Opened 12 months ago

Last modified 12 months ago

#16174 assigned defect

ISOLDE: sim start: Error compiling kernel

Reported by: shfan@… Owned by: Tristan Croll
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-4.18.0-477.15.1.el8_8.x86_64-x86_64-with-glibc2.28
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
When I ran "isolde sim start sel", it happened.

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  

UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> help help:quickstart

> isolde start

> set selectionWidth 4

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  

> isolde tutorial

> isolde demo cryo_em_intro modelOnly true startIsolde false

6out.pdb title:  
Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP
asymmetric unit In T=3 symmetry [more info...]  

Chain information for 6out.pdb #1  
---  
Chain | Description | UniProt  
A B C | capsid protein VP1 | CAPSD_NVN68 9-520  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 51 residues in model #1 to IUPAC-IUB
standards.  
6out.pdb title:  
Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP
asymmetric unit In T=3 symmetry [more info...]  

Chain information for 6out.pdb  
---  
Chain | Description | UniProt  
1.2/A 1.2/B 1.2/C | capsid protein VP1 | CAPSD_NVN68 9-520  

Loaded cryo-EM demo: PDB ID 6out, EMDB ID 20205  

> open 20205 fromDatabase emdb

Opened emdb 20205 as #2, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at
level 0.287, step 1, values float32  

> volume #2 level 0.1761

> volume #2 level 0.2117

> volume #2 level 0.2766

> clipper associate #2 toModel #1

Opened emdb 20205 as #1.1.1.1, grid size 98,112,104, pixel 1.07,1.07,1.07,
shown at step 1, values float32  

> ui tool show "Command Line Interface"

[Repeated 1 time(s)]

> hide #1.3 models

> show #1.3 models

> hide #1.3 models

> show #1.3 models

> hide #1.3 models

> show #1.3 models

> hide #1.3 models

> show #1.3 models

> hide #!1.2 models

> hide #1.3 models

> hide #!1.1 models

> hide #!1 models

> show #!1.1 models

> show #!1.2 models

> select add #1.1

11505 atoms, 11622 bonds, 1720 residues, 7 models selected  

> select subtract #1.1

11505 atoms, 11622 bonds, 1720 residues, 2 models selected  

> hide #!1.1 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1 models

> show #!1.1 models

> show #1.3 models

> volume #1.1.1.1 level 0.1328

> close #1.1.1.1

> isolde tutorial

> select add #1

11505 atoms, 11622 bonds, 1720 residues, 13 models selected  

> select add #1.1

11505 atoms, 11622 bonds, 1720 residues, 13 models selected  

> select subtract #1.3

11505 atoms, 11622 bonds, 1720 residues, 12 models selected  

> select add #1.2

11505 atoms, 11622 bonds, 1720 residues, 12 models selected  

> select add #1.3

11505 atoms, 11622 bonds, 1720 residues, 13 models selected  

> close #1

> open /programs/x86_64-linux/chimerax/1.6.1_c8/libexec/UCSF-
> ChimeraX/lib/python3.9/site-packages/chimerax/isolde/demo_data/6out/6out.pdb
> format pdb

6out.pdb title:  
Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP
asymmetric unit In T=3 symmetry [more info...]  

Chain information for 6out.pdb #1  
---  
Chain | Description | UniProt  
A B C | capsid protein VP1 | CAPSD_NVN68 9-520  


> hide target m

> show target m

> close

> open 20205 format ccp4 fromDatabase emdb

Opened emdb 20205 as #1, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at
level 0.287, step 1, values float32  

> isolde demo cryo_em_intro modelOnly true startIsolde false

6out.pdb title:  
Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP
asymmetric unit In T=3 symmetry [more info...]  

Chain information for 6out.pdb #2  
---  
Chain | Description | UniProt  
A B C | capsid protein VP1 | CAPSD_NVN68 9-520  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 51 residues in model #2 to IUPAC-IUB
standards.  
6out.pdb title:  
Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP
asymmetric unit In T=3 symmetry [more info...]  

Chain information for 6out.pdb  
---  
Chain | Description | UniProt  
2.2/A 2.2/B 2.2/C | capsid protein VP1 | CAPSD_NVN68 9-520  

Loaded cryo-EM demo: PDB ID 6out, EMDB ID 20205  

> hide #2.3 models

> show #2.3 models

> hide #!1 models

> hide #2.3 models

> show #!1 models

> hide #2.1 models

> hide #!2 models

> show #!2 models

> show #2.3 models

> hide #2.3 models

> show #2.3 models

> clipper associate #2 toModel #1

Invalid "toModel" argument: must specify 1 structure, got 0 for "#1"  

> hide #!2.2 models

> hide #2.3 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> show #!2.2 models

> hide #!2 models

> hide #!1 models

> show #!2 models

> select add #2.3

11505 atoms, 11622 bonds, 1720 residues, 3 models selected  

> close #2.3

> close #

Expected a models specifier or a keyword  

> close

> help help:quickstart

> ui tool show ISOLDE

> set selectionWidth 4

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  

> ui tool show ISOLDE

> set selectionWidth 4

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  

> isolde tutorial

> isolde demo cryo_em_intro modelOnly true startIsolde false

6out.pdb title:  
Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP
asymmetric unit In T=3 symmetry [more info...]  

