ISOLDE start sim: OpenMMException: Error compiling kernel

[yasaitoh@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/y_saitoh/Documents/3D/Nramps/OsNr5-2Fabs/Nr5_22-471fin_2Fab-
> all.pdb

Chain information for Nr5_22-471fin_2Fab-all.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
H | No description available  
L | No description available  
  

> style stick

Changed 9892 atom styles  

> hide atoms

> show atoms

> hide atoms

> show atoms

> hide cartoons

> show cartoons

> style sphere

Changed 9892 atom styles  

> hide cartoons

> show cartoons

> hide cartoons

> show cartoons

> style sphere

Changed 9892 atom styles  

> style ball

Changed 9892 atom styles  

> hide cartoons

> show cartoons

> style stick

Changed 9892 atom styles  

> hide cartoons

> show cartoons

> show surfaces

> hide surfaces

> style sphere

Changed 9892 atom styles  

> style ball

Changed 9892 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> nucleotides fill

> style nucleic stick

Changed 0 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> nucleotides tube/slab shape box

> nucleotides ladder

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> color byhetero

[Repeated 1 time(s)]

> color bychain

> color bypolymer

> rainbow

> coulombic

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
/A LYS 156  
/A GLU 158  
/A CYS 240  
/A ARG 241  
/A PHE 242  
/A PHE 243  

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for Nr5_22-471fin_2Fab-all.pdb_A SES surface #1.2: minimum,
-16.47, mean 0.51, maximum 16.52  
Coulombic values for Nr5_22-471fin_2Fab-all.pdb_B SES surface #1.3: minimum,
-13.79, mean -1.47, maximum 9.31  
Coulombic values for Nr5_22-471fin_2Fab-all.pdb_C SES surface #1.4: minimum,
-15.64, mean -0.27, maximum 14.80  
Coulombic values for Nr5_22-471fin_2Fab-all.pdb_H SES surface #1.5: minimum,
-12.72, mean -0.46, maximum 15.40  
Coulombic values for Nr5_22-471fin_2Fab-all.pdb_L SES surface #1.6: minimum,
-12.96, mean -1.82, maximum 10.55  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp

Map values for surface "Nr5_22-471fin_2Fab-all.pdb_A SES surface": minimum
-31.5, mean 0.123, maximum 26.05  
Map values for surface "Nr5_22-471fin_2Fab-all.pdb_B SES surface": minimum
-31.6, mean -6.413, maximum 23.55  
Map values for surface "Nr5_22-471fin_2Fab-all.pdb_C SES surface": minimum
-26.45, mean -5.562, maximum 24.38  
Map values for surface "Nr5_22-471fin_2Fab-all.pdb_H SES surface": minimum
-26.47, mean -5.222, maximum 22.76  
Map values for surface "Nr5_22-471fin_2Fab-all.pdb_L SES surface": minimum
-31.47, mean -6.836, maximum 22.23  
To also show corresponding color key, enter the above mlp command and add key
true  

> color bfactor

9892 atoms, 1479 residues, 5 surfaces, atom bfactor range 15.9 to 93.7  

> color bynucleotide

> hbonds reveal true

1252 hydrogen bonds found  

> ~hbonds

> style sphere

Changed 9892 atom styles  

> style ball

Changed 9892 atom styles  

> hide surfaces

> color byhetero

[Repeated 1 time(s)]

> color bychain

> color byhetero

> hbonds reveal true

1252 hydrogen bonds found  

> open
> C:/Users/y_saitoh/Documents/3D/Nramps/OsNr5-2Fabs/J95_007_volume_map_sharp.mrc

Opened J95_007_volume_map_sharp.mrc as #2, grid size 362,362,362, pixel 0.752,
shown at level 0.0626, step 2, values float32  

> volume hide

> volume show

> volume style surface

> volume style mesh

> volume style image

> transparency #1.2-6 50

> volume style surface

> transparency 0

> volume showOutlineBox true

> volume showOutlineBox false

> volume showOutlineBox true

> transparency 50

> volume showOutlineBox false

> volume step 1

> volume step 2

> volume step 1

> volume #2 change image level -0.01641,0 level 0.06246,0.8 level 1.579,1

> volume #2 level -0.04891

> volume #2 level 0.01481

> volume step 2

> volume #2 level 0.062

> volume step 1

> volume #2 level 0.09917

> transparency 0

> volume #2 level 0.1841

> volume planes z style image imageMode "full region"

