ChimeraX bug report submission

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-6.6.99-09000-gd3ae1caecf39-x86_64-with-glibc2.41
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "/home/calvingunther66/Imaging/Gunther, Calvin/Head_MRI_2025.cxs"

Opened 1 MR (LOC) as #1.1.1, grid size 256,256,21, pixel 0.938,0.938,8.66,
shown at step 1, values int16  
Opened 2 MR (SAG 3D T1 MP-RAGE) as #1.1.2, grid size 512,512,208, pixel
0.5,0.5,1.41, shown at step 1, values int16  
Opened 3 MR (SAG T1 FLAIR) as #1.1.3, grid size 1024,1024,32, pixel
0.225,0.225,4.36, shown at step 1, values int16  
Opened 4 MR (AX T2 FLAIR) as #1.1.4, grid size 512,512,32, pixel
0.43,0.43,4.84, shown at step 1, values int16  
Opened 5 MR (AX MUSE DWI) as #1.1.5, grid size 256,256,80, pixel
0.859,0.859,1.95, shown at step 1, values int16  
Opened 6 MR (COR T2 OBL THIN) as #1.1.6, grid size 1024,1024,30, pixel
0.176,0.176,2.9, shown at step 1, values int16  
Opened 7 MR (COR T2 FLAIR OBL THIN) as #1.1.7, grid size 512,512,30, pixel
0.352,0.352,2.9, shown at step 1, values int16  
Opened 8 MR (AX T2) as #1.1.8, grid size 1024,1024,36, pixel 0.215,0.215,4.38,
shown at step 1, values int16  
Opened 9 MR (AX 3D SWAN) as #1.1.9, grid size 512,512,134, pixel
0.43,0.43,1.19, shown at step 1, values int16  
Opened 10 MR (AX T1 FLAIR) as #1.1.10, grid size 1024,1024,36, pixel
0.215,0.215,4.38, shown at step 1, values int16  
Opened 11 MR (AX 3D ASL) as #1.1.11, grid size 128,128,56, pixel
1.88,1.88,2.41, shown at step 1, values int16  
Opened 12 MR (COR T2) as #1.1.12, grid size 1024,1024,42, pixel
0.215,0.215,4.39, shown at step 1, values int16  
Opened 200 MR (AX 3D T1 MP-RAGE REFORMAT) as #1.1.13, grid size 512,512,257,
pixel 0.5,0.5,0.996, shown at step 1, values int16  
Opened 201 MR (COR 3D T1 MP-RAGE REFORMAT) as #1.1.14, grid size 512,512,257,
pixel 0.5,0.5,1.41, shown at step 1, values int16  
Opened 510 MR (ORIG: AX MUSE DWI) as #1.1.15, grid size 256,256,80, pixel
0.859,0.859,1.95, shown at step 1, values int16  
Opened 550 MR (ADC (10^-6 mm²/s)) as #1.1.16, grid size 256,256,40, pixel
0.859,0.859,3.9, shown at step 1, values int16  
Opened 551 MR (eADC) as #1.1.17, grid size 256,256,40, pixel 0.859,0.859,3.9,
shown at step 1, values float32  
Opened 900 MR (FILT_PHA: AX 3D SWAN) as #1.1.18, grid size 512,512,134, pixel
0.43,0.43,1.19, shown at step 1, values int16  
Opened 901 MR (AX SWAN MIN IP) as #1.1.19, grid size 512,512,81, pixel
0.43,0.43,1.98, shown at step 1, values int16  
Opened multi-channel map 1150 MR (CBF) as #1.1.20, 0 channels  
Opened 1150 MR (CBF) red as #1.1.20.1, grid size 512,512,28, pixel 1, shown at
step 1, values uint8  
Opened 1150 MR (CBF) green as #1.1.20.2, grid size 512,512,28, pixel 1, shown
at step 1, values uint8  
Opened 1150 MR (CBF) blue as #1.1.20.3, grid size 512,512,28, pixel 1, shown
at step 1, values uint8  
Opened 1151 MR (CBF) as #1.1.21, grid size 128,128,28, pixel 1.88,1.88,4.82,
shown at step 1, values int16  
Log from Mon Nov 17 07:27:39 2025UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/home/calvingunther66/Imaging/Gunther, Calvin/Head MRI w-o contrast
> 2025/dicom/SER00001" format dicom

Summary of feedback from opening /home/calvingunther66/Imaging/Gunther,
Calvin/Head MRI w-o contrast 2025/dicom/SER00001  
---  
note | Opened 1 MR (LOC) as #1.1.1, grid size 256,256,21, pixel 0.938,0.938,8.66, shown at step 1, values int16  
  

> hide #!1.1.1 models

> open "/home/calvingunther66/Imaging/Gunther, Calvin/Head MRI w-o contrast
> 2025/dicom/SER00002" format dicom

