ChimeraX bug report submission

[karolin.luger@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26200
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
electron density surface transparency cannot be changed in this versio

Log:
UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "C:/Users/kalu4386/OneDrive - UCB-O365/From Google
> Drive/users/projects/HIRA/Mar2_Figure_color (2).cxs"

Opened composite_for_coot.mrc as #1, grid size 265,264,265, pixel
1.51,1.51,1.51, shown at level 0.368, step 1, values float32  
Log from Mon Mar 2 10:59:12 2026UCSF 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 /Users/weitian/Library/CloudStorage/OneDrive-
> UCB-O365/HIRA/HIRA_maps/composite_for_coot.mrc

Opened composite_for_coot.mrc as #1, grid size 265,264,265, pixel
1.51,1.51,1.51, shown at level 0.302, step 2, values float32  

> open /Users/weitian/Library/CloudStorage/OneDrive-
> UCB-O365/HIRA/HIRA_models/Mar2_best.pdb

Chain information for Mar2_best.pdb #2  
---  
Chain | Description  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F G H I 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  
S | No description available  
X Y | No description available  
Z | No description available  
  

> volume #1 step 1

> volume #1 color #b2b2b245

> select add #2

43775 atoms, 45346 bonds, 14 pseudobonds, 4981 residues, 2 models selected  

> show sel cartoons

> hide sel atoms

> set bgColor white

> split #2

Split Mar2_best.pdb (#2) into 20 models  
Chain information for Mar2_best.pdb B #2.1  
---  
Chain | Description  
B | No description available  
  
Chain information for Mar2_best.pdb C #2.2  
---  
Chain | Description  
C | No description available  
  
Chain information for Mar2_best.pdb D #2.3  
---  
Chain | Description  
D | No description available  
  
Chain information for Mar2_best.pdb E #2.4  
---  
Chain | Description  
E | No description available  
  
Chain information for Mar2_best.pdb F #2.5  
---  
Chain | Description  
F | No description available  
  
Chain information for Mar2_best.pdb G #2.6  
---  
Chain | Description  
G | No description available  
  
Chain information for Mar2_best.pdb H #2.7  
---  
Chain | Description  
H | No description available  
  
Chain information for Mar2_best.pdb I #2.8  
---  
Chain | Description  
I | No description available  
  
Chain information for Mar2_best.pdb J #2.9  
---  
Chain | Description  
J | No description available  
  
Chain information for Mar2_best.pdb K #2.10  
---  
Chain | Description  
K | No description available  
  
Chain information for Mar2_best.pdb L #2.11  
---  
Chain | Description  
L | No description available  
  
Chain information for Mar2_best.pdb M #2.12  
---  
Chain | Description  
M | No description available  
  
Chain information for Mar2_best.pdb N #2.13  
---  
Chain | Description  
N | No description available  
  
Chain information for Mar2_best.pdb O #2.14  
---  
Chain | Description  
O | No description available  
  
Chain information for Mar2_best.pdb P #2.15  
---  
Chain | Description  
P | No description available  
  
Chain information for Mar2_best.pdb Q #2.16  
---  
Chain | Description  
Q | No description available  
  
Chain information for Mar2_best.pdb S #2.17  
---  
Chain | Description  
S | No description available  
  
Chain information for Mar2_best.pdb X #2.18  
---  
Chain | Description  
X | No description available  
  
Chain information for Mar2_best.pdb Y #2.19  
---  
Chain | Description  
Y | No description available  
  
Chain information for Mar2_best.pdb Z #2.20  
---  
Chain | Description  
Z | No description available  
  

> hide #2.1 models

> show #2.1 models

> hide #2.1 models

> show #2.1 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> volume #1 level 0.3679

