kvfinder error with multiple structures

[Elaine Meng]

The following bug report has been submitted:
Platform:        macOS-14.7-arm64-arm-64bit
ChimeraX Version: 1.9.dev202410040848 (2024-10-04 08:48:56 UTC)
Description
Tried to run Cavity Finder on 2 structures

I had 8iyx (with surface, from pre-existing session) then opened 2gbp and 2mnr and chose the 2 latter from the dialog to run KVFinder.  Got rainbow pinwheel for a minute or so and then the error.

Log:
UCSF ChimeraX version: 1.9.dev202410040848 (2024-10-04)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/meng/Library/Application Support/ChimeraX/Schol-
> AR/chimeraXscholartest/NI9FAIQHQY/N77O/cxs/mlp coloring-session.cxs" format
> session

Log from Tue Oct 1 17:53:33 2024UCSF ChimeraX version: 1.9.dev202409280129
(2024-09-28)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> scholar openAugSession chimeraXscholartest "8iyx binding site" "mlp
> coloring"

Log from Tue Oct 1 17:51:32 2024UCSF ChimeraX version: 1.9.dev202409280129
(2024-09-28)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> scholar openAugSession chimeraXscholartest "8iyx binding site" "mlp
> coloring"

Log from Tue Sep 24 15:52:28 2024UCSF ChimeraX version: 1.9.dev202409170516
(2024-09-17)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open project.cxs

Log from Mon Sep 23 17:59:22 2024

> open /Users/meng/Desktop/startup.cxc

> alias reset view orient; view initial

> alias start tool show $1

> alias whereprefs info path user unversioned config

> alias captut open help:user/tutorials/binding-sites.html#cap-example

> alias previewts toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu;toolshed reload available

> alias normalts toolshed url https://cxtoolshed.rbvi.ucsf.edu;toolshed reload
> available

> alias btut open
> https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/tutorials/binding-
> sites.html; ui dockable false "Help Viewer"

> alias stut open https://www.rbvi.ucsf.edu/chimerax/data/conservation-
> coloring/conservation-coloring.html; ui dockable false "Help Viewer"

> alias ltut open https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop-
> modeling.html; ui dockable false "Help Viewer"

> alias mtut open https://www.rbvi.ucsf.edu/chimerax/data/mole-channel/mole-
> channel.html; ui dockable false "Help Viewer"; windowsize 600 800

executed startup.cxc  
UCSF ChimeraX version: 1.9.dev202409170516 (2024-09-17)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 8iyx

Summary of feedback from opening 8iyx fetched from pdb  
---  
notes | https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/S6R/S6R.cif  

8iyx title:  
Cryo-EM structure of the GPR34 receptor in complex with the antagonist YL-365
[more info...]  

Chain information for 8iyx #1  
---  
Chain | Description | UniProt  
C | Probable G-protein coupled receptor 34,YL-365 | GPR34_HUMAN 1-242 250-381  

Non-standard residues in 8iyx #1  
---  
S6R \u2014
1-[4-(3-chlorophenyl)phenyl]carbonyl-4-[2-(4-phenylmethoxyphenyl)ethanoylamino]piperidine-4-carboxylic
acid  


> label delete

> hide atoms

> show ligand

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 8iyx_C SES surface #1.2: minimum, -12.46, mean 2.74,
maximum 16.85  

> size ligand stickRadius .4

Changed 46 bond radii  

> lighting soft

> lighting simple

> lighting soft

> lighting full

> lighting flat

> lighting full

> lighting flat

> set bgColor white

> lighting full

> hide sel

> mlp

Map values for surface "8iyx_C SES surface": minimum -25.99, mean 1.235,
maximum 23.7  

> save project.cxs

\u2014\u2014\u2014 End of log from Mon Sep 23 17:59:22 2024 \u2014\u2014\u2014

opened ChimeraX session  

> scholar project chimeraXscholartest "test project: 8iyx binding site"
> projectType other discUrl ""

Invalid project title. Project titles can only contain letters, numbers, and
spaces.  

> scholar project chimeraXscholartest "8iyx binding site" projectType other
> discUrl ""

> scholar project chimeraXscholartest "8iyx binding site"

> scholar augmentation chimeraXscholartest "8iyx binding site" "mlp coloring"

An error occurred while making the API call:  
HTTPSConnectionPool(host='www.schol-ar.io', port=443): Max retries exceeded
with url: /api/EditAug/NI9FAIQHQY/N77O (Caused by SSLError(SSLEOFError(8, 'EOF
occurred in violation of protocol (_ssl.c:2423)')))  
Failed to update augmentation mlp coloring for project 8iyx binding site  
An error occurred while making the API call:  
https://www.schol-ar.io/api/EditAug/NI9FAIQHQY/N77O  
Error:  
503 Server Error: Service Unavailable for url: https://www.schol-
ar.io/api/EditAug/NI9FAIQHQY/N77O  
Failed to update augmentation mlp coloring for project 8iyx binding site  

