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Opened 7 hours ago
#20225 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-14.3-arm64-arm-64bit
ChimeraX Version: 1.8rc202406102315 (2024-06-10 23:15:52 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 0x00000001d9369c40 (most recent call first):
File "/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, PIL._imagingmath, chimerax.mlp._mlp (total: 65)
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{
"uptime" : 170000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,12",
"coalitionID" : 1661,
"osVersion" : {
"train" : "macOS 14.3",
"build" : "23D2057",
"releaseType" : "User"
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"captureTime" : "2026-04-26 23:15:02.2491 -0500",
"codeSigningMonitor" : 1,
"incident" : "09C3E735-2CFF-4443-B118-49FEA74222EB",
"pid" : 45672,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2026-04-26 02:59:55.5025 -0500",
"procStartAbsTime" : 3753384270442,
"procExitAbsTime" : 4183889873508,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8-rc2024.06.10.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"61DCCA4C-8BBE-566F-8CCC-1D1EFAE87F42","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "31D03CEA-B4B7-1878-D34B-04A35F37F001",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 6,
"sleepWakeUUID" : "6663A7AC-BDCA-47D2-9CCE-437EE572D9AF",
"sip" : "enabled",
"vmRegionInfo" : "0x169 is not in any region. Bytes before following region: 105559558717079\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO 600180000000-6001a0000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000169","rawCodes":[1,361],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000169"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":45672},
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===== Log before crash start =====
UCSF ChimeraX version: 1.8rc202406102315 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/aninditosen/Documents/P1/baseplate/main_baseplate/h_bonf_triplex.cxs
> format session
Opened flip_base.mrc as #9, grid size 512,512,512, pixel 1.39, shown at level
0.272, step 1, values float32
opened ChimeraX session
> lighting soft
> lighting full
> coulombic #1,10-11#!2,5-6,12,17
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for UpfC_af.pdb_9 SES surface #1.1: minimum, -8.94, mean
-0.37, maximum 7.77
Coulombic values for gp5_af.pdb_6 SES surface #10.1: minimum, -15.35, mean
-0.92, maximum 15.28
Coulombic values for gp5_af.pdb_7 SES surface #10.2: minimum, -11.39, mean
-0.89, maximum 14.28
Coulombic values for gp5_af.pdb_8 SES surface #10.3: minimum, -18.47, mean
-0.93, maximum 13.00
Coulombic values for gp6_af.pdb_3 SES surface #11.1: minimum, -15.10, mean
-0.17, maximum 14.54
Coulombic values for gp6_af.pdb_4 SES surface #11.2: minimum, -20.20, mean
-0.16, maximum 16.17
Coulombic values for gp6_af.pdb_5 SES surface #11.3: minimum, -14.77, mean
-0.17, maximum 15.83
Coulombic values for BplAminus.pdb_d SES surface #2.1: minimum, -16.51, mean
-1.43, maximum 17.71
Coulombic values for gp26.cif_X SES surface #5.1: minimum, -17.97, mean -1.93,
maximum 8.40
Coulombic values for pmgA.cif_R SES surface #6.1: minimum, -18.54, mean -4.68,
maximum 6.81
Coulombic values for gp16.pdb_p SES surface #12.1: minimum, -19.32, mean
-2.22, maximum 12.53
Coulombic values for pmgG.cif_G SES surface #17.2: minimum, -14.33, mean
-1.98, maximum 8.86
Coulombic values for pmgG.cif_H SES surface #17.3: minimum, -14.49, mean
-1.97, maximum 9.31
Coulombic values for pmgG.cif_I SES surface #17.4: minimum, -14.63, mean
-1.97, maximum 8.52
Coulombic values for pmgG.cif_J SES surface #17.5: minimum, -14.51, mean
-1.97, maximum 8.67
Coulombic values for pmgG.cif_K SES surface #17.6: minimum, -14.32, mean
-1.97, maximum 10.17
Coulombic values for pmgG.cif_L SES surface #17.7: minimum, -14.45, mean
-1.96, maximum 11.02
