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Opened 3 hours ago
#20155 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-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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{
"uptime" : 18000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac16,5",
"coalitionID" : 1924,
"osVersion" : {
"train" : "macOS 15.7.4",
"build" : "24G517",
"releaseType" : "User"
},
"captureTime" : "2026-04-10 15:06:33.3721 -0400",
"codeSigningMonitor" : 2,
"incident" : "F1AAF4EB-2940-405F-98E4-6D47CE520BEC",
"pid" : 1821,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2026-04-10 11:35:42.2201 -0400",
"procStartAbsTime" : 147287659970,
"procExitAbsTime" : 450914783497,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.1","CFBundleVersion":"1.10.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"091F18F9-4828-5E7C-8280-88FCDF77F2BD","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "10D78415-FD42-E1D3-B36A-F181F7F76893",
"appleIntelligenceStatus" : {"reasons":["siriAssetIsNotReady","notOptedIn","assetIsNotReady"],"state":"unavailable"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
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"sip" : "enabled",
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"exception" : {"codes":"0x0000000000000001, 0x000016c6fec24070","rawCodes":[1,25043933479024],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000016c6fec24070"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":1821},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
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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:
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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
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ihm: 2.2
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ipykernel: 6.29.5
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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
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