> scholar openAugSession chimeraXscholartest "8iyx binding site" "mlp
> coloring"

No session file found for Augmentation: mlp coloring  

Failed to send bug report. Bug report server www.rbvi.ucsf.edu is unavailable  

QTextHtmlParser::applyAttributes: Unknown color name '{link}'  

Failed to send bug report. Bug report server www.rbvi.ucsf.edu is unavailable  

QTextHtmlParser::applyAttributes: Unknown color name '{link}'  

> scholar storeQRImage chimeraXscholartest "8iyx binding site"
> /Users/meng/Desktop/scholar-project/qr.png

> scholar saveAugSession chimeraXscholartest "8iyx binding site" "mlp
> coloring"

\u2014\u2014\u2014 End of log from Tue Sep 24 15:52:28 2024 \u2014\u2014\u2014

opened ChimeraX session  

> scholar saveAugSession chimeraXscholartest "8iyx binding site" "mlp
> coloring" filePath ~/Desktop

Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/meng/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/scholar/cmd.py", line 349, in save_aug_session  
ScARFileManager.save_file_copy(file_path, aug_session_dir)  
File "/Users/meng/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/scholar/io.py", line 784, in save_file_copy  
shutil.copy(full_file_for_copy_path, destination_file_path)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/shutil.py",
line 419, in copy  
copyfile(src, dst, follow_symlinks=follow_symlinks)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/shutil.py",
line 256, in copyfile  
with open(src, 'rb') as fsrc:  
^^^^^^^^^^^^^^^  
IsADirectoryError: [Errno 21] Is a directory: '/Users/meng/Desktop'  

IsADirectoryError: [Errno 21] Is a directory: '/Users/meng/Desktop'  

File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/shutil.py",
line 256, in copyfile  
with open(src, 'rb') as fsrc:  
^^^^^^^^^^^^^^^  

See log for complete Python traceback.  


> scholar saveAugSession chimeraXscholartest "8iyx binding site" "mlp
> coloring" filePath ~/Desktop/test.cxs

> scholar saveAugSession chimeraXscholartest "8iyx binding site" "mlp
> coloring" filePath browse

> ui tool show Shell

> pwd

Current working directory is: /Users/meng/Desktop  

> browse

Expected a keyword  

> browse

Expected a keyword  

> browse

Expected a keyword  

> scholar storeQRImage chimeraXscholartest "8iyx binding site"
> /Users/meng/Desktop/junk.png

> scholar storeAllAugFiles chimeraXscholartest "8iyx binding site" "mlp
> coloring" /Users/meng/Desktop/junk

> scholar saveAugSession chimeraXscholartest "8iyx binding site" "mlp
> coloring" filePath browse

> scholar saveAugSession chimeraXscholartest "8iyx binding site" "mlp
> coloring" filePath ~/Desktop/junk.cxs

> save nerts.cxs

> scholar saveAugSession chimeraXscholartest "8iyx binding site" "mlp
> coloring" filePath ~/Desktop/nerts.cxs

[Repeated 1 time(s)]

\u2014\u2014\u2014 End of log from Tue Oct 1 17:51:32 2024 \u2014\u2014\u2014

opened ChimeraX session  

> scholar saveAugSession chimeraXscholartest "8iyx binding site" "mlp
> coloring"

\u2014\u2014\u2014 End of log from Tue Oct 1 17:53:33 2024 \u2014\u2014\u2014

opened ChimeraX session  

> ui tool show "Find Cavities"

> open 2gbp

2gbp title:  
Sugar and signal-transducer binding sites of the escherichia coli galactose
chemoreceptor protein [more info...]  

Chain information for 2gbp #2  
---  
Chain | Description | UniProt  
A | D-GALACTOSE/D-GLUCOSE BINDING PROTEIN | DGAL_ECOLI 1-309  

Non-standard residues in 2gbp #2  
---  
BGC \u2014 \u03b2-D-glucose  
CA \u2014 calcium ion  


> open 2mnr

2mnr title:  
Mechanism of the reaction catalyzed by mandelate racemase. 2. Crystal
structure of mandelate racemase At 2.5 angstroms resolution: identification of
the active site and possible catalytic residues [more info...]  

Chain information for 2mnr #3  
---  
Chain | Description | UniProt  
A | MANDELATE RACEMASE | MANR_PSEPU 3-359  

Non-standard residues in 2mnr #3  
---  
MN \u2014 manganese (II) ion  
SO4 \u2014 sulfate ion  

2mnr mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  


> ui tool show "Find Cavities"

pyKVFinder module not installed; fetching from PyPi repository...  

