Isolde sim start: OpenMMException: Error initializing context

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-6.8.0-65-generic-x86_64-with-glibc2.35
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
> /home/kimlab/Downloads/fold_2025_08_26_17_15_124nuc_scfv_wgr_model_0.cif

Chain information for fold_2025_08_26_17_15_124nuc_scfv_wgr_model_0.cif #1  
---  
Chain | Description  
A | .  
B C | .  
D E | .  
F G | .  
H I | .  
J K | .  
L | .  
M | .  
N | .  
  

> open /home/kimlab/Downloads/cryosparc_P40_J212_map_sharp.mrc

Opened cryosparc_P40_J212_map_sharp.mrc as #2, grid size 250,250,250, pixel
0.828, shown at level 0.0446, step 1, values float32  

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 19006 atom styles  
Computing secondary structure  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> ui mousemode right "translate selected models"

> select add #1

19006 atoms, 19981 bonds, 1945 residues, 1 model selected  

> view matrix models #1,1,0,0,8.3258,0,1,0,8.5306,0,0,1,11.467

> select clear

> select add #1

19006 atoms, 19981 bonds, 1945 residues, 1 model selected  

> view matrix models #1,1,0,0,64.94,0,1,0,70.262,0,0,1,94.056

> view matrix models #1,1,0,0,77.015,0,1,0,-8.9639,0,0,1,21.711

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 54, in event  
if self.handle_drag_and_drop(event):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 124, in handle_drag_and_drop  
mw.dropEvent(event)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py",
line 765, in dropEvent  
md = event.mimeData()  
^^^^^^^^^^^^^^  
AttributeError: 'QMouseEvent' object has no attribute 'mimeData'  
  
AttributeError: 'QMouseEvent' object has no attribute 'mimeData'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py",
line 765, in dropEvent  
md = event.mimeData()  
^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> close session

> open /home/kimlab/Documents/J212_z_flipped.mrc

Opened J212_z_flipped.mrc as #1, grid size 250,250,250, pixel 0.828, shown at
level 0.0446, step 1, values float32  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 54, in event  
if self.handle_drag_and_drop(event):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 124, in handle_drag_and_drop  
mw.dropEvent(event)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py",
line 765, in dropEvent  
md = event.mimeData()  
^^^^^^^^^^^^^^  
AttributeError: 'QMouseEvent' object has no attribute 'mimeData'  
  
AttributeError: 'QMouseEvent' object has no attribute 'mimeData'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py",
line 765, in dropEvent  
md = event.mimeData()  
^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> open
> /home/kimlab/Downloads/fold_2025_08_26_17_15_124nuc_scfv_wgr_model_0.cif

Chain information for fold_2025_08_26_17_15_124nuc_scfv_wgr_model_0.cif #2  
---  
Chain | Description  
A | .  
B C | .  
D E | .  
F G | .  
H I | .  
J K | .  
L | .  
M | .  
N | .  
  

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 19006 atom styles  
Computing secondary structure  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> select add #1

2 models selected  

> select subtract #1

Nothing selected  

> select add #2

19006 atoms, 19981 bonds, 1945 residues, 1 model selected  

> view matrix models #2,1,0,0,50.268,0,1,0,19.996,0,0,1,67.38

> view matrix models #2,1,0,0,58.017,0,1,0,100.1,0,0,1,110.56

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.99071,0.13058,-0.037899,56.063,-0.13199,0.85659,-0.49883,98.013,-0.032674,0.4992,0.86587,103.17

> view matrix models
> #2,0.99464,-0.031657,0.098395,59.149,0.077134,0.861,-0.50272,98.204,-0.068804,0.50761,0.85883,102.97

> view matrix models
> #2,0.99632,0.043068,0.074126,58.021,0.00325,0.84505,-0.53467,98.069,-0.085668,0.53294,0.8418,102.49

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.99632,0.043068,0.074126,98.713,0.00325,0.84505,-0.53467,102.5,-0.085668,0.53294,0.8418,105.11

> view matrix models
> #2,0.99632,0.043068,0.074126,103.9,0.00325,0.84505,-0.53467,105.25,-0.085668,0.53294,0.8418,93.001

