isolde sim start: OpenMMException: Error compiling kernel

[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
Starting an ISOLDE simulation worked before on my computer, but after updating my Windows system it does not work any more and gives me that error message whenever I try to start a simulation. I already tried to reinstall ChimeraX and ISOLDE, but the problem remained.

Log:
Startup Messages  
---  
warning | QWindowsWindow::setGeometry: Unable to set geometry 3840x1410-1920+90 (frame: 3856x1449-1928+59) on QWidgetWindow/"MainWindowClassWindow" on "DELL U2721DE". Resulting geometry: 3846x1427-1923+76 (frame: 3862x1466-1931+45) margins: 8, 31, 8, 8 minimum size: 63x49 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=79, y=88)))  
  
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\birte\Documents\01 Universität\Lübeck\Blockpraktikum Maya
> Topf\BAM_SurA\cryosparc_P423_J83_map.mrc" format mrc

Opened cryosparc_P423_J83_map.mrc as #1, grid size 300,300,300, pixel 0.71,
shown at level 0.0506, step 2, values float32  

> open 8pz2

8pz2 title:  
Wait Complex: Lateral open BAM bound Extended SurA [more info...]  
  
Chain information for 8pz2 #2  
---  
Chain | Description | UniProt  
A | Outer membrane protein assembly factor BamA | BAMA_ECOLI 21-810  
B | Outer membrane protein assembly factor BamB | BAMB_ECOLI 20-392  
C | Outer membrane protein assembly factor BamC | BAMC_ECOLI 25-344  
D | Outer membrane protein assembly factor BamD | BAMD_ECOLI 20-245  
E | Outer membrane protein assembly factor BamE | BAME_ECOLI 20-113  
F | Chaperone SurA | SURA_ECOLI 21-428  
  

> ui tool show Matchmaker

QWindowsWindow::setGeometry: Unable to set geometry 768x710+1536+773 (frame:
790x766+1525+728) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY2". Resulting geometry: 762x693+1539+787 (frame:
784x749+1528+742) margins: 11, 45, 11, 11 minimum size: 486x330 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=786453, y=786487), mintrack=POINT(x=751, y=551)))  

> ui tool show "Fit in Map"

> fitmap #2 inMap #1

Fit molecule 8pz2 (#2) to map cryosparc_P423_J83_map.mrc (#1) using 13121
atoms  
average map value = 0.02474, steps = 124  
shifted from previous position = 10.3  
rotated from previous position = 10.4 degrees  
atoms outside contour = 11465, contour level = 0.050603  
  
Position of 8pz2 (#2) relative to cryosparc_P423_J83_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99968278 0.01275379 0.02171810 5.60151969  
-0.01642908 0.98380297 0.17849872 -19.52805938  
-0.01908979 -0.17879890 0.98370043 20.79653901  
Axis -0.99028561 0.11310309 -0.08088322  
Axis point 0.00000000 101.77311460 112.65642684  
Rotation angle (degrees) 10.39313522  
Shift along axis -9.43787930  
  

> select add #2

13121 atoms, 13385 bonds, 2 pseudobonds, 1678 residues, 2 models selected  

> show sel cartoons

> style sel stick

Changed 13121 atom styles  

> hide sel atoms

> ui mousemode right "move picked models"

> view matrix models
> #2,0.99968,0.012754,0.021718,-26.254,-0.016429,0.9838,0.1785,-11.331,-0.01909,-0.1788,0.9837,10.929

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.59121,-0.79382,-0.14257,236.6,-0.39919,0.13441,0.90696,40.503,-0.7008,0.59312,-0.39635,143.02

> ui mousemode right "move picked models"

> view matrix models
> #2,-0.59121,-0.79382,-0.14257,270.86,-0.39919,0.13441,0.90696,38.602,-0.7008,0.59312,-0.39635,160.36

