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Opened 109 minutes ago
#19833 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: Linux-4.18.0-553.89.1.el8_10.x86_64-x86_64-with-glibc2.28
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Error occurs trying to open a tomogram in ArtiaX. The same tomogram opens fine in ChimeraX
Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open rec_24-08_G2_53Kx_ts_2.mrc
Opened rec_24-08_G2_53Kx_ts_2.mrc as #1, grid size 1440,1023,512, pixel
6.76,6.76,6.76, shown at step 1, values float32
> volume #1 level -0.7506,0 level 1.219,0.8 level 4.17,1
> volume #1 level -1.983,0.03125 level 1.219,0.8 level 4.17,1
> volume #1 level -2.442,0 level 1.219,0.8 level 4.17,1
> volume #1 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 1730 tiltedSlabSpacing 6.756 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> ui mousemode right "rotate slab"
> volume #1 tiltedSlabAxis 0.1715,-0.3461,0.9224 tiltedSlabOffset 1413
> ui mousemode right clip
[Repeated 1 time(s)]
> ui mousemode right "move planes"
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> ui mousemode right clip
> ui mousemode right "move planes"
> volume #1 region 0,0,274,1439,1022,274
> volume #1 region 0,0,264,1439,1022,264
> ui mousemode right "rotate slab"
> volume #1 tiltedSlabAxis -0.1408,-0.2173,0.9659 tiltedSlabOffset 193
> ui mousemode right "move planes"
> volume #1 tiltedSlabOffset 172.8 tiltedSlabPlaneCount 25
> volume planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume #1 level -2.867,0 level 1.219,0.8 level 4.17,1
> volume #1 region 0,0,292,1439,1022,292
> volume #1 region 0,0,0,1439,1022,511 step 4
> volume #1 region 0,0,0,1439,1022,511 step 4 imageMode "tilted slab"
> tiltedSlabAxis -0.1245,-0.1489,0.981 tiltedSlabOffset 482.2
> ui mousemode right "rotate slab"
> volume #1 tiltedSlabAxis 0.1857,-0.07503,0.9797 tiltedSlabOffset 1984
> volume #1 tiltedSlabAxis 0.2222,-0.2026,0.9537 tiltedSlabOffset 1628
> ui mousemode right "move planes"
> volume #1 tiltedSlabOffset 1763 tiltedSlabPlaneCount 25
> volume #1 tiltedSlabOffset 1756 tiltedSlabPlaneCount 25
> volume #1 tiltedSlabOffset 1675 tiltedSlabPlaneCount 25
> volume #1 tiltedSlabOffset 1445 tiltedSlabPlaneCount 25
> volume #1 tiltedSlabOffset 2155 tiltedSlabPlaneCount 25
> volume planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume #1 region 0,0,275,1439,1022,275
> volume #1 region 0,0,265,1439,1022,265
> volume #1 region 0,0,251,1439,1022,251
> volume #1 region 0,0,275,1439,1022,275
> ui mousemode right "mark point"
[Repeated 1 time(s)]
> marker #2 position 3274,3460,692.6 color yellow radius 1
> marker #2 position 3752,3517,540.9 color yellow radius 1
> marker link #2:1,2 color #659cef radius 0.5
> marker #2 position 4340,3590,508.1 color yellow radius 1
> marker link #2:2,3 color #659cef radius 0.5
> marker #2 position 5026,3630,529.8 color yellow radius 1
> marker link #2:3,4 color #659cef radius 0.5
> marker #2 position 5996,3634,616.1 color yellow radius 1
> marker link #2:4,5 color #659cef radius 0.5
> marker #2 position 6805,3770,743.3 color yellow radius 1
> marker link #2:5,6 color #659cef radius 0.5
> ui mousemode right "move markers"
