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Opened 88 minutes ago
#20075 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-26.3.1-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error
Current thread 0x0000000203de3100 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 248 in swap_buffers
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 561 in swap_buffers
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py", line 166 in status
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py", line 98 in _expose_event
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 122 in make_current
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 555 in make_current
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 584 in use_shared_context
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 146 in render
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 115 in _redraw
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 100 in draw_new_frame
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 169 in update_graphics_now
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py", line 153 in resizeEvent
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py", line 61 in event
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 414 in event_loop
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, chimerax.map._map, chimerax.surface._surface, PIL._imaging, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.alignment_algs._sw (total: 60)
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REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
MALLOC_SMALL 513000000-513400000 [ 4096K] rw-\/rwx SM=PRV
GAP OF 0x28ac00000 BYTES
---> commpage (reserved) 79e000000-a99400000 [ 11.9G] ---\/--- SM=NUL reserved VM address space (unallocated)
MALLOC_SMALL a99400000-a99800000 [ 4096K] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000002, 0x0000000a00001b40","rawCodes":[2,42949679936],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_PROTECTION_FAILURE at 0x0000000a00001b40"},
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REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
MALLOC_SMALL 513000000-513400000 [ 4096K] rw-\/rwx SM=PRV
GAP OF 0x28ac00000 BYTES
---> commpage (reserved) 79e000000-a99400000 [ 11.9G] ---\/--- SM=NUL reserved VM address space (unallocated)
MALLOC_SMALL a99400000-a99800000 [ 4096K] rw-\/rwx SM=PRV ",
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===== Log before crash start =====
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 "/Users/SSVirdee/Library/CloudStorage/OneDrive-
> UniversityofDundee/Mehmet Gundogdu (Staff)'s files -
> MYCBP2_NMNAT2_manuscript/figures/raw_data/chimera_sessions/7_MYCBP2_FBXO45_SKP1_overall/7_chimera_figure_5.cxs"
> format session
> view name session-start
opened ChimeraX session
> hide #!2-7 surfaces
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> save "/Users/SSVirdee/OneDrive - University of Dundee/35575 home
> backup/Documents/Projects/MYCBP2/SKP1-MYCBP2-FBXO45 Manuscript/Isolated
> domains/FBD.pdb" models #2
> combine #2a
Expected a keyword
> combine #2
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> show #!9 surfaces
> coulombic #!9
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for copy of copy of
ESRF20240426_p1s9_grenadesfp_aimless_refmac7_fixed2.pdb_A SES surface #9.2:
minimum, -11.07, mean 0.41, maximum 12.64
To also show corresponding color key, enter the above coulombic command and
add key true
> open 9r94
Summary of feedback from opening 9r94 fetched from pdb
---
note | Fetching compressed mmCIF 9r94 from http://files.rcsb.org/download/9r94.cif
9r94 title:
Cryo-EM structure of the E3 ligase HECTD3 [more info...]