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.086365,-0.97286,0.21465,186,0.017928,0.21694,0.97602,-18.632,-0.9961,-0.080446,0.036178,216.83

> fitmap #2 inMap #1

Fit molecule 8pz2 (#2) to map cryosparc_P423_J83_map.mrc (#1) using 13121
atoms  
average map value = 0.06714, steps = 168  
shifted from previous position = 10.3  
rotated from previous position = 13.7 degrees  
atoms outside contour = 5118, contour level = 0.050603  
  
Position of 8pz2 (#2) relative to cryosparc_P423_J83_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.01247290 -0.91002163 0.41437310 158.33668056  
0.09496249 0.41361034 0.90548805 -42.58045911  
-0.99540271 0.02805584 0.09157684 206.82608505  
Axis -0.45205960 0.72632697 0.51777529  
Axis point 175.96660653 0.00000000 32.24787480  
Rotation angle (degrees) 103.95560256  
Shift along axis 4.58448326  
  

> volume #1 level 0.03651

> open C:/Users/birte/Downloads/cryosparc_P423_J74_class_00_00266_volume.mrc

Opened cryosparc_P423_J74_class_00_00266_volume.mrc as #3, grid size 72,72,72,
pixel 2.96, shown at level 0.419, step 1, values float32  

> hide #!2 models

> hide #!1 models

> select subtract #2

Nothing selected  

> volume #3 level 0.4192

> volume #1 step 1

> volume #3 level 0.4456

> volume #3 level 0.2756

Drag select of 3 cryosparc_P423_J74_class_00_00266_volume.mrc  

> volume #3 level 0.1936

> close #3

> show #!2 models

> show #!1 models

> select add #2

13121 atoms, 13385 bonds, 2 pseudobonds, 1678 residues, 2 models selected  

> addh

Summary of feedback from adding hydrogens to 8pz2 #2  
---  
warnings | Not adding hydrogens to /A ILE 806 C because it is missing heavy-atom bond partners  
Not adding hydrogens to /D SER 243 C because it is missing heavy-atom bond
partners  
Not adding hydrogens to /E LEU 110 C because it is missing heavy-atom bond
partners  
Not adding hydrogens to /F VAL 164 C because it is missing heavy-atom bond
partners  
Not adding hydrogens to /F SER 427 C because it is missing heavy-atom bond
partners  
notes | Termini for 8pz2 (#2) chain A determined from SEQRES records  
Termini for 8pz2 (#2) chain B determined from SEQRES records  
Termini for 8pz2 (#2) chain C determined from SEQRES records  
Termini for 8pz2 (#2) chain D determined from SEQRES records  
Termini for 8pz2 (#2) chain E determined from SEQRES records  
1 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /C CYS 25  
Chain-initial residues that are not actual N termini: /A PHE 24, /B ASN 24, /D
GLU 26, /E ARG 25, /F VAL 25, /F LEU 123, /F ASP 395  
Chain-final residues that are actual C termini: /B ARG 392  
Chain-final residues that are not actual C termini: /A ILE 806, /C PRO 85, /D
SER 243, /E ASN 113, /F ASN 107, /F VAL 164, /F SER 427  
1114 hydrogen bonds  
Adding 'H' to /A PHE 24  
Adding 'H' to /B ASN 24  
Adding 'H' to /D GLU 26  
Adding 'H' to /E ARG 25  
Adding 'H' to /F VAL 25  
2 messages similar to the above omitted  
/C PRO 85 is not terminus, removing H atom from 'C'  
/E ASN 113 is not terminus, removing H atom from 'C'  
12721 hydrogens added  
  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  

QWindowsWindow::setGeometry: Unable to set geometry 981x885+1430+684 (frame:
1003x941+1419+639) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY2". Resulting geometry: 975x868+1433+698 (frame:
997x924+1422+653) margins: 11, 45, 11, 11 minimum size: 454x524 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=786453, y=786487), mintrack=POINT(x=703, y=842)))  

