ChimeraX bug report submission

[olibclarke@…]

The following bug report has been submitted:
Platform:        macOS-15.7.4-arm64-arm-64bit
ChimeraX Version: 1.12.dev202603110023 (2026-03-11 00:23:15 UTC)
Description
Hi,

Not sure whether this counts as a bug, but I notice that when I use the "pick blobs" mousemode, the color changes automatically, but the transparency is not inherited from the parent surface. It would be nice, I think, if the opicked blob changed color, but kept the transparency of the parent surface. It would also be nice if there was a way to default to not showing the bounding boxes (apologies if there is and I missed it).

Cheers
Oli

Log:
> runscript /Users/oc2188/chimerax_startup.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 cofroff cofr centerofview showpivot false

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

> alias selmodel sel ##num_residues

> alias selmap sel ~##num_residues

> 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; ~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 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; ~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 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; ~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 project_map set bgColor black; lighting depthcue false; volume $1
> style image sdlevel 0,0 color white sdlevel 100,0.15 color white
> projectionmode 3d maximumIntensityProjection false dimTransparentVoxels
> false btcorrection true showOutlineBox false linearinterpolation true

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

> alias map_unsphere volume unzone ~##num_residues

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

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

> alias hidemaps surface unzone ~##num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ~##num_residues nearAtoms sel
> distance 0; close #10000

> 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 "Fits the selected model or map to the
> target map, using a zone around the center of rotation for fitting." $1
> "model to fit" $2 "map to fit to" $3 "Radius of local zone"

> alias showmaps surface unzone ~##num_residues

> alias caps_off surface cap false

> alias caps_on surface cap true

> alias open_vseries "open browse vseries true"

> alias selbetween ks ri

> alias helix setattr $1 res is_helix true

> alias strand setattr $1 res is_strand true

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

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

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

> 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 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 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

> functionkey F1 prevmodel

> functionkey F2 nextmodel

> functionkey F3 centersel

> functionkey F4 view all

> 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 hidemaps command hidemaps

> buttonpanel Shortcuts add showmaps command showmaps

> 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: 1.12.dev202603110023 (2026-03-11)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/oc2188/Downloads/semc_2026_tutorial/emd_34705.map

Opened emd_34705.map as #1, grid size 120,120,120, pixel 1.11, shown at level
0.0314, step 1, values float32  

> open /Users/oc2188/Downloads/semc_2026_tutorial/SGLT2_AF.cif

Chain information for SGLT2_AF.cif #2  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> cofron

> move cofr #2

> fitmap #2 inMap #1 search 100 radius 5

Found 100 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).  
  
Average map values and times found:  
0.007378 (1), 0.007286 (1), 0.00719 (1), 0.007164 (1), 0.007084 (1), 0.007081
(1), 0.007048 (1), 0.007038 (1), 0.007004 (1), 0.007 (1), 0.006981 (1),
0.006937 (1), 0.00689 (1), 0.006877 (1), 0.006828 (1), 0.006827 (1), 0.006826
(1), 0.00682 (1), 0.006787 (1), 0.006779 (1), 0.006775 (1), 0.006752 (1),
0.006752 (1), 0.006736 (1), 0.0067 (1), 0.006692 (1), 0.006679 (1), 0.006672
(1), 0.006671 (1), 0.00667 (1), 0.006655 (1), 0.006641 (1), 0.006636 (1),
0.006635 (1), 0.006632 (1), 0.006632 (1), 0.006615 (1), 0.0066 (1), 0.006597
(1), 0.006592 (1), 0.006581 (1), 0.00656 (1), 0.006549 (1), 0.006548 (1),
0.006542 (1), 0.00654 (1), 0.006528 (1), 0.006525 (1), 0.006509 (1), 0.006504
(1), 0.006493 (1), 0.006482 (1), 0.006481 (1), 0.006471 (1), 0.006463 (1),
0.006461 (1), 0.006453 (1), 0.006451 (1), 0.00643 (1), 0.006427 (1), 0.006427
(1), 0.006424 (1), 0.00642 (1), 0.006418 (1), 0.006408 (1), 0.006397 (1),
0.006391 (1), 0.006379 (1), 0.006378 (1), 0.006356 (1), 0.006325 (1), 0.006302
(1), 0.006291 (1), 0.006282 (1), 0.006258 (1), 0.00625 (1), 0.006213 (1),
0.00618 (1), 0.006175 (1), 0.006172 (1), 0.006161 (1), 0.006144 (1), 0.006138
(1), 0.006117 (1), 0.00611 (1), 0.00611 (1), 0.0061 (1), 0.006079 (1),
0.006063 (1), 0.006042 (1), 0.006006 (1), 0.006 (1), 0.005996 (1), 0.00597
(1), 0.005949 (1), 0.005926 (1), 0.0059 (1), 0.0059 (1), 0.005896 (1),
0.005696 (1)  
  