Summary of feedback from opening /home/calvingunther66/Imaging/Gunther,
Calvin/Head MRI w-o contrast 2025/dicom/SER00002  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Opened 2 MR (SAG 3D T1 MP-RAGE) as #1.1.2, grid size 512,512,208, pixel 0.5,0.5,1.41, shown at step 1, values int16  
  

> hide #!1.1.2 models

> open "/home/calvingunther66/Imaging/Gunther, Calvin/Head MRI w-o contrast
> 2025/dicom/SER00003" format dicom

Summary of feedback from opening /home/calvingunther66/Imaging/Gunther,
Calvin/Head MRI w-o contrast 2025/dicom/SER00003  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Opened 3 MR (SAG T1 FLAIR) as #1.1.3, grid size 1024,1024,32, pixel 0.225,0.225,4.36, shown at step 1, values int16  
  

> hide #!1.1.3 models

> open "/home/calvingunther66/Imaging/Gunther, Calvin/Head MRI w-o contrast
> 2025/dicom/SER00004" format dicom

Summary of feedback from opening /home/calvingunther66/Imaging/Gunther,
Calvin/Head MRI w-o contrast 2025/dicom/SER00004  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Opened 4 MR (AX T2 FLAIR) as #1.1.4, grid size 512,512,32, pixel 0.43,0.43,4.84, shown at step 1, values int16  
  

> hide #!1.1.4 models

> open "/home/calvingunther66/Imaging/Gunther, Calvin/Head MRI w-o contrast
> 2025/dicom/SER00005" format dicom

Summary of feedback from opening /home/calvingunther66/Imaging/Gunther,
Calvin/Head MRI w-o contrast 2025/dicom/SER00005  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Opened 5 MR (AX MUSE DWI) as #1.1.5, grid size 256,256,80, pixel 0.859,0.859,1.95, shown at step 1, values int16  
  

> hide #!1.1.5 models

> open "/home/calvingunther66/Imaging/Gunther, Calvin/Head MRI w-o contrast
> 2025/dicom/SER00006" format dicom

Summary of feedback from opening /home/calvingunther66/Imaging/Gunther,
Calvin/Head MRI w-o contrast 2025/dicom/SER00006  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Opened 6 MR (COR T2 OBL THIN) as #1.1.6, grid size 1024,1024,30, pixel 0.176,0.176,2.9, shown at step 1, values int16  
  

> hide #!1.1.6 models

> open "/home/calvingunther66/Imaging/Gunther, Calvin/Head MRI w-o contrast
> 2025/dicom/SER00007" format dicom

Summary of feedback from opening /home/calvingunther66/Imaging/Gunther,
Calvin/Head MRI w-o contrast 2025/dicom/SER00007  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Opened 7 MR (COR T2 FLAIR OBL THIN) as #1.1.7, grid size 512,512,30, pixel 0.352,0.352,2.9, shown at step 1, values int16  
  

> hide #!1.1.7 models

> open "/home/calvingunther66/Imaging/Gunther, Calvin/Head MRI w-o contrast
> 2025/dicom/SER00008" format dicom

Summary of feedback from opening /home/calvingunther66/Imaging/Gunther,
Calvin/Head MRI w-o contrast 2025/dicom/SER00008  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Opened 8 MR (AX T2) as #1.1.8, grid size 1024,1024,36, pixel 0.215,0.215,4.38, shown at step 1, values int16  
  

> hide #!1.1.8 models

> open "/home/calvingunther66/Imaging/Gunther, Calvin/Head MRI w-o contrast
> 2025/dicom/SER00009" format dicom

Summary of feedback from opening /home/calvingunther66/Imaging/Gunther,
Calvin/Head MRI w-o contrast 2025/dicom/SER00009  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Opened 9 MR (AX 3D SWAN) as #1.1.9, grid size 512,512,134, pixel 0.43,0.43,1.19, shown at step 1, values int16  
  

> hide #!1.1.9 models

> open "/home/calvingunther66/Imaging/Gunther, Calvin/Head MRI w-o contrast
> 2025/dicom/SER00010" format dicom

Summary of feedback from opening /home/calvingunther66/Imaging/Gunther,
Calvin/Head MRI w-o contrast 2025/dicom/SER00010  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Opened 10 MR (AX T1 FLAIR) as #1.1.10, grid size 1024,1024,36, pixel 0.215,0.215,4.38, shown at step 1, values int16  
  

> hide #!1.1.10 models

> open "/home/calvingunther66/Imaging/Gunther, Calvin/Head MRI w-o contrast
> 2025/dicom/SER00011" format dicom

