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Opened 96 minutes ago
#20059 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 0x00000001f34a7100 (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.pdb_lib._load_libs, chimerax.map._map, chimerax.surface._surface, PIL._imaging, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, 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.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, PIL._imagingmath, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw, cython.cimports.libc.math, scipy._lib._ccallback_c, 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.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.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct (total: 115)
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{
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"version" : 2,
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"procLaunch" : "2026-03-24 19:39:26.9014 -0400",
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"procPath" : "\/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX",
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"appleIntelligenceStatus" : {"reasons":["assetIsNotReady","notOptedIn"],"state":"unavailable"},
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"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
MALLOC_LARGE 516c00000-519bf8000 [ 48.0M] rw-\/rwx SM=PRV
GAP OF 0xca408000 BYTES
---> commpage (reserved) 5e4000000-8ddc00000 [ 11.9G] ---\/--- SM=NUL reserved VM address space (unallocated)
MALLOC_SMALL 8ddc00000-8de000000 [ 4096K] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000002, 0x0000000800003a00","rawCodes":[2,34359753216],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_PROTECTION_FAILURE at 0x0000000800003a00"},
"termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":66532},
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REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
MALLOC_LARGE 516c00000-519bf8000 [ 48.0M] rw-\/rwx SM=PRV
GAP OF 0xca408000 BYTES
---> commpage (reserved) 5e4000000-8ddc00000 [ 11.9G] ---\/--- SM=NUL reserved VM address space (unallocated)
MALLOC_SMALL 8ddc00000-8de000000 [ 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/todbutenschon/Desktop/Rieder Lab/AlphaFold/PRR and
> WW/fold_2026_03_24_12_05_prr_ww_model_0.cif" format mmcif
Chain information for fold_2026_03_24_12_05_prr_ww_model_0.cif #1
---
Chain | Description
A | .
B | .
Computing secondary structure
> close
> open "/Users/todbutenschon/Desktop/Rieder Lab/AlphaFold/PRR and
> WW/fold_2026_03_24_12_05_prr_ww_model_0.cif" format mmcif
Chain information for fold_2026_03_24_12_05_prr_ww_model_0.cif #1
---
Chain | Description
A | .
B | .
Computing secondary structure
> open "/Users/todbutenschon/Desktop/Rieder Lab/AlphaFold/Mxc to
> Prp40/fold_2026_03_24_11_30_mxc_prp40_summary_confidences_0.json"
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open /Users/todbutenschon/Desktop/Rieder Lab/AlphaFold/Mxc to
Prp40/fold_2026_03_24_11_30_mxc_prp40_summary_confidences_0.json structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> close
> open "/Users/todbutenschon/Desktop/Rieder Lab/AlphaFold/Mxc to
> Prp40/fold_2026_03_24_11_30_mxc_prp40_full_data_0_pae.json"
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open /Users/todbutenschon/Desktop/Rieder Lab/AlphaFold/Mxc to
Prp40/fold_2026_03_24_11_30_mxc_prp40_full_data_0_pae.json structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open "/Users/todbutenschon/Desktop/Rieder Lab/AlphaFold/Mxc to
> Prp40/fold_2026_03_24_11_30_mxc_prp40_model_0.cif"
Chain information for fold_2026_03_24_11_30_mxc_prp40_model_0.cif #1
---
Chain | Description
A | .
B | .
