | No description available
B E G | No description available
C D F H | No description available
> set bgColor white
> graphics silhouettes true
> show cartoons
> hide atoms
> select /g,h
2831 atoms, 2890 bonds, 363 residues, 1 model selected
> delete ~sel
> select add #1
2831 atoms, 2890 bonds, 363 residues, 1 model selected
> select subtract #1
Nothing selected
> select /d
Nothing selected
> select /g
1857 atoms, 1900 bonds, 233 residues, 1 model selected
> color sel green
> ui tool show "Color Actions"
> color sel yellow green
> color sel lime
> color sel spring green
> color sel lime green
> color sel medium sea green
> color sel sea green
> color sel spring green
> ui tool show "Color Actions"
> color sel #8eff8cff
> color sel #7cff61ff
> color sel #63ff3dff
> color sel #67ff2eff
> color sel #50ff2eff
> color sel #47ff34ff
> color sel #57ff47ff
> color sel #2fff23ff
> color sel #45ff3aff
> color sel #41ff52ff
> color sel #47ff7fff
> color sel #36ff55ff
> color sel #0cff67ff
> color sel #09ff3bff
> color sel #0eff1fff
> color sel #3eff10ff
> color sel #fff55aff
> color sel #86ff65ff
> color sel #77ff77ff
> color sel #77ff76ff
> color sel #8dff99ff
> color sel #70ff8bff
> color sel #61ff57ff
> color sel #56ff64ff
> color sel #3eff52ff
> select add #1
2831 atoms, 2890 bonds, 363 residues, 1 model selected
> select subtract #1
Nothing selected
> select /h
974 atoms, 990 bonds, 130 residues, 1 model selected
> color sel plum
> select add #1
2831 atoms, 2890 bonds, 363 residues, 1 model selected
> select subtract #1
Nothing selected
> select /h
974 atoms, 990 bonds, 130 residues, 1 model selected
> color sel hot pink
> color sel #ffc7e6ff
> color sel #e5b1ffff
> color sel #e5b0ffff
> color sel #ffabd4ff
> color sel #ff6fb6ff
> color sel #ff87cfff
> color sel #ff8ce4ff
> color sel #ff9efcff
> color sel #ff96d6ff
> color sel #ff5d7dff
> color sel #ff74adff
> color sel #ff89c6ff
> select add #1
2831 atoms, 2890 bonds, 363 residues, 1 model selected
> select subtract #1
Nothing selected
> save /Users/h.b/Desktop/gfpnB.png width 3000 height 2000
> transparentBackground true supersample 3
> select /h
974 atoms, 990 bonds, 130 residues, 1 model selected
> select /g
1857 atoms, 1900 bonds, 233 residues, 1 model selected
> color sel #ff89c6ff
> color sel #a4ff9eff
> color sel #8cff6cff
> color sel #6cff39ff
> color sel #57ff3aff
> color sel #6dff1fff
> color sel #53ff38ff
> color sel #3cff3aff
> color sel #4bff47ff
> select add #1
2831 atoms, 2890 bonds, 363 residues, 1 model selected
> select subtract #1
Nothing selected
> save /Users/h.b/Desktop/gfpnB.png width 3000 height 2000
> transparentBackground true supersample 3
> select /G:190
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /G:191
12 atoms, 10 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel byhetero
> hide sel surfaces
> select add #1
2831 atoms, 2890 bonds, 363 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #1
2831 atoms, 2890 bonds, 363 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 2831 atom styles
> hide sel atoms
> select subtract #1
Nothing selected
> select /G:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select /H:55
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select /H:34
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select /H:56
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #1
2831 atoms, 2890 bonds, 363 residues, 1 model selected
> select subtract #1
Nothing selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel byhetero
> select add #1
2831 atoms, 2890 bonds, 363 residues, 1 model selected
> select subtract #1
Nothing selected
> undo
> select subtract #1
Nothing selected
> select /G:117@CD
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select add #1
2831 atoms, 2890 bonds, 363 residues, 1 model selected
> select subtract #1
Nothing selected
> select /G:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #1
2831 atoms, 2890 bonds, 363 residues, 1 model selected
> select subtract #1
Nothing selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel byhetero
> select add #1
2831 atoms, 2890 bonds, 363 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #1
2831 atoms, 2890 bonds, 363 residues, 1 model selected
> select subtract #1
Nothing selected
> select /H:106
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select add #1
2831 atoms, 2890 bonds, 363 residues, 1 model selected
> select subtract #1
Nothing selected
> select /H:103
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select add #1
2831 atoms, 2890 bonds, 363 residues, 1 model selected
> select subtract #1
Nothing selected
> select /G:92
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select /G:91
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select /G:90
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #1
2831 atoms, 2890 bonds, 363 residues, 1 model selected
> select subtract #1
Nothing selected
> color byhetero
> select /H:103
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add /H:104
15 atoms, 13 bonds, 2 residues, 1 model selected
> select add /H:105
26 atoms, 24 bonds, 3 residues, 1 model selected
> select add /H:106
32 atoms, 29 bonds, 4 residues, 1 model selected
> select add /H:107
39 atoms, 35 bonds, 5 residues, 1 model selected
> show sel atoms
> select add #1
2831 atoms, 2890 bonds, 363 residues, 1 model selected
> select subtract #1
Nothing selected
> select /G:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add /G:118
13 atoms, 11 bonds, 2 residues, 1 model selected
> select add /G:119
21 atoms, 18 bonds, 3 residues, 1 model selected
> show sel atoms
> select add #1
2831 atoms, 2890 bonds, 363 residues, 1 model selected
> select subtract #1
Nothing selected
> select /G:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #1
2831 atoms, 2890 bonds, 363 residues, 1 model selected
> select subtract #1
Nothing selected
> select /G:115
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #1
2831 atoms, 2890 bonds, 363 residues, 1 model selected
> select subtract #1
Nothing selected
> select /H:32
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add /H:33
14 atoms, 12 bonds, 2 residues, 1 model selected
> select add /H:34
20 atoms, 17 bonds, 3 residues, 1 model selected
> show sel atoms
> select add #1
2831 atoms, 2890 bonds, 363 residues, 1 model selected
> select subtract #1
