Opened 7 months ago

Last modified 7 months ago

#17489 assigned defect

ArtiaX: save particle list: KeyError: 'rlnTomoName'

Reported by: chimerax-bug-report@… Owned by: Utz Ermel
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:        Linux-5.14.0-578.el9.x86_64-x86_64-with-glibc2.34
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> artiax start

Using preset: ArtiaX / Artiax Default  
Preset expands to these ChimeraX commands:

    
    
    set bgColor black
    lighting depthCue false
    camera ortho

  
Opened Position_38_7p52A.mrc as #1.1.1, grid size 1024,1024,376, pixel
7.52,7.52,7.52, shown at level 0.0385, step 1, values float32  

> artiax tomo #1.1.1 sliceDirection 0,0,1

> artiax view xy

> open
> /data1/luyichen/YFH/matching/pixel_star/Position_38/Position_38_mod_00.star
> /data1/luyichen/YFH/matching/pixel_star/Position_38/Position_38_mod_01.star
> /data1/luyichen/YFH/matching/pixel_star/Position_38/Position_38_mod_02.star
> /data1/luyichen/YFH/matching/pixel_star/Position_38/Position_38_mod_03.star
> /data1/luyichen/YFH/matching/pixel_star/Position_38/Position_38_mod_04.star
> /data1/luyichen/YFH/matching/pixel_star/Position_38/Position_38_mod_05.star
> /data1/luyichen/YFH/matching/pixel_star/Position_38/Position_38_mod_06.star
> /data1/luyichen/YFH/matching/pixel_star/Position_38/Position_38_mod_07.star
> /data1/luyichen/YFH/matching/pixel_star/Position_38/Position_38_mod_08.star
> /data1/luyichen/YFH/matching/pixel_star/Position_38/Position_38_mod_09.star
> /data1/luyichen/YFH/matching/pixel_star/Position_38/Position_38_mod_10.star
> /data1/luyichen/YFH/matching/pixel_star/Position_38/Position_38_mod_11.star
> /data1/luyichen/YFH/matching/pixel_star/Position_38/Position_38_mod_12.star
> /data1/luyichen/YFH/matching/pixel_star/Position_38/Position_38_mod_13.star
> /data1/luyichen/YFH/matching/pixel_star/Position_38/Position_38_mod_14.star
> /data1/luyichen/YFH/matching/pixel_star/Position_38/Position_38_mod_15.star
> /data1/luyichen/YFH/matching/pixel_star/Position_38/Position_38_mod_16.star
> /data1/luyichen/YFH/matching/pixel_star/Position_38/Position_38_mod_17.star
> /data1/luyichen/YFH/matching/pixel_star/Position_38/Position_38_mod_18.star
> /data1/luyichen/YFH/matching/pixel_star/Position_38/Position_38_mod_19.star
> format star

Opened Particle list Position_38_mod_00.star with 1882 particles.  
Opened Particle list Position_38_mod_01.star with 1882 particles.  
Opened Particle list Position_38_mod_02.star with 1882 particles.  
Opened Particle list Position_38_mod_03.star with 1882 particles.  
Opened Particle list Position_38_mod_04.star with 1882 particles.  
Opened Particle list Position_38_mod_05.star with 1882 particles.  
Opened Particle list Position_38_mod_06.star with 1882 particles.  
Opened Particle list Position_38_mod_07.star with 1882 particles.  
Opened Particle list Position_38_mod_08.star with 1882 particles.  
Opened Particle list Position_38_mod_09.star with 1882 particles.  
Opened Particle list Position_38_mod_10.star with 1882 particles.  
Opened Particle list Position_38_mod_11.star with 1882 particles.  
Opened Particle list Position_38_mod_12.star with 1881 particles.  
Opened Particle list Position_38_mod_13.star with 1881 particles.  
Opened Particle list Position_38_mod_14.star with 1881 particles.  
Opened Particle list Position_38_mod_15.star with 1881 particles.  
Opened Particle list Position_38_mod_16.star with 1881 particles.  
Opened Particle list Position_38_mod_17.star with 1881 particles.  
Opened Particle list Position_38_mod_18.star with 1881 particles.  
Opened Particle list Position_38_mod_19.star with 1881 particles.  