Computing secondary structure
> color bychain
> open "/Users/todbutenschon/Desktop/Rieder Lab/AlphaFold/Mxc to
> Prp40/fold_2026_03_24_11_30_mxc_prp40_full_data_0_pae.json"
Opened AlphaFold PAE with values for 2643 residues and atoms
> color /A:675-694 lime
> color /B:358-433 magenta
> color /A:1636 lime
> color /B:166 magenta
> hide #1 models
> show #1 models
> select add #1
20264 atoms, 20642 bonds, 2643 residues, 1 model selected
> select subtract #1
Nothing selected
> color bychain
> alphafold contacts /A toAtoms /B distance 4.5
Found 524 residue or atom pairs within distance 4.5
> color /A:680-689 lime
> color /B:353-454 magenta
> color bychain
> alphafold contacts /A toAtoms /B distance 8
Found 3071 residue or atom pairs within distance 8
> alphafold contacts /A toAtoms /B distance 10
Found 6273 residue or atom pairs within distance 10
> color bychain
> hide #1.1 models
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #1/B
Alignment identifier is 1/B
> select
> /A:7-20,24-33,35-45,55-78,81-89,92-102,117-131,140-146,152-163,170-182,187-196,199-202,204-214,220-238,240-257,262-282,284-297,300-305,309-328,342-354,364-377,382-399,402-411,417-426,428-433,435-437,440-444,449-466,472-487,489-494,498-500,503-520,522-536,539-561,564-580,582-585,589-596,601-635,643-656,662-665,669-672,675-708,714-742,751-766,771-791,798-826,828-855,857-874,877-900,906-925,930-952,961-985,989-998,1011-1023,1028-1044,1052-1067,1073-1100,1104-1135,1145-1169,1176-1200,1205-1216,1223-1231,1233-1258,1272-1290,1293-1295,1300-1303,1315-1329,1349-1352,1360-1375,1378-1397,1404-1425,1433-1453,1455-1464,1467-1474,1478-1499,1507-1519,1521-1527,1535-1552,1554-1558,1561-1587,1592-1597,1601-1609,1613-1626,1635-1649,1651-1669,1676-1688,1693-1708,1711-1741,1744-1768,1770-1773,1776-1813,1815-1836
10868 atoms, 10952 bonds, 1439 residues, 1 model selected
> select /A:1340
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:1340-1362
159 atoms, 175 bonds, 23 residues, 1 model selected
> color sel bychain
> select add #1
20264 atoms, 20642 bonds, 6273 pseudobonds, 2643 residues, 2 models selected
> select subtract #1
Nothing selected
> ui tool show AlphaFold
> alphafold match #1
Fetching compressed AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
Fetching compressed AlphaFold Q9W363 from
https://alphafold.ebi.ac.uk/files/AF-Q9W363-F1-model_v6.cif
Fetching compressed AlphaFold Q9VQK5 from
https://alphafold.ebi.ac.uk/files/AF-Q9VQK5-F1-model_v6.cif
2 AlphaFold models found using sequence similarity searches: Q9W363 (chain A),
Q9VQK5 (chain B)
AlphaFold prediction matching fold_2026_03_24_11_30_mxc_prp40_model_0.cif
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
B | Q9VQK5 | Q9VQK5_DROME | 56.76 | 806 | 806 | 100
A | Q9W363 | Q9W363_DROME | 82.59 | 1837 | 1837 | 100
Opened 2 AlphaFold models
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> hide #2.2 models
> show #2.2 models
> hide #2.2 models
> hide #2.1 models
> show #2.1 models
> show #2.2 models
> hide #2.2 models
> show #2.2 models
> hide #2.2 models
> hide #2.1 models
> show #2.1 models
> show #2.2 models
> hide #2.2 models
> hide #2.1 models
> show #2.1 models
> show #2.2 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #2.1 models
> hide #2.2 models
> show #2.2 models
> show #2.1 models
> hide #2.2 models
> show #2.2 models
> hide #2.2 models
> show #2.2 models
> hide #2.2 models
> show #2.2 models
> hide #2.2 models
> show #2.2 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!1 models
> hide #2.2 models
> show #2.2 models
> show #!1 models
> hide #!1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> color #2.1 lightgray
> color #2.2 white
> color #2.2 #d9d9d9ff
> hide #2.2 models
> show #!1 models
> hide #2.1 models
> show #2.2 models
> color #2.1::c_alpha_distance>=5.0 red
> show #2.1 models
> hide #2.1 models
> color #2.2::c_alpha_distance>=5.0 red
Desktop color scheme is dark
Unsupported scale factor (0.000000) detected on Display0
===== 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
> open "/Users/todbutenschon/Desktop/Rieder Lab/AlphaFold/PRR and
> WW/fold_2026_03_24_12_05_prr_ww_model_0.cif" format mmcif
Chain information for fold_2026_03_24_12_05_prr_ww_model_0.cif #1
---
Chain | Description
A | .
