log hyperlink: 'PySide6.QtCore.QUrl.toString' called with wrong argument types

[Eric Pettersen]

The following bug report has been submitted:
Platform:        macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.11.dev202508270038 (2025-08-27 00:38:49 UTC)
Description
With 5QYH open, clicked on "T9V" in the log (which is supposed to select residue T9V)

Log:
UCSF ChimeraX version: 1.11.dev202508270038 (2025-08-27)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1A0I

Summary of feedback from opening 1A0I fetched from pdb  
---  
note | Fetching compressed mmCIF 1a0i from http://files.rcsb.org/download/1a0i.cif  
  
1a0i title:  
ATP-dependent DNA ligase from bacteriophage T7 complex with atp [more info...]  
  
Chain information for 1a0i #1  
---  
Chain | Description | UniProt  
A | DNA LIGASE | DNLI_BPT7 3-349  
  
Non-standard residues in 1a0i #1  
---  
ATP — adenosine-5'-triphosphate  
  

> minimize

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Filling out missing side chains  
/A ARG 349: phi -172.3, psi none trans  
Applying ARG rotamer (chi angles: -170.0 -92.9 -72.5 104.0) to /A ARG 349  
Summary of feedback from adding hydrogens to 1a0i #1  
---  
notes | Termini for 1a0i (#1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A VAL 2  
Chain-initial residues that are not actual N termini: /A ARG 130, /A ASP 315  
Chain-final residues that are actual C termini: /A ARG 349  
Chain-final residues that are not actual C termini: /A HIS 121, /A PHE 306  
Missing OXT added to C-terminal residue /A ARG 349  
292 hydrogen bonds  
Adding 'H' to /A ARG 130  
Adding 'H' to /A ASP 315  
2654 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> view :atp

> close

> open 1atn

Summary of feedback from opening 1atn fetched from pdb  
---  
note | Fetching compressed mmCIF 1atn from http://files.rcsb.org/download/1atn.cif  
  
1atn title:  
Atomic structure of the actin:DNASE I complex [more info...]  
  
Chain information for 1atn #1  
---  
Chain | Description | UniProt  
A | ACTIN | ACTS_HUMAN 1-372  
D | DEOXYRIBONUCLEASE I | DRN1_BOVIN 1-260  
  
Non-standard residues in 1atn #1  
---  
ACE — acetyl group  
ATP — adenosine-5'-triphosphate  
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)  
CA — calcium ion  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> minimize

