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Opened 8 hours ago
#19788 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-26.2-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: Segmentation fault
Current thread 0x00000001f1956c40 (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/atomic/structure.py", line 1487 in apply_auto_styling
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 206 in added_to_session
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 1385 in added_to_session
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/models.py", line 827 in add
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 297 in provider_open
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3237 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 132 in cmd_open
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3237 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/dialog.py", line 355 in _qt_safe
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.pdb_lib._load_libs, chimerax.surface._surface, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, 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, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath (total: 50)
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{
"uptime" : 42000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac16,6",
"coalitionID" : 7734,
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"build" : "25C56",
"releaseType" : "User"
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"captureTime" : "2026-02-01 17:25:58.0598 -0800",
"codeSigningMonitor" : 2,
"incident" : "F340948D-0A29-4CED-B39F-103AD6093B43",
"pid" : 39562,
"translated" : false,
"cpuType" : "ARM-64",
"procLaunch" : "2026-02-01 17:21:30.0889 -0800",
"procStartAbsTime" : 1013964688501,
"procExitAbsTime" : 1020395554180,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.11.1","CFBundleVersion":"1.11.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"8AB6E830-A965-505B-A827-4DF2C6CB1339","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "D8BF9185-89E6-3F5A-A82B-FD7DE51DFE3F",
"appleIntelligenceStatus" : {"state":"available"},
"developerMode" : 1,
"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" : "84A50A5F-91E0-47F1-9594-9244B0A8C231",
"wakeTime" : 4400,
"sleepWakeUUID" : "B58F06C5-3704-4A8F-A3A2-744411642E25",
"sip" : "enabled",
"vmRegionInfo" : "0x16c643fc0 is in 0x168e40000-0x16c644000; bytes after start: 58736576 bytes before end: 63
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
VM_ALLOCATE 1670ec000-1671ec000 [ 1024K] r--\/r-- SM=PRV
GAP OF 0x1c54000 BYTES
---> Stack Guard 168e40000-16c644000 [ 56.0M] ---\/rwx SM=NUL
Stack 16c644000-16ce40000 [ 8176K] rw-\/rwx SM=SHM ",
"exception" : {"codes":"0x0000000000000002, 0x000000016c643fc0","message":"Could not determine thread index for stack guard region","rawCodes":[2,6113476544],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_PROTECTION_FAILURE at 0x000000016c643fc0"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":39562},
"vmregioninfo" : "0x16c643fc0 is in 0x168e40000-0x16c644000; bytes after start: 58736576 bytes before end: 63
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
VM_ALLOCATE 1670ec000-1671ec000 [ 1024K] r--\/r-- SM=PRV
GAP OF 0x1c54000 BYTES
---> Stack Guard 168e40000-16c644000 [ 56.0M] ---\/rwx SM=NUL
Stack 16c644000-16ce40000 [ 8176K] rw-\/rwx SM=SHM ",
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Foundation 48K 2
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shared memory 3728K 26
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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/vivekadarsh/Downloads/4JX3.pdb
4JX3.pdb title:
Crystal structure of PIM1 kinase [more info...]
Chain information for 4JX3.pdb #1
---
Chain | Description | UniProt
A | PIM1 kinase | PIM1_HUMAN 1-313
> set bgColor white
> lighting full
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> open /Users/vivekadarsh/Downloads/4JX3.pdb
4JX3.pdb title:
Crystal structure of PIM1 kinase [more info...]
Chain information for 4JX3.pdb #2
---
Chain | Description | UniProt
A | PIM1 kinase | PIM1_HUMAN 1-313
> open /Users/vivekadarsh/Downloads/PIM1/251121094721-2ef9a718_cmpx.pdb
> /Users/vivekadarsh/Downloads/PIM1/251121101614-a628c515_cmpx.pdb
> /Users/vivekadarsh/Downloads/PIM1/251121102040-36a71612_cmpx.pdb
