Render by Attr select histogram: cannot subtract numpy booleans

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
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.  
How to cite UCSF ChimeraX  

> open C:\Users\sidba314\Downloads\cryosparc_P474_J72_006_volume_map.mrc
> format mrc

Opened cryosparc_P474_J72_006_volume_map.mrc as #1, grid size 600,600,600,
pixel 0.828, shown at level 0.0375, step 4, values float32  

> volume #1 step 1

> volume #1 level 0.046

> ui tool show "Hide Dust"

> surface dust #1 size 4.97

> open C:/Users/sidba314/Downloads/pdb_extract_out_7811568935.cif

Summary of feedback from opening
C:/Users/sidba314/Downloads/pdb_extract_out_7811568935.cif  
---  
warning | Missing or incorrect sequence information. Inferred polymer connectivity.  
  
  
Chain information for pdb_extract_out_7811568935.cif #2  
---  
Chain | Description  
1 | No description available  
2 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
8 | No description available  
9 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
  
11 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide atoms

> show cartoons

> surface zone #2 nearAtoms #1/x

No surfaces specified  

> surface zone #1 nearAtoms #2/x

> surface zone #1 nearAtoms #2/x,v,w

> transparency 50

> set bgColor white

> lighting soft

> select / A,B,C,D,E,F,G,H,I,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,1,2,4,5,6,7,8,9

95519 atoms, 104099 bonds, 6 pseudobonds, 6719 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel white smoke

> select / a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u

51082 atoms, 55235 bonds, 3883 residues, 1 model selected  

> color sel lemon chiffon

> select /x

4073 atoms, 4165 bonds, 527 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel dodger blue

> color sel cornflower blue

> select / v,w

3287 atoms, 3672 bonds, 154 residues, 1 model selected  

> select / v

1643 atoms, 1835 bonds, 77 residues, 1 model selected  

> color sel brown

> nucleotides sel tube/slab shape box

> show sel atoms

> select ~sel & ##selected

153081 atoms, 165574 bonds, 1400 pseudobonds, 11766 residues, 3 models
selected  

> select ~sel & ##selected

1643 atoms, 1835 bonds, 77 residues, 1 model selected  

> select / w

1644 atoms, 1837 bonds, 77 residues, 1 model selected  

> color sel orchid

> color sel lime green

> show sel atoms

> nucleotides sel tube/slab shape muffler

> select clear

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> lighting soft

> lighting full

[Repeated 1 time(s)]

> lighting soft

> lighting simple

> lighting soft

> select / a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u

51082 atoms, 55235 bonds, 3883 residues, 1 model selected  

> transperency / a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u 50

Unknown command: transperency / a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u 50  

> transperency /a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u 50

Unknown command: transperency /a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u 50  

> set transperency /a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u 50

Expected a keyword  

> set transperency /a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u/ 50

Expected a keyword  

> transparency #2/ a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u 80 ribbons

> transparency #2/ a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u 70 ribbons

> transparency #2/
> A,B,C,D,E,F,G,H,I,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,1,2,4,5,6,7,8,9 70 ribbons

> select clear

> select / A,B,C,D,E,F,G,H,I,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,1,2,4,5,6,7,8,9

95519 atoms, 104099 bonds, 6 pseudobonds, 6719 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel beige

> select clear

> transparency #2/
> A,B,C,D,E,F,G,H,I,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,1,2,4,5,6,7,8,9 40 ribbons

> lighting flat

> graphics silhouettes false

> transparency #2/
> A,B,C,D,E,F,G,H,I,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,1,2,4,5,6,7,8,9 0 ribbons

> transparency #2/ a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u 0 ribbons

> select / A,B,C,D,E,F,G,H,I,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,1,2,4,5,6,7,8,9

95519 atoms, 104099 bonds, 6 pseudobonds, 6719 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel khaki

> select clear

> graphics silhouettes true

> graphics silhouettes false

> lighting soft

> lighting simple

> lighting flat

> graphics silhouettes false

> lighting soft

> graphics silhouettes true

> graphics silhouettes false

> lighting full

> graphics silhouettes true

> graphics silhouettes false

> lighting shadows false

> graphics silhouettes true

> graphics silhouettes false

> lighting flat

> graphics silhouettes false

> select / a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u

51082 atoms, 55235 bonds, 3883 residues, 1 model selected  

> color sel blue violet

> color sel hot pink

> color sel pale green

> color sel gainsboro

> color sel light cyan

> color sel lavender

> color sel rosy brown

> select clear

> select / a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u

51082 atoms, 55235 bonds, 3883 residues, 1 model selected  

> color sel light goldenrod yellow

> select clear

> set bgColor black

> set bgColor transparent

> set bgColor white

> set bgColor #ffffff00

> lighting simple

> transparency #2/
> A,B,C,D,E,F,G,H,I,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,1,2,4,5,6,7,8,9 70 ribbons

> transparency #2/ a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u 70 ribbons

> select clear

> graphics silhouettes true

> graphics silhouettes false

> lighting soft

[Repeated 1 time(s)]

> lighting simple

> lighting flat

> graphics silhouettes false

> lighting simple

> cartoon style helix width 1.1

> cartoon style helix width 1.5

> cartoon style width 1.5 thickness 0.3

> ui tool show "Color Zone"

> color zone #1 near #2 distance 2.54

> transparency 0

> lighting flat

> graphics silhouettes false

> lighting soft

> select / a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u

51082 atoms, 55235 bonds, 3883 residues, 1 model selected  

> color sel hot pink

> select clear

> lighting soft

> lighting simple

> lighting soft

> view orient

[Repeated 2 time(s)]