B | .
Computing secondary structure
> open "/Users/todbutenschon/Desktop/Rieder Lab/AlphaFold/Mxc to
> Prp40/fold_2026_03_24_11_30_mxc_prp40_model_0.cif"
Chain information for fold_2026_03_24_11_30_mxc_prp40_model_0.cif #2
---
Chain | Description
A | .
B | .
Computing secondary structure
> hide #1 models
> ui autostart false "Model Panel"
> close #1
> color bychain
> select #2/A:1-1837
13848 atoms, 14105 bonds, 1837 residues, 1 model selected
> select #2/B:1-806
6416 atoms, 6537 bonds, 806 residues, 1 model selected
> select add #2
20264 atoms, 20642 bonds, 2643 residues, 1 model selected
> select subtract #2
Nothing selected
> select #2/A:1-1837
13848 atoms, 14105 bonds, 1837 residues, 1 model selected
> select add #2
20264 atoms, 20642 bonds, 2643 residues, 1 model selected
> select subtract #2
Nothing selected
> sequence chain #2/A
Alignment identifier is 2/A
> sequence chain #2/B
Alignment identifier is 2/B
> select /A:1362-1363
16 atoms, 16 bonds, 2 residues, 1 model selected
> select /A:1340-1363
168 atoms, 184 bonds, 24 residues, 1 model selected
> select
> /A:7-20,24-33,35-45,55-78,81-89,92-102,117-131,140-146,152-163,170-182,187-196,199-202,204-214,220-238,240-257,262-282,284-297,300-305,309-328,342-354,364-377,382-399,402-411,417-426,428-433,435-437,440-444,449-466,472-487,489-494,498-500,503-520,522-536,539-561,564-580,582-585,589-596,601-635,643-656,662-665,669-672,675-708,714-742,751-766,771-791,798-826,828-855,857-874,877-900,906-925,930-952,961-985,989-998,1011-1023,1028-1044,1052-1067,1073-1100,1104-1135,1145-1169,1176-1200,1205-1216,1223-1231,1233-1258,1272-1290,1293-1295,1300-1303,1315-1329,1349-1352,1360-1375,1378-1397,1404-1425,1433-1453,1455-1464,1467-1474,1478-1499,1507-1519,1521-1527,1535-1552,1554-1558,1561-1587,1592-1597,1601-1609,1613-1626,1635-1649,1651-1669,1676-1688,1693-1708,1711-1741,1744-1768,1770-1773,1776-1813,1815-1836
10868 atoms, 10952 bonds, 1439 residues, 1 model selected
> select /A:1340-1363
168 atoms, 184 bonds, 24 residues, 1 model selected
> select /A:1342
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:1342-1362
145 atoms, 160 bonds, 21 residues, 1 model selected
> select /A:1342-1343
14 atoms, 15 bonds, 2 residues, 1 model selected
> select /A:1342-1361
138 atoms, 152 bonds, 20 residues, 1 model selected
> select /A:1342-1361
138 atoms, 152 bonds, 20 residues, 1 model selected
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M3
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: Mac15,3
Model Number: MR7J3LL/A
Chip: Apple M3
Total Number of Cores: 8 (4 Performance and 4 Efficiency)
Memory: 8 GB
System Firmware Version: 13822.81.10
OS Loader Version: 13822.81.10
Software:
System Software Overview:
System Version: macOS 26.3.1 (25D2128)
Kernel Version: Darwin 25.3.0
Time since boot: 13 days, 20 hours, 22 minutes
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
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
DELL S2721QS:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
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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