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to 1atn #1  
---  
notes | Termini for 1atn (#1) chain A determined from SEQRES records  
Termini for 1atn (#1) chain D determined from SEQRES records  
Chain-initial residues that are actual N termini: /A ACE 0, /D LEU 1  
Chain-initial residues that are not actual N termini: /D CYS 104  
Chain-final residues that are actual C termini: /A ARG 372, /D THR 260  
Chain-final residues that are not actual C termini: /D CYS 101  
612 hydrogen bonds  
Adding 'H' to /D CYS 104  
4887 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue HIC (net charge +0) with am1-bcc method  
Running ANTECHAMBER command:
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/p6/r5049lvm8xj99q001s6g8l_00000gn/T/tmpn27pz4b1/ante.in.mol2 -fi
mol2 -o
/var/folders/p6/r5049lvm8xj99q001s6g8l_00000gn/T/tmpn27pz4b1/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n  
(HIC) ``  
(HIC) `Welcome to antechamber 20.0: molecular input file processor.`  
(HIC) ``  
(HIC) `Info: Finished reading file
(/var/folders/p6/r5049lvm8xj99q001s6g8l_00000gn/T/tmpn27pz4b1/ante.in.mol2);
atoms read (32), bonds read (32).`  
(HIC) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(HIC) `Running:
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/bin/bondtype -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(HIC) ``  
(HIC) ``  
(HIC) `Running:
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(HIC) `Info: Total number of electrons: 120; net charge: 0`  
(HIC) ``  
(HIC) `Running:
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/bin/sqm -O -i
sqm.in -o sqm.out`  
(HIC) ``  
(HIC) `Running:
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(HIC) ``  
(HIC) `Running:
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/bin/atomtype -f ac
-p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(HIC) ``  
Charges for residue HIC determined  
Assigning partial charges to residue CA (net charge +2) with am1-bcc method  
Assigning partial charges to residue NAG+ASN+NAG+BMA (net charge +0) with
am1-bcc method  
Running ANTECHAMBER command:
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/p6/r5049lvm8xj99q001s6g8l_00000gn/T/tmplehys0tl/ante.in.mol2 -fi
mol2 -o
/var/folders/p6/r5049lvm8xj99q001s6g8l_00000gn/T/tmplehys0tl/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n  
(NAG+ASN+NAG+BMA) ``  
(NAG+ASN+NAG+BMA) `Welcome to antechamber 20.0: molecular input file
processor.`  
(NAG+ASN+NAG+BMA) ``  
(NAG+ASN+NAG+BMA) `Info: Finished reading file
(/var/folders/p6/r5049lvm8xj99q001s6g8l_00000gn/T/tmplehys0tl/ante.in.mol2);
atoms read (99), bonds read (101).`  
(NAG+ASN+NAG+BMA) `Info: Determining atomic numbers from atomic symbols which
are case sensitive.`  
(NAG+ASN+NAG+BMA) `Running:
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/bin/bondtype -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(NAG+ASN+NAG+BMA) ``  
(NAG+ASN+NAG+BMA) ``  
(NAG+ASN+NAG+BMA) `Running:
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(NAG+ASN+NAG+BMA) `Info: Total number of electrons: 400; net charge: 0`  
(NAG+ASN+NAG+BMA) ``  
(NAG+ASN+NAG+BMA) `Running:
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/bin/sqm -O -i
sqm.in -o sqm.out`  
(NAG+ASN+NAG+BMA) ``  
(NAG+ASN+NAG+BMA) `Running:
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(NAG+ASN+NAG+BMA) ``  
(NAG+ASN+NAG+BMA) `Running:
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/bin/atomtype -f ac
-p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(NAG+ASN+NAG+BMA) ``  
Charges for residue NAG+ASN+NAG+BMA determined  
Dock prep finished  

> select /A:373@CA

1 atom, 1 residue, 1 model selected  

> display sel :<4

> save /Users/pett/rm/min.pdb

> close

> open 2CT2

Summary of feedback from opening 2CT2 fetched from pdb  
---  
note | Fetching compressed mmCIF 2ct2 from http://files.rcsb.org/download/2ct2.cif  
  
2ct2 title:  
Solution Structure of the RING domain of the Tripartite motif protein 32 [more
info...]  
  
Chain information for 2ct2  
---  
Chain | Description | UniProt  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A 1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A | Tripartite motif protein 32 | TRI32_HUMAN 8-82  
  

> close #1.2-end

> minimize

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Filling out missing side chains  
Swapping /A GLY 88 to GLY  
Summary of feedback from adding hydrogens to 2ct2 #1.1  
---  
notes | Termini for 2ct2 (#1.1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A GLY 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A GLY 88  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue /A GLY 88  
25 hydrogen bonds  
12 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue ZN (net charge +2) with am1-bcc method  
Dock prep finished  

> display Zn :<4

> save /Users/pett/rm/min.pdb

> close

> open 8ERE

Summary of feedback from opening 8ERE fetched from pdb  
---  
note | Fetching compressed mmCIF 8ere from http://files.rcsb.org/download/8ere.cif  
  
8ere title:  
HTLV-1 capsid protein N-terminal domain triclinic crystal form [more info...]  
  
Chain information for 8ere #1  
---  
Chain | Description | UniProt  
A | capsid protein p24 | U3RC00_9DELA 1-127  
  
176 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
1150 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.  