> kvfinder #2-3

8 cavities found for 2gbp #2  
Traceback (most recent call last):  
File "/Users/meng/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/kvfinder/tool.py", line 67, in find_cavities  
run(self.session, "kvfinder %s" % concise_model_spec(self.session, structures,  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/meng/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/kvfinder/cmd.py", line 47, in cmd_kvfinder  
struct_input, vertices = prep_input(s, origin, extent, probe_in, probe_out,
step)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/meng/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/kvfinder/prep.py", line 42, in prep_input  
"p2": [origin[0], origin[1], origin[2] + extents[2]],  
~~~~~~~^^^  
TypeError: 'NoneType' object is not subscriptable  

TypeError: 'NoneType' object is not subscriptable  

File "/Users/meng/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/kvfinder/prep.py", line 42, in prep_input  
"p2": [origin[0], origin[1], origin[2] + extents[2]],  
~~~~~~~^^^  

See log for complete Python traceback.  





OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

   Hardware Overview:

     Model Name: MacBook Pro
     Model Identifier: MacBookPro18,1
     Model Number: MK1F3LL/A
     Chip: Apple M1 Pro
     Total Number of Cores: 10 (8 performance and 2 efficiency)
     Memory: 16 GB
     System Firmware Version: 11881.1.1
     OS Loader Version: 10151.140.19.700.2

Software:

   System Software Overview:

     System Version: macOS 14.7 (23H124)
     Kernel Version: Darwin 23.6.0
     Time since boot: 3 hours, 56 minutes

Graphics/Displays:

   Apple M1 Pro:

     Chipset Model: Apple M1 Pro
     Type: GPU
     Bus: Built-In
     Total Number of Cores: 16
     Vendor: Apple (0x106b)
     Metal Support: Metal 3
     Displays:
       Color LCD:
         Display Type: Built-in Liquid Retina XDR Display
         Resolution: 3456 x 2234 Retina
         Main Display: Yes
         Mirror: Off
         Online: Yes
         Automatically Adjust Brightness: Yes
         Connection Type: Internal