> artiax particles #1.2.6 originScaleFactor 7.52

> artiax view xy

> artiax particles #1.2.6 transScaleFactor 1.0

> artiax view xy

> hide #!1.1.1 models

> hide #!1.2.7 models

> hide #!1.2.8 models

> hide #!1.2.9 models

> hide #!1.2.10 models

> hide #!1.2.11 models

> hide #!1.2.12 models

> hide #!1.2.13 models

> hide #!1.2.14 models

> hide #!1.2.15 models

> hide #!1.2.16 models

> hide #!1.2.17 models

> hide #!1.2.18 models

> hide #!1.2.19 models

> hide #!1.2.20 models

> hide #!1.2.6 models

> hide #!1.2.1 models

> hide #!1.2.2 models

> hide #!1.2.3 models

> hide #!1.2.4 models

> show #!1.2.4 models

> hide #!1.2.4 models

> hide #!1.2.5 models

> show #!1.2.1 models

> artiax particles #1.2.1 originScaleFactor 7.52

> artiax view xy

> artiax particles #1.2.1 transScaleFactor 1.0

> artiax view xy

> ui mousemode right select

Drag select of axes, 317 of 1882 instances, 318 atoms  
Drag select of axes, 154 of 1558 instances, 152 atoms  
Drag select of axes, 43 of 1400 instances, 41 atoms  
Drag select of axes, 3 of 1354 instances, 4 atoms  

> select clear

[Repeated 1 time(s)]Drag select of axes, 9 of 1354 instances, 7 atoms  

> select clear

Drag select of axes, 18 of 1354 instances, 17 atoms  
Drag select of axes, 16 of 1337 instances, 17 atoms  
Drag select of axes, 3 of 1320 instances  

> select clear

Drag select of 1 atoms  
Drag select of axes, 100 of 1319 instances, 107 atoms  
Drag select of axes, 38 of 1208 instances, 36 atoms  
Drag select of 2 atoms  
Drag select of axes, 23 of 1169 instances, 23 atoms  

> select clear

Drag select of axes, 39 of 1169 instances, 40 atoms  
Drag select of axes, 113 of 1129 instances, 112 atoms  
Drag select of axes, 2 of 1012 instances, 1 atoms  
Drag select of axes, 42 of 1010 instances, 46 atoms  
Drag select of axes, 2 of 962 instances, 2 atoms  
Drag select of axes, 2 of 960 instances, 2 atoms  
Drag select of axes, 31 of 958 instances, 28 atoms  

> select clear

Drag select of axes, 35 of 958 instances, 34 atoms  

> select clear

[Repeated 1 time(s)]Drag select of axes, 30 of 958 instances, 28 atoms  

> select #1.2.1.3/M:587@M

1 atom, 1 residue, 1 model selected  
Drag select of axes, 40 of 958 instances, 39 atoms  

> select clear

Drag select of axes, 34 of 958 instances, 33 atoms  

> select clear

Drag select of axes, 31 of 958 instances, 29 atoms  

> select clear

Drag select of axes, 1 of 958 instances  
Drag select of axes, 16 of 958 instances, 14 atoms  

> artiax view xy

Drag select of axes, 9 of 942 instances, 11 atoms  
Drag select of axes, 13 of 931 instances, 15 atoms  

> select clear

Drag select of axes, 4 of 931 instances, 2 atoms  
Drag select of axes, 9 of 931 instances, 7 atoms  
Drag select of 2 atoms  
Drag select of axes, 5 of 919 instances, 7 atoms  
Drag select of axes, 10 of 912 instances, 10 atoms  
Drag select of axes, 1 of 902 instances, 1 atoms  
Drag select of axes, 10 of 902 instances, 11 atoms  
Drag select of axes, 20 of 890 instances, 20 atoms  
Drag select of axes, 2 of 869 instances, 3 atoms  
Drag select of axes, 4 of 866 instances, 3 atoms  
Drag select of axes, 1 of 862 instances, 1 atoms  
Drag select of axes, 4 of 861 instances, 3 atoms  
Drag select of axes, 16 of 857 instances, 14 atoms  
Drag select of axes, 1 of 841 instances, 1 atoms  
Drag select of axes, 5 of 840 instances, 7 atoms  
Drag select of axes, 3 of 833 instances, 4 atoms  
Drag select of axes, 2 of 829 instances  
Drag select of 2 atoms  
Drag select of axes, 2 of 829 instances, 3 atoms  
Drag select of axes, 2 of 826 instances, 2 atoms  
Drag select of axes, 1 of 823 instances, 1 atoms  
Drag select of axes, 1 of 822 instances, 1 atoms  
Drag select of 1 atoms  