To also show corresponding color key, enter the above coulombic command and
add key true
> ui tool show "Side View"
> hide #!17 models
> hide #16 models
> hide #!11 models
> hide #!10 models
> hide #!5 models
> hide #!6 models
> show #!3 models
> hide #!1 models
> coulombic #!2-3,12
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for BplAminus.pdb_d SES surface #2.1: minimum, -16.51, mean
-1.43, maximum 17.71
Coulombic values for BplAplus.pdb_j SES surface #3.1: minimum, -16.70, mean
-1.85, maximum 13.05
Coulombic values for gp16.pdb_p SES surface #12.1: minimum, -19.32, mean
-2.22, maximum 12.53
To also show corresponding color key, enter the above coulombic command and
add key true
> graphics silhouettes false
> ~label #2-3,12 residues
> select #3/j:3@NZ
1 atom, 1 residue, 1 model selected
> select #12/p:55@OD1
1 atom, 1 residue, 1 model selected
> select add #3/j:3@NZ
2 atoms, 2 residues, 3 models selected
> label (#!3,12 & sel) text "/{0.chain_id} {0.name}
> {0.number}{0.insertion_code}"
> ~label (#!3,12 & sel) residues
> label (#!3,12 & sel) text "{0.name} {0.number}{0.insertion_code}"
> label height 3
> ui mousemode right "move label"
> label height 2
> select clear
> label color white
> save /Users/aninditosen/Desktop/image17.png supersample 3
> open /Users/aninditosen/Documents/P1/final_images/mocell/FigS2.tif
Opened multi-channel map FigS2.tif as #18, 3 channels, grid size 2700,3300,1,
pixel 1, shown at step 1, values uint8
> close #18.1
> close #18.2
> close #18.3
> close #9
> hide #18 models
> close #18
> hide #!12 models
> hide #!2 models
> show #!12 models
> hide #!3 models
> show #!3 models
> select add #3
7498 atoms, 7582 bonds, 8 pseudobonds, 477 residues, 3 models selected
> transparency sel 50
> hide sel cartoons
> hide sel atoms
> hide #!12 models
> show #!2 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!12 models
> select subtract #3
1 model selected
> select add #3
7498 atoms, 7582 bonds, 8 pseudobonds, 477 residues, 3 models selected
> transparency sel 0
> select subtract #3
1 model selected
> select #2/d:14@OE2
1 atom, 1 residue, 1 model selected
> select #3/j:47@NH1
1 atom, 1 residue, 1 model selected
> select add #2/d:14@OE2
2 atoms, 2 residues, 3 models selected
> label (#!2-3 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #3/j:47@1HH1
1 atom, 1 residue, 1 model selected
> select add #3/j:47@NH1
2 atoms, 1 residue, 2 models selected
> select add #3/j:47@2HH1
3 atoms, 1 residue, 2 models selected
> label (#!3 & sel) text "{0.name} {0.number}{0.insertion_code}"
> ~label (#!3 & sel) residues
> select add #3
7498 atoms, 7582 bonds, 8 pseudobonds, 477 residues, 4 models selected
> select subtract #3
1 model selected
> ~label #2-3 residues
> select #2/d:14@OE2
1 atom, 1 residue, 1 model selected
> select add #2/d:14@CG
2 atoms, 1 residue, 2 models selected
> select add #2/d:14@CD
3 atoms, 1 residue, 2 models selected
> select add #3/j:47@NH1
4 atoms, 2 residues, 3 models selected
> select subtract #3/j:47@NH1
3 atoms, 1 residue, 3 models selected
> select add #3/j:47@1HH1
4 atoms, 2 residues, 3 models selected
> select add #3/j:47@NH1
5 atoms, 2 residues, 4 models selected
> select add #3/j:47@CD
6 atoms, 2 residues, 4 models selected
> select add #3/j:47@CZ
7 atoms, 2 residues, 4 models selected
> label (#!2-3 & sel) text "{0.name} {0.number}{0.insertion_code}"
> ui mousemode right "translate selected atoms"
> undo
> coulombic sel
Coulombic values for BplAminus.pdb_d SES surface #2.1: minimum, -16.51, mean
-1.43, maximum 17.71
Coulombic values for BplAplus.pdb_j SES surface #3.1: minimum, -16.70, mean
-1.85, maximum 13.05
To also show corresponding color key, enter the above coulombic command and
add key true
> select #3/j:47@1HH1
1 atom, 1 residue, 1 model selected
> select #3/j:47@NH1
1 atom, 1 residue, 1 model selected
> select #3/j:47@CZ
1 atom, 1 residue, 1 model selected
> label (#!3 & sel) text "{0.name} {0.number}{0.insertion_code}"