> color #2.10 #2.11 #4A6FA5

> color #2.12 #2.1 #4C9A2A

> color #2.13 #2.2 #E6C44A

> color #2.14 #2.3 #B2182B

> color #2.15 #2.16 #A09EA0

> hide #2.5 models

> show #2.5 models

> color #2.20 #86cdab

> hide #!2.4 models

> show #!2.4 models

> hide #2.17 models

> show #2.17 models

> color #2.17 #86cdab

> color #2.18 #86cdab

> hide #!2.4 models

> show #!2.4 models

> hide #2.13 models

> show #2.13 models

> hide #!2.19 models

> show #!2.19 models

> color #2.19 #86cdab

> color #2.9 #C190AF

> hide #2.5 models

> show #2.5 models

> hide #2.5 models

> show #2.5 models

> hide #2.6 models

> show #2.6 models

> hide #2.7 models

> show #2.7 models

> hide #2.8 models

> show #2.8 models

> color #2.5 #2.6 #2.7 #2.8 #C190AF

> color #2.4 #C190AF

> show #!1 models

> hide #2.17 models

> show #2.17 models

> hide #2.1 models

> show #2.1 models

> hide #!2.20 models

> show #!2.20 models

> hide #!2.19 models

> show #!2.19 models

> hide #!2.18 models

> show #!2.18 models

> hide #!2.18 models

> show #!2.18 models

> color #2.18:1-250 #A3D1D8

> hide #!2.18 models

> show #!2.18 models

> hide #!2.18 models

> show #!2.18 models

> hide #!2.18 models

> show #!2.18 models

> hide #!2.18 models

> show #!2.18 models

> color #2.18:1-250 #d8eff0

> hide #!1 models

> color #2.18:251-307 #A3D1D8

> color #2.18:460-686 #A3D1D8

> hide #!2.18 models

> show #!2.18 models

> hide #!2.19 models

> show #!2.19 models

> hide #!2.20 models

> show #!2.20 models

> color #2.20:974-1310 #1F9EA0

> color #2.18:1-250 #E8F5E9

> hide #!2.18 models

> show #!2.18 models

> hide #!2.19 models

> show #!2.19 models

> hide #2.17 models

> show #2.17 models

> hide #!2.20 models

> show #!2.20 models

> select add #2.20

6958 atoms, 7116 bonds, 2 pseudobonds, 867 residues, 2 models selected  

> ~hbonds

Alignment identifier is 2.20/Z  

> select clear

> color #2.20: 1311-1922#1F9EA0

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color #2.20: 1311-1922 #1F9EA0

> color #2.20: 1311-1922 #0B775E

> color #2.18:1-250 #A6D96A

> show #!1 models

> volume #1 color #b2b2b200

> volume #1 color #b2b2b21e

> volume #1 color #e6e6e61e

> color #2.18:251-307 #86cdab

> color #2.18:460-686 #86cdab

> hide #!2.18 models

> show #!2.18 models

> hide #2.17 models

> show #2.17 models

> hide #2.17 models

> show #2.17 models

> color #2.17 #1A9850

> color #2.17 #1F9EA0

> hide #!2.18 models

> show #!2.18 models

> hide #!2.19 models

> show #!2.19 models

> hide #!2.20 models

> show #!2.20 models

> color #2.20:706-973 #1F9EA0

> color #2.20:974-1310 #006837

> color #2.20:974-1310 #0B775E

> color #2.20: 1311-1922 #006837

> (optional) Domain 5 (dark teal-green): #0B775E

Unknown command: (optional) Domain 5 (dark teal-green): #0B775E  

> Then within each domain, apply a subtle internal ramp (e.g., lighten at
> domain start, darken at domain end). This gives “domain context” without
> leaving the green family.

Unknown command: Then within each domain, apply a subtle internal ramp (e.g.,
lighten at domain start, darken at domain end). This gives “domain context”
without leaving the green family.  

> Option C: Green gradient + neutral domains (if you want domains to be the
> primary message)

Unknown command: Option C: Green gradient + neutral domains (if you want
domains to be the primary message)  

> Make domains distinct in neutral grays, and overlay a green ramp only on the
> domain you’re focusing on (or on an active site region).

Unknown command: Make domains distinct in neutral grays, and overlay a green
ramp only on the domain you’re focusing on (or on an active site region).  

> Neutrals:

Unknown command: Neutrals:  

> lighting gray #D9D9D9

Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a
keyword  

> mid gray #9E9E9E

Unknown command: mid gray #9E9E9E  

> dark gray #616161

Unknown command: dark gray #616161  

> Highlight gradient: use Option A ramp.

Unknown command: Highlight gradient: use Option A ramp.  

> Practical tips (so it looks good in figures)

Unknown command: Practical tips (so it looks good in figures)  

> Avoid super-bright neon greens (they blow out on white background and look
> noisy).

Unknown command: Avoid super-bright neon greens (they blow out on white
background and look noisy).  

> If you’ll show secondary structure cartoons, keep greens a bit muted (Option
> A) so helices/sheets remain readable.

Unknown command: If you’ll show secondary structure cartoons, keep greens a
bit muted (Option A) so helices/sheets remain readable.  

> If you have domains adjacent, use either (1) thin white separators or (2)
> slightly different green tints (Option B) to prevent the gradient from
> “hiding” boundaries.

Unknown command: If you have domains adjacent, use either (1) thin white
separators or (2) slightly different green tints (Option B) to prevent the
gradient from “hiding” boundaries.  

> If you tell me how many domains you have and roughly their residue ranges, I
> can propose an exact palette per domain (still green-themed) and give the
> exact Chimera/ChimeraX commands to apply it by residue ranges.

Unknown command: If you tell me how many domains you have and roughly their
residue ranges, I can propose an exact palette per domain (still green-themed)
and give the exact Chimera/ChimeraX commands to apply it by residue ranges.  

