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Opened 89 minutes ago
#20058 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, 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, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 50)
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"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,3",
"coalitionID" : 23042,
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"codeSigningMonitor" : 2,
"incident" : "D454B68A-8F82-4D84-A04F-677064AF8147",
"pid" : 63991,
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"cpuType" : "ARM-64",
"procLaunch" : "2026-03-24 15:57:17.8286 -0400",
"procStartAbsTime" : 8974760589887,
"procExitAbsTime" : 9222661242251,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX",
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"crashReporterKey" : "F762FC1B-2639-FC18-CCDC-E0C815E73B8F",
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"developerMode" : 1,
"bootProgressRegister" : "0x2f000000",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRFOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkQng\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "09950ED0-D802-4E2E-8F23-1BA1F23E54F8",
"wakeTime" : 15,
"sleepWakeUUID" : "1DA3CFF9-B63B-49D3-86F2-2A0E37FE2F69",
"sip" : "enabled",
"vmRegionInfo" : "0xc00002d40 is in 0x95e000000-0xc5ac00000; bytes after start: 11307855168 bytes before end: 1522520767
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
MALLOC_LARGE 444800000-445160000 [ 9600K] rw-\/rwx SM=PRV
GAP OF 0x518ea0000 BYTES
---> commpage (reserved) 95e000000-c5ac00000 [ 11.9G] ---\/--- SM=NUL reserved VM address space (unallocated)
MALLOC_SMALL c5ac00000-c5b000000 [ 4096K] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000002, 0x0000000c00002d40","rawCodes":[2,51539619136],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_PROTECTION_FAILURE at 0x0000000c00002d40"},
"termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":63991},
"vmregioninfo" : "0xc00002d40 is in 0x95e000000-0xc5ac00000; bytes after start: 11307855168 bytes before end: 1522520767
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
MALLOC_LARGE 444800000-445160000 [ 9600K] rw-\/rwx SM=PRV
GAP OF 0x518ea0000 BYTES
---> commpage (reserved) 95e000000-c5ac00000 [ 11.9G] ---\/--- SM=NUL reserved VM address space (unallocated)
MALLOC_SMALL c5ac00000-c5b000000 [ 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
> select /A:1-21
146 atoms, 161 bonds, 21 residues, 1 model selected
> select /B:1-124
957 atoms, 999 bonds, 124 residues, 1 model selected
> select /A:1-21
146 atoms, 161 bonds, 21 residues, 1 model selected
> color bfactor #1 palette alphafold
1103 atoms, 145 residues, atom bfactor range 33.9 to 96.3
> select /A:1-21
146 atoms, 161 bonds, 21 residues, 1 model selected
> select /B:1-124
957 atoms, 999 bonds, 124 residues, 1 model selected
> select /A:1-21
146 atoms, 161 bonds, 21 residues, 1 model selected
> alphafold contacts /A toAtoms /B distance 8
Structure fold_2026_03_24_12_05_prr_ww_model_0.cif #1 does not have PAE data
opened
> open "/Users/todbutenschon/Desktop/Rieder Lab/AlphaFold/PRR and
> WW/fold_2026_03_24_12_05_prr_ww_full_data_0.json"
Opened AlphaFold PAE with values for 145 residues and atoms
> open "/Users/todbutenschon/Desktop/Rieder Lab/AlphaFold/PRR and
> WW/fold_2026_03_24_12_05_prr_ww_full_data_0.json" format pae
Opened AlphaFold PAE with values for 145 residues and atoms
> alphafold contacts /A toAtoms /B distance 8
Found 145 residue or atom pairs within distance 8
> select /A:1-21
146 atoms, 161 bonds, 21 residues, 1 model selected
> select /B:1-124
957 atoms, 999 bonds, 124 residues, 1 model selected
> select /A:1-21
146 atoms, 161 bonds, 21 residues, 1 model selected
> select /A:1-21
146 atoms, 161 bonds, 21 residues, 1 model selected
> set bgColor white
> set bgColor black
> color /B:55-99 lime
> color /A:1-15 lime
> color /B:58-92 magenta
> color /A:12-21/B:1 lime
> color /B:95-123 magenta
> color /A:19 lime
> color /B:120 magenta
> color /A:1-19 lime
> color /B:95-121 magenta
> color /A:11 lime
> color /B:95 magenta