Summary of feedback from opening /home/calvingunther66/Imaging/Gunther,
Calvin/Head MRI w-o contrast 2025/dicom/SER00011  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Opened 11 MR (AX 3D ASL) as #1.1.11, grid size 128,128,56, pixel 1.88,1.88,2.41, shown at step 1, values int16  
  

> hide #!1.1.11 models

> open "/home/calvingunther66/Imaging/Gunther, Calvin/Head MRI w-o contrast
> 2025/dicom/SER00012" format dicom

Summary of feedback from opening /home/calvingunther66/Imaging/Gunther,
Calvin/Head MRI w-o contrast 2025/dicom/SER00012  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Opened 12 MR (COR T2) as #1.1.12, grid size 1024,1024,42, pixel 0.215,0.215,4.39, shown at step 1, values int16  
  

> view orient

> hide #!1.1.12 models

> open "/home/calvingunther66/Imaging/Gunther, Calvin/Head MRI w-o contrast
> 2025/dicom/SER00013" format dicom

Summary of feedback from opening /home/calvingunther66/Imaging/Gunther,
Calvin/Head MRI w-o contrast 2025/dicom/SER00013  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Opened 200 MR (AX 3D T1 MP-RAGE REFORMAT) as #1.1.13, grid size 512,512,257, pixel 0.5,0.5,0.996, shown at step 1, values int16  
  

> view orient

> hide #!1.1.13 models

> open "/home/calvingunther66/Imaging/Gunther, Calvin/Head MRI w-o contrast
> 2025/dicom/SER00014" format dicom

Summary of feedback from opening /home/calvingunther66/Imaging/Gunther,
Calvin/Head MRI w-o contrast 2025/dicom/SER00014  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Opened 201 MR (COR 3D T1 MP-RAGE REFORMAT) as #1.1.14, grid size 512,512,257, pixel 0.5,0.5,1.41, shown at step 1, values int16  
  

> view orient

> hide #!1.1.14 models

> open "/home/calvingunther66/Imaging/Gunther, Calvin/Head MRI w-o contrast
> 2025/dicom/SER00015" format dicom

Summary of feedback from opening /home/calvingunther66/Imaging/Gunther,
Calvin/Head MRI w-o contrast 2025/dicom/SER00015  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Opened 510 MR (ORIG: AX MUSE DWI) as #1.1.15, grid size 256,256,80, pixel 0.859,0.859,1.95, shown at step 1, values int16  
  

> view orient

> hide #!1.1.15 models

> open "/home/calvingunther66/Imaging/Gunther, Calvin/Head MRI w-o contrast
> 2025/dicom/SER00016" format dicom

Summary of feedback from opening /home/calvingunther66/Imaging/Gunther,
Calvin/Head MRI w-o contrast 2025/dicom/SER00016  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Opened 550 MR (ADC (10^-6 mm²/s)) as #1.1.16, grid size 256,256,40, pixel 0.859,0.859,3.9, shown at step 1, values int16  
  

> hide #!1.1.16 models

> open "/home/calvingunther66/Imaging/Gunther, Calvin/Head MRI w-o contrast
> 2025/dicom/SER00017" format dicom

Summary of feedback from opening /home/calvingunther66/Imaging/Gunther,
Calvin/Head MRI w-o contrast 2025/dicom/SER00017  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Opened 551 MR (eADC) as #1.1.17, grid size 256,256,40, pixel 0.859,0.859,3.9, shown at step 1, values float32  
  

> hide #!1.1.17 models

> open "/home/calvingunther66/Imaging/Gunther, Calvin/Head MRI w-o contrast
> 2025/dicom/SER00018" format dicom

Summary of feedback from opening /home/calvingunther66/Imaging/Gunther,
Calvin/Head MRI w-o contrast 2025/dicom/SER00018  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Opened 900 MR (FILT_PHA: AX 3D SWAN) as #1.1.18, grid size 512,512,134, pixel 0.43,0.43,1.19, shown at step 1, values int16  
  

> hide #!1.1.18 models

> open "/home/calvingunther66/Imaging/Gunther, Calvin/Head MRI w-o contrast
> 2025/dicom/SER00019" format dicom

Summary of feedback from opening /home/calvingunther66/Imaging/Gunther,
Calvin/Head MRI w-o contrast 2025/dicom/SER00019  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Opened 901 MR (AX SWAN MIN IP) as #1.1.19, grid size 512,512,81, pixel 0.43,0.43,1.98, shown at step 1, values int16  
  

> hide #!1.1.19 models

> open "/home/calvingunther66/Imaging/Gunther, Calvin/Head MRI w-o contrast
> 2025/dicom/SER00020" format dicom

Summary of feedback from opening /home/calvingunther66/Imaging/Gunther,
Calvin/Head MRI w-o contrast 2025/dicom/SER00020  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Opened multi-channel map 1150 MR (CBF) as #1.1.20, 3 channels, grid size 512,512,28, pixel 1, shown at step 1, values uint8  
  