Chain information for 6out.pdb #1  
---  
Chain | Description | UniProt  
A B C | capsid protein VP1 | CAPSD_NVN68 9-520  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 51 residues in model #1 to IUPAC-IUB
standards.  
6out.pdb title:  
Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP
asymmetric unit In T=3 symmetry [more info...]  

Chain information for 6out.pdb  
---  
Chain | Description | UniProt  
1.2/A 1.2/B 1.2/C | capsid protein VP1 | CAPSD_NVN68 9-520  

Loaded cryo-EM demo: PDB ID 6out, EMDB ID 20205  

> open 20205 fromDatabase emdb

Opened emdb 20205 as #2, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at
level 0.287, step 1, values float32  

> clipper associate #2 toModel #1

Opened emdb 20205 as #1.1.1.1, grid size 98,112,104, pixel 1.07,1.07,1.07,
shown at step 1, values float32  

> isolde start

> set selectionWidth 4

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  

> set bgColor white

> addh

Summary of feedback from adding hydrogens to 6out.pdb #1.2  
---  
notes | Termini for 6out.pdb (#1.2) chain A determined from SEQRES records  
Termini for 6out.pdb (#1.2) chain B determined from SEQRES records  
Termini for 6out.pdb (#1.2) chain C determined from SEQRES records  
Chain-initial residues that are actual N termini: /B THR 9  
Chain-initial residues that are not actual N termini: /A ASP 29, /C ASP 29  
Chain-final residues that are actual C termini: /A SER 520  
Chain-final residues that are not actual C termini: /B ALA 519, /C ALA 519  
Missing OXT added to C-terminal residue /A SER 520  
1438 hydrogen bonds  
Adding 'H' to /A ASP 29  
Adding 'H' to /C ASP 29  
/B ALA 519 is not terminus, removing H atom from 'C'  
/C ALA 519 is not terminus, removing H atom from 'C'  
11439 hydrogens added  


> isolde restrain ligands #1

No visible Surface models selected  

> volume #1.1.1.1 style surface

> transparency (#!1.2 & sel) 20

> transparency (#!1.2 & sel) 50

> volume #1.1.1.1 color #aaffff

> volume #1.1.1.1 step 2

> volume #1.1.1.1 step 1

> volume #1.1.1.1 color #00ffff32

> ui tool show "Ramachandran Plot"

[Repeated 1 time(s)]

> select #1

22945 atoms, 23062 bonds, 1720 residues, 18 models selected  

> ui tool show ISOLDE

> isolde sim start sel

Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.6.1_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 319, in
execute  
cmd.run(cmd_text)  
File "/programs/x86_64-linux/chimerax/1.6.1_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line
2897, in run  
result = ci.function(session, **kw_args)  
File "/programs/x86_64-linux/chimerax/1.6.1_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/isolde/cmd/cmd.py", line 122, in
isolde_sim  
isolde.start_sim()  
File "/programs/x86_64-linux/chimerax/1.6.1_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/isolde/isolde.py", line 896, in
start_sim  
sm.start_sim()  
File "/programs/x86_64-linux/chimerax/1.6.1_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 401, in start_sim  
sh.start_sim()  
File "/programs/x86_64-linux/chimerax/1.6.1_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1432, in start_sim  
self._prepare_sim()  
File "/programs/x86_64-linux/chimerax/1.6.1_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1377, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
File "/programs/x86_64-linux/chimerax/1.6.1_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/openmm/app/simulation.py", line 103, in
__init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "/programs/x86_64-linux/chimerax/1.6.1_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/openmm/openmm.py", line 5931, in __init__  
this = _openmm.new_Context(*args)  
openmm.OpenMMException: Error compiling kernel:  

openmm.OpenMMException: Error compiling kernel:  

File "/programs/x86_64-linux/chimerax/1.6.1_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/openmm/openmm.py", line 5931, in __init__  
this = _openmm.new_Context(*args)  

See log for complete Python traceback.  