> color /A:10-21 lime
> color /B:96-122 magenta
> color /A:2-15 lime
> color /B:57-92 magenta
> color /A:1-5 lime
> color /B:95-122 magenta
> alphafold contacts /A toAtoms /B distance 4
Found 29 residue or atom pairs within distance 4
> color /B:34 lime
> color /B:75 magenta
> alphafold contacts /A toAtoms /B distance 3
Found 3 residue or atom pairs within distance 3
> alphafold contacts /A toAtoms /B distance 4
Found 29 residue or atom pairs within distance 4
> set bgColor white
> set bgColor black
> color /A:1-14 lime
> color /B:57-91 magenta
> color /A:9-20 lime
> color /B:96-121 magenta
> color /B:56-81 lime
> color /A:4-10 magenta
> color /B:93-122 lime
> color /A:15-21 magenta
> color /A:4 lime
> color /B:72 magenta
> color /B:10 lime
> color /B:66 magenta
> color /A:11 lime
> color /B:67 magenta
> color /B:14 lime
> color /B:65 magenta
> select /B:1-124
957 atoms, 999 bonds, 124 residues, 1 model selected
> select /A:1-21
146 atoms, 161 bonds, 21 residues, 1 model selected
> select /B:1-124
957 atoms, 999 bonds, 124 residues, 1 model selected
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> select add #1
1103 atoms, 1160 bonds, 29 pseudobonds, 145 residues, 2 models selected
> select subtract #1
Nothing selected
> select add #1
1103 atoms, 1160 bonds, 29 pseudobonds, 145 residues, 2 models selected
> select subtract #1.1
1103 atoms, 1160 bonds, 145 residues, 1 model selected
> select add #1.1
1103 atoms, 1160 bonds, 29 pseudobonds, 145 residues, 2 models selected
> select subtract #1.1
1103 atoms, 1160 bonds, 145 residues, 1 model selected
> color /A:1-16 lime
> color /B:58-91 magenta
> color /A:11-19 lime
> color /B:96-120 magenta
> color /B:5 lime
> color /B:78 magenta
> select /A:1-21
146 atoms, 161 bonds, 21 residues, 1 model selected
> select /B:1-124
957 atoms, 999 bonds, 124 residues, 1 model selected
> hide #!1 models
> hide #1.1 models
> open "/Users/todbutenschon/Desktop/Rieder Lab/AlphaFold/PRR and
> WW/fold_2026_03_24_12_05_prr_ww_model_0.cif"
Chain information for fold_2026_03_24_12_05_prr_ww_model_0.cif #2
---
Chain | Description
A | .
B | .
Computing secondary structure
> open "/Users/todbutenschon/Desktop/Rieder Lab/AlphaFold/PRR and
> WW/fold_2026_03_24_12_05_prr_ww_full_data_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/PRR and
WW/fold_2026_03_24_12_05_prr_ww_full_data_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
> show #!1 models
> hide #!1 models
> hide #2 models
> close #2
> open "/Users/todbutenschon/Desktop/Rieder Lab/AlphaFold/Bait and
> Prp40/fold_2026_03_24_12_27_bait_prp40_model_0.cif"
Chain information for fold_2026_03_24_12_27_bait_prp40_model_0.cif #2
---
Chain | Description
A | .
B | .
Computing secondary structure
> open "/Users/todbutenschon/Desktop/Rieder Lab/AlphaFold/Bait and
> Prp40/fold_2026_03_24_12_27_bait_prp40_full_data_0.json"
Opened AlphaFold PAE with values for 1567 residues and atoms
> color #2/A:31-56 lime
> color #2/B:297-494 magenta
> alphafold contacts /A toAtoms /B distance 4
Interface PAE pseudobonds can only be computed for a single structure, got 2.
> select add #1
1103 atoms, 1160 bonds, 29 pseudobonds, 145 residues, 2 models selected
> select subtract #1
Nothing selected
> alphafold contacts /A toAtoms /B distance 4
Interface PAE pseudobonds can only be computed for a single structure, got 2.
> select #2/A:1-761
5753 atoms, 5863 bonds, 761 residues, 1 model selected
> select #2/B:1-806
6416 atoms, 6537 bonds, 806 residues, 1 model selected
> select #2/A:1-761
5753 atoms, 5863 bonds, 761 residues, 1 model selected
> select #2/A:1-761
5753 atoms, 5863 bonds, 761 residues, 1 model selected
> select #2/B:1-806
6416 atoms, 6537 bonds, 806 residues, 1 model selected
> select #2/A:1-761
5753 atoms, 5863 bonds, 761 residues, 1 model selected
> select add #2
12169 atoms, 12400 bonds, 1567 residues, 1 model selected
> color #2/A:28-64 lime
> color #2/B:274-517 magenta
> select subtract #2
Nothing selected
> color #2/A:26-62 lime
> color #2/B:278-532 magenta
> alphafold contacts /A toAtoms /B distance 4
Interface PAE pseudobonds can only be computed for a single structure, got 2.
