![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 hours ago
#19793 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 (2025-12-17 06:45:39 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
"uptime" : 8700,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac15,3",
"coalitionID" : 2153,
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"build" : "25C56",
"releaseType" : "User"
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"captureTime" : "2026-02-02 22:39:15.5667 +0900",
"codeSigningMonitor" : 2,
"incident" : "91DA5C83-B76D-4EE1-BADA-28BC419EDD24",
"pid" : 14913,
"translated" : false,
"cpuType" : "ARM-64",
"procLaunch" : "2026-02-02 22:24:49.0708 +0900",
"procStartAbsTime" : 190214651534,
"procExitAbsTime" : 211010169415,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.11.app\/Contents\/MacOS\/ChimeraX",
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "B764343E-6690-75E4-BB9E-16AB9F8A0AF2",
"lowPowerMode" : 1,
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["siriAssetIsNotReady","assetIsNotReady","notOptedIn"]},
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"bootProgressRegister" : "0x2f000000",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
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"vmRegionInfo" : "0x8 is not in any region. Bytes before following region: 4367220728
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 1044e8000-1044ec000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.11.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000008","rawCodes":[1,8],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000008"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":14913},
"vmregioninfo" : "0x8 is not in any region. Bytes before following region: 4367220728
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
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Log:
UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling
> Workspaces/PCH45_Gp63Beta_Feb_Finalizing.cxs"
Opened PCH45_Gp63Beta_Segmap_Jan.mrc as #6, grid size 416,416,204, pixel
1.37,1.37,1.37, shown at level 0.711, step 1, values float32
Log from Mon Feb 2 22:54:37 2026UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/Desktop/PCH45_Gp63Beta_1-90AAFit.pdb
Chain information for PCH45_Gp63Beta_1-90AAFit.pdb #1
---
Chain | Description
A | No description available
> open "/Users/croal939/Downloads/output_output (5).cif"
Summary of feedback from opening /Users/croal939/Downloads/output_output
(5).cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for output_output (5).cif #2
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
8 | No description available
9 | No description available
A | No description available
AA | No description available
AB | No description available
AC | No description available
AD | No description available
AE | No description available
AF | No description available
AG | No description available
AH | No description available
AI | No description available
AJ | No description available
AK | No description available
AL | No description available
AM | No description available
AN | No description available
AO | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
N | No description available
O | No description available
S | No description available
X | No description available
Z | No description available
g | No description available
j | No description available
q | No description available
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/Gp63ing Pt.2/PCH45_Gp63b_Fitted1-coot-1.pdb"
Summary of feedback from opening
/Users/croal939/Library/CloudStorage/OneDrive-UniversityofOtago/PCH45/PCH45
Modelling Workspaces/Gen 3 Models for Distribution!/Gp63ing
Pt.2/PCH45_Gp63b_Fitted1-coot-1.pdb
---
warnings | End residue of secondary structure not found: HELIX 8 8 ALA A 171 GLU A 198 1 28
Start residue of secondary structure not found: HELIX 9 9 LEU A 199 LYS A 201
1 3
Chain information for PCH45_Gp63b_Fitted1-coot-1.pdb #3
---
Chain | Description
A | No description available
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/Gp63ing Pt.2/63b_test2.mrc"
Opened 63b_test2.mrc as #4, grid size 416,416,416, pixel 1.37, shown at level
0.000262, step 2, values float32
> hide #2 models
> show #2 models
> select add #1
713 atoms, 730 bonds, 90 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #4
2 models selected