> open
> /Users/aninditosen/Documents/P1/baseplate/main_baseplate/h_bonf_triplex.cxs
> format session
Opened flip_base.mrc as #9, grid size 512,512,512, pixel 1.39, shown at level
0.272, step 1, values float32
opened ChimeraX session
> coulombic #1,10-11#!2,5-6,12,17
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for UpfC_af.pdb_9 SES surface #1.1: minimum, -8.94, mean
-0.37, maximum 7.77
Coulombic values for gp5_af.pdb_6 SES surface #10.1: minimum, -15.35, mean
-0.92, maximum 15.28
Coulombic values for gp5_af.pdb_7 SES surface #10.2: minimum, -11.39, mean
-0.89, maximum 14.28
Coulombic values for gp5_af.pdb_8 SES surface #10.3: minimum, -18.47, mean
-0.93, maximum 13.00
Coulombic values for gp6_af.pdb_3 SES surface #11.1: minimum, -15.10, mean
-0.17, maximum 14.54
Coulombic values for gp6_af.pdb_4 SES surface #11.2: minimum, -20.20, mean
-0.16, maximum 16.17
Coulombic values for gp6_af.pdb_5 SES surface #11.3: minimum, -14.77, mean
-0.17, maximum 15.83
Coulombic values for BplAminus.pdb_d SES surface #2.1: minimum, -16.51, mean
-1.43, maximum 17.71
Coulombic values for gp26.cif_X SES surface #5.1: minimum, -17.97, mean -1.93,
maximum 8.40
Coulombic values for pmgA.cif_R SES surface #6.1: minimum, -18.54, mean -4.68,
maximum 6.81
Coulombic values for gp16.pdb_p SES surface #12.1: minimum, -19.32, mean
-2.22, maximum 12.53
Coulombic values for pmgG.cif_G SES surface #17.2: minimum, -14.33, mean
-1.98, maximum 8.86
Coulombic values for pmgG.cif_H SES surface #17.3: minimum, -14.49, mean
-1.97, maximum 9.31
Coulombic values for pmgG.cif_I SES surface #17.4: minimum, -14.63, mean
-1.97, maximum 8.52
Coulombic values for pmgG.cif_J SES surface #17.5: minimum, -14.51, mean
-1.97, maximum 8.67
Coulombic values for pmgG.cif_K SES surface #17.6: minimum, -14.32, mean
-1.97, maximum 10.17
Coulombic values for pmgG.cif_L SES surface #17.7: minimum, -14.45, mean
-1.96, maximum 11.02
To also show corresponding color key, enter the above coulombic command and
add key true
> ui tool show "Side View"
No visible residues selected
> select add #16
43 pseudobonds, 1 model selected
> select subtract #16
Nothing selected
> hide #16 models
> hide #!17 models
> hide #!10 models
> hide #!11 models
> hide #!5 models
> hide #!6 models
> ~label #1-2,12 residues
> show #!3 models
> hide #!1 models
> show #!2-3,12 surfaces
> coulombic #!2-3,12
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for BplAminus.pdb_d SES surface #2.1: minimum, -16.51, mean
-1.43, maximum 17.71
Coulombic values for BplAplus.pdb_j SES surface #3.1: minimum, -16.70, mean
-1.85, maximum 13.05
Coulombic values for gp16.pdb_p SES surface #12.1: minimum, -19.32, mean
-2.22, maximum 12.53
To also show corresponding color key, enter the above coulombic command and
add key true
> ~label #2-3,12 residues
> hide #!12 models
> lighting full
> graphics silhouettes false
> select add #2
7498 atoms, 7582 bonds, 6 pseudobonds, 477 residues, 3 models selected
> transparency sel 50
> transparency sel 0
> select subtract #2
1 model selected
> select #2/d:14@OE2
1 atom, 1 residue, 1 model selected
> select add #3/j:47@NH1
2 atoms, 2 residues, 3 models selected
> label (#!2-3 & sel) text "{0.name} {0.number}{0.insertion_code}"
> label color white
> ui mousemode right "move label"
> select add #2
7499 atoms, 7582 bonds, 6 pseudobonds, 478 residues, 8 models selected
> select subtract #2
1 atom, 1 residue, 3 models selected
> select add #3
7498 atoms, 7582 bonds, 8 pseudobonds, 477 residues, 4 models selected
> select subtract #3
1 model selected
> label height 2
> save /Users/aninditosen/Desktop/image17.png supersample 3
> select add #2
7498 atoms, 7582 bonds, 6 pseudobonds, 477 residues, 5 models selected
> transparency sel 50
> select subtract #2
1 model selected
> transparency #2.1#3.1 0
> hide #!3 models
> show #!12 models
> select add #12
4399 atoms, 4444 bonds, 10 pseudobonds, 278 residues, 2 models selected