Best fit found:  
Fit molecule SGLT2_AF.cif (#2) to map emd_34705.map (#1) using 5146 atoms  
average map value = 0.007378, steps = 56  
shifted from previous position = 1.59  
rotated from previous position = 1.41 degrees  
atoms outside contour = 4344, contour level = 0.03136  
Position of SGLT2_AF.cif (#2) relative to emd_34705.map (#1) coordinates:  
Matrix rotation and translation  
0.76640778 0.16086434 0.62188567 67.03975095  
0.34483385 0.71377338 -0.60960410 64.64350727  
-0.54194899 0.68165253 0.49156998 67.55131792  
Axis 0.73868152 0.66578800 0.10524234  
Axis point 0.00000000 -63.55266506 27.02646500  
Rotation angle (degrees) 60.93014626  
Shift along axis 99.66915559  
  
Found 100 fits.  

Populating font family aliases took 185 ms. Replace uses of missing font
family "Courier" with one that exists to avoid this cost.  

> volume gaussian #1 sDev 2

Opened emd_34705.map gaussian as #3, grid size 120,120,120, pixel 1.11, shown
at step 1, values float32  

> transparency #* 50

> fitmap #2 inMap #3 search 100 radius 5

Found 90 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).  
  
Average map values and times found:  
0.00785 (3), 0.005593 (4), 0.00558 (1), 0.005574 (1), 0.00557 (1), 0.00556
(2), 0.005529 (1), 0.005504 (1), 0.005501 (1), 0.00549 (2), 0.005463 (1),
0.005462 (1), 0.005452 (1), 0.005451 (1), 0.00544 (1), 0.00543 (1), 0.005428
(1), 0.005414 (2), 0.005414 (1), 0.005413 (1), 0.005411 (1), 0.005407 (1),
0.005407 (1), 0.005401 (1), 0.005397 (1), 0.005387 (2), 0.005383 (1), 0.005381
(1), 0.005376 (1), 0.005374 (1), 0.005369 (1), 0.005368 (1), 0.005361 (1),
0.005359 (1), 0.005354 (1), 0.005353 (1), 0.005352 (1), 0.005349 (1), 0.005348
(2), 0.005344 (1), 0.00534 (1), 0.005339 (1), 0.005335 (1), 0.005333 (1),
0.005332 (1), 0.005328 (1), 0.005327 (1), 0.005322 (1), 0.005316 (1), 0.005315
(1), 0.005314 (1), 0.005307 (1), 0.005306 (1), 0.005296 (1), 0.005294 (1),
0.005291 (1), 0.005287 (1), 0.005287 (1), 0.005276 (1), 0.005273 (1), 0.005261
(1), 0.005253 (1), 0.005249 (1), 0.005249 (1), 0.005248 (1), 0.005242 (1),
0.005241 (1), 0.005241 (1), 0.005224 (1), 0.005221 (1), 0.005212 (1), 0.005208
(1), 0.005199 (1), 0.005199 (1), 0.005197 (1), 0.005185 (1), 0.00518 (1),
0.005165 (1), 0.005161 (1), 0.005161 (1), 0.005158 (1), 0.005154 (1), 0.005152
(1), 0.005135 (1), 0.005115 (1), 0.005114 (1), 0.005111 (1), 0.005107 (1),
0.005075 (1), 0.004992 (1)  
  
Best fit found:  
Fit molecule SGLT2_AF.cif (#2) to map emd_34705.map gaussian (#3) using 5146
atoms  
average map value = 0.00785, steps = 196  
shifted from previous position = 7.37  
rotated from previous position = 36.8 degrees  
atoms outside contour = 2956, contour level = 0.0091429  
Position of SGLT2_AF.cif (#2) relative to emd_34705.map gaussian (#3)
coordinates:  
Matrix rotation and translation  
0.38542617 -0.33537699 0.85963305 71.35528782  
0.70605454 0.70698433 -0.04074484 69.46195606  
-0.59408220 0.62265191 0.50928464 68.76198858  
Axis 0.34781172 0.76216713 0.54601125  
Axis point 25.02230043 0.00000000 -18.46477385  
Rotation angle (degrees) 72.49148285  
Shift along axis 115.30464368  
  
Found 90 fits.  

> color bfactor pal alpha key true

> key alphafold :0 :50 :70 :90 :100 showTool true

> ui mousemode right "color key"

5146 atoms, 676 residues, atom bfactor range 17 to 98.4  

> select #2/A:1

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select add #2/A:26

12 atoms, 10 bonds, 2 residues, 1 model selected  

> selbetween

> select #2/A:1-26

181 atoms, 183 bonds, 26 residues, 1 model selected  

> delete sel

> cofron

> symclip 10

> select #2/A:649

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select add #2/A:571

18 atoms, 16 bonds, 2 residues, 1 model selected  

> selbetween

> select #2/A:571-649

595 atoms, 606 bonds, 79 residues, 1 model selected  

> delete sel

> symclip 30

> save /Users/oc2188/Downloads/SGLT2_AF_trim.pdb relModel #1

> fitmap #2 #1

Missing required "in_map" argument  

> fitmap #2 inMap #1

Fit molecule SGLT2_AF.cif (#2) to map emd_34705.map (#1) using 4370 atoms  
average map value = 0.05204, steps = 48  
shifted from previous position = 0.122  
rotated from previous position = 0.26 degrees  
atoms outside contour = 1370, contour level = 0.03136  
  