Chain information for 9r94 #10
---
Chain | Description | UniProt
A | E3 ubiquitin-protein ligase HECTD3 | HECD3_HUMAN 1-861
> hide #!9 models
> show #!9 models
> hide #!10 models
> show #!10 models
> mmaker #10/a to #9/a pair bs alg sw matrix PAM-150 ss false cut 5.0
Parameters
---
Chain pairing | bs
Alignment algorithm | Smith-Waterman
Similarity matrix | PAM-150
No secondary-structure guidance used
Gap open | 12
Gap extend | 1
Iteration cutoff | 5
Matchmaker copy of copy of
ESRF20240426_p1s9_grenadesfp_aimless_refmac7_fixed2.pdb (#9) with 9r94 (#10),
sequence alignment score = 43
RMSD between 41 pruned atom pairs is 2.148 angstroms; (across all 43 pairs:
2.803)
> hide #!9 models
> ui tool show "Side View"
> show #!9 models
> hide #!9 models
> show #!10 surfaces
> coulombic #!10
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 9r94_A SES surface #10.2: minimum, -24.22, mean -2.46,
maximum 15.02
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!10 surfaces
> show #!9 models
> hide #!9-10 surfaces
> hide #!10 models
> select #9/A:2482
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel ball
Changed 11 atom styles
> show sel atoms
> hide #!9 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> show #!9 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!9 models
> hide #!10 models
> show #!2 models
> show #!1 models
> show #!3 models
> show #!4 models
> show #!5 models
> save "/Users/SSVirdee/OneDrive - University of Dundee/Mehmet Gundogdu
> (Staff)'s files -
> MYCBP2_NMNAT2_manuscript/figures/raw_data/chimera_sessions/7_MYCBP2_FBXO45_SKP1_overall/7_chimera_figure_5_SV.cxs"
> close session
> open "/Users/SSVirdee/Library/CloudStorage/OneDrive-
> UniversityofDundee/Mehmet Gundogdu (Staff)'s files -
> MYCBP2_NMNAT2_manuscript/figures/raw_data/chimera_sessions/6_MYCBP2_FBXO45_SKP1_ASU/6_chimera_figure_1_ASU.cxs"
Opened ESRF20240426_p1s9_grenadesfp_aimless_refmac7.ccp4 as #2, grid size
249,267,231, pixel 0.877,0.82,0.887, shown at level 0.12, step 1, values
float32
Opened ESRF20240426_p1s9_grenadesfp_aimless_refmac7.ccp4 zone as #3, grid size
249,267,231, pixel 0.877,0.82,0.887, shown at level 0.12, step 1, values
float32
Opened ESRF20240426_p1s9_grenadesfp_aimless_refmac7.ccp4 zone as #4, grid size
249,267,231, pixel 0.877,0.82,0.887, shown at level 0.12, step 1, values
float32
Opened ESRF20240426_p1s9_grenadesfp_aimless_refmac7.ccp4 zone as #5, grid size
249,267,231, pixel 0.877,0.82,0.887, shown at level 0.12, step 1, values
float32
Opened ESRF20240426_p1s9_grenadesfp_aimless_refmac7.ccp4 zone as #6, grid size
249,267,231, pixel 0.877,0.82,0.887, shown at level 0.12, step 1, values
float32
Opened ESRF20240426_p1s9_grenadesfp_aimless_refmac7.ccp4 zone as #7, grid size
249,267,231, pixel 0.877,0.82,0.887, shown at level 0.12, step 1, values
float32
Opened ESRF20240426_p1s9_grenadesfp_aimless_refmac7.ccp4 zone as #8, grid size
249,267,231, pixel 0.877,0.82,0.887, shown at level 0.12, step 1, values
float32
> view name session-start
opened ChimeraX session
> close session
> open "/Users/SSVirdee/Library/CloudStorage/OneDrive-
> UniversityofDundee/Mehmet Gundogdu (Staff)'s files -
> MYCBP2_NMNAT2_manuscript/figures/raw_data/chimera_sessions/6_MYCBP2_FBXO45_SKP1_ASU/6_chimera_figure_2_ASU.cxs"
Opened ESRF20240426_p1s9_grenadesfp_aimless_refmac7.ccp4 as #2, grid size
249,267,231, pixel 0.877,0.82,0.887, shown at level 0.12, step 1, values
float32
Opened ESRF20240426_p1s9_grenadesfp_aimless_refmac7.ccp4 zone as #12, grid
size 249,267,231, pixel 0.877,0.82,0.887, shown at level 0.12, step 1, values
float32
Opened ESRF20240426_p1s9_grenadesfp_aimless_refmac7.ccp4 zone as #13, grid
size 249,267,231, pixel 0.877,0.82,0.887, shown at level 0.12, step 1, values
float32
Opened ESRF20240426_p1s9_grenadesfp_aimless_refmac7.ccp4 zone as #14, grid
size 249,267,231, pixel 0.877,0.82,0.887, shown at level 0.12, step 1, values
float32
Opened ESRF20240426_p1s9_grenadesfp_aimless_refmac7.ccp4 zone as #15, grid