> mousemode rightMode "move planes"

> volume #2 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 136.1 tiltedSlabSpacing 0.752 tiltedSlabPlaneCount 10

> mousemode rightMode "rotate slab"

> volume #2 level -0.01641,0 level 0.1103,0.8154 level 1.579,1

> volume #2 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 136.1 tiltedSlabSpacing 0.752 tiltedSlabPlaneCount 10

> mousemode rightMode "rotate slab"

> volume planes z style image imageMode "full region"

> mousemode rightMode "move planes"

> volume planes z style image imageMode "full region"

> mousemode rightMode "move planes"

> volume planes z style image imageMode "full region"

> mousemode rightMode "move planes"

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

> volume showOutlineBox false

> volume #2 orthoplanes xyz positionPlanes 181,181,181 style image region all

> mousemode rightMode "move planes"

> volume zone #2 nearAtoms #1 range 4.51

> volume #2 orthoplanes xyz positionPlanes 181,181,181 style image region all

> mousemode rightMode "move planes"

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

> volume zone #2 nearAtoms #1 range 4.51

[Repeated 3 time(s)]

> volume planes z style image imageMode "full region"

> mousemode rightMode "move planes"

> volume #2 level -0.01641,0 level 0.1103,0.8154 level 1.069,0.9385

> volume #2 level -0.01641,0 level 0.1103,0.8154 level 0.9458,0.4769

> volume #2 level -0.01641,0 level 0.1103,0.8154 level 0.326,0.6769

> volume #2 level -0.01641,0 level 0.1103,0.8154 level 0.2327,0.8154

> volume #2 level -0.02641,0 level 0.1103,0.8154 level 0.2327,0.8154

> volume #2 level -0.02641,0 level 0.003618,0.8615 level 0.2327,0.8154

> volume #2 level -0.02641,0 level 0.003618,0.8615 level 0.3294,0.9846

> volume #2 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 136.1 tiltedSlabSpacing 0.752 tiltedSlabPlaneCount 10

> mousemode rightMode "rotate slab"

> volume #2 level -0.02641,0 level 0.003618,0.8615 level 0.324,0.7385

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

> volume zone #2 nearAtoms #1 range 4.51

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

> volume showOutlineBox false

> volume showOutlineBox true

> volume style surface

> color zone #2 near #1 distance 4.51

> surface dust #2 size 7.52

[Repeated 1 time(s)]

> color zone #2 near #1 distance 4.51

> surface dust #2 size 7.52

> volume #2 level 0.1204

> surface dust #2 size 7.52

> color zone #2 near #1 distance 4.51

> surface dust #2 size 7.52

> volume hide

> volume show

> volume showOutlineBox false

> transparency 50

> transparency 0

> color zone #2 near #1 distance 4.51

> surface dust #2 size 7.52

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

> volume zone #2 nearAtoms #1 range 4.51

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

> surface dust #2 size 7.52

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

> color zone #2 near #1 distance 4.51

> clipper associate #2 toModel #1

Opened J95_007_volume_map_sharp.mrc as #1.1.1.1, grid size 362,362,362, pixel
0.752, shown at level 0.261, step 1, values float32  
Chain information for Nr5_22-471fin_2Fab-all.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/H | No description available  
1.2/L | No description available  
  

> volume #1.1.1.1 region 164,146,150,196,177,181

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 43 residues in model #1.2 to IUPAC-IUB
standards.  

