![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 months ago
Closed 7 weeks ago
#18432 closed defect (fixed)
kvfinder KeyError: 'KAA'
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
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.
> open "C:\Users\Amanda\UC Enterprise Dropbox\Amanda Board\My Papers\DHDPS
> Allostery\Tunnnel analysis\Chimera\417U .cxs" format session
Log from Thu Aug 14 14:07:07 2025UCSF 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 "C:/Users/Amanda/UC Enterprise Dropbox/Amanda Board/My Papers/DHDPS
> Allostery/Tunnnel analysis/Chimera/4I7U_dimer.cif"
Summary of feedback from opening C:/Users/Amanda/UC Enterprise Dropbox/Amanda
Board/My Papers/DHDPS Allostery/Tunnnel analysis/Chimera/4I7U_dimer.cif
---
warnings | Unknown polymer entity '1' on line 36
Unable to infer polymer connectivity due to unspecified label_seq_id for
residue "LYS" on line 2348
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for 4I7U_dimer.cif #1
---
Chain | Description
A | No description available
B | No description available
162 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
> show surfaces
> ui tool show "Side View"
> ui tool show "Find Cavities"
> kvfinder
24 cavities found for 4I7U_dimer.cif #1
4I7U_dimer.cif Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.4.8 | | 1820.02 | 1565.37 | 8426 | 11.89 | 4.19
1.4.15 | | 81.65 | 90.47 | 378 | 4.02 | 1.49
1.4.5 | | 77.54 | 95.64 | 359 | 0 | 0
1.4.12 | | 69.34 | 80.51 | 321 | 0 | 0
1.4.2 | | 66.96 | 76.05 | 310 | 2.75 | 1.14
1.4.13 | | 60.91 | 79.98 | 282 | 3.06 | 1.57
1.4.9 | | 55.08 | 60.02 | 255 | 2.47 | 0.83
1.4.3 | | 53.57 | 71.1 | 248 | 3.89 | 2.04
1.4.14 | | 50.54 | 57.97 | 234 | 2.16 | 0.79
1.4.1 | | 49.03 | 50.06 | 227 | 2.4 | 0.65
1.4.17 | | 39.53 | 60.13 | 183 | 0 | 0
1.4.4 | | 37.58 | 54.99 | 174 | 2.47 | 1.14
1.4.16 | | 28.51 | 30.94 | 132 | 1.8 | 0.51
1.4.7 | | 27.86 | 39.74 | 129 | 1.7 | 0.54
1.4.19 | | 21.82 | 40.63 | 101 | 0 | 0
1.4.18 | | 19.87 | 25.08 | 92 | 1.47 | 0.41
1.4.23 | | 13.82 | 24 | 64 | 1.2 | 0.24
1.4.6 | | 12.31 | 29.54 | 57 | 0 | 0
1.4.11 | | 12.31 | 29.54 | 57 | 0 | 0
1.4.21 | | 12.31 | 29.54 | 57 | 0 | 0
1.4.22 | | 12.1 | 21.88 | 56 | 1.34 | 0.46
1.4.20 | | 7.56 | 17.37 | 35 | 0.6 | 0.21
1.4.10 | | 7.13 | 18.01 | 33 | 0.6 | 0.11
1.4.24 | | 6.26 | 13.64 | 29 | 0.6 | 0.04
> kvfinder volumeCutoff 150
1 cavities found for 4I7U_dimer.cif #1
4I7U_dimer.cif Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.4.1 | | 1820.02 | 1565.37 | 8426 | 11.89 | 4.19
> kvfinder probeOut 5 volumeCutoff 120
1 cavities found for 4I7U_dimer.cif #1
4I7U_dimer.cif Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.4.1 | | 1984.18 | 1696.67 | 9186 | 12.49 | 4.56
> kvfinder probeOut 7 volumeCutoff 120
2 cavities found for 4I7U_dimer.cif #1
4I7U_dimer.cif Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.4.1 | | 2362.82 | 1902.5 | 10939 | 13.7 | 5.04
1.4.2 | | 650.38 | 561.42 | 3011 | 3.45 | 0.89
> kvfinder probeIn 5 probeOut 5 volumeCutoff 120
0 cavities found for 4I7U_dimer.cif #1
> kvfinder probeIn 5 probeOut 5 volumeCutoff 120
0 cavities found for 4I7U_dimer.cif #1
> kvfinder probeIn 4 probeOut 5 volumeCutoff 120
0 cavities found for 4I7U_dimer.cif #1
> kvfinder probeIn 3 probeOut 5 volumeCutoff 120