Position of SGLT2_AF.cif (#2) relative to emd_34705.map (#1) coordinates:  
Matrix rotation and translation  
0.38212315 -0.33721123 0.86038975 71.45030917  
0.70602425 0.70725300 -0.03637253 69.51991612  
-0.59624799 0.62135477 0.50833699 68.74730244  
Axis 0.34461314 0.76319854 0.54659836  
Axis point 25.15492631 0.00000000 -18.81525744  
Rotation angle (degrees) 72.61106103  
Shift along axis 115.25737706  
  

> tool show Models

> hide #!3 models

> show #!1 models

> cootmode

> surface cap false

Changed 4370 atom styles  
Changed 0 atom styles  
[Repeated 1 time(s)]Changed 1 ball scales  
Changed 4489 bond radii  

> tool show Models

> hide #!3 models

> symclip 10

> ca_and_sidechains #2

Changed 4370 atom styles  
Changed 4489 bond radii  
Changed 1 pseudobond radii  

> symclip 5

> volume #1 level 0.0222

> volume gaussian #1 sDev 1

Opened emd_34705.map gaussian as #5, grid size 120,120,120, pixel 1.11, shown
at step 1, values float32  

> transparency #* 50

> volume #5 level 0.01491

> 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"

> help https://github.com/olibclarke/chimerax-
> trimmings/blob/main/default_mousemodes.md

> measure blob #!5.1 triangleNumber 43552 color #0000ccff outline true

Surface emd_34705.map gaussian #5.1 blob:  
volume = 100.23  
area = 169.66  
size = 12.949 7.3646 5.3283  
  

> transparency #* 50

> symclip 5

> measure blob #!5.1 triangleNumber 23556 color #cc7e56ff

Surface emd_34705.map gaussian #5.1 blob:  
volume = 884.43  
area = 1307.6  
size = 46.217 14.823 12.066  
  

> transparency #* 50

> help mousemode




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple

Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PySide6 6.10.1, Qt 6.10.1
Qt runtime version: 6.10.1
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,5
      Model Number: Z17J00171LL/A
      Chip: Apple M2 Max
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 64 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: 13 days, 3 hours, 13 minutes

Graphics/Displays:

    Apple M2 Max:

      Chipset Model: Apple M2 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 30
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    accessible-pygments: 0.0.5
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.12.1
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.1
    attrs: 25.4.0
    babel: 2.18.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 4.1.2
    build: 1.3.0
    certifi: 2025.7.14
    cftime: 1.6.5
    charset-normalizer: 3.4.5
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.2
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.65
    ChimeraX-AtomicLibrary: 14.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4.1
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-Cluster: 1.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.1
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.12.dev202603110023
    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: 1.2
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.8.2
    ChimeraX-Label: 1.3
    ChimeraX-LightingGUI: 1.0
    ChimeraX-ListInfo: 1.3.1
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.2.0
    ChimeraX-MDcrds: 2.18
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.6
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.23
    ChimeraX-ModelPanel: 1.6.1
    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: 1.0.1
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.15.4
    ChimeraX-OpenFold: 1.0
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.12
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PhenixUI: 1.4.12
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.5.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.8
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.12
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.18
    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-SNFG: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.3
    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: 2.5.3
    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: 1.50.3
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.6.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    click: 8.3.1
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.13.4
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.2.4
    debugpy: 1.8.20
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.62.0
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.16.0
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.11
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 2.0.0
    iniconfig: 2.3.0
    ipykernel: 7.1.0
    ipython: 9.9.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.8
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.8.0
    jupyter_core: 5.9.1
    jupyterlab_widgets: 3.0.16
    kiwisolver: 1.5.0
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.1
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.1
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    numpy: 1.26.4
    OpenMM: 8.4.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.6
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.9.4
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.4.1
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.12.5
    pydantic-settings: 2.13.1
    pydantic_core: 2.41.5
    pydata-sphinx-theme: 0.16.1
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.5.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.3.2
    pyproject_hooks: 1.2.0
    PySide6: 6.10.1
    PySide6_Addons: 6.10.1
    PySide6_Essentials: 6.10.1
    pytest: 9.0.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.2
    python-multipart: 0.0.22
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2.1
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.1.0
    rpds-py: 0.30.0
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    shiboken6: 6.10.1
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8.3
    Sphinx: 9.0.4
    sphinx-autodoc-typehints: 3.6.1
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    sse-starlette: 3.3.2
    stack-data: 0.6.3
    starlette: 0.52.1
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.5
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    urllib3: 2.6.3
    uvicorn: 0.41.0
    wcwidth: 0.6.0
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.15
    yarl: 1.23.0