> ui tool show "Side View"

> view

> ui tool show "Side View"

> select / a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u

51082 atoms, 55235 bonds, 3883 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel gray

> select clear

> lighting flat

> graphics silhouettes false

> lighting soft

> lighting simple

> graphics silhouettes true

> graphics silhouettes false

> lighting flat

> graphics silhouettes false

> lighting soft

> select / A,B,C,D,E,F,G,H,I,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,1,2,4,5,6,7,8,9

95519 atoms, 104099 bonds, 6 pseudobonds, 6719 residues, 2 models selected  

> color sel gold

> select clear

> lighting soft

> lighting full

> volume #1 style mesh

> volume #1 style surface

> transparency 50

> lighting soft

[Repeated 1 time(s)]

> lighting simple

> lighting soft

> view orient

> lighting simple

> lighting soft

> lighting flat

> graphics silhouettes false

> lighting simple

> transparency #2/
> A,B,C,D,E,F,G,H,I,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,1,2,4,5,6,7,8,9 70

> transparency #2/
> A,B,C,D,E,F,G,H,I,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,1,2,4,5,6,7,8,9 70 ribbons

> transparency #2/ a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u 70 ribbons

> select / a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u

51082 atoms, 55235 bonds, 3883 residues, 1 model selected  

> transparency #2/ a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u 70 ribbons

> transparency #2/ a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u 90 ribbons

> select clear

> transparency #2/
> A,B,C,D,E,F,G,H,I,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,1,2,4,5,6,7,8,9 90 ribbons

> lighting soft

> lighting simple

> lighting full

> graphics silhouettes true

> graphics silhouettes false

> lighting flat

> graphics silhouettes false

> lighting simple

> lighting full

> graphics silhouettes true

> graphics silhouettes false

> lighting soft

> select /y

213 atoms, 238 bonds, 10 residues, 1 model selected  

> show sel atoms

> nucleotides sel tube/slab shape ellipsoid

> nucleotides sel tube/slab shape muffler

> cartoon hide sel

> hide sel target a

> transparency #2/
> A,B,C,D,E,F,G,H,I,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,1,2,4,5,6,7,8,9 80 ribbons

> lighting simple

> lighting soft

> lighting full

> lighting soft

> save "C:/Users/sidba314/Documents/Msmeg RF3 figures/RF3 bound.tif" width
> 1326 height 923 supersample 4 transparentBackground true

> lighting simple

> save "C:/Users/sidba314/Documents/Msmeg RF3 figures/RF3 bound.tif" width
> 1326 height 923 supersample 4 transparentBackground true

> transparency #2/
> A,B,C,D,E,F,G,H,I,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,1,2,4,5,6,7,8,9 50 ribbons

> transparency #2/ a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u 50 ribbons

> ui mousemode right clip

> ui mousemode right select

> ui mousemode right rotate

> lighting flat

> graphics silhouettes false

> lighting soft

> lighting simple

> save "C:/Users/sidba314/Documents/Msmeg RF3 figures/RF3 bound.tif" width
> 1326 height 923 supersample 4 transparentBackground true

> volume #1 style image

> volume #1 style surface

> volume style surface

> transparency 0

> save "C:/Users/sidba314/Documents/Msmeg RF3 figures/RF3 bound.tif" width
> 1326 height 923 supersample 4 transparentBackground true

[Repeated 1 time(s)]

> view :GNP

No displayed objects specified.  

> view : GNP

No displayed objects specified.  

> select ::name="GNP"

32 atoms, 34 bonds, 1 residue, 1 model selected  

> view : GNP

No displayed objects specified.  

> ui tool show "Render/Select by Attribute"

> save "C:/Users/sidba314/Documents/Msmeg RF3 figures/GG.tif" width 1326
> height 923 supersample 3

> ui mousemode right clip

> save "C:/Users/sidba314/Documents/Msmeg RF3 figures/GG.tif" width 1326
> height 923 supersample 4 transparentBackground true

> view : GNP

No displayed objects specified.  

> select ::name="GNP"

32 atoms, 34 bonds, 1 residue, 1 model selected  

> show sel atoms

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\\__init__.py", line 175, in handler  
callback()  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 831, in update_hist  
self._update_histogram(self.select_histogram, attr_name)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 865, in _update_histogram  
histogram.data_source = (min_val, max_val, lambda num_bins:  
^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\histogram.py", line 350, in data_source  
self._new_data()  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\histogram.py", line 615, in _new_data  
self._redraw_cb()  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\histogram.py", line 638, in _redraw_cb  
filled_range = self._max_val - self._min_val  
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~  
TypeError: numpy boolean subtract, the `-` operator, is not supported, use the
bitwise_xor, the `^` operator, or the logical_xor function instead.  
  
Error processing trigger "changes":  
TypeError: numpy boolean subtract, the `-` operator, is not supported, use the
bitwise_xor, the `^` operator, or the logical_xor function instead.  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\widgets\histogram.py", line 638, in _redraw_cb  
filled_range = self._max_val - self._min_val  
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 576.52
OpenGL renderer: NVIDIA GeForce RTX 5070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_SE.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: ASUSTeK COMPUTER INC.
Model: ROG G700TF
OS: Microsoft Windows 11 Education (Build 26100)
Memory: 33,848,745,984
MaxProcessMemory: 137,438,953,344
CPU: 20 Intel(R) Core(TM) Ultra 7 265F
OSLanguage: en-US

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-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
    comtypes: 1.4.10
    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
    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
    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
    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
    pywin32: 310
    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
    WMI: 1.5.1