id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
20155	ChimeraX bug report submission	psrini7@…		"{{{
The following bug report has been submitted:
Platform:        macOS-15.7.4-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
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Log:
> runscript /Users/poojasrinivas/Downloads/chimerax-trimmings-
> main/chimerax_trimmings.py

> runscript /Users/poojasrinivas/Downloads/chimerax-trimmings-
> main/map_salami.py

> camera ortho

> cofr centerOfView

> mousemode alt rightMode ""contour level""

> mousemode rightMode clip

> mousemode alt leftMode ""translate selected models""

> mousemode shift leftMode ""rotate selected models""

> mousemode alt control leftMode ""pick blobs""

> alias cofron cofr centerofview showpivot 7,0.25

> alias usage cofron synopsis ""Center the rotation point on the view and show
> the pivot""

FYI: alias is hiding existing command: ""usage""  

> alias cofroff cofr centerofview showpivot false

> alias usage cofroff synopsis ""Recenter the rotation point on the view and
> hide the pivot marker""

> alias symclip cofr centerofview; clip near -$1 far $1 position cofr

> alias usage symclip synopsis ""Set symmetric clip planes around the center of
> rotation"" $1 ""half-distance""

> alias modelsel select ##num_residues

> alias usage modelsel synopsis ""Select atomic models""

> alias mapsel select ~##num_residues

> alias usage mapsel synopsis ""Select non-atomic models such as maps""

> alias sidesel select sidechain & $1 | ~backbone & nucleic & $1

> alias usage sidesel synopsis ""Select protein sidechains and nucleic-acid
> bases"" $1 ""atom-spec""

> alias sidedisp select sidechain & $1 | ~backbone & nucleic & $1; display sel

> alias usage sidedisp synopsis ""Display protein sidechains and nucleic-acid
> bases"" $1 ""atom-spec""

> alias cootmode_white set bgColor white; surface cap false; surface style
> solid; nucleotides #* atoms; lighting flat; graphics silhouettes false;
> style stick; ~rib; color ##num_residues orange; color byhet ; disp
> ##num_residues & ##display; ~disp @H*; style ions sphere; style solvent
> ball; size ballscale 0.2; size stickradius 0.07; transparency 85; cofr
> centerofview; clip near -10 far 10 position cofr; color ~##num_residues
> medium blue

> alias usage cootmode_white synopsis ""Apply the white-background Coot-style
> display preset""

> alias cootmode set bgColor black; surface cap false; surface style solid;
> nucleotides #* atoms; lighting flat; graphics silhouettes false; style
> stick; ~rib; color ##num_residues gold; color byhet ; disp ##num_residues &
> ##display; ~disp @H*; style ions sphere; style solvent ball; size ballscale
> 0.2; size stickradius 0.07; transparency 70; cofr centerofview; clip near
> -10 far 10 position cofr; color ~##num_residues cornflower blue

> alias usage cootmode synopsis ""Apply the dark-background Coot-style display
> preset""

> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> nucleotides #* atoms; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp ##num_residues & ##display; ~disp
> @H*; style solvent ball; style ions sphere; size ballscale 0.2; size
> stickradius 0.07; cofr centerofview; clip near -10 far 10 position cofr;
> color ~##num_residues #3d60ffff; transparency 50

> alias usage cootmode_mesh synopsis ""Apply the mesh Coot-style display
> preset""

> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1

> alias usage ca_and_sidechains synopsis ""Show CA or phosphate trace plus
> sidechains or bases"" $1 ""model-spec""

> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1

> alias usage ca_trace synopsis ""Show a CA or phosphate trace"" $1 ""model-spec""

> alias expand_sym ~disp $1; rib $1; sym $1 assembly 1 copies false newModel
> true

> alias usage expand_sym synopsis ""Expand an asymmetric unit to biological
> assembly 1 as ribbon copies"" $1 ""model-spec""

> alias map_sphere_15 volume unzone ~##num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; volume zone ~##num_residues nearAtoms sel
> minimalBounds true range 15; close #10000

> alias usage map_sphere_15 synopsis ""Zone maps to a 15 A sphere around the
> center of rotation""

> alias cubic_map shape sphere radius $1 modelid #10000; volume onesmask
> #10000 spacing 1 border -0.5

> alias usage cubic_map synopsis ""Create a spherical mask map on a cubic grid""
> $1 ""sphere radius""

> alias map_unsphere volume unzone ~##num_residues

> alias usage map_unsphere synopsis ""Remove map zoning from all maps""