> color #2.20: 1311-1922 #006837

> color #2.20: 1311-1922 #1B5E20

> hide #!1 models

> show #!1 models

> color #2.20:974-1310 #BFECC8

> color #2.18:251-307 #BFECC8

> color #2.18:460-686 #BFECC8

> color #2.20:706-973 #1F9EA0

> color #2.20:706-973 #2A9D8F

> color #2.20:706-973 #1B9E77

> hide #!2.19 models

> show #!2.19 models

> hide #2.17 models

> show #2.17 models

> color #2.17 #1B9E77

> color #2.20:974-1310 #1A9850

> save /Users/weitian/Library/CloudStorage/OneDrive-
> UCB-O365/HIRA/Chimera/Mar2_Figure_color.cxs includeMaps true

——— End of log from Mon Mar 2 10:59:12 2026 ———

> view name session-start

opened ChimeraX session  

> hide #!2.20 models

> show #!2.20 models

> hide #!2.20 models

> show #!2.20 models

> hide #!2.19 models

> show #!2.19 models

> hide #!2.18 models

> show #!2.18 models

> hide #2.17 models

> show #2.17 models

> hide #2.9 models

> show #2.9 models

> select #1

2 models selected  

> select #1

2 models selected  

> hide #!1 models

> select #2.17/S:398

11 atoms, 10 bonds, 1 residue, 1 model selected  

> cofr sel

> show #!1 models

> volume #1 level 0.3136

> set bgColor black

> transparency sel 50

> select add #1

11 atoms, 10 bonds, 1 residue, 3 models selected  

> select subtract #1

11 atoms, 10 bonds, 1 residue, 1 model selected  

> volume #1 color #cccccc1e

> transparency sel 20

> volume #1 color #ffff7f1e

> volume #1 color #b3b3b31e

> lighting simple

> lighting soft

> lighting simple

> select add #1

11 atoms, 10 bonds, 1 residue, 3 models selected  

> select subtract #1

11 atoms, 10 bonds, 1 residue, 1 model selected  

> volume #1 style image

> ui tool show "Volume Viewer"

> volume #1 style mesh

> volume #1 style surface

> ui tool show "Side View"

> select up

166 atoms, 165 bonds, 20 residues, 1 model selected  

> select up

260 atoms, 262 bonds, 31 residues, 1 model selected  

> style sel stick

Changed 260 atom styles  

> show sel atoms

> color sel byhetero

> select clear

> volume #1 change image level -0.03931,0 level 0.3025,0.8 level 2.696,1

> volume #1 level 0.549

> volume #1 level 0.3559

> volume #1 level 0.3981

> select #1

4 models selected  

> select #1

4 models selected  

> hide #!1 models

> select #2.12/M:17

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

67 atoms, 67 bonds, 7 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 67 atom styles  

> color sel byhetero

> show #!1 models

> volume #1 level 0.4283

> select clear

> select #1

4 models selected  

> select add #1

4 models selected  

> hide #!1 models

> select #2.20/Z:963

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

187 atoms, 190 bonds, 23 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 187 atom styles  

> color sel byhetero

> select clear

> show #!1 models

> volume #1 level 0.3438

> volume #1 level 0.3679

> select #1

4 models selected  

> hide #!1 models

> select #2.20/Z:1287

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

100 atoms, 100 bonds, 13 residues, 1 model selected  

> select up

4834 atoms, 4950 bonds, 605 residues, 1 model selected  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for Mar2_best.pdb Z_Z SES surface #2.20.2: minimum, -23.76,
mean -1.22, maximum 26.25  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select #2.20/Z:1853

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

163 atoms, 165 bonds, 20 residues, 2 models selected  

> select up

624 atoms, 630 bonds, 79 residues, 2 models selected  

> select up

642 atoms, 648 bonds, 81 residues, 2 models selected  

> select up

2124 atoms, 2166 bonds, 262 residues, 2 models selected  

> select up

2186 atoms, 2228 bonds, 270 residues, 2 models selected  

> select up

6958 atoms, 7116 bonds, 867 residues, 2 models selected  

> coulombic sel

Coulombic values for Mar2_best.pdb Z_Z SES surface #2.20.2: minimum, -23.76,
mean -1.22, maximum 26.25  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select clear




OpenGL version: 3.3.0 - Build 32.0.101.7077
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel

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

Manufacturer: Dell Inc.
Model: XPS 13 9310
OS: Microsoft Windows 11 Pro (Build 26200)
Memory: 16,855,638,016
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i7-1185G7 @ 3.00GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.5.0
    build: 1.2.2.post1
    certifi: 2025.6.15
    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: 14.1.18
    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
    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: 1.1.2
    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: 7.9.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.58.4
    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: 4.4.4
    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-cuda-cupti-cu12: 12.9.79
    nvidia-cuda-nvcc-cu12: 12.9.86
    nvidia-cuda-nvrtc-cu12: 12.9.86
    nvidia-cuda-runtime-cu12: 12.9.79
    nvidia-cufft-cu12: 11.4.1.4
    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
    pyelftools: 0.32
    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: 4.14.0
    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