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/Gp63ing Pt.2/PCH45_Gp63b_VZr4_Segmap1.mrc"
Opened PCH45_Gp63b_VZr4_Segmap1.mrc as #5, grid size 416,416,86, pixel
1.37,1.37,1.37, shown at level 0.000157, step 1, values float32
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/PCH45_Gp63Beta_Segmap_Jan.mrc"
Opened PCH45_Gp63Beta_Segmap_Jan.mrc as #6, grid size 416,416,204, pixel
1.37,1.37,1.37, shown at level 6.36e-05, step 2, values float32
> hide #!5 models
> hide #!4 models
> hide #3 models
> color #2 #929292ff
> hide #1-2 atoms
> show #1-2 cartoons
Computing secondary structure
> set bgColor white
> graphics silhouettes true
> select add #6
4 models selected
> volume #4 step 1
> show #!4 models
> close #4
> show #!5 models
> select add #5
4 models selected
> close #5
> volume #6 step 1
> volume #6 level 0.711
> select clear
> select add #2
2000 atoms, 1972 bonds, 250 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,22.818,0,1,0,-22.448,0,0,1,119.93
> view matrix models #2,1,0,0,0.25713,0,1,0,-0.55439,0,0,1,145.02
> select add #6
2000 atoms, 1972 bonds, 250 residues, 3 models selected
> fitmap #2 inMap #6
Fit molecule output_output (5).cif (#2) to map PCH45_Gp63Beta_Segmap_Jan.mrc
(#6) using 2000 atoms
average map value = 0.6873, steps = 48
shifted from previous position = 0.667
rotated from previous position = 0.128 degrees
atoms outside contour = 1009, contour level = 0.71102
Position of output_output (5).cif (#2) relative to
PCH45_Gp63Beta_Segmap_Jan.mrc (#6) coordinates:
Matrix rotation and translation
0.99999891 -0.00023246 -0.00146098 0.35866017
0.00023492 0.99999856 0.00168288 -0.40799733
0.00146059 -0.00168323 0.99999752 144.65036076
Axis -0.75109584 -0.65190410 0.10428850
Axis point 0.00000000 85010.15091267 -5526.98173801
Rotation angle (degrees) 0.12838840
Shift along axis 15.08195578
> transparency sel 50
> select clear
> select add #1
713 atoms, 730 bonds, 90 residues, 1 model selected
> view matrix models #1,1,0,0,-48.292,0,1,0,-26.491,0,0,1,229.92
> select add #6
713 atoms, 730 bonds, 90 residues, 3 models selected
> surface dust #6 size 13.7
> select clear
> select add #1
713 atoms, 730 bonds, 90 residues, 1 model selected
> rainbow sel
> select clear
> select add #1
713 atoms, 730 bonds, 90 residues, 1 model selected
> view matrix models #1,1,0,0,-91.309,0,1,0,-43.034,0,0,1,253.92
> view matrix models #1,1,0,0,-92.519,0,1,0,-39.23,0,0,1,240.64
> view matrix models #1,1,0,0,-95.536,0,1,0,-44.111,0,0,1,242.82
> select clear
> select add #1
713 atoms, 730 bonds, 90 residues, 1 model selected
> select add #6
713 atoms, 730 bonds, 90 residues, 3 models selected
> fitmap #1 inMap #6
Fit molecule PCH45_Gp63Beta_1-90AAFit.pdb (#1) to map
PCH45_Gp63Beta_Segmap_Jan.mrc (#6) using 713 atoms
average map value = 0.6914, steps = 60
shifted from previous position = 4.29
rotated from previous position = 0.0258 degrees
atoms outside contour = 349, contour level = 0.71102
Position of PCH45_Gp63Beta_1-90AAFit.pdb (#1) relative to
PCH45_Gp63Beta_Segmap_Jan.mrc (#6) coordinates:
Matrix rotation and translation
0.99999990 -0.00042223 -0.00012889 -97.79218147
0.00042222 0.99999991 -0.00008503 -44.93692375
0.00012893 0.00008498 0.99999999 239.25086380
Axis 0.18907213 -0.28673116 0.93916823
Axis point -42428.15039300 -329704.41775435 0.00000000
Rotation angle (degrees) 0.02575883
Shift along axis 219.09185132
> select clear
> open
> /Users/croal939/Downloads/fold_pch45_gp63beta_91_end/fold_pch45_gp63beta_91_end_model_0.cif
Chain information for fold_pch45_gp63beta_91_end_model_0.cif #4
---
Chain | Description
A | .
> open
> /Users/croal939/Downloads/fold_pch45_gp63beta_91_end/fold_pch45_gp63beta_91_end_model_1.cif
Chain information for fold_pch45_gp63beta_91_end_model_1.cif #5
---
Chain | Description
A | .
> open
> /Users/croal939/Downloads/fold_pch45_gp63beta_91_end/fold_pch45_gp63beta_91_end_model_2.cif
Chain information for fold_pch45_gp63beta_91_end_model_2.cif #7
---
Chain | Description
A | .
> open
> /Users/croal939/Downloads/fold_pch45_gp63beta_91_end/fold_pch45_gp63beta_91_end_model_3.cif
Chain information for fold_pch45_gp63beta_91_end_model_3.cif #8
---
Chain | Description
A | .
> open
> /Users/croal939/Downloads/fold_pch45_gp63beta_91_end/fold_pch45_gp63beta_91_end_model_4.cif
Chain information for fold_pch45_gp63beta_91_end_model_4.cif #9
---
Chain | Description
A | .