> minimize

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to 8ere #1  
---  
notes | Termini for 8ere (#1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A PRO 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A SER 127  
Chain-final residues that are not actual C termini:  
116 hydrogen bonds  
0 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> dssp

> close

> open 5QYH

Summary of feedback from opening 5QYH fetched from pdb  
---  
notes | Fetching compressed mmCIF 5qyh from http://files.rcsb.org/download/5qyh.cif  
Fetching CCD T9V from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/V/T9V/T9V.cif  
  
5qyh title:  
PanDDA analysis group deposition -- Aar2/RNaseH in complex with fragment
F2X-Entry G04a [more info...]  
  
Chain information for 5qyh #1  
---  
Chain | Description | UniProt  
A | Pre-mRNA-splicing factor 8 | PRP8_YEAST 1836-2090  
B | A1 cistron-splicing factor AAR2 | AAR2_YEAST 1-152 171-317  
  
Non-standard residues in 5qyh #1  
---  
PGR — R-1,2-propanediol  
SO4 — sulfate ion  
T9V — N-(4-methoxyphenyl)acetamide  
  
416 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Traceback (most recent call last):  
File
"/Users/pett/src/chimerax/ChimeraX.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
"/Users/pett/src/chimerax/ChimeraX.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
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 218, in link_intercept  
cmd = qurl.toString(no_formatting)[6:].lstrip() # skip cxcmd:  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
TypeError: 'PySide6.QtCore.QUrl.toString' called with wrong argument types:  
PySide6.QtCore.QUrl.toString(UrlFormattingOption)  
Supported signatures:  
PySide6.QtCore.QUrl.toString(options:
PySide6.QtCore.QUrl.ComponentFormattingOption =
<ComponentFormattingOption.PrettyDecoded: 0>)  
  
TypeError: 'PySide6.QtCore.QUrl.toString' called with wrong argument types:  
PySide6.QtCore.QUrl.toString(UrlFormattingOption)  
Supported signatures:  
PySide6.QtCore.QUrl.toString(options:
PySide6.QtCore.QUrl.ComponentFormattingOption = )  
  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 218, in link_intercept  
cmd = qurl.toString(no_formatting)[6:].lstrip() # skip cxcmd:  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3
OpenGL vendor: Apple

Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PySide6 6.9.2, Qt 6.9.2
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: Mac15,5
      Model Number: Z19K0011DLL/A
      Chip: Apple M3
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.140.96
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.6.1 (24G90)
      Kernel Version: Darwin 24.6.0
      Time since boot: 8 hours, 25 minutes

Graphics/Displays:

    Apple M3:

      Chipset Model: Apple M3
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 4.5K (4480 x 2520)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.7.2
    build: 1.3.0
    certifi: 2025.8.3
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.3
    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: 3.0.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.14
    ChimeraX-AtomicLibrary: 14.1.22
    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.dev202508270038
    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: 1.7.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    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-MDcrds: 2.17.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.2
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.5.1
    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: 1.0.1
    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: 1.15.1
    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: 1.3.1
    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: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.2.1
    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: 2.17.2
    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: 1.48.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.3.2
    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
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.10.5
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.3
    debugpy: 1.8.16
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.19.1
    fonttools: 4.59.1
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2025.4.15
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.30.1
    ipython: 9.4.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.7
    jedi: 0.19.2
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 6.0.1
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.5
    matplotlib-inline: 0.1.7
    msgpack: 1.1.1
    narwhals: 1.38.0
    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: 2.2.5
    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: 4.4.0
    plotly: 6.0.1
    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
    pybind11: 3.0.1
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
    pyKVFinder: 0.8.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PySide6: 6.9.2
    PySide6_Addons: 6.9.2
    PySide6_Essentials: 6.9.2
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.0.2
    qtconsole: 5.6.1
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    requests: 2.32.4
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    shiboken6: 6.9.2
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    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
    stack-data: 0.6.3
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tomlkit: 0.13.2
    tornado: 6.5.2
    traitlets: 5.14.3
    typing_extensions: 4.15.0
    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

[Zach Pearson]

PySide6 expects a QUrl.ComponentFormatingOption, not a QUrl.UrlFormattingOption

I have branched on whether we're using PyQt6 or PySide6 and set no_formatting to the appropriate value for the library used.