> color #2/A:362 lime
> color #2/B:417 magenta
> color #2/A:364 lime
> color #2/B:181 magenta
> select add #2
12169 atoms, 12400 bonds, 1567 residues, 1 model selected
> alphafold contacts /A toAtoms /B distance 4
Interface PAE pseudobonds can only be computed for a single structure, got 2.
> select subtract #2
Nothing selected
> open "/Users/todbutenschon/Desktop/Rieder Lab/AlphaFold/Bait and
> Prp40/fold_2026_03_24_12_27_bait_prp40_full_data_0.json"
Opened AlphaFold PAE with values for 1567 residues and atoms
> color #2/A:28-56 lime
> color #2/B:285-502 magenta
> color #2/A:617-648 lime
> color #2/B:58-143 magenta
> alphafold contacts /A toAtoms /B distance 4
Interface PAE pseudobonds can only be computed for a single structure, got 2.
> alphafold contacts /A toAtoms /B distance 8
Interface PAE pseudobonds can only be computed for a single structure, got 2.
> hide #2 models
> show #!1 models
> color #1/A:2-14 lime
> color #1/B:58-92 magenta
> color #1/A:11 lime
> color #1/B:75 magenta
> alphafold contacts /A toAtoms /B distance 8
Interface PAE pseudobonds can only be computed for a single structure, got 2.
> close #2
> close #1
> open "/Users/todbutenschon/Desktop/Rieder Lab/AlphaFold/Bait and
> Prp40/fold_2026_03_24_12_27_bait_prp40_model_0.cif" format mmcif
Chain information for fold_2026_03_24_12_27_bait_prp40_model_0.cif #1
---
Chain | Description
A | .
B | .
Computing secondary structure
> close
> open "/Users/todbutenschon/Desktop/Rieder Lab/AlphaFold/Bait and
> Prp40/fold_2026_03_24_12_27_bait_prp40_full_data_0.json" format pae
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/Bait and
Prp40/fold_2026_03_24_12_27_bait_prp40_full_data_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
> open "/Users/todbutenschon/Desktop/Rieder Lab/AlphaFold/Bait and
> Prp40/fold_2026_03_24_12_27_bait_prp40_model_0.cif" format mmcif
Chain information for fold_2026_03_24_12_27_bait_prp40_model_0.cif #1
---
Chain | Description
A | .
B | .
Computing secondary structure
> open "/Users/todbutenschon/Desktop/Rieder Lab/AlphaFold/Bait and
> Prp40/fold_2026_03_24_12_27_bait_prp40_full_data_0.json" format pae
Opened AlphaFold PAE with values for 1567 residues and atoms
> open "/Users/todbutenschon/Desktop/Rieder Lab/AlphaFold/Bait and
> Prp40/fold_2026_03_24_12_27_bait_prp40_full_data_0.json" format pae
Opened AlphaFold PAE with values for 1567 residues and atoms
> open "/Users/todbutenschon/Desktop/Rieder Lab/AlphaFold/Bait and
> Prp40/fold_2026_03_24_12_27_bait_prp40_model_0.cif" format mmcif
Chain information for fold_2026_03_24_12_27_bait_prp40_model_0.cif #2
---
Chain | Description
A | .
B | .
Computing secondary structure
> close #2
> color /A:28-56 lime
> color /B:284-496 magenta
> alphafold contacts /A toAtoms /B distance 8
Found 990 residue or atom pairs within distance 8
> alphafold contacts /A toAtoms /B distance 4
Found 148 residue or atom pairs within distance 4
> color /A:617-648 lime
> color /B:59-142 magenta
> alphafold contacts /A toAtoms /B distance 4
Found 148 residue or atom pairs within distance 4
> alphafold contacts /A toAtoms /B distance 8
Found 990 residue or atom pairs within distance 8
> color /B:56-151 lime
> color /B:217-654 lime
> color /A:26-56 lime
> color /B:278-509 magenta
> color /A:615-648 lime
> color /B:63-139 magenta
> alphafold contacts /A toAtoms /B distance 10
Found 1974 residue or atom pairs within distance 10
> alphafold contacts /A toAtoms /B distance 4.5
Found 190 residue or atom pairs within distance 4.5
> close
> open "/Users/todbutenschon/Desktop/Rieder Lab/AlphaFold/Bait and
> Prp40/fold_2026_03_24_12_27_bait_prp40_full_data_0.json" format pae
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/Bait and
Prp40/fold_2026_03_24_12_27_bait_prp40_full_data_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
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
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, 19 hours, 35 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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