> alias fit_by_chain split $1; fitmap $1.* inmap $2 eachmodel true; combine
> $1.* close true

> alias usage fit_by_chain synopsis ""Split a model by chain, fit each chain
> into a map, and recombine"" $1 ""model-spec"" $2 ""map-spec""

> alias rainbow_new rainbow palette RdYlBu-5

> alias usage rainbow_new synopsis ""Color models by rainbow using the RdYlBu-5
> palette""

> alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5;
> lighting soft

> alias usage default_mol_display synopsis ""Restore the default cartoon
> molecular display""

> alias local_fitmap ~sel; close #10000-10001; marker #10000 position cofr;
> sel #10000; volume zone $2 nearAtoms sel range $3 newMap true modelid 10001
> minimalbounds true; fitmap $1 inmap #10001 eachmodel true; close #10001;
> close sel; show $2

> alias usage local_fitmap synopsis ""Fit a model or map into a local zone
> around the center of rotation"" $1 ""model or map to fit"" $2 ""target map"" $3
> ""zone radius""

> alias hidemodels hide ##num_residues models

> alias usage hidemodels synopsis ""Hide all atomic models""

> alias showmodels show ##num_residues models

> alias usage showmodels synopsis ""Show all atomic models""

> alias caps_off surface cap false

> alias usage caps_off synopsis ""Turn clipped surface caps off""

> alias caps_on surface cap true

> alias usage caps_on synopsis ""Turn clipped surface caps on""

> alias open_vseries ""open browse vseries true""

> alias usage open_vseries synopsis ""Open a file browser with volume series
> enabled""

> alias selbetween ks ri

> alias usage selbetween synopsis ""Select residues between the current
> selection endpoints""

> alias helix setattr $1 res is_helix true

> alias usage helix synopsis ""Mark residues as helix"" $1 ""residue-spec""

> alias strand setattr $1 res is_strand true

> alias usage strand synopsis ""Mark residues as strand"" $1 ""residue-spec""

> alias coil setattr $1 res is_strand false; setattr $1 res is_helix false

> alias usage coil synopsis ""Clear helix and strand assignment for residues""
> $1 ""residue-spec""

> alias rock_movie cofr showpivot false; movie record; rock y 50; wait 600;
> movie encode ~/Desktop/rock_movie.mp4; stop

> alias usage rock_movie synopsis ""Record a rocking movie and save it to the
> default Desktop file""

> alias centersel cofr sel; clip near 10 position cofr; clip far -10 position
> cofr; cofr centerOfView showpivot true; view sel

> alias usage centersel synopsis ""Center the view on the selection and apply
> local clipping""

> alias volume_project set bgColor black; volume $1 step 1 sd_level 0,0
> sd_level 50,1 color white color white style image projection_mode auto
> maximum_intensity_projection true bt_correction true linear_interpolation
> true; lighting depth_cue false

> alias usage volume_project synopsis ""Display a map as a maximum-intensity
> projection"" $1 ""map-spec""

> alias split_diff_map volume scale $1 rms 1 modelId $2; close $1; volume $2
> capFaces false meshLighting false squareMesh false level -3 color
> #da1200000000 level 3 color #0000bda00000; lighting depthCue true; volume $2
> style mesh

> alias usage split_diff_map synopsis ""Replace a map with a scaled positive
> and negative mesh difference map"" $1 ""input map"" $2 ""output model-id""

> alias local_diff_map view name tmp; close #1001,1002,1003,1004,1005; fitmap
> $1 inMap $2; vol zone $2 near $1 range 5 newMap true modelId 1000
> minimalBounds true; fitmap $1 inMap $3; vol zone $3 near $1 range 5 newMap
> true modelId 1001 minimalBounds true; volume scale #1000 sd 0.1 modelId
> 1002; volume scale #1001 sd 0.1 modelId 1003; fitmap #1003 inMap #1002;
> volume resample #1003 onGrid #1002 modelId 1004; volume subtract #1002 #1004
> modelId 1005 minRms true; volume #1005 step 1; split_diff_map #1005 #1006;
> close #1000,1001,1002,1003,1004,1005; view tmp

> alias usage local_diff_map synopsis ""Build a local difference map between
> two fitted maps around a model"" $1 ""model-spec"" $2 ""first map"" $3 ""second
> map""