> view matrix models
> #2,0.99632,0.043068,0.074126,106.69,0.00325,0.84505,-0.53467,104.85,-0.085668,0.53294,0.8418,98.735

> view matrix models
> #2,0.99632,0.043068,0.074126,100.5,0.00325,0.84505,-0.53467,100.93,-0.085668,0.53294,0.8418,92.648

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.95728,0.038758,0.28656,102.1,0.14956,0.78178,-0.60535,101.4,-0.24749,0.62235,0.74258,90.556

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.95728,0.038758,0.28656,113.57,0.14956,0.78178,-0.60535,103.62,-0.24749,0.62235,0.74258,103.8

> view matrix models
> #2,0.95728,0.038758,0.28656,114.52,0.14956,0.78178,-0.60535,100.6,-0.24749,0.62235,0.74258,107.1

> view matrix models
> #2,0.95728,0.038758,0.28656,112.93,0.14956,0.78178,-0.60535,100.67,-0.24749,0.62235,0.74258,107.04

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.9076,0.40824,0.098031,106.76,-0.15919,0.55068,-0.8194,101.59,-0.38849,0.72808,0.56478,104.18

> view matrix models
> #2,0.93255,0.015367,0.3607,113.75,0.22697,0.75201,-0.61885,101.05,-0.28076,0.65898,0.6978,106.2

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.92016,0.26986,0.28368,109.93,-0.063621,0.81796,-0.57175,100.18,-0.38633,0.50805,0.76983,108.51

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.92016,0.26986,0.28368,105.58,-0.063621,0.81796,-0.57175,100.58,-0.38633,0.50805,0.76983,108.55

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.94984,0.31063,-0.036331,102.7,-0.23271,0.62435,-0.74567,101.51,-0.20895,0.71672,0.66532,105.35

> ui tool show "Fit in Map"

> fitmap #2 inMap #1

Fit molecule fold_2025_08_26_17_15_124nuc_scfv_wgr_model_0.cif (#2) to map
J212_z_flipped.mrc (#1) using 19006 atoms  
average map value = 0.07947, steps = 152  
shifted from previous position = 3.67  
rotated from previous position = 11.5 degrees  
atoms outside contour = 6392, contour level = 0.044624  
  
Position of fold_2025_08_26_17_15_124nuc_scfv_wgr_model_0.cif (#2) relative to
J212_z_flipped.mrc (#1) coordinates:  
Matrix rotation and translation  
0.95991304 0.24037511 0.14417617 103.68304615  
-0.04478566 0.63928800 -0.76766210 104.90615052  
-0.27669695 0.73043183 0.62442625 104.35710454  
Axis 0.94695971 0.26603799 -0.18025289  
Axis point 0.00000000 -95.19587106 144.20843701  
Rotation angle (degrees) 52.27924295  
Shift along axis 107.28201859  
  

> save /home/kimlab/Downloads/model1_v1.pdb

> select clear

> volume #1 level 0.0951

> Clipper associate #2 to #1

Unknown command: Clipper associate #2 to #1  

> clipper associate #2 toModel #1

Invalid "toModel" argument: must specify 1 structure, got 0 for "#1"  

> clipper associate #1 toModel #2

Opened J212_z_flipped.mrc as #1.1.1.1, grid size 250,250,250, pixel 0.828,
shown at level 0.0737, step 1, values float32  
Chain information for fold_2025_08_26_17_15_124nuc_scfv_wgr_model_0.cif  
---  
Chain | Description  
1.2/A | .  
1.2/B 1.2/C | .  
1.2/D 1.2/E | .  
1.2/F 1.2/G | .  
1.2/H 1.2/I | .  
1.2/J 1.2/K | .  
1.2/L | .  
1.2/M | .  
1.2/N | .  
  