Computing secondary structure
[Repeated 4 time(s)]
> ui tool show Matchmaker
> matchmaker #4-5,7-9 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker output_output (5).cif, chain 2 (#2) with
fold_pch45_gp63beta_91_end_model_0.cif, chain A (#4), sequence alignment score
= 42.2
RMSD between 12 pruned atom pairs is 0.780 angstroms; (across all 28 pairs:
4.670)
Matchmaker output_output (5).cif, chain 2 (#2) with
fold_pch45_gp63beta_91_end_model_1.cif, chain A (#5), sequence alignment score
= 42.2
RMSD between 13 pruned atom pairs is 1.191 angstroms; (across all 28 pairs:
3.647)
Matchmaker output_output (5).cif, chain 2 (#2) with
fold_pch45_gp63beta_91_end_model_2.cif, chain A (#7), sequence alignment score
= 42.2
RMSD between 10 pruned atom pairs is 1.414 angstroms; (across all 28 pairs:
3.978)
Matchmaker output_output (5).cif, chain 2 (#2) with
fold_pch45_gp63beta_91_end_model_3.cif, chain A (#8), sequence alignment score
= 42.2
RMSD between 11 pruned atom pairs is 1.177 angstroms; (across all 28 pairs:
3.973)
Matchmaker output_output (5).cif, chain 2 (#2) with
fold_pch45_gp63beta_91_end_model_4.cif, chain A (#9), sequence alignment score
= 42.2
RMSD between 5 pruned atom pairs is 1.465 angstroms; (across all 28 pairs:
8.716)
> hide #9 models
> select add #6
2 models selected
> select add #7
877 atoms, 890 bonds, 113 residues, 3 models selected
> fitmap #7 inMap #6
Fit molecule fold_pch45_gp63beta_91_end_model_2.cif (#7) to map
PCH45_Gp63Beta_Segmap_Jan.mrc (#6) using 877 atoms
average map value = 0.5335, steps = 68
shifted from previous position = 1.44
rotated from previous position = 10.1 degrees
atoms outside contour = 558, contour level = 0.71102
Position of fold_pch45_gp63beta_91_end_model_2.cif (#7) relative to
PCH45_Gp63Beta_Segmap_Jan.mrc (#6) coordinates:
Matrix rotation and translation
-0.86379141 0.30097549 -0.40407692 333.87967102
-0.35199663 -0.93429107 0.05655594 193.26113261
-0.36050350 0.19108625 0.91297496 351.44246211
Axis 0.20135982 -0.06521902 -0.97734370
Axis point 218.48834281 50.41390684 0.00000000
Rotation angle (degrees) 160.48494727
Shift along axis -288.85442718
> select subtract #7
2 models selected
> select add #8
877 atoms, 890 bonds, 113 residues, 3 models selected
> fitmap #8 inMap #6
Fit molecule fold_pch45_gp63beta_91_end_model_3.cif (#8) to map
PCH45_Gp63Beta_Segmap_Jan.mrc (#6) using 877 atoms
average map value = 0.5154, steps = 180
shifted from previous position = 1.14
rotated from previous position = 14 degrees
atoms outside contour = 565, contour level = 0.71102
Position of fold_pch45_gp63beta_91_end_model_3.cif (#8) relative to
PCH45_Gp63Beta_Segmap_Jan.mrc (#6) coordinates:
Matrix rotation and translation
-0.37992807 -0.14267041 -0.91394738 335.20161826
-0.37136621 -0.88138741 0.29196467 195.41925835
-0.84719644 0.45033475 0.28188085 351.54518251
Axis 0.55359759 -0.23333425 -0.79942782
Axis point 296.62850733 27.82302033 0.00000000
Rotation angle (degrees) 171.77636703
Shift along axis -141.06619499
> select subtract #8
2 models selected
> select add #5
877 atoms, 890 bonds, 113 residues, 3 models selected
> fitmap #5 inMap #6
Fit molecule fold_pch45_gp63beta_91_end_model_1.cif (#5) to map
PCH45_Gp63Beta_Segmap_Jan.mrc (#6) using 877 atoms
average map value = 0.4988, steps = 96
shifted from previous position = 2.04
rotated from previous position = 13.4 degrees
atoms outside contour = 581, contour level = 0.71102
Position of fold_pch45_gp63beta_91_end_model_1.cif (#5) relative to
PCH45_Gp63Beta_Segmap_Jan.mrc (#6) coordinates:
Matrix rotation and translation
0.97610708 -0.20200812 -0.08004804 335.05559155
-0.14914265 -0.35494475 -0.92291424 195.46808550
0.15802354 0.91280170 -0.37659211 351.41021431
Axis 0.99129086 -0.12855921 0.02854748
Axis point 0.00000000 3.40483896 250.95847808
Rotation angle (degrees) 112.19220911
Shift along axis 317.04019826
> select clear
> select add #7
877 atoms, 890 bonds, 113 residues, 1 model selected
> select clear
> select add #7
877 atoms, 890 bonds, 113 residues, 1 model selected
> fitmap #7 inMap #6