1 cavities found for 4I7U_dimer.cif #1
4I7U_dimer.cif Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.4.1 | | 200.02 | 168.6 | 926 | 6.95 | 3.81
> kvfinder probeIn 3 probeOut 5 volumeCutoff 150
1 cavities found for 4I7U_dimer.cif #1
4I7U_dimer.cif Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.4.1 | | 200.02 | 168.6 | 926 | 6.95 | 3.81
> kvfinder probeIn 3 probeOut 5 volumeCutoff 80
1 cavities found for 4I7U_dimer.cif #1
4I7U_dimer.cif Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.4.1 | | 200.02 | 168.6 | 926 | 6.95 | 3.81
> kvfinder probeIn 2 probeOut 5 volumeCutoff 80
3 cavities found for 4I7U_dimer.cif #1
4I7U_dimer.cif Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.4.3 | | 627.05 | 377.33 | 2903 | 8.16 | 3.47
1.4.1 | | 150.55 | 130.04 | 697 | 5.13 | 1.96
1.4.2 | | 131.54 | 115.47 | 609 | 4.69 | 1.67
> kvfinder probeIn 1 probeOut 5 volumeCutoff 80
9 cavities found for 4I7U_dimer.cif #1
4I7U_dimer.cif Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.4.1 | | 2550.31 | 2512.09 | 11807 | 14.37 | 4.55
1.4.8 | | 136.3 | 169.84 | 631 | 5.3 | 1
1.4.9 | | 133.06 | 171.05 | 616 | 3.84 | 0.63
1.4.3 | | 131.76 | 186.75 | 610 | 9.69 | 4.98
1.4.4 | | 130.25 | 191.2 | 603 | 6.79 | 1.9
1.4.5 | | 122.9 | 161.47 | 569 | 9.02 | 5.04
1.4.6 | | 112.97 | 158.33 | 523 | 6.63 | 1.79
1.4.7 | | 112.97 | 121.27 | 523 | 6.03 | 2.39
1.4.2 | | 92.45 | 104.62 | 428 | 5.23 | 2
> kvfinder probeIn 1.5 probeOut 5 volumeCutoff 80
6 cavities found for 4I7U_dimer.cif #1
4I7U_dimer.cif Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.4.3 | | 1059.05 | 704.8 | 4903 | 14.52 | 5.63
1.4.1 | | 488.59 | 455.76 | 2262 | 11.8 | 4.03
1.4.2 | | 402.41 | 386.08 | 1863 | 9.33 | 3.3
1.4.4 | | 102.38 | 104.23 | 474 | 5.97 | 2.35
1.4.5 | | 101.95 | 116.9 | 472 | 2.16 | 0.57
1.4.6 | | 82.3 | 89.01 | 381 | 1.7 | 0.4
> save "C:/Users/Amanda/UC Enterprise Dropbox/Amanda Board/My Papers/DHDPS
> Allostery/Tunnnel analysis/Chimera/417U .cxs"
——— End of log from Thu Aug 14 14:07:07 2025 ———
> view name session-start
opened ChimeraX session
> set bgColor white
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> lighting full
> lighting soft
> lighting simple
> graphics silhouettes false
> volume style surface
No volumes specified
> transparency 50
> transparency 0
> transparency 50
> hide cartoons
> color blue
> undo
> ui tool show "Color Actions"
> color cyan target s
> color forest green target s
[Repeated 1 time(s)]
> color lime target s
> color white target s
> color light gray target s
> show surfaces
> transparency 0
> ui tool show "Find Cavities"
> ui tool show "Color Actions"
> color light sea green target s
> color magenta target s
> color cyan target s
> color light sea green target s
> ui tool show "Side View"
> kvfinder volumeCutoff 120
1 cavities found for 4I7U_dimer.cif #1
4I7U_dimer.cif Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.4.1 | | 1820.02 | 1565.37 | 8426 | 11.89 | 4.19
> kvfinder probeIn 4 volumeCutoff 120
0 cavities found for 4I7U_dimer.cif #1
> kvfinder probeIn 4 volumeCutoff 100
0 cavities found for 4I7U_dimer.cif #1
> kvfinder probeIn 2 volumeCutoff 100
3 cavities found for 4I7U_dimer.cif #1
4I7U_dimer.cif Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.4.3 | | 564.62 | 352.06 | 2614 | 7.42 | 2.95
