Opened 5 weeks ago

Closed 5 weeks ago

#19021 closed defect (limitation)

Didn't find section 'Peptide bond' in tab 'ISOLDE'

Reported by: chimerax-bug-report@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc: Greg Couch
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.14.0-427.22.1.el9_4.x86_64-x86_64-with-glibc2.34
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
happens when you click on a qscore residue in the chimerx window

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/walter/refine/CEM-1332D4-KP311/S-closed-1332D4/J518_005_volume_map.mrc

Opened J518_005_volume_map.mrc as #1, grid size 512,512,512, pixel 0.73, shown
at level 0.0147, step 2, values float32  

> volume #1 level 0.04289

> open
> /home/walter/refine/CEM-1332D4-KP311/S-closed-1332D4/RealSpaceRefine_18/trimer-717-v1-remove-
> header_real_space_refined_018.pdb

Chain information for trimer-717-v1-remove-header_real_space_refined_018.pdb
#2  
---  
Chain | Description  
A E | No description available  
B | No description available  
  

> toolshed show

Downloading bundle ChimeraX_QScore-1.2-cp311-cp311-linux_x86_64.whl  
Installed ChimeraX-QScore (1.2)  

> qscore #2 toVolume #1

When the "qscore" command is called with "useGui True", the analysis will be
run on the entire model.  

> ui tool show "Model-map Q-Score"

> style #2 stick

Changed 24700 atom styles  

> color #2 byhetero

> transparency #1 60

Overall mean Q-Score: 0.00  

> open /home/walter/refine/CEM-1332D4-KP311/S-closed-1332D4/vox-
> test/p32-j518-voxel717.ccp4

Opened p32-j518-voxel717.ccp4 as #3, grid size 512,512,512, pixel 0.717, shown
at level 0.0147, step 2, values float32  

> color #3 #1c71d8ff models

> close #1

> qscore #2 toVolume #3

When the "qscore" command is called with "useGui True", the analysis will be
run on the entire model.  

> ui tool show "Model-map Q-Score"

> style #2 stick

Changed 24700 atom styles  

> color #2 byhetero

> transparency #3 60

Overall mean Q-Score: 0.63  

> open /home/walter/refine/CEM-1332D4-KP311/S-closed-1332D4/ward-
> structure/embd-48150.mrc

Opened embd-48150.mrc as #1, grid size 512,512,512, pixel 0.718, shown at
level 0.061, step 2, values float32  

> volume #1 level 0.07983

> volume #1 step 1

> open /home/walter/refine/CEM-1332D4-KP311/S-closed-1332D4/ward-
> structure/9eli-48150.pdb

Chain information for 9eli-48150.pdb #4  
---  
Chain | Description  
A B C | No description available  
  

> volume #1 level 0.3307

> hide #!2 models

> qscore #4 toVolume #1

When the "qscore" command is called with "useGui True", the analysis will be
run on the entire model.  

> ui tool show "Model-map Q-Score"

> style #4 stick

Changed 25509 atom styles  

> color #4 byhetero

> transparency #1 60

Overall mean Q-Score: 0.60  

> qscore #4 toVolume #1 useGui true

When the "qscore" command is called with "useGui True", the analysis will be
run on the entire model.  

> ui tool show "Model-map Q-Score"

> transparency #1 60

Overall mean Q-Score: 0.60  

> style #2 stick

Changed 24700 atom styles  

> color #2 byhetero

> style #4 stick

Changed 25509 atom styles  

> color #4 byhetero

> volume #3 step 1

> qscore #2 toVolume #3

When the "qscore" command is called with "useGui True", the analysis will be
run on the entire model.  

> ui tool show "Model-map Q-Score"

> style #2 stick

Changed 24700 atom styles  

> color #2 byhetero

> transparency #3 60

Overall mean Q-Score: 0.63  

> qscore #4 toVolume #1

When the "qscore" command is called with "useGui True", the analysis will be
run on the entire model.  

> ui tool show "Model-map Q-Score"

> style #4 stick

Changed 25509 atom styles  

> color #4 byhetero

> transparency #1 60

Overall mean Q-Score: 0.60  

> qscore #2 toVolume #3

When the "qscore" command is called with "useGui True", the analysis will be
run on the entire model.  

> ui tool show "Model-map Q-Score"

> style #2 stick

Changed 24700 atom styles  

> color #2 byhetero

> transparency #3 60

Overall mean Q-Score: 0.63  
Downloading bundle chimerax_isolde-1.10.1-cp311-cp311-linux_x86_64.whl  
/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/pkginfo/distribution.py:175: NewMetadataVersion: New metadata version
(2.4) higher than latest supported version: parsing as 2.3  
warnings.warn(NewMetadataVersion(self.metadata_version))  
Installed ChimeraX-Clipper (0.25.2)  
Installed ChimeraX-ISOLDE (1.10.1)  

> open /home/walter/refine/CEM-1332D4-KP311/ResolveCryoEM_48/j460-denmod-
> voxel717.ccp4

Opened j460-denmod-voxel717.ccp4 as #5, grid size 115,85,139, pixel
0.717,0.717,0.717, shown at level 1.44, step 1, values float32  

> open /home/walter/refine/CEM-1332D4-KP311/RealSpaceRefine_50/1332d4-rbd-
> vox717_real_space_refined_050.log

Install the SEQCROW bundle to open "Gaussian output file" format files.  
Opener for format 'Gaussian output file' is not installed; see log for more
info  

> open /home/walter/refine/CEM-1332D4-KP311/RealSpaceRefine_50/1332d4-rbd-
> vox717_real_space_refined_050.pdb

Chain information for 1332d4-rbd-vox717_real_space_refined_050.pdb #6  
---  
Chain | Description  
B | No description available  
D | No description available  
E | No description available  
  

> qscore #6 toVolume #5

When the "qscore" command is called with "useGui True", the analysis will be
run on the entire model.  