> transparency sel 50
> select subtract #12
1 model selected
> ~label #2,12 residues
> transparency #2.1#12.1 0
> select #12/p:148@CB
1 atom, 1 residue, 1 model selected
> select add #12/p:148@2HD2
2 atoms, 1 residue, 2 models selected
> select add #12/p:148@CD2
3 atoms, 1 residue, 2 models selected
> select add #2/d:335@CE
4 atoms, 2 residues, 3 models selected
> select add #2/d:335@1HZ
5 atoms, 2 residues, 4 models selected
> select add #2/d:334@1HB
6 atoms, 3 residues, 4 models selected
> select add #2/d:335@NZ
7 atoms, 3 residues, 4 models selected
> select add #2/d:333@O
8 atoms, 4 residues, 4 models selected
> label (#!2,12 & sel) text "{0.name} {0.number}{0.insertion_code}"
> label height 2
> ui mousemode right "move label"
> label color white
> select clear
> save /Users/aninditosen/Desktop/image17.png supersample 3
> select add #12
4399 atoms, 4444 bonds, 10 pseudobonds, 278 residues, 4 models selected
> transparency sel 50
> transparency sel 0
> hide #!12 models
> select subtract #12
1 model selected
> show #!3 models
> select add #2
7498 atoms, 7582 bonds, 6 pseudobonds, 477 residues, 5 models selected
> ~label (#!2 & sel) residues
> select subtract #2
1 model selected
> ~label #2-3 residues
> select #2/d:289@1HB
1 atom, 1 residue, 1 model selected
> select #2/d:289@CB
1 atom, 1 residue, 1 model selected
> select add #2/d:289@1HB
2 atoms, 1 residue, 2 models selected
> select add #2/d:282@NH1
3 atoms, 2 residues, 2 models selected
> select add #2/d:289@N
4 atoms, 2 residues, 2 models selected
> select add #3/j:217@1HD1
5 atoms, 3 residues, 3 models selected
> select add #3/j:217@CD1
6 atoms, 3 residues, 4 models selected
> select add #3/j:217@CG1
7 atoms, 3 residues, 4 models selected
> label (#!2-3 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select clear
> label color white
> label height 2
> label height 1.5
> save /Users/aninditosen/Desktop/image17.png supersample 3
> show #!12 models
> hide #!2 models
> ~label #3,12 residues
> select add #12
4399 atoms, 4444 bonds, 10 pseudobonds, 278 residues, 2 models selected
> hide #!12 models
> show #!12 models
> select clear
> select #3/j:53@OD1
1 atom, 1 residue, 1 model selected
> select add #12/p:41@NH1
2 atoms, 2 residues, 3 models selected
> select add #12/p:41@NH2
3 atoms, 2 residues, 4 models selected
> label (#!3,12 & sel) text "{0.name} {0.number}{0.insertion_code}"
> label height 1.5
> label color white
> select clear
> save /Users/aninditosen/Desktop/image17.png supersample 3
> hide #!3 models
> show #4 models
> hide #4 models
> show #!3 models
> show #!2 models
> hide #!12 models
> ~label #2-3 residues
> mlp #!2-3
Map values for surface "BplAminus.pdb_d SES surface": minimum -29.61, mean
-3.276, maximum 25.53
Map values for surface "BplAplus.pdb_j SES surface": minimum -29.52, mean
-3.189, maximum 29.02
To also show corresponding color key, enter the above mlp command and add key
true
> select add #2
7498 atoms, 7582 bonds, 6 pseudobonds, 477 residues, 4 models selected
> transparency sel 50
> hide sel cartoons
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8rc202406102315 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac15,12
Model Number: MXCU3LL/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.81.1
OS Loader Version: 10151.81.1
Software:
System Software Overview:
System Version: macOS 14.3 (23D2057)
Kernel Version: Darwin 23.3.0
Time since boot: 10 days, 12 hours, 58 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 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8rc202406102315
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
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
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
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
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
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