> alias local_diff_map_sphere ~sel; close
> #10000,#1001,#1002,#1003,#1004,#1005; marker #10000 position cofr; sel
> #10000; vol zone $1 near sel range $3 newMap true modelId 1000 minimalBounds
> true; vol zone $2 near sel range $3 newMap true modelId 1001 minimalBounds
> true; volume scale #1000 sd 0.1 modelId 1002; volume scale #1001 sd 0.1
> modelId 1003; fitmap #1003 inMap #1002; volume resample #1003 onGrid #1002
> modelId 1004; volume subtract #1002 #1004 modelId 1005 minRms true; volume
> #1005 step 1; split_diff_map #1005 #1006; close
> #10000,#1000,#1001,#1002,#1003,#1004,#1005

> alias usage local_diff_map_sphere synopsis ""Build a local difference map
> between two maps around the center of rotation"" $1 ""first map"" $2 ""second
> map"" $3 ""radius""

> alias binary_mask volume threshold $1 minimum $2 set 0 maximum $2 setMaximum
> 1 modelId 2000; volume #2000 level 0.5

> alias usage binary_mask synopsis ""Create a binary mask map at a chosen
> contour level"" $1 ""map-spec"" $2 ""contour level""

> alias soft_mask volume threshold $1 minimum $2 set 0 maximum $2 setMaximum 1
> modelId 2000; volume falloff #2000 iterations 20 modelId 2001; volume #2001
> level 0.5; close #2000

> alias usage soft_mask synopsis ""Create a soft-edged mask map at a chosen
> contour level"" $1 ""map-spec"" $2 ""contour level""

> alias delh delete @H*

> alias usage delh synopsis ""Delete all hydrogen atoms""

> alias delh_sel delete sel & @H*

> alias usage delh_sel synopsis ""Delete hydrogen atoms from the current
> selection""

> alias carve surface zone ~##num_residues nearAtoms sel distance $1

> alias usage carve synopsis ""Carve displayed map surfaces to the current
> selection"" $1 ""distance""

> alias uncarve surface unzone ~##num_residues

> alias usage uncarve synopsis ""Remove surface carving from displayed map
> surfaces""

> functionkey F1 prevmodel

> functionkey F2 nextmodel

> functionkey F3 centersel

> functionkey F4 view all

> functionkey F5 togglemaps

> functionkey F6 togglemodels

> functionkey F7 cyclelighting

> functionkey F8 cyclemodeldisplay

> functionkey F9 prevmap

> functionkey F10 nextmap

> buttonpanel Shortcuts rows 3 columns 5

> buttonpanel Shortcuts add Vol_Viewer command ""tool show 'Volume Viewer'""

> buttonpanel Shortcuts add Model_Panel command ""tool show Models""

> buttonpanel Shortcuts add Log command ""tool show Log""

> buttonpanel Shortcuts add default_disp command default_mol_display

> buttonpanel Shortcuts add map_sphere command map_sphere_15

> buttonpanel Shortcuts add map_unsphere command map_unsphere

> buttonpanel Shortcuts add cofron command cofron

> buttonpanel Shortcuts add cofroff command cofroff

> buttonpanel Shortcuts add cootmode command cootmode

> buttonpanel Shortcuts add mark_cofr command ""marker #20000 position cofr
> radius 1""

> buttonpanel Shortcuts add togglemaps command togglemaps

> buttonpanel Shortcuts add togglemodels command togglemodels

> buttonpanel Shortcuts add reset_mouse_and_help command ""mousemode alt right
> contour ; mousemode right clip ; mousemode alt left 'translate selected
> models' ; mousemode shift left 'rotate selected models' ; mousemode alt
> control left 'pick blobs'; help https://github.com/olibclarke/chimerax-
> trimmings/blob/main/default_mousemodes.md""

> buttonpanel Shortcuts add previous_model command prevmodel

> buttonpanel Shortcuts add next_model command nextmodel

> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true

Saved volume settings  
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4 Max
OpenGL vendor: Apple

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: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac16,5
      Model Number: MX303LL/A
      Chip: Apple M4 Max
      Total Number of Cores: 14 (10 performance and 4 efficiency)
      Memory: 36 GB
      System Firmware Version: 13822.81.10
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.7.4 (24G517)
      Kernel Version: Darwin 24.6.0
      Time since boot: 5 hours, 13 minutes

Graphics/Displays:

    Apple M4 Max:

      Chipset Model: Apple M4 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      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
        PA27DCE:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    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: 2023.11.17
    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-Clipper: 0.25.2
    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-ISOLDE: 1.10.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    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
    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
    OpenMM: 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-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 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
}}}
"	defect	new	normal		Unassigned