Nothing selected
> select /H:102
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #1
2831 atoms, 2890 bonds, 363 residues, 1 model selected
> select subtract #1
Nothing selected
> select /G:90@CG
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 2 residues, 1 model selected
> select up
15 atoms, 15 bonds, 2 residues, 1 model selected
> hide sel atoms
> select /G:9
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> hide sel atoms
> select add #1
2831 atoms, 2890 bonds, 363 residues, 1 model selected
> select subtract #1
Nothing selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /G:119@OD2
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
12 atoms, 11 bonds, 2 residues, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /H:34@CB
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> select add #1
2831 atoms, 2890 bonds, 363 residues, 1 model selected
> select subtract #1
Nothing selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> select add #1
2831 atoms, 2890 bonds, 363 residues, 1 model selected
> select subtract #1
Nothing selected
> select /H:102@OG1
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
62 atoms, 62 bonds, 8 residues, 1 model selected
> select add #1
2831 atoms, 2890 bonds, 363 residues, 1 model selected
> select subtract #1
Nothing selected
> select /H:102@OG1
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select add #1
2831 atoms, 2890 bonds, 363 residues, 1 model selected
> select subtract #1
Nothing selected
Drag select of 1 atoms, 15 residues
> select add #1
2831 atoms, 2890 bonds, 363 residues, 1 model selected
> select subtract #1
Nothing selected
> ui tool show "Side View"
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> select /G:117@OE1
1 atom, 1 residue, 1 model selected
> select add /H:56@OG1
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance /G:117@OE1 /H:56@OG1
Distance between /G GLU 117 OE1 and /H THR 56 OG1: 2.866Å
> distance style decimalPlaces 2
> distance style decimalPlaces 1
> select add #1
2831 atoms, 2890 bonds, 1 pseudobond, 363 residues, 2 models selected
> select subtract #1
Nothing selected
> select /G:92@OE1
1 atom, 1 residue, 1 model selected
> select add /H:103@NH1
2 atoms, 2 residues, 1 model selected
> distance /G:92@OE1 /H:103@NH1
Distance between /G GLU 92 OE1 and /H ARG 103 NH1: 4.2Å
> select add #1
2831 atoms, 2890 bonds, 2 pseudobonds, 363 residues, 2 models selected
> select subtract #1
Nothing selected
> distance style symbol false
> hide #2.1 models
> save /Users/h.b/Desktop/gfpnBclose.png width 3000 height 2000
> transparentBackground true supersample 3
> hide #!2 models
Drag select of 24 atoms, 37 residues, 20 bonds
> show sel atoms
> select add #1
2831 atoms, 2890 bonds, 2 pseudobonds, 363 residues, 2 models selected
> select subtract #1
Nothing selected
> save /Users/h.b/Desktop/gfpnBclosemore res.png width 3000 height 2000
> transparentBackground true supersample 3
'/Users/h.b/Desktop/gfpnBclosemore' has only compression suffix; cannot
determine format from suffix
> save /Users/h.b/Desktop/gfpnBclosemoreres.png width 3000 height 2000
> transparentBackground true supersample 3
> hide atoms
> save /Users/h.b/Desktop/Ginny.cxs
===== Log before crash end =====
Log:
Startup Errors
---
error | Bundle 'ChimeraX-Clipper' custom initialization failed
warning | Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 501, in get_module
m = importlib.import_module(self.package_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/importlib/__init__.py",
line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "<frozen importlib._bootstrap>", line 1204, in _gcd_import
File "<frozen importlib._bootstrap>", line 1176, in _find_and_load
File "<frozen importlib._bootstrap>", line 1147, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 690, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 940, in exec_module
File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
File "/Users/h.b/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/clipper/__init__.py", line 32, in <module>
__version__ = _version()
^^^^^^^^^^
File "/Users/h.b/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/clipper/__init__.py", line 30, in _version
return pkg_resources.require('ChimeraX-Clipper')[0].version
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/pkg_resources/__init__.py", line 937, in require
needed = self.resolve(parse_requirements(requirements))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/pkg_resources/__init__.py", line 798, in resolve
dist = self._resolve_dist(
^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/pkg_resources/__init__.py", line 844, in _resolve_dist
raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (ChimeraX-Core 1.8rc202405282004
(/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages), Requirement.parse('ChimeraX-Core~=1.8.0'), {'ChimeraX-Clipper'})
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 375, in initialize
api = self._get_api(session.logger)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 520, in _get_api
m = self.get_module()
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 503, in get_module
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-
Clipper's module: (ChimeraX-Core 1.8rc202405282004
(/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages), Requirement.parse('ChimeraX-Core~=1.8.0'), {'ChimeraX-Clipper'})
UCSF ChimeraX version: 1.8rc202405282004 (2024-05-28)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,7
Model Number: MNEH3LL/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 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: 183 days, 13 hours, 54 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57
ChimeraX-AtomicLibrary: 14.0.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.23.1
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8rc202405282004
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.16
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.4
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.13
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.52.4
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.45
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.2
typing-extensions: 4.12.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
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