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Opened 4 hours ago
#20359 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 0x0000000209527100 (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/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.map._map, chimerax.surface._surface, PIL._imaging, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, chimerax.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.xtc_utils, openmm.app.internal.compiled, 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._imagingmath, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.special._ellip_harm_2, scipy.interpolate._fitpack, scipy.interpolate._dfitpack, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.spatial.transform._rotation, scipy.optimize._direct, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, kiwisolver._cext, chimerax.atom_search.ast, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.chem_group._chem_group (total: 123)
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"codeSigningMonitor" : 2,
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"procLaunch" : "2026-05-19 17:00:26.4567 -0400",
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REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
MALLOC_LARGE 46d800000-4709fc000 [ 50.0M] rw-\/rwx SM=PRV
GAP OF 0x1b5604000 BYTES
---> commpage (reserved) 626000000-917c00000 [ 11.8G] ---\/--- SM=NUL reserved VM address space (unallocated)
MALLOC_SMALL 917c00000-918000000 [ 4096K] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000002, 0x0000000900000900","rawCodes":[2,38654707968],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_PROTECTION_FAILURE at 0x0000000900000900"},
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"vmregioninfo" : "0x900000900 is in 0x626000000-0x917c00000; bytes after start: 12247369984 bytes before end: 398456575
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
MALLOC_LARGE 46d800000-4709fc000 [ 50.0M] rw-\/rwx SM=PRV
GAP OF 0x1b5604000 BYTES
---> commpage (reserved) 626000000-917c00000 [ 11.8G] ---\/--- SM=NUL reserved VM address space (unallocated)
MALLOC_SMALL 917c00000-918000000 [ 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/guidopetrovich/Documents/DmelIR25a_IR93a-VcarIR40a/DmelIR25a_IR93a-VcarIR40a-Isolde5.pdb
Chain information for DmelIR25a_IR93a-VcarIR40a-Isolde5.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> open
> /Users/guidopetrovich/Documents/DmelIR25a_IR93a-VcarIR40a/cryosparc_P54_J755_004_volume_map_sharp.mrc
Opened cryosparc_P54_J755_004_volume_map_sharp.mrc as #2, grid size
360,360,360, pixel 0.987, shown at level 0.0686, step 2, values float32
> open /Users/guidopetrovich/Documents/DmelIR25a_IR93a-VcarIR40a/IR40a_LBD-
> lobe2.pdb
Chain information for IR40a_LBD-lobe2.pdb #3
---
Chain | Description
A | No description available
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1 to IUPAC-IUB
standards.
Chain information for DmelIR25a_IR93a-VcarIR40a-Isolde5.pdb #1.2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> clipper associate #2 toModel #1
Opened cryosparc_P54_J755_004_volume_map_sharp.mrc as #1.1.1.1, grid size
360,360,360, pixel 0.987, shown at step 1, values float32
> set bgColor white
> lighting soft
> graphics silhouettes true
> select clear
> sequence chain #1.2/A
Alignment identifier is 1.2/A
> select #1.2/A:23
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1.2/A:23
20 atoms, 20 bonds, 1 residue, 1 model selected
> isolde stepto #1.2/A:23
> transparency 50
> volume style surface
> volume #1.1.1.1 level 0.1
> isolde stepto next
> select #1.2/A:24-25
33 atoms, 32 bonds, 2 residues, 1 model selected
> select #1.2/A:24-27
58 atoms, 57 bonds, 4 residues, 1 model selected
> select #1.2/A:23
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1.2/A:23-67
717 atoms, 721 bonds, 45 residues, 1 model selected
> isolde sim start #1.2/A:23-67
ISOLDE: started sim
> select #1.2/A:39
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1.2/A:39-40
32 atoms, 32 bonds, 2 residues, 1 model selected
> select #1.2/A:43
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1.2/A:43-44
29 atoms, 28 bonds, 2 residues, 1 model selected
> select #1.2/A:40
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1.2/A:40-50
156 atoms, 157 bonds, 11 residues, 1 model selected
> isolde stepto prev
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde stepto next
> volume #1.1.1.1 level 0.2
> isolde stepto next
> isolde stepto prev
> isolde sim start #1.2/A:108
ISOLDE: started sim
> select #1.2/A:109
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1.2/A:109-111
40 atoms, 39 bonds, 3 residues, 1 model selected
> select #1.2/A:93
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1.2/A:93-108
264 atoms, 266 bonds, 16 residues, 1 model selected
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> isolde stepto prev
> isolde sim start #1.2/A:120
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> isolde sim start #1.2/A:123
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde stepto next
> isolde stepto prev
> isolde sim start #1.2/A:179
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> select #1.2/A:182
