The following bug report has been submitted:
Platform: Windows-10-10.0.22631
ChimeraX Version: 1.11 (2025-12-17 06:45:39 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:\\\Users\\\dgp15\\\Desktop\\\gjcl_PLP_CYS.pdbqt
Chain information for gjcl_PLP_CYS.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
Opened gjcl_PLP_CYS.pdbqt containing 1 structures (5262 atoms, 5336 bonds)
Drag select of 4 atoms, 13 residues, 4 bonds
> select clear
> select /A:99@CD
1 atom, 1 residue, 1 model selected
> select /A:300
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:245@OG1
1 atom, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select /A:211@OH
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
18 atoms, 16 bonds, 3 residues, 1 model selected
> select up
20 atoms, 18 bonds, 3 residues, 1 model selected
> hide sel atoms
> show sel atoms
> hide sel cartoons
> hide sel atoms
> select /A:136@HG
1 atom, 1 residue, 1 model selected
> select clear
> select /?:0@@serial_number=24
1 atom, 1 residue, 1 model selected
> select clear
> select /A:136@HN
1 atom, 1 residue, 1 model selected
> select /A:80
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
34 atoms, 33 bonds, 3 residues, 1 model selected
> select up
5232 atoms, 5308 bonds, 557 residues, 1 model selected
> hide sel atoms
> select clear
> select /?:0@@serial_number=24
1 atom, 1 residue, 1 model selected
> hide sel atoms
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Traceback (most recent call last):
File "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\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 "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\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 "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1420, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\shortcuts\\__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1393, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 403, in try_shortcut
self.run_shortcut(keys)
File "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 421, in run_shortcut
sc.run(self.session, status = self._enabled)
File "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 340, in run
f(s)
File "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 72, in func_plus_tip
func(cmd + " %s")(session)
File "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 594, in run_expanded_command
run(session, cmd)
File "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 537, in run
run_command(session, command, **kw)
File "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-packages\chimerax\coulombic\cmd.py",
line 102, in cmd_coulombic
assign_charges(session, needs_assignment, his_scheme, charge_method,
File "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\coulombic\coulombic.py", line 110, in assign_charges
add_charges(session, charged_residues, method=charge_method, status=status,
File "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\add_charge\charge.py", line 34, in add_charges
uncharged_res_types = add_standard_charges(session, residues, status=status,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\add_charge\charge.py", line 204, in add_standard_charges
br_type = "%s[non-%s]" % (br_type, a.name)
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
MemoryError
MemoryError
File "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\add_charge\charge.py", line 204, in add_standard_charges
br_type = "%s[non-%s]" % (br_type, a.name)
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
See log for complete Python traceback.
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Traceback (most recent call last):
File "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\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 "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\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 "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1420, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\shortcuts\\__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1393, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 403, in try_shortcut
self.run_shortcut(keys)
File "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 421, in run_shortcut
sc.run(self.session, status = self._enabled)
File "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 340, in run
f(s)
File "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 72, in func_plus_tip
func(cmd + " %s")(session)
File "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 594, in run_expanded_command
run(session, cmd)
File "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 537, in run
run_command(session, command, **kw)
File "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-packages\chimerax\coulombic\cmd.py",
line 102, in cmd_coulombic
assign_charges(session, needs_assignment, his_scheme, charge_method,
File "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\coulombic\coulombic.py", line 110, in assign_charges
add_charges(session, charged_residues, method=charge_method, status=status,
File "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\add_charge\charge.py", line 34, in add_charges
uncharged_res_types = add_standard_charges(session, residues, status=status,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\add_charge\charge.py", line 204, in add_standard_charges
br_type = "%s[non-%s]" % (br_type, a.name)
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
MemoryError
MemoryError
File "D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\add_charge\charge.py", line 204, in add_standard_charges
br_type = "%s[non-%s]" % (br_type, a.name)
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
See log for complete Python traceback.
Invalid texture upload for 0x1b8bc0d5e80 layer=0 mip=0
OpenGL version: 3.3.0 NVIDIA 546.92
OpenGL renderer: NVIDIA GeForce RTX 3050 Ti Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.9
Locale: zh_CN.cp936
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: windows
Manufacturer: LENOVO
Model: 82TF
OS: Microsoft Windows 11 \u5bb6\u5ead\u7248 (Build 22631)
Memory: 16,979,447,808
MaxProcessMemory: 137,438,953,344
CPU: 16 12th Gen Intel(R) Core(TM) i5-12500H
OSLanguage: zh-CN
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.0
appdirs: 1.4.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.11.12
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
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: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
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: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11
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: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
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-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
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: 1.0.1
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: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.11
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
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: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
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
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
comtypes: 1.4.11
contourpy: 1.3.3
coverage: 7.13.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.25.1
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
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: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.2.5
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pytz: 2025.2
pywin32: 311
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.0.0
roman-numerals-py: 4.0.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
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
sse-starlette: 3.0.4
stack-data: 0.6.3
starlette: 0.50.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2025.3
urllib3: 2.6.2
uvicorn: 0.38.0
wcwidth: 0.2.14
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
WMI: 1.5.1
yarl: 1.22.0
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
No idea how adding charges to a 5000 atom structure could run out of memory.