> view orient

> hide #!1.1.20 models

> open "/home/calvingunther66/Imaging/Gunther, Calvin/Head MRI w-o contrast
> 2025/dicom/SER00021" format dicom

Summary of feedback from opening /home/calvingunther66/Imaging/Gunther,
Calvin/Head MRI w-o contrast 2025/dicom/SER00021  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Opened 1151 MR (CBF) as #1.1.21, grid size 128,128,28, pixel 1.88,1.88,4.82, shown at step 1, values int16  
  

> view orient

> hide #!1.1.21 models

> open "/home/calvingunther66/Imaging/Gunther, Calvin/Head MRI w-o contrast
> 2025/dicom/SER00022" format dicom

Summary of feedback from opening /home/calvingunther66/Imaging/Gunther,
Calvin/Head MRI w-o contrast 2025/dicom/SER00022  
---  
warnings | Merged incoming unique studies with existing patient with same ID  
No model created for Series #9990 from patient 24340846 because it had no
pixel data. Metadata will still be available.  
  

> view orient

> open "/home/calvingunther66/Imaging/Gunther, Calvin/Head MRI w-o contrast
> 2025/dicom/SER00022" format dicom

Summary of feedback from opening /home/calvingunther66/Imaging/Gunther,
Calvin/Head MRI w-o contrast 2025/dicom/SER00022  
---  
warnings | Merged incoming unique studies with existing patient with same ID  
No model created for Series #9990 from patient 24340846 because it had no
pixel data. Metadata will still be available.  
  

> save "/home/calvingunther66/Imaging/Gunther, Calvin/Head_MRI_2025.cxs"

——— End of log from Mon Nov 17 07:27:39 2025 ———

> view name session-start

opened ChimeraX session  

> show #!1.1.1 models

> hide #!1.1.1 models

> show #!1.1.9 models

> volume #!1.1.9 projectionMode 2d-xyz

> volume #!1.1.9 appearance brain

> volume #!1.1.9 appearance initial

> volume #1.1.9 orthoplanes xyz positionPlanes 256,256,67 style image region
> all

> mousemode rightMode "move planes"

> ui mousemode right windowing

> volume #1.1.9 level 149.8,0 level 833.8,0.9 level 2255,1

> volume #1.1.9 level 417.1,0 level 954.5,0.9 level 2071,1

> hide #!1.1.9 models

> show #!1.1.16 models

> hide #!1.1.16 models

> show #!1.1.2 models

> view orient

> volume #1.1.2 level -1121,0 level 270.5,0.9 level 3161,1

> ui mousemode right "move planes"

> volume #1.1.2 region 0,0,182,511,511,182

> volume #1.1.2 region 0,0,111,511,511,111

> hide #!1.1.2 models

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 230, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1419, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/segmentations/bundle.py", line 68, in run_provider  
from chmerax.segmentations.actions import run_toolbar_button  
ModuleNotFoundError: No module named 'chmerax'  
  
ModuleNotFoundError: No module named 'chmerax'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/segmentations/bundle.py", line 68, in run_provider  
from chmerax.segmentations.actions import run_toolbar_button  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 230, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1419, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/segmentations/bundle.py", line 68, in run_provider  
from chmerax.segmentations.actions import run_toolbar_button  
ModuleNotFoundError: No module named 'chmerax'  
  
ModuleNotFoundError: No module named 'chmerax'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/segmentations/bundle.py", line 68, in run_provider  
from chmerax.segmentations.actions import run_toolbar_button  
  
See log for complete Python traceback.  
  




OpenGL version: 4.3 (Core Profile) Mesa 25.0.7-2
OpenGL renderer: virgl (Mesa Intel(R) Graphics (MTL))
OpenGL vendor: Mesa

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: xcb

XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=
XDG_SESSION_DESKTOP=
XDG_CURRENT_DESKTOP=X-Generic
WAYLAND_DISPLAY=wayland-0
DISPLAY=:0
Manufacturer: ChromiumOS
Model: crosvm
OS: Debian GNU/Linux 13
Architecture: 64bit ELF
Virtual Machine: lxc
CPU: 10 Intel(R) Core(TM) Ultra 5 115U
Cache Size: 10240 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           6.1Gi       3.2Gi       2.1Gi       248Mi       909Mi       3.0Gi
	Swap:             0B          0B          0B

Graphics:
	unknown

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.6.1
    build: 1.2.2.post1
    certifi: 2025.7.14
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.19
    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: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    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
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.1
    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: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    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-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    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-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: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    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: 1.1.3
    ChimeraX-ProfileGrids: 1.1.3
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    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: 1.45.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.10.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.15
    decorator: 5.2.1
    distro: 1.9.0
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.59.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.3.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    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
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.1
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14