Installed Packages:
   alabaster: 1.0.0
   appdirs: 1.4.4
   appnope: 0.1.4
   asttokens: 2.4.1
   babel: 2.16.0
   beautifulsoup4: 4.12.3
   blockdiag: 3.0.0
   blosc2: 2.7.1
   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: 2.14
   ChimeraX-AlphaFold: 1.0.1
   ChimeraX-AltlocExplorer: 1.1.2
   ChimeraX-AmberInfo: 1.0
   ChimeraX-Arrays: 1.1
   ChimeraX-Atomic: 1.58.7
   ChimeraX-AtomicLibrary: 14.1.7
   ChimeraX-AtomSearch: 2.0.1
   ChimeraX-AxesPlanes: 2.4
   ChimeraX-BasicActions: 1.1.2
   ChimeraX-BILD: 1.0
   ChimeraX-BlastProtein: 2.4.7
   ChimeraX-BondRot: 2.0.4
   ChimeraX-BugReporter: 1.0.1
   ChimeraX-BuildStructure: 2.13
   ChimeraX-Bumps: 1.0
   ChimeraX-BundleBuilder: 1.3.4
   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: 2.3
   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: 1.9.dev202410040848
   ChimeraX-CoreFormats: 1.2
   ChimeraX-coulombic: 1.4.4
   ChimeraX-Crosslinks: 1.0
   ChimeraX-Crystal: 1.0
   ChimeraX-CrystalContacts: 1.0.1
   ChimeraX-DataFormats: 1.2.3
   ChimeraX-DeepMutationalScan: 1.0
   ChimeraX-Dicom: 1.2.5
   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: 1.4.1
   ChimeraX-Hbonds: 2.5
   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: 1.0
   ChimeraX-Label: 1.1.11
   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: 2.1.6
   ChimeraX-MCopy: 1.0
   ChimeraX-MDcrds: 2.7.1
   ChimeraX-MedicalToolbar: 1.1
   ChimeraX-Meeting: 1.0.1
   ChimeraX-MLP: 1.1.1
   ChimeraX-mmCIF: 2.14.2
   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: 1.14
   ChimeraX-OrthoPick: 1.0.1
   ChimeraX-PDB: 2.7.6
   ChimeraX-PDBBio: 1.0.1
   ChimeraX-PDBLibrary: 1.0.4
   ChimeraX-PDBMatrices: 1.0
   ChimeraX-PhenixUI: 1.3
   ChimeraX-PickBlobs: 1.0.1
   ChimeraX-Positions: 1.0
   ChimeraX-PresetMgr: 1.1.2
   ChimeraX-PubChem: 2.2
   ChimeraX-ReadPbonds: 1.0.1
   ChimeraX-Registration: 1.1.2
   ChimeraX-RemoteControl: 1.0
   ChimeraX-RenderByAttr: 1.6
   ChimeraX-RenumberResidues: 1.1
   ChimeraX-ResidueFit: 1.0.1
   ChimeraX-RestServer: 1.3
   ChimeraX-RNALayout: 1.0
   ChimeraX-RotamerLibMgr: 4.0
   ChimeraX-RotamerLibsDunbrack: 2.0
   ChimeraX-RotamerLibsDynameomics: 2.0
   ChimeraX-RotamerLibsRichardson: 2.0
   ChimeraX-SaveCommand: 1.5.1
   ChimeraX-SchemeMgr: 1.0
   ChimeraX-ScholAR: 0.4.2
   ChimeraX-SDF: 2.0.2
   ChimeraX-Segger: 1.0
   ChimeraX-Segment: 1.0.1
   ChimeraX-Segmentations: 3.2.0
   ChimeraX-SelInspector: 1.0
   ChimeraX-SeqView: 2.13
   ChimeraX-Shape: 1.0.1
   ChimeraX-Shell: 1.0.1
   ChimeraX-Shortcuts: 1.2.0
   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: 1.18.1
   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
   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: 1.41
   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: 1.1.4
   ChimeraX-Zone: 1.0.1
   colorama: 0.4.6
   comm: 0.2.2
   contourpy: 1.3.0
   cxservices: 1.2.3
   cycler: 0.12.1
   Cython: 3.0.10
   debugpy: 1.8.6
   decorator: 5.1.1
   docutils: 0.21.2
   executing: 2.1.0
   filelock: 3.15.4
   fonttools: 4.54.1
   funcparserlib: 2.0.0a0
   glfw: 2.7.0
   grako: 3.16.5
   h5py: 3.12.1
   html2text: 2024.2.26
   idna: 3.10
   ihm: 1.3
   imagecodecs: 2024.6.1
   imagesize: 1.4.1
   ipykernel: 6.29.5
   ipython: 8.26.0
   ipywidgets: 8.1.5
   jedi: 0.19.1
   Jinja2: 3.1.4
   jupyter_client: 8.6.2
   jupyter_core: 5.7.2
   jupyterlab_widgets: 3.0.13
   kiwisolver: 1.4.7
   line_profiler: 4.1.3
   lxml: 5.2.2
   lz4: 4.3.3
   MarkupSafe: 2.1.5
   matplotlib: 3.9.2
   matplotlib-inline: 0.1.7
   msgpack: 1.0.8
   ndindex: 1.9.2
   nest-asyncio: 1.6.0
   netCDF4: 1.6.5
   networkx: 3.3
   nibabel: 5.2.0
   nptyping: 2.5.0
   numexpr: 2.10.1
   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: 10.4.0
   pip: 24.2
   pkginfo: 1.11.1
   platformdirs: 4.3.6
   plotly: 5.24.1
   prompt_toolkit: 3.0.48
   psutil: 6.0.0
   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
   pyKVFinder: 0.7.0
   pynmrstar: 3.3.4
   pynrrd: 1.0.0
   PyOpenGL: 3.1.7
   PyOpenGL-accelerate: 3.1.7
   pyopenxr: 1.0.3401
   pyparsing: 3.1.4
   pyproject_hooks: 1.2.0
   PyQt6-commercial: 6.7.1
   PyQt6-Qt6: 6.7.3
   PyQt6-WebEngine-commercial: 6.7.0
   PyQt6-WebEngine-Qt6: 6.7.3
   PyQt6-WebEngineSubwheel-Qt6: 6.7.3
   PyQt6_sip: 13.8.0
   python-dateutil: 2.9.0.post0
   pytz: 2024.2
   pyzmq: 26.2.0
   qtconsole: 5.5.2
   QtPy: 2.4.1
   qtshim: 1.0
   RandomWords: 0.4.0
   requests: 2.32.3
   scipy: 1.14.0
   setuptools: 72.1.0
   sfftk-rw: 0.8.1
   six: 1.16.0
   snowballstemmer: 2.2.0
   sortedcontainers: 2.4.0
   soupsieve: 2.6
   Sphinx: 8.0.2
   sphinx-autodoc-typehints: 2.2.3
   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: 0.6.3
   tables: 3.10.1
   tcia_utils: 1.5.1
   tenacity: 9.0.0
   tifffile: 2024.7.24
   tinyarray: 1.2.4
   toml: 0.10.2
   tornado: 6.4.1
   traitlets: 5.14.3
   typing_extensions: 4.12.2
   tzdata: 2024.2
   urllib3: 2.2.3
   wcwidth: 0.2.13
   webcolors: 24.6.0
   wheel: 0.43.0
   wheel-filename: 1.4.1
   widgetsnbextension: 4.0.13