> ui mousemode right select
Drag select of 6 atoms, 5 bonds
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,-95.403,0,1,0,6.031,0,0,1,1350.9
> view matrix models #2,1,0,0,-89.742,0,1,0,-203.13,0,0,1,1363.3
> close #2
> ui mousemode right "mark point"
> marker #2 position 3278,3210,838.7 color yellow radius 1
> marker #2 position 3897,3219,582 color yellow radius 1
> marker #2 position 4520,3305,540.8 color yellow radius 1
> marker #2 position 5166,3359,585.4 color yellow radius 1
> marker #2 position 6001,3416,697 color yellow radius 1
> marker #2 position 5926,3447,685.1 color yellow radius 1
> volume planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume #1 region 0,0,256,1439,1022,256
> volume #1 region 0,0,258,1439,1022,258
> volume #1 region 0,0,282,1439,1022,282
> volume #1 region 0,0,264,1439,1022,264
> ui mousemode right "mark point"
> marker #2 position 5997,3503,679.4 color yellow radius 1
> marker #2 position 6505,3592,769.5 color yellow radius 1
> marker #2 position 7086,3674,893.6 color yellow radius 1
> ui mousemode right "move planes"
> volume #1 region 0,0,255,1439,1022,255
> close #2
> volume #1 region 0,0,265,1439,1022,265
> ui mousemode right "mark point"
> marker #2 position 3563,3335,792.3 color yellow radius 1
> marker #2 position 4452,3376,554.2 color yellow radius 1
> marker link #2:1,2 color #659cef radius 0.5
> marker #2 position 4913,3407,519.3 color yellow radius 1
> marker link #2:2,3 color #659cef radius 0.5
> ui mousemode right "move planes"
> volume #1 region 0,0,267,1439,1022,267
> ui mousemode right "mark point"
> marker #2 position 5818,3546,614.1 color yellow radius 1
> marker link #2:3,4 color #659cef radius 0.5
> marker #2 position 6294,3613,688.4 color yellow radius 1
> marker link #2:4,5 color #659cef radius 0.5
> marker #2 position 6749,3679,773.6 color yellow radius 1
> marker link #2:5,6 color #659cef radius 0.5
> ui mousemode right select
Drag select of 6 atoms, 5 bonds
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,-30.178,0,1,0,-4.0581,0,0,1,1260.3
> view matrix models #2,1,0,0,-100.6,0,1,0,-82.336,0,0,1,1197.3
> view matrix models #2,1,0,0,141.94,0,1,0,26.882,0,0,1,1155.9
> marker change #2 radius 50 links false
> view matrix models #2,1,0,0,131.12,0,1,0,22.082,0,0,1,1254.6
> view matrix models #2,1,0,0,149.45,0,1,0,23.555,0,0,1,1261.9
> view matrix models #2,1,0,0,155.27,0,1,0,16.686,0,0,1,1260.5
> ui mousemode right "move planes"
> volume #1 region 0,0,318,1439,1022,318
> volume #1 region 0,0,419,1439,1022,419
> volume #1 region 0,0,277,1439,1022,277
> volume #1 region 0,0,274,1439,1022,274
> ui mousemode right "move planes"
> volume #1 region 0,0,268,1439,1022,268
> volume #1 region 0,0,243,1439,1022,243
> volume #1 region 0,0,278,1439,1022,278
> close #2
> close #1
> artiax start
Using preset: ArtiaX / Artiax Default
Preset expands to these ChimeraX commands:
set bgColor black
lighting depthCue false
camera ortho
Opened rec_24-08_G2_53Kx_ts_2.mrc as #1.1.1, grid size 1440,1023,512, pixel
6.76,6.76,6.76, shown at level 1.35, step 1, values float32
> artiax clip off
> artiax tomo #1.1.1 sliceDirection 0,0,1
> artiax view xy
An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.