> /Users/vivekadarsh/Downloads/PIM1/251121103201-eb44cdb8_cmpx.pdb
> /Users/vivekadarsh/Downloads/PIM1/251121103852-1c15afa8_cmpx.pdb
> /Users/vivekadarsh/Downloads/PIM1/251121110540-941bf4a5_cmpx.pdb
Summary of feedback from opening
/Users/vivekadarsh/Downloads/PIM1/251121094721-2ef9a718_cmpx.pdb
---
warnings | Ignored bad PDB record found on line 2228
REMARK VINA RESULT: -12.2 0.000 0.000
Ignored bad PDB record found on line 2229
REMARK CORE O=c3[nH]ccc4c(N2CCOc1ccccc1C2)nc([*:1])cc34
Ignored bad PDB record found on line 2230
REMARK SMILES O=C(c1cc2c(=O)[nH]ccc2c(N2CCOc3ccccc3C2)n1)c1ccccc1C(=O)N1CCCC1
Ignored bad PDB record found on line 2231
REMARK SMILES IDX 25 1 26 2 27 3 28 4 29 5 30 6 2 7 1 8 3 9 4 10 24 11 5 12
Ignored bad PDB record found on line 2232
REMARK SMILES IDX 12 13 6 14 11 15 8 16 10 17 9 18 7 19 13 21 14 22 23 23
3 messages similar to the above omitted
notes | Combining 110 symmetry atoms into GLN /A:285 CG
Combining 31 symmetry atoms into GLN /A:285 NE2
Combining 33 symmetry atoms into GLN /A:285 O
Summary of feedback from opening
/Users/vivekadarsh/Downloads/PIM1/251121101614-a628c515_cmpx.pdb
---
warnings | Ignored bad PDB record found on line 2228
REMARK VINA RESULT: -12.2 0.000 0.000
Ignored bad PDB record found on line 2229
REMARK CORE O=c3[nH]ccc4c(N2CCOc1ccccc1C2)nc([*:1])cc34
Ignored bad PDB record found on line 2230
REMARK SMILES O=C(c1ccc2c(c1)CNCC2)c1cc2c(=O)[nH]ccc2c(N2CCOc3ccccc3C2)n1
Ignored bad PDB record found on line 2231
REMARK SMILES IDX 1 1 2 2 3 3 4 4 8 5 5 6 7 7 6 8 9 9 12 10 10 11 11 12 13 14
Ignored bad PDB record found on line 2232
REMARK SMILES IDX 14 15 34 16 15 17 22 18 16 19 21 20 18 21 20 22 19 23 17 24
3 messages similar to the above omitted
notes | /Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py:519: RuntimeWarning: overflow encountered in cast
xyzr[:, :3] = atoms.coords
Combining 6 symmetry atoms into GLN /A:285 CG
Combining 3 symmetry atoms into GLN /A:285 NE2
Combining 4 symmetry atoms into GLN /A:285 O
Combining 2 symmetry atoms into HIS /A:287 CD2
Combining 3 symmetry atoms into GLN /A:291 NE2
Combining 4 symmetry atoms into PRO /A:296 CG
Combining 4 symmetry atoms into ASP /A:292 CG
Combining 5 symmetry atoms into MET /A:290 CA
Combining 2 symmetry atoms into TRP /A:289 CG
Combining 5 symmetry atoms into MET /A:290 C
Combining 3 symmetry atoms into GLN /A:297 O
Combining 2 symmetry atoms into TRP /A:289 C
Combining 2 symmetry atoms into THR /A:299 CB
Summary of feedback from opening
/Users/vivekadarsh/Downloads/PIM1/251121102040-36a71612_cmpx.pdb
---
warnings | Ignored bad PDB record found on line 2228
REMARK VINA RESULT: -11.9 0.000 0.000
Ignored bad PDB record found on line 2229
REMARK CORE O=c3[nH]ccc4c(N2CCOc1ccccc1C2)nc([*:1])cc34
Ignored bad PDB record found on line 2230
REMARK SMILES
O=C1C[C@@H](c2cccc(-c3cc4c(=O)[nH]ccc4c(N4CCOc5ccccc5C4)n3)c2)CN1
Ignored bad PDB record found on line 2231
REMARK SMILES IDX 5 1 6 2 7 3 8 4 9 5 32 6 4 7 2 8 3 9 34 10 33 11 1 12 10 14
Ignored bad PDB record found on line 2232
REMARK SMILES IDX 11 15 31 16 12 17 19 18 13 19 18 20 15 21 17 22 16 23 14 24
3 messages similar to the above omitted
notes | Combining 110 symmetry atoms into GLN /A:285 CG
Combining 31 symmetry atoms into GLN /A:285 NE2
Combining 33 symmetry atoms into GLN /A:285 O
Summary of feedback from opening
/Users/vivekadarsh/Downloads/PIM1/251121103201-eb44cdb8_cmpx.pdb
---
warnings | Ignored bad PDB record found on line 2228
REMARK VINA RESULT: -12.0 0.000 0.000
Ignored bad PDB record found on line 2229
REMARK CORE O=c3[nH]ccc4c(N2CCOc1ccccc1C2)nc([*:1])cc34
Ignored bad PDB record found on line 2230
REMARK SMILES
O=C1CC[C@@H]2COc3ccc(Cc4cc5c(=O)[nH]ccc5c(N5CCOc6ccccc6C5)n4)cc3N12
Ignored bad PDB record found on line 2231
REMARK SMILES IDX 12 1 11 2 2 3 3 4 37 5 4 6 5 7 36 8 6 9 8 10 35 11 7 12 9 13
Ignored bad PDB record found on line 2232
REMARK SMILES IDX 10 14 1 15 13 16 14 17 34 18 15 19 22 20 16 21 21 22 18 23
3 messages similar to the above omitted
Some X/Y/Z coordinate values in the '251121103201-eb44cdb8_cmpx.pdb' PDB file
are not finite numbers
> open /Users/vivekadarsh/Downloads/PIM1/251121103852-1c15afa8_cmpx.pdb
Summary of feedback from opening
/Users/vivekadarsh/Downloads/PIM1/251121103852-1c15afa8_cmpx.pdb
---
warnings | Ignored bad PDB record found on line 2228
REMARK VINA RESULT: -12.4 0.000 0.000