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1.2/A:182-183
31 atoms, 30 bonds, 2 residues, 1 model selected
> isolde sim start #1.2/A:182-183
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> select #1.2/A:185
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1.2/A:185-192
131 atoms, 132 bonds, 8 residues, 1 model selected
> isolde sim start #1.2/A:185-192
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> isolde sim start #1.2/A:192
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> select #1.2/A:199
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/A:199-200
18 atoms, 17 bonds, 2 residues, 1 model selected
> isolde sim start #1.2/A:199-200
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> isolde sim start #1.2/A:259
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> isolde sim start #1.2/A:267
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> isolde sim start #1.2/A:293
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save
> /Users/guidopetrovich/Documents/DmelIR25a_IR93a-VcarIR40a/DmelIR25a_IR93a-VcarIR40a-Isolde6.pdb
> models #1
> isolde stepto next
> isolde sim start #1.2/A:299
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> isolde stepto prev
> isolde sim start #1.2/A:319
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> isolde sim start #1.2/A:320
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> isolde stepto prev
> isolde sim start #1.2/A:330
ISOLDE: started sim
> select #1.2/A:329
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1.2/A:329-331
50 atoms, 50 bonds, 3 residues, 1 model selected
> select #1.2/A:320
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1.2/A:320-331
172 atoms, 173 bonds, 12 residues, 1 model selected
> isolde stepto prev
> isolde stepto next
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde stepto next
> select #1.2/A:263
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1.2/A:263-346
1341 atoms, 1360 bonds, 84 residues, 1 model selected
> select #1.2/A:263-264
34 atoms, 34 bonds, 2 residues, 1 model selected
> select #1.2/A:263-347
1365 atoms, 1384 bonds, 85 residues, 1 model selected
> isolde sim start #1.2/A:263-347
ISOLDE: started sim
> select #1.2/A:260
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1.2/A:260
22 atoms, 21 bonds, 1 residue, 1 model selected
> isolde stepto #1.2/A:260
> isolde stepto next
> select #1.2/A:319-320
39 atoms, 39 bonds, 2 residues, 1 model selected
> select #1.2/A:319-320
39 atoms, 39 bonds, 2 residues, 1 model selected
> select #1.2/A:321
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1.2/A:319-321
53 atoms, 53 bonds, 3 residues, 1 model selected
> select #1.2/A:331
17 atoms, 17 bonds, 1 residue, 1 model selected
> select #1.2/A:319-331
192 atoms, 194 bonds, 13 residues, 1 model selected
> select #1.2/A:319
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1.2/A:319
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1.2/A:320-321
33 atoms, 32 bonds, 2 residues, 1 model selected
> select #1.2/A:320-321
33 atoms, 32 bonds, 2 residues, 1 model selected
> select #1.2/A:320
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1.2/A:320
19 atoms, 18 bonds, 1 residue, 1 model selected
> isolde stepto next
> select #1.2/A:322
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1.2/A:322-331
139 atoms, 140 bonds, 10 residues, 1 model selected
> select #1.2/A:321
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1.2/A:321-328
103 atoms, 103 bonds, 8 residues, 1 model selected
> select #1.2/A:320
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1.2/A:320-331
172 atoms, 173 bonds, 12 residues, 1 model selected
> select #1.2/A:320
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1.2/A:320
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1.2/A:321
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1.2/A:321
14 atoms, 13 bonds, 1 residue, 1 model selected
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1.2/A:342
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1.2/A:342-343
38 atoms, 37 bonds, 2 residues, 1 model selected
> select #1.2/A:347
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2/A:341-347
130 atoms, 131 bonds, 7 residues, 1 model selected
> isolde sim start #1.2/A:341-347
ISOLDE: started sim
> isolde stepto next
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save
> /Users/guidopetrovich/Documents/DmelIR25a_IR93a-VcarIR40a/DmelIR25a_IR93a-VcarIR40a-Isolde7.pdb
> models #1
===== 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 M5
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: Mac17,2
Model Number: MDE34LL/A
Chip: Apple M5
Total Number of Cores: 10 (4 Super and 6 Efficiency)
Memory: 24 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: 1 day, 5 hours, 51 minutes
Graphics/Displays:
Apple M5:
Chipset Model: Apple M5
Type: GPU
Bus: Built-In
Total Number of Cores: 10
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: No
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-Clipper: 0.26.1
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-ISOLDE: 1.11.1
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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