size 249,267,231, pixel 0.877,0.82,0.887, shown at level 0.12, step 1, values
float32
Opened ESRF20240426_p1s9_grenadesfp_aimless_refmac7.ccp4 zone as #16, grid
size 249,267,231, pixel 0.877,0.82,0.887, shown at level 0.12, step 1, values
float32
Opened ESRF20240426_p1s9_grenadesfp_aimless_refmac7.ccp4 zone as #17, grid
size 249,267,231, pixel 0.877,0.82,0.887, shown at level 0.12, step 1, values
float32
Opened ESRF20240426_p1s9_grenadesfp_aimless_refmac7.ccp4 zone as #18, grid
size 249,267,231, pixel 0.877,0.82,0.887, shown at level 0.12, step 1, values
float32
Opened ESRF20240426_p1s9_grenadesfp_aimless_refmac7.ccp4 zone as #19, grid
size 249,267,231, pixel 0.877,0.82,0.887, shown at level 0.12, step 1, values
float32
Opened ESRF20240426_p1s9_grenadesfp_aimless_refmac7.ccp4 zone as #20, grid
size 249,267,231, pixel 0.877,0.82,0.887, shown at level 0.12, step 1, values
float32
> view name session-start
opened ChimeraX session
> close session
> open "/Users/SSVirdee/Library/CloudStorage/OneDrive-
> UniversityofDundee/Mehmet Gundogdu (Staff)'s files -
> MYCBP2_NMNAT2_manuscript/figures/raw_data/chimera_sessions/7_MYCBP2_FBXO45_SKP1_overall/7_chimera_figure_3.cxs"
> view name session-start
opened ChimeraX session
> cartoon tether scale 0
> hide #1.1 models
> tuen y 180
Unknown command: tuen y 180
> turn y 180
> cartoon tether scale 0
> turn y 180
> save "/Users/SSVirdee/OneDrive - University of Dundee/35575 home
> backup/Documents/Projects/MYCBP2/SKP1-MYCBP2-FBXO45 Manuscript/Full
> scale_single-0_degrees.png" width 1922 height 1205 supersample 3
> turn y 180
> save "/Users/SSVirdee/OneDrive - University of Dundee/35575 home
> backup/Documents/Projects/MYCBP2/SKP1-MYCBP2-FBXO45 Manuscript/Full
> scale_single-180_degrees.png" width 1922 height 1205 supersample 3
> turn y 180
> save "/Users/SSVirdee/OneDrive - University of Dundee/35575 home
> backup/Documents/Projects/MYCBP2/SKP1-MYCBP2-FBXO45 Manuscript/Full
> scale_single-0_degrees.png" width 3000 height 1881 supersample 3
> turn y 180
> save "/Users/SSVirdee/OneDrive - University of Dundee/35575 home
> backup/Documents/Projects/MYCBP2/SKP1-MYCBP2-FBXO45 Manuscript/Full
> scale_single-180_degrees.png" width 3000 height 1881 supersample 3
> close session
> open "/Users/SSVirdee/Library/CloudStorage/OneDrive-
> UniversityofDundee/Mehmet Gundogdu (Staff)'s files -
> MYCBP2_NMNAT2_manuscript/figures/raw_data/chimera_sessions/7_MYCBP2_FBXO45_SKP1_overall/7_chimera_figure_3.cxs"
> format session
> view name session-start
opened ChimeraX session
> turn y 180
===== Log before crash end =====
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
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,5
Model Number: MPHG3B/A
Chip: Apple M2 Max
Total Number of Cores: 12 (8 Performance and 4 Efficiency)
Memory: 32 GB
System Firmware Version: 13822.81.10
OS Loader Version: 13822.81.10
Software:
System Software Overview:
System Version: macOS 26.3.1 (a) (25D771280a)
Kernel Version: Darwin 25.3.0
Time since boot: 4 days, 15 hours, 3 minutes
Graphics/Displays:
Apple M2 Max:
Chipset Model: Apple M2 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 30
Vendor: Apple (0x106b)
Metal Support: Metal 4
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:
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
appnope: 0.1.4
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: 2025.7.14
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-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-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
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
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
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
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
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
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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