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Opened 3 days ago
Last modified 3 days ago
#19888 assigned defect
SEQCROW: mol_builder: URLError
| Reported by: | Owned by: | Tony Schaefer | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-26.3-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
File "/private/var/folders/61/j_ycxrgd4v96ytc5crb63t3h0000gn/T/AppTranslocation/0502E6DB-68E3-4D74-92DB-33D826D0CEFB/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py", line 1351, in do_open
raise URLError(err) shows up when I attempt to view a molecule in 3d
Log:
> open "/var/folders/61/j_ycxrgd4v96ytc5crb63t3h0000gn/T/UCSF ChimeraX-
> AXTmbZ/download.svg"
Can only save, not open, .svg files
getting structure
failed to retrieve structure from CACTUS web API
https://cactus.nci.nih.gov/cgi-
bin/translate.tcl?smiles=&format=sdf&astyle=kekule&dim=3D&file=Molecule+from+ChemDoodle+Web+Components%0A%0Ahttp%3A%2F%2Fwww.ichemlabs.com%0A++3++2++0++0++0++0++++++++++++999+V2000%0A++++0.0000++++0.4330++++0.0000+O+++0++0++0++0++0++0%0A+++-0.5000+++-0.4330++++0.0000+H+++0++0++0++0++0++0%0A++++0.5000+++-0.4330++++0.0000+H+++0++0++0++0++0++0%0A++1++2++1++0++0++0++0%0A++1++3++1++0++0++0++0%0AM++END
structure in V3000 format:
Molecule from ChemDoodle Web Components (Modified for SEQCROW)
http://www.ichemlabs.com
0 0 0 0 0 0 0 0 0 0 0 V3000
M V30 BEGIN CTAB
M V30 COUNTS 3 2 0 0 0
M V30 BEGIN ATOM
M V30 1 O 0.0000 0.4330 0.0000
M V30 2 H -0.5000 -0.4330 0.0000
M V30 3 H 0.5000 -0.4330 0.0000
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 1 3
M V30 END BOND
M V30 END CTAB
M END
structure in V2000 format:
Molecule from ChemDoodle Web Components
http://www.ichemlabs.com
3 2 0 0 0 0 999 V2000
0.0000 0.4330 0.0000 O 0 0 0 0 0 0
-0.5000 -0.4330 0.0000 H 0 0 0 0 0 0
0.5000 -0.4330 0.0000 H 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
M END
Traceback (most recent call last):
File
"/private/var/folders/61/j_ycxrgd4v96ytc5crb63t3h0000gn/T/AppTranslocation/0502E6DB-68E3-4D74-92DB-33D826D0CEFB/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 1348, in do_open
h.request(req.get_method(), req.selector, req.data, headers,
File
"/private/var/folders/61/j_ycxrgd4v96ytc5crb63t3h0000gn/T/AppTranslocation/0502E6DB-68E3-4D74-92DB-33D826D0CEFB/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1303, in request
self._send_request(method, url, body, headers, encode_chunked)
File
"/private/var/folders/61/j_ycxrgd4v96ytc5crb63t3h0000gn/T/AppTranslocation/0502E6DB-68E3-4D74-92DB-33D826D0CEFB/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1349, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File
"/private/var/folders/61/j_ycxrgd4v96ytc5crb63t3h0000gn/T/AppTranslocation/0502E6DB-68E3-4D74-92DB-33D826D0CEFB/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1298, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File
"/private/var/folders/61/j_ycxrgd4v96ytc5crb63t3h0000gn/T/AppTranslocation/0502E6DB-68E3-4D74-92DB-33D826D0CEFB/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1058, in _send_output
self.send(msg)
File
"/private/var/folders/61/j_ycxrgd4v96ytc5crb63t3h0000gn/T/AppTranslocation/0502E6DB-68E3-4D74-92DB-33D826D0CEFB/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 996, in send
self.connect()
File
"/private/var/folders/61/j_ycxrgd4v96ytc5crb63t3h0000gn/T/AppTranslocation/0502E6DB-68E3-4D74-92DB-33D826D0CEFB/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1468, in connect
super().connect()
File
"/private/var/folders/61/j_ycxrgd4v96ytc5crb63t3h0000gn/T/AppTranslocation/0502E6DB-68E3-4D74-92DB-33D826D0CEFB/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 962, in connect
self.sock = self._create_connection(
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/61/j_ycxrgd4v96ytc5crb63t3h0000gn/T/AppTranslocation/0502E6DB-68E3-4D74-92DB-33D826D0CEFB/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/socket.py",
line 827, in create_connection
for res in getaddrinfo(host, port, 0, SOCK_STREAM):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/61/j_ycxrgd4v96ytc5crb63t3h0000gn/T/AppTranslocation/0502E6DB-68E3-4D74-92DB-33D826D0CEFB/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/socket.py",
line 962, in getaddrinfo
for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
socket.gaierror: [Errno 8] nodename nor servname provided, or not known
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/61/j_ycxrgd4v96ytc5crb63t3h0000gn/T/AppTranslocation/0502E6DB-68E3-4D74-92DB-33D826D0CEFB/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 316, in interceptRequest
self._callback(info)
File