Ignored bad PDB record found on line 2229
REMARK CORE O=c3[nH]ccc4c(N2CCOc1ccccc1C2)nc([*:1])cc34
Ignored bad PDB record found on line 2230
REMARK SMILES CN1CCc2cc(C(=O)c3cc4c(=O)[nH]ccc4c(N4CCOc5ccccc5C4)n3)ccc2C1
Ignored bad PDB record found on line 2231
REMARK SMILES IDX 8 1 9 2 7 3 2 4 3 5 35 6 4 7 34 8 5 9 33 10 6 11 32 12 1 13
Ignored bad PDB record found on line 2232
REMARK SMILES IDX 10 14 11 15 31 16 12 17 19 18 13 19 18 20 15 21 17 22 16 23
3 messages similar to the above omitted
notes | Combining 1381 symmetry atoms into TYR /A:38 CA
Combining 380 symmetry atoms into GLN /A:37 NE2
Combining 394 symmetry atoms into GLN /A:37 OE1
Combining 8 symmetry atoms into MET /A:88 SD
Chain information for 251121103852-1c15afa8_cmpx.pdb #3
---
Chain | Description
A | No description available
/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py:1607: RuntimeWarning: invalid value
encountered in subtract
lv = translation(center - radius * ld) * orthonormal_frame(-ld)
/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py:972: RuntimeWarning: invalid value
encountered in scalar add
return (d-r, d+r)
/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/camera.py:254: RuntimeWarning: invalid value
encountered in subtract
bc = bounds.box_corners() - center
/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/camera.py:259: RuntimeWarning: invalid value
encountered in multiply
camera_center = center - d*view_direction
/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/camera.py:259: RuntimeWarning: invalid value
encountered in subtract
camera_center = center - d*view_direction
/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py:177: RuntimeWarning: invalid value
encountered in scalar multiply
\+ m1[r][2] * m2[2][c])
/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py:176: RuntimeWarning: invalid value
encountered in scalar multiply
p[r][c] = (m1[r][0] * m2[0][c] + m1[r][1] * m2[1][c]
> open /Users/vivekadarsh/Downloads/PIM1/251123220754-33c69291-7_cmpx.pdb
Summary of feedback from opening
/Users/vivekadarsh/Downloads/PIM1/251123220754-33c69291-7_cmpx.pdb
---
warnings | Ignored bad PDB record found on line 2484
REMARK VINA RESULT: -11.842 0.000 0.000
Ignored bad PDB record found on line 2485
REMARK INTER + INTRA: -14.445
Ignored bad PDB record found on line 2486
REMARK INTER: -14.265
Ignored bad PDB record found on line 2487
REMARK INTRA: -0.180
Ignored bad PDB record found on line 2488
REMARK UNBOUND: -0.180
5 messages similar to the above omitted
notes | Combining 11 symmetry atoms into GLN /A:140 CG
Combining 2 symmetry atoms into ARG /A:122 NH1
Combining 15 symmetry atoms into ILE /A:133 O
Combining 789 symmetry atoms into GLN /A:37 CA
Combining 209 symmetry atoms into GLN /A:37 NE2
Combining 472 symmetry atoms into SER /A:36 O
Combining 6 symmetry atoms into MET /A:88 SD
Combining 2 symmetry atoms into PHE /A:281 C
Combining 2 symmetry atoms into LYS /A:67 O
Combining 3 symmetry atoms into VAL /A:69 C
Combining 3 symmetry atoms into LYS /A:71 CB
Combining 2 symmetry atoms into ASP /A:239 N
Combining 4 symmetry atoms into VAL /A:69 CG1
Combining 2 symmetry atoms into GLU /A:79 OE2
Combining 5 symmetry atoms into LEU /A:62 CB
Combining 2 symmetry atoms into LEU /A:107 N
Combining 3 symmetry atoms into LYS /A:71 CE
Combining 3 symmetry atoms into VAL /A:64 CG2
Combining 2 symmetry atoms into GLY /A:162 CA
Combining 3 symmetry atoms into ARG /A:73 CZ
Combining 2 symmetry atoms into LEU /A:92 O
Combining 4 symmetry atoms into PRO /A:113 CD
Combining 2 symmetry atoms into ASN /A:160 ND2
Combining 10 symmetry atoms into PHE /A:116 O
Combining 2 symmetry atoms into ILE /A:213 CG1
Combining 2 symmetry atoms into ILE /A:119 N
===== 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 M4 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: Mac16,6
Model Number: Z1FG000AVLL/A
Chip: Apple M4 Max
Total Number of Cores: 16 (12 performance and 4 efficiency)
Memory: 128 GB
System Firmware Version: 13822.61.10
OS Loader Version: 13822.61.10
Software:
System Software Overview:
System Version: macOS 26.2 (25C56)
Kernel Version: Darwin 25.2.0
Time since boot: 2 days, 9 hours, 16 minutes
Graphics/Displays:
Apple M4 Max:
Chipset Model: Apple M4 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 40
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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