GLError(
err = 1285,
description = b'out of memory',
baseOperation = glTexImage3D,
pyArgs = (
GL_TEXTURE_3D,
0,
GL_R32F,
1440,
1023,
512,
0,
GL_RED,
GL_FLOAT,
array([[[ 0.15100943, -0.40536138, -0.11823019, ..., 1.154046 ,
1.8430679 , 2.3593435 ],
[ 0.014...,
),
cArgs = (
GL_TEXTURE_3D,
0,
GL_R32F,
1440,
1023,
512,
0,
GL_RED,
GL_FLOAT,
array([[[ 0.15100943, -0.40536138, -0.11823019, ..., 1.154046 ,
1.8430679 , 2.3593435 ],
[ 0.014...,
),
cArguments = (
GL_TEXTURE_3D,
0,
GL_R32F,
1440,
1023,
512,
0,
GL_RED,
GL_FLOAT,
array([[[ 0.15100943, -0.40536138, -0.11823019, ..., 1.154046 ,
1.8430679 , 2.3593435 ],
[ 0.014...,
)
)
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 84, in draw_new_frame
view.draw(check_for_changes = False)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 188, in draw
self._draw_scene(camera, drawings)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 259, in _draw_scene
draw_opaque(r, opaque_drawings)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1559, in draw_opaque
_draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1572, in _draw_multiple
d.draw(renderer, draw_pass)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 936, in draw
drawing = self._update_view_axis(renderer)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 662, in _update_view_axis
pd = self._update_3d_texture_planes(view_dir)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 714, in _update_3d_texture_planes
pd = self._texture_3d_planes()
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 724, in _texture_3d_planes
pd = Texture3dPlanes(self)
^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1551, in __init__
self._fill_textures()
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1668, in _fill_textures
t.reload_texture(td, now=True)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 3210, in reload_texture
self.fill_opengl_texture()
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 3220, in fill_opengl_texture
self.initialize_texture(size, format, iformat, tdtype, ncomp, data)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 3100, in initialize_texture
GL.glTexImage3D(gl_target, 0, iformat, size[0], size[1], size[2],
File "src/latebind.pyx", line 40, in
OpenGL_accelerate.latebind.LateBind.__call__
File "src/wrapper.pyx", line 319, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src/wrapper.pyx", line 312, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1285,
description = b'out of memory',
baseOperation = glTexImage3D,
pyArgs = (
GL_TEXTURE_3D,
0,
GL_R32F,
1440,
1023,
512,
0,
GL_RED,
GL_FLOAT,
array([[[ 0.15100943, -0.40536138, -0.11823019, ..., 1.154046 ,
1.8430679 , 2.3593435 ],
[ 0.014...,
),
cArgs = (
GL_TEXTURE_3D,
0,
GL_R32F,
1440,
1023,
512,
0,
GL_RED,
GL_FLOAT,
array([[[ 0.15100943, -0.40536138, -0.11823019, ..., 1.154046 ,
1.8430679 , 2.3593435 ],
[ 0.014...,
),
cArguments = (
GL_TEXTURE_3D,
0,
GL_R32F,
1440,
1023,
512,
0,
GL_RED,
GL_FLOAT,
array([[[ 0.15100943, -0.40536138, -0.11823019, ..., 1.154046 ,
1.8430679 , 2.3593435 ],
[ 0.014...,
)
)
Exception ignored in: <function Drawing.__del__ at 0x7f8ee84aba60>
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1222, in __del__
self.delete()
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1242, in delete
raise RuntimeError("Don't have opengl context needed to delete texture from
drawing '%s' because drawing was never drawn" % self.name)
RuntimeError: Don't have opengl context needed to delete texture from drawing
'Image3D 3d texture planes' because drawing was never drawn
Exception ignored in: <function Texture.__del__ at 0x7f8ee3bfdbc0>
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 3165, in __del__
raise OpenGLError('OpenGL texture was not deleted before graphics.Texture
destroyed')
chimerax.graphics.opengl.OpenGLError: OpenGL texture was not deleted before
graphics.Texture destroyed
OpenGL version: 4.5 (Core Profile) Mesa 23.1.4
OpenGL renderer: llvmpipe (LLVM 17.0.6, 256 bits)
OpenGL vendor: Mesa
Python: 3.11.13
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=gnome
XDG_SESSION_DESKTOP=gnome
XDG_CURRENT_DESKTOP=GNOME
DISPLAY=:2
Manufacturer: ASUS
Model: System Product Name
OS: Rocky Linux 8.10
Architecture: 64bit ELF
Virtual Machine: none
CPU: 128 AMD Ryzen Threadripper PRO 9985WX 64-Cores
Cache Size: 1024 KB
Memory:
total used free shared buff/cache available
Mem: 250Gi 137Gi 108Gi 147Mi 4.7Gi 110Gi
Swap: 31Gi 0B 31Gi
Graphics:
01:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:2c31] (rev a1)
Subsystem: NVIDIA Corporation Device [10de:2051]
Kernel driver in use: nvidia
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2026.1.4
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-ArtiaX: 0.6.0
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
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: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
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: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.1
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: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
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-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
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: 1.0.1
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: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
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: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
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: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
distro: 1.9.0
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
geomdl: 5.4.0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 25.0
pandas: 3.0.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pyarrow: 23.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
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
sse-starlette: 3.2.0
stack-data: 0.6.3
starfile: 0.5.13
starlette: 0.52.1
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
urllib3: 2.6.3
uvicorn: 0.40.0
wcwidth: 0.3.2
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
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