> ui tool show "Model-map Q-Score"

> style #6 stick

Changed 3300 atom styles  

> color #6 byhetero

> transparency #5 60

Overall mean Q-Score: 0.59  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/walter/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/toolbar.py", line 332, in _selection_changed_cb  
self._enable_if_single_peptide_selected_cb()  
File "/home/walter/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/toolbar.py", line 318, in
_enable_if_single_peptide_selected_cb  
self.set_enabled(key, enable)  
File "/home/walter/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/toolbar.py", line 129, in set_enabled  
self.session.toolbar.set_enabled(enabled, tab, section, display_name)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/toolbar/manager.py", line 205, in set_enabled  
tb.set_enabled(enabled, tab_title, section_title, button_title)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 271, in set_enabled  
self.ttb.set_enabled(enabled, tab_title, section_title, button_title)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/ui/widgets/tabbedtoolbar.py", line 559, in set_enabled  
raise ValueError(  
ValueError: Didn't find section 'Peptide bond' in tab 'ISOLDE'  
  
Error processing trigger "selection changed":  
ValueError: Didn't find section 'Peptide bond' in tab 'ISOLDE'  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/ui/widgets/tabbedtoolbar.py", line 559, in set_enabled  
raise ValueError(  
  
See log for complete Python traceback.  
  

> volume #5 level 0.2313

[Repeated 1 time(s)]Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/walter/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/toolbar.py", line 332, in _selection_changed_cb  
self._enable_if_single_peptide_selected_cb()  
File "/home/walter/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/toolbar.py", line 318, in
_enable_if_single_peptide_selected_cb  
self.set_enabled(key, enable)  
File "/home/walter/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/toolbar.py", line 129, in set_enabled  
self.session.toolbar.set_enabled(enabled, tab, section, display_name)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/toolbar/manager.py", line 205, in set_enabled  
tb.set_enabled(enabled, tab_title, section_title, button_title)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 271, in set_enabled  
self.ttb.set_enabled(enabled, tab_title, section_title, button_title)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/ui/widgets/tabbedtoolbar.py", line 559, in set_enabled  
raise ValueError(  
ValueError: Didn't find section 'Peptide bond' in tab 'ISOLDE'  
  
Error processing trigger "selection changed":  
ValueError: Didn't find section 'Peptide bond' in tab 'ISOLDE'  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/ui/widgets/tabbedtoolbar.py", line 559, in set_enabled  
raise ValueError(  
  
See log for complete Python traceback.  
  

> volume #5 level 0.8065

Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/walter/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/toolbar.py", line 332, in _selection_changed_cb  
self._enable_if_single_peptide_selected_cb()  
File "/home/walter/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/toolbar.py", line 318, in
_enable_if_single_peptide_selected_cb  
self.set_enabled(key, enable)  
File "/home/walter/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/toolbar.py", line 129, in set_enabled  
self.session.toolbar.set_enabled(enabled, tab, section, display_name)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/toolbar/manager.py", line 205, in set_enabled  
tb.set_enabled(enabled, tab_title, section_title, button_title)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 271, in set_enabled  
self.ttb.set_enabled(enabled, tab_title, section_title, button_title)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/ui/widgets/tabbedtoolbar.py", line 559, in set_enabled  
raise ValueError(  
ValueError: Didn't find section 'Peptide bond' in tab 'ISOLDE'  
  
Error processing trigger "selection changed":  
ValueError: Didn't find section 'Peptide bond' in tab 'ISOLDE'  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/ui/widgets/tabbedtoolbar.py", line 559, in set_enabled  
raise ValueError(  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 550.54.14
OpenGL renderer: NVIDIA RTX A5000/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=gnome
XDG_SESSION_DESKTOP=gnome
XDG_CURRENT_DESKTOP=GNOME
DISPLAY=:3
Manufacturer: To Be Filled By O.E.M.
Model: WRX80 Creator R2.0
OS: Rocky Linux 9.6
Architecture: 64bit ELF
Virtual Machine: none
CPU: 128 AMD Ryzen Threadripper PRO 5995WX 64-Cores
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           503Gi        18Gi       473Gi       161Mi        15Gi       484Gi
	Swap:            9Gi          0B         9Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA102GL [RTX A5000] [10de:2231] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:147e]	
	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-QScore: 1.2
    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

Change History (3)

comment:1 by Eric Pettersen, 5 weeks ago

Cc: Greg Couch added
Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Didn't find section 'Peptide bond' in tab 'ISOLDE'

comment:2 by Tristan Croll, 5 weeks ago 

User installed ISOLDE in this session, and must have ignored the pop-up
window saying a ChimeraX restart is needed. The traceback is why: ISOLDE’s
section of the Toolbar is only created on ChimeraX startup, so trying to
use it in the “installation” session leads to tracebacks like this.

I’ve lost login access to Trac again… been meaning to chase that up, but,
y’know, life. Eric, could you go ahead and close the ticket?

On Mon, 6 Oct 2025 at 19:27, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>
>

comment:3 by Eric Pettersen, 5 weeks ago

Resolution: → limitation
Status: assigned → closed
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