> select add #1

13121 atoms, 13385 bonds, 2 pseudobonds, 1678 residues, 4 models selected  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  

QWindowsWindow::setGeometry: Unable to set geometry 981x885+1430+684 (frame:
1003x941+1419+639) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY2". Resulting geometry: 975x868+1433+698 (frame:
997x924+1422+653) margins: 11, 45, 11, 11 minimum size: 454x524 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=786453, y=786487), mintrack=POINT(x=703, y=842)))  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 100 residues in model #2 to IUPAC-IUB
standards.  
8pz2 title:  
Wait Complex: Lateral open BAM bound Extended SurA [more info...]  
  
Chain information for 8pz2  
---  
Chain | Description | UniProt  
2.2/A | Outer membrane protein assembly factor BamA | BAMA_ECOLI 21-810  
2.2/B | Outer membrane protein assembly factor BamB | BAMB_ECOLI 20-392  
2.2/C | Outer membrane protein assembly factor BamC | BAMC_ECOLI 25-344  
2.2/D | Outer membrane protein assembly factor BamD | BAMD_ECOLI 20-245  
2.2/E | Outer membrane protein assembly factor BamE | BAME_ECOLI 20-113  
2.2/F | Chaperone SurA | SURA_ECOLI 21-428  
  

> clipper associate #1 toModel #2

Opened cryosparc_P423_J83_map.mrc as #2.1.1.1, grid size 300,300,300, pixel
0.71, shown at step 1, values float32  

> hide #!2.1 models

> show #!2.1 models

> select clear

[Repeated 1 time(s)]

> select up

11 atoms, 10 bonds, 1 residue, 2 models selected  

> select up

291 atoms, 294 bonds, 20 residues, 2 models selected  

> select down

11 atoms, 10 bonds, 1 residue, 2 models selected  

> select up

291 atoms, 294 bonds, 20 residues, 2 models selected  

> isolde sim start /B:96-115

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 230, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1419, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\birte\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\\__init__.py", line 166, in run_provider  
toolbar_command(session, name)  
File "C:\Users\birte\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\toolbar.py", line 23, in toolbar_command  
run(session, f'isolde sim start {_current_residue_sel_string(session)}')  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\birte\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\cmd\cmd.py", line 122, in isolde_sim  
isolde.start_sim()  
File "C:\Users\birte\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\isolde.py", line 896, in start_sim  
sm.start_sim()  
File "C:\Users\birte\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 401, in start_sim  
sh.start_sim()  
File "C:\Users\birte\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1432, in start_sim  
self._prepare_sim()  
File "C:\Users\birte\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1377, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\openmm\app\simulation.py", line 106, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\openmm\openmm.py", line 5082, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
openmm.OpenMMException: Error compiling kernel:  
error: undefined reference to
`__builtin_spirv_OpAtomicIAdd_p1i64_i32_i32_i64()'  
  
error: backend compiler failed build.  
  
  
openmm.OpenMMException: Error compiling kernel:  
error: undefined reference to
`__builtin_spirv_OpAtomicIAdd_p1i64_i32_i32_i64()'  
  
error: backend compiler failed build.  
  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\openmm\openmm.py", line 5082, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

QWindowsWindow::setGeometry: Unable to set geometry 900x731+1470+762 (frame:
922x787+1459+717) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY2". Resulting geometry: 894x714+1473+776 (frame:
916x770+1462+731) margins: 11, 45, 11, 11 minimum size: 600x333 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=786453, y=786487), mintrack=POINT(x=922, y=556)))  




OpenGL version: 3.3.0 - Build 25.20.100.6577
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel

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

Manufacturer: Acer
Model: Swift SF514-53T
OS: Microsoft Windows 11 Home (Build 26100)
Memory: 17,022,767,104
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-8565U CPU @ 1.80GHz
OSLanguage: de-DE

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-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
    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