> set bgColor white

> addH

Unknown command: addH  

> addh

Summary of feedback from adding hydrogens to
fold_2025_08_26_17_15_124nuc_scfv_wgr_model_0.cif #1.2  
---  
notes | Termini for fold_2025_08_26_17_15_124nuc_scfv_wgr_model_0.cif (#1.2) chain A determined from SEQRES records  
Termini for fold_2025_08_26_17_15_124nuc_scfv_wgr_model_0.cif (#1.2) chain B
determined from SEQRES records  
Termini for fold_2025_08_26_17_15_124nuc_scfv_wgr_model_0.cif (#1.2) chain C
determined from SEQRES records  
Termini for fold_2025_08_26_17_15_124nuc_scfv_wgr_model_0.cif (#1.2) chain D
determined from SEQRES records  
Termini for fold_2025_08_26_17_15_124nuc_scfv_wgr_model_0.cif (#1.2) chain E
determined from SEQRES records  
9 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A GLY 1, /B MET 1, /C MET
1, /D MET 1, /E MET 1, /F GLY 1, /G GLY 1, /H MET 1, /I MET 1, /J MET 1, /K
MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A THR 123, /B ALA 269, /C ALA
269, /D ALA 124, /E ALA 124, /F LYS 125, /G LYS 125, /H ALA 136, /I ALA 136,
/J GLY 104, /K GLY 104  
Chain-final residues that are not actual C termini:  
1941 hydrogen bonds  
16536 hydrogens added  
  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 246 residues in model #1.2 to IUPAC-IUB
standards.  
Done loading forcefield  

> 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  

> isolde restrain basepairs sel

ISOLDE: created disulfide bonds between the following residues:  
B183-B248; C46-C120; C183-C248; B46-B120  
Deleted the following atoms from residue DA L1: OP1  
Deleted the following atoms from residue DA M1: OP1  
Deleted the following atoms from residue DG N1: OP1  

> select clear

> isolde sim start /A-N

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 230, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1419, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/kimlab/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/__init__.py", line 166, in run_provider  
toolbar_command(session, name)  
File "/home/kimlab/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/toolbar.py", line 23, in toolbar_command  
run(session, f'isolde sim start {_current_residue_sel_string(session)}')  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/kimlab/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/cmd/cmd.py", line 122, in isolde_sim  
isolde.start_sim()  
File "/home/kimlab/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/isolde.py", line 896, in start_sim  
sm.start_sim()  
File "/home/kimlab/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 401, in start_sim  
sh.start_sim()  
File "/home/kimlab/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1432, in start_sim  
self._prepare_sim()  
File "/home/kimlab/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1377, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/openmm/app/simulation.py", line 106, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/openmm/openmm.py",
line 15354, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
openmm.OpenMMException: Error initializing context: clCreateContext (-5)  
  
openmm.OpenMMException: Error initializing context: clCreateContext (-5)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/openmm/openmm.py",
line 15354, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> isolde sim start /A-N

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 230, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1419, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/kimlab/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/__init__.py", line 166, in run_provider  
toolbar_command(session, name)  
File "/home/kimlab/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/toolbar.py", line 23, in toolbar_command  
run(session, f'isolde sim start {_current_residue_sel_string(session)}')  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/kimlab/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/cmd/cmd.py", line 122, in isolde_sim  
isolde.start_sim()  
File "/home/kimlab/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/isolde.py", line 896, in start_sim  
sm.start_sim()  
File "/home/kimlab/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 401, in start_sim  
sh.start_sim()  
File "/home/kimlab/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1432, in start_sim  
self._prepare_sim()  
File "/home/kimlab/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1377, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/openmm/app/simulation.py", line 106, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/openmm/openmm.py",
line 15354, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
openmm.OpenMMException: Error initializing context: clCreateContext (-5)  
  
openmm.OpenMMException: Error initializing context: clCreateContext (-5)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/openmm/openmm.py",
line 15354, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 575.64.03
OpenGL renderer: NVIDIA GeForce RTX 3060 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: XPS 8950
OS: Ubuntu 22.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700
Cache Size: 25600 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            62Gi       5.2Gi        49Gi       107Mi       8.2Gi        56Gi
	Swap:          2.0Gi          0B       2.0Gi

Graphics:
	0000:01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA104 [GeForce RTX 3060 Ti Lite Hash Rate] [10de:2489] (rev a1)	
	Subsystem: Dell GA104 [GeForce RTX 3060 Ti Lite Hash Rate] [1028:c976]	
	Kernel driver in use: nvidia

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-LinuxSupport: 1.0.1
    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
    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
    distro: 1.9.0
    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
    pexpect: 4.9.0
    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
    ptyprocess: 0.7.0
    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: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine: 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
    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