"/private/var/folders/61/j_ycxrgd4v96ytc5crb63t3h0000gn/T/AppTranslocation/0502E6DB-68E3-4D74-92DB-33D826D0CEFB/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/61/j_ycxrgd4v96ytc5crb63t3h0000gn/T/AppTranslocation/0502E6DB-68E3-4D74-92DB-33D826D0CEFB/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/private/var/folders/61/j_ycxrgd4v96ytc5crb63t3h0000gn/T/AppTranslocation/0502E6DB-68E3-4D74-92DB-33D826D0CEFB/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 527, in thread_safe
func(*args, **kw)
File "/Users/dusandbarrow/Library/Application
Support/ChimeraX/1.11/lib/python/site-packages/SEQCROW/tools/mol_builder.py",
line 683, in handle_scheme
raise e
File "/Users/dusandbarrow/Library/Application
Support/ChimeraX/1.11/lib/python/site-packages/SEQCROW/tools/mol_builder.py",
line 612, in handle_scheme
s_sd_get = urlopen(url, context=ssl.SSLContext())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/61/j_ycxrgd4v96ytc5crb63t3h0000gn/T/AppTranslocation/0502E6DB-68E3-4D74-92DB-33D826D0CEFB/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 216, in urlopen
return opener.open(url, data, timeout)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/61/j_ycxrgd4v96ytc5crb63t3h0000gn/T/AppTranslocation/0502E6DB-68E3-4D74-92DB-33D826D0CEFB/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 519, in open
response = self._open(req, data)
^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/61/j_ycxrgd4v96ytc5crb63t3h0000gn/T/AppTranslocation/0502E6DB-68E3-4D74-92DB-33D826D0CEFB/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 536, in _open
result = self._call_chain(self.handle_open, protocol, protocol +
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/61/j_ycxrgd4v96ytc5crb63t3h0000gn/T/AppTranslocation/0502E6DB-68E3-4D74-92DB-33D826D0CEFB/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 496, in _call_chain
result = func(*args)
^^^^^^^^^^^
File
"/private/var/folders/61/j_ycxrgd4v96ytc5crb63t3h0000gn/T/AppTranslocation/0502E6DB-68E3-4D74-92DB-33D826D0CEFB/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 1391, in https_open
return self.do_open(http.client.HTTPSConnection, req,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/61/j_ycxrgd4v96ytc5crb63t3h0000gn/T/AppTranslocation/0502E6DB-68E3-4D74-92DB-33D826D0CEFB/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 1351, in do_open
raise URLError(err)
urllib.error.URLError: <urlopen error [Errno 8] nodename nor servname
provided, or not known>
urllib.error.URLError:
File
"/private/var/folders/61/j_ycxrgd4v96ytc5crb63t3h0000gn/T/AppTranslocation/0502E6DB-68E3-4D74-92DB-33D826D0CEFB/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 1351, in do_open
raise URLError(err)
See log for complete Python traceback.
getting structure
structure will appear when optimization completes
job started: local sqm job "water"
job finished: local sqm job "water"
> open "/Users/dusandbarrow/SEQCROW_SCRATCH/water Tue Feb 24 13.43.22
> 2026/water.sqmout" format sqmout
Opened water.sqmout as an sqm output file
> style ball
Changed 3 atom styles
> style sphere
Changed 3 atom styles
> style ball
Changed 3 atom styles
> ui tool show Angles/Torsions
Exactly two atoms must be selected!
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac14,2
Model Number: MLY33LL/A
Chip: Apple M2
Total Number of Cores: 8 (4 Performance and 4 Efficiency)
Memory: 8 GB
System Firmware Version: 13822.81.10
OS Loader Version: 13822.81.10
Software:
System Software Overview:
System Version: macOS 26.3 (25D125)
Kernel Version: Darwin 25.3.0
Time since boot: 3 hours, 43 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
appnope: 0.1.4
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: 2025.7.14
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: 1.11.1
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: 2.5.3
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: 2.7.12
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
contourpy: 1.3.3
coverage: 7.13.1
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: 4.26.0
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
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
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
ptyprocess: 0.7.0
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: 3.3.2
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
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: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
Send2Trash: 2.1.0
SEQCROW: 1.9.7
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
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: 3.2.0
stack-data: 0.6.3
starlette: 0.52.1
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
urllib3: 2.6.3
uvicorn: 0.40.0
wcwidth: 0.3.2
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
Change History (2)
comment:1 by , 3 days ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → SEQCROW: mol_builder: URLError |
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