> isolde set simFidelityMode Highest/Slowest

ISOLDE: setting sim fidelity mode to Highest/Slowest  
nonbonded_cutoff_distance = 1.700000  
use_gbsa = True  
gbsa_cutoff = 2.000000  

> addh

Summary of feedback from adding hydrogens to Nr5_22-471fin_2Fab-all.pdb #1.2  
---  
warnings | Not adding hydrogens to /A LYS 156 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A GLU 158 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A CYS 240 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ARG 241 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A PHE 242 CB because it is missing heavy-atom bond
partners  
1 messages similar to the above omitted  
notes | No usable SEQRES records for Nr5_22-471fin_2Fab-all.pdb (#1.2) chain
A; guessing termini instead  
No usable SEQRES records for Nr5_22-471fin_2Fab-all.pdb (#1.2) chain B;
guessing termini instead  
No usable SEQRES records for Nr5_22-471fin_2Fab-all.pdb (#1.2) chain C;
guessing termini instead  
No usable SEQRES records for Nr5_22-471fin_2Fab-all.pdb (#1.2) chain H;
guessing termini instead  
No usable SEQRES records for Nr5_22-471fin_2Fab-all.pdb (#1.2) chain L;
guessing termini instead  
Chain-initial residues that are actual N termini: /A ALA 18, /B ASP 1, /C GLN
1, /H GLU 1, /L ASP 2  
Chain-initial residues that are not actual N termini: /A CYS 240, /B THR 109,
/C GLY 142, /H GLY 142  
Chain-final residues that are actual C termini: /B ARG 211, /C PRO 221, /H PRO
221  
Chain-final residues that are not actual C termini: /A VAL 472, /A LYS 228, /B
GLU 105, /C GLY 135, /H GLY 135, /L GLY 201  
1243 hydrogen bonds  
Adding 'H' to /A CYS 240  
Adding 'H' to /B THR 109  
Adding 'H' to /C GLY 142  
Adding 'H' to /H GLY 142  
/A VAL 472 is not terminus, removing H atom from 'C'  
/L GLY 201 is not terminus, removing H atom from 'C'  
10071 hydrogens added  
  

> ui tool show "Ramachandran Plot"

> hide #1.3 models

> show #1.3 models

> hide #1.3 models

> show #1.3 models

> hide #1.3 models

> show #1.3 models

> hide #!1.2 models

> hide #1.3 models

> show #1.3 models

> show #!1.2 models

> select #1.2

19963 atoms, 19983 bonds, 1256 pseudobonds, 1479 residues, 11 models selected  

> isolde sim start sel

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Users\y_saitoh\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\cmd\cmd.py", line 122, in isolde_sim  
isolde.start_sim()  
File "C:\Users\y_saitoh\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\isolde.py", line 896, in start_sim  
sm.start_sim()  
File "C:\Users\y_saitoh\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 401, in start_sim  
sh.start_sim()  
File "C:\Users\y_saitoh\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1432, in start_sim  
self._prepare_sim()  
File "C:\Users\y_saitoh\AppData\Local\UCSF\ChimeraX\1.6\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\bin\lib\site-
packages\openmm\app\simulation.py", line 103, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\openmm\openmm.py", line
4584, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
openmm.OpenMMException: Error compiling kernel:  
  
openmm.OpenMMException: Error compiling kernel:  
  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\openmm\openmm.py", line
4584, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
  
See log for complete Python traceback.  
  

> isolde sim start sel

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Users\y_saitoh\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\cmd\cmd.py", line 122, in isolde_sim  
isolde.start_sim()  
File "C:\Users\y_saitoh\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\isolde.py", line 896, in start_sim  
sm.start_sim()  
File "C:\Users\y_saitoh\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 401, in start_sim  
sh.start_sim()  
File "C:\Users\y_saitoh\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1432, in start_sim  
self._prepare_sim()  
File "C:\Users\y_saitoh\AppData\Local\UCSF\ChimeraX\1.6\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\bin\lib\site-
packages\openmm\app\simulation.py", line 103, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\openmm\openmm.py", line
4584, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
openmm.OpenMMException: Error compiling kernel:  
  
openmm.OpenMMException: Error compiling kernel:  
  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\openmm\openmm.py", line
4584, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 431.94
OpenGL renderer: Quadro RTX 4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: ja_JP.cp932
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: To Be Filled By O.E.M.
Model: To Be Filled By O.E.M.
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 68,636,749,824
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz
OSLanguage: ja-JP

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.21.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.6.0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    comtypes: 1.1.14
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pywin32: 305
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    WMI: 1.5.1
    zipp: 3.15.0

[Eric Pettersen]

Reported by Yasunori Saitoh