Fit molecule fold_pch45_gp63beta_91_end_model_2.cif (#7) to map
PCH45_Gp63Beta_Segmap_Jan.mrc (#6) using 877 atoms
average map value = 0.5334, steps = 64
shifted from previous position = 0.0191
rotated from previous position = 0.0104 degrees
atoms outside contour = 559, contour level = 0.71102
Position of fold_pch45_gp63beta_91_end_model_2.cif (#7) relative to
PCH45_Gp63Beta_Segmap_Jan.mrc (#6) coordinates:
Matrix rotation and translation
-0.86387301 0.30094938 -0.40392189 333.87142005
-0.35193005 -0.93431665 0.05654771 193.27643367
-0.36037295 0.19100229 0.91304406 351.44981825
Axis 0.20127884 -0.06519287 -0.97736212
Axis point 218.46861706 50.43487334 0.00000000
Rotation angle (degrees) 160.48821242
Shift along axis -288.89273304
> select add #6
877 atoms, 890 bonds, 113 residues, 3 models selected
> fitmap #7 inMap #6
Fit molecule fold_pch45_gp63beta_91_end_model_2.cif (#7) to map
PCH45_Gp63Beta_Segmap_Jan.mrc (#6) using 877 atoms
average map value = 0.5334, steps = 40
shifted from previous position = 0.00155
rotated from previous position = 0.00256 degrees
atoms outside contour = 558, contour level = 0.71102
Position of fold_pch45_gp63beta_91_end_model_2.cif (#7) relative to
PCH45_Gp63Beta_Segmap_Jan.mrc (#6) coordinates:
Matrix rotation and translation
-0.86386400 0.30093943 -0.40394857 333.87213141
-0.35193807 -0.93431167 0.05657999 193.27513580
-0.36038672 0.19104229 0.91303026 351.45018069
Axis 0.20129025 -0.06521215 -0.97735849
Axis point 218.47066884 50.43021511 0.00000000
Rotation angle (degrees) 160.48819695
Shift along axis -288.89149822
> select clear
> hide #1 models
> show #1 models
> hide #5 models
> hide #4 models
> hide #7 models
> hide #8 models
> show #7 models
> select add #7
877 atoms, 890 bonds, 113 residues, 1 model selected
> sequence chain #7/A
Alignment identifier is 7/A
> select clear
> select add #1
713 atoms, 730 bonds, 90 residues, 1 model selected
> sequence chain #1/A
Alignment identifier is 1/A
> combine #1 #7
Remapping chain ID 'A' in fold_pch45_gp63beta_91_end_model_2.cif #7 to 'B'
> select add #10
2303 atoms, 2350 bonds, 293 residues, 2 models selected
> changechains #10 A,B,C A,A,A
Proposed chain ID change would produce multiple residues with the samechain-
ID/number/insertion-code combo (A/1/)
> changechains chains #10 A,B,C A,A,A
Expected ',' or a keyword
> sequence chain #1/A#10/A
Alignment identifier is 1
> sequence chain #10/B
Alignment identifier is 10/B
> changechains chains #10 1,B,C A,A,A
Expected ',' or a keyword
> changechains chains #10 A,B,C A,A,A
Expected ',' or a keyword
> changechains chains #10 A, B , C A,A,A
Expected ',' or a keyword
> sequence chain #1/A#10/A
Alignment identifier is 1
> sequence chain #10/B
Alignment identifier is 10/B
> select clear
> save "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling
> Workspaces/PCH45_Gp63Beta_Feb_Finalizing.cxs" includeMaps true
——— End of log from Mon Feb 2 22:54:37 2026 ———
> view name session-start
opened ChimeraX session
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: Z1C80004VX/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 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 hours, 45 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: 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: 4.12.0
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
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: 2.7.11
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: 7.13.0
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: 4.25.1
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: 3.2.5
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
pytz: 2025.2
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: 4.0.0
roman-numerals-py: 4.0.0
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
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: 3.0.4
stack-data: 0.6.3
starlette: 0.50.0
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
tzdata: 2025.3
urllib3: 2.6.2
uvicorn: 0.38.0
wcwidth: 0.2.14
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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