> save /data1/luyichen/YFH/matching/pixel_star/Position_38/Position_38_00.star
> partlist #1.2.1

Traceback (most recent call last):  
File "/home/luyichen/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/chimerax/artiax/tool.py", line 344, in _save_partlist  
show_save_file_dialog(self.session)  
File "/home/luyichen/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/chimerax/artiax/widgets/ArtiaXSaveDialog.py", line 52, in
show_save_file_dialog  
_dlg.display(session, **kw)  
File "/home/luyichen/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/chimerax/artiax/widgets/ArtiaXSaveDialog.py", line 43, in display  
run(session, cmd)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "/home/luyichen/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/chimerax/artiax/io/formats.py", line 44, in save  
save_particle_list(session, path, partlist, format_name=self.name)  
File "/home/luyichen/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/chimerax/artiax/io/io.py", line 137, in save_particle_list  
save_data.write_file(file_name=file_name, additional_files=additional_files)  
File "/home/luyichen/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 317, in
write_file  
data.pop('rlnTomoName')  
KeyError: 'rlnTomoName'  
  
KeyError: 'rlnTomoName'  
  
File "/home/luyichen/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 317, in
write_file  
data.pop('rlnTomoName')  
  
See log for complete Python traceback.  
  

> save /data1/luyichen/YFH/matching/pixel_star/Position_38/Position_38_00.star
> partlist #1.2.1

Traceback (most recent call last):  
File "/home/luyichen/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/chimerax/artiax/tool.py", line 344, in _save_partlist  
show_save_file_dialog(self.session)  
File "/home/luyichen/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/chimerax/artiax/widgets/ArtiaXSaveDialog.py", line 52, in
show_save_file_dialog  
_dlg.display(session, **kw)  
File "/home/luyichen/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/chimerax/artiax/widgets/ArtiaXSaveDialog.py", line 43, in display  
run(session, cmd)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "/home/luyichen/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/chimerax/artiax/io/formats.py", line 44, in save  
save_particle_list(session, path, partlist, format_name=self.name)  
File "/home/luyichen/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/chimerax/artiax/io/io.py", line 137, in save_particle_list  
save_data.write_file(file_name=file_name, additional_files=additional_files)  
File "/home/luyichen/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 317, in
write_file  
data.pop('rlnTomoName')  
KeyError: 'rlnTomoName'  
  
KeyError: 'rlnTomoName'  
  
File "/home/luyichen/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 317, in
write_file  
data.pop('rlnTomoName')  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 570.133.20
OpenGL renderer: Quadro P4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: xcb

XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=gnome
XDG_SESSION_DESKTOP=gnome
XDG_CURRENT_DESKTOP=GNOME
WAYLAND_DISPLAY=wayland-0
GNOME_SETUP_DISPLAY=:1
DISPLAY=:0
Manufacturer: Dell Inc.
Model: Precision 7920 Tower
OS: CentOS Stream 9
Architecture: 64bit ELF
Virtual Machine: none
CPU: 16 Intel(R) Xeon(R) Silver 4110 CPU @ 2.10GHz
Cache Size: 11264 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            62Gi       4.9Gi        54Gi        49Mi       3.0Gi        57Gi
	Swap:           15Gi       1.1Gi        14Gi

Graphics:
	b3:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104GL [Quadro P4000] [10de:1bb1] (rev a1)	
	Subsystem: Dell Device [1028:11a3]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-ArtiaX: 0.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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
    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: 1.2.1
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    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
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    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: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    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: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    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: 1.18.1
    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
    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: 1.41
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    distro: 1.9.0
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    pandas: 2.2.3
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pyarrow: 19.0.1
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    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
    starfile: 0.5.12
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13

Change History (1)

comment:1 by Eric Pettersen, 7 months ago

Component: Unassigned → Third Party
Owner: set to Utz Ermel
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ArtiaX: save particle list: KeyError: 'rlnTomoName'
Note: See TracTickets for help on using tickets.