1.4.1 | | 119.45 | 102.19 | 553 | 4.84 | 1.91
1.4.2 | | 114.26 | 101.03 | 529 | 4.02 | 1.46
> view #1.4.3 @< 3.5
> zoom 0.75
moved plane near -24.149157428816153 [-0.838716 -0.4664705 0.28099963]
moved plane far -24.149157428816153 [-0.838716 -0.4664705 0.28099963]
> surface #1.4.1-3 probeRadius 2.0 transparency 50
> ~surface #1.4
> surface #1.4.3 probeRadius 2.0
> show #!1/A:48-53,56,78-81,84,88,106/B:42,48-53,56,78-81,84,88,106-107
> kvfinder probeIn 0.5 volumeCutoff 100
5 cavities found for 4I7U_dimer.cif #1
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 136, in find_cavities
run(self.session, cmd)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\cmd.py", line 118, in cmd_kvfinder
contacting[cav_s] = contacting[k_index]
~~~~~~~~~~^^^^^^^^^
KeyError: 'KAA'
KeyError: 'KAA'
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\cmd.py", line 118, in cmd_kvfinder
contacting[cav_s] = contacting[k_index]
~~~~~~~~~~^^^^^^^^^
See log for complete Python traceback.
> kvfinder probeIn 0.5 volumeCutoff 100
5 cavities found for 4I7U_dimer.cif #1
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 136, in find_cavities
run(self.session, cmd)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\cmd.py", line 118, in cmd_kvfinder
contacting[cav_s] = contacting[k_index]
~~~~~~~~~~^^^^^^^^^
KeyError: 'KAA'
KeyError: 'KAA'
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\cmd.py", line 118, in cmd_kvfinder
contacting[cav_s] = contacting[k_index]
~~~~~~~~~~^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 516.69
OpenGL renderer: Quadro M1000M/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_NZ.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows
Manufacturer: HP
Model: HP ZBook 17 G3
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 17,054,662,656
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-6700HQ CPU @ 2.60GHz
OSLanguage: en-US
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-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-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
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
comtypes: 1.4.10
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
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
narwhals: 2.0.1
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: 2.2.6
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
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
plotly: 6.0.1
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pyKVFinder: 0.8.1
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-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 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
pywin32: 310
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
tomlkit: 0.13.2
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
WMI: 1.5.1
Change History (4)
comment:1 by , 3 months ago
| Component: | Unassigned → Structure Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → kvfinder KeyError: 'KAA' |
comment:2 by , 3 months ago
| Status: | assigned → accepted |
|---|
comment:3 by , 7 weeks ago
Note:
See TracTickets
for help on using tickets.
Only happens for small probes. Sent mail to João asking for guidance.