OpenGL version: 4.5 (Core Profile) Mesa 22.3.0
OpenGL renderer: llvmpipe (LLVM 15.0.0, 256 bits)
OpenGL vendor: Mesa/X.org

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=plasma
XDG_SESSION_DESKTOP=plasma
XDG_CURRENT_DESKTOP=KDE
DISPLAY=:1
Manufacturer: Hewlett-Packard
Model: HP Z620 Workstation
OS: Rocky Linux 8.8 Green Obsidian
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 Intel(R) Xeon(R) CPU E5-2609 0 @ 2.40GHz
Cache Size: 10240 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           31Gi        13Gi       3.6Gi       1.7Gi        14Gi        15Gi
	Swap:          23Gi       1.5Gi        22Gi

Graphics:
	05:00.0 VGA compatible controller [0300]: NVIDIA Corporation GM107GL [Quadro K2200] [10de:13ba] (rev a2)	
	Subsystem: Hewlett-Packard Company Device [103c:1097]	
	Kernel driver in use: nvidia

Installed Packages:
   alabaster: 0.7.13
   appdirs: 1.4.4
   asttokens: 2.2.1
   Babel: 2.12.1
   backcall: 0.2.0
   beautifulsoup4: 4.11.2
   blockdiag: 3.0.0
   build: 0.10.0
   certifi: 2023.5.7
   cftime: 1.6.2
   charset-normalizer: 3.1.0
   ChimeraX-AddCharge: 1.5.9.1
   ChimeraX-AddH: 2.2.5
   ChimeraX-AlignmentAlgorithms: 2.0.1
   ChimeraX-AlignmentHdrs: 3.3.1
   ChimeraX-AlignmentMatrices: 2.1
   ChimeraX-Alignments: 2.9.3
   ChimeraX-AlphaFold: 1.0
   ChimeraX-AltlocExplorer: 1.0.3
   ChimeraX-AmberInfo: 1.0
   ChimeraX-Arrays: 1.1
   ChimeraX-Atomic: 1.43.10
   ChimeraX-AtomicLibrary: 10.0.6
   ChimeraX-AtomSearch: 2.0.1
   ChimeraX-AxesPlanes: 2.3.2
   ChimeraX-BasicActions: 1.1.2
   ChimeraX-BILD: 1.0
   ChimeraX-BlastProtein: 2.1.2
   ChimeraX-BondRot: 2.0.1
   ChimeraX-BugReporter: 1.0.1
   ChimeraX-BuildStructure: 2.8
   ChimeraX-Bumps: 1.0
   ChimeraX-BundleBuilder: 1.2.2
   ChimeraX-ButtonPanel: 1.0.1
   ChimeraX-CageBuilder: 1.0.1
   ChimeraX-CellPack: 1.0
   ChimeraX-Centroids: 1.3.2
   ChimeraX-ChangeChains: 1.0.2
   ChimeraX-CheckWaters: 1.3.1
   ChimeraX-ChemGroup: 2.0.1
   ChimeraX-Clashes: 2.2.4
   ChimeraX-Clipper: 0.21.0
   ChimeraX-ColorActions: 1.0.3
   ChimeraX-ColorGlobe: 1.0
   ChimeraX-ColorKey: 1.5.3
   ChimeraX-CommandLine: 1.2.5
   ChimeraX-ConnectStructure: 2.0.1
   ChimeraX-Contacts: 1.0.1
   ChimeraX-Core: 1.6.1
   ChimeraX-CoreFormats: 1.1
   ChimeraX-coulombic: 1.4.2
   ChimeraX-Crosslinks: 1.0
   ChimeraX-Crystal: 1.0
   ChimeraX-CrystalContacts: 1.0.1
   ChimeraX-DataFormats: 1.2.3
   ChimeraX-Dicom: 1.2
   ChimeraX-DistMonitor: 1.4
   ChimeraX-DockPrep: 1.1.1
   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: 1.1.1
   ChimeraX-Hbonds: 2.4
   ChimeraX-Help: 1.2.1
   ChimeraX-HKCage: 1.3
   ChimeraX-IHM: 1.1
   ChimeraX-ImageFormats: 1.2
   ChimeraX-IMOD: 1.0
   ChimeraX-IO: 1.0.1
   ChimeraX-ISOLDE: 1.6.0
   ChimeraX-ItemsInspection: 1.0.1
   ChimeraX-Label: 1.1.7
   ChimeraX-LinuxSupport: 1.0.1
   ChimeraX-ListInfo: 1.1.1
   ChimeraX-Log: 1.1.5
   ChimeraX-LookingGlass: 1.1
   ChimeraX-Maestro: 1.8.2
   ChimeraX-Map: 1.1.4
   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: 2.0.12
   ChimeraX-MDcrds: 2.6
   ChimeraX-MedicalToolbar: 1.0.2
   ChimeraX-Meeting: 1.0.1
   ChimeraX-MLP: 1.1.1
   ChimeraX-mmCIF: 2.12
   ChimeraX-MMTF: 2.2
   ChimeraX-Modeller: 1.5.9
   ChimeraX-ModelPanel: 1.3.7
   ChimeraX-ModelSeries: 1.0.1
   ChimeraX-Mol2: 2.0
   ChimeraX-Mole: 1.0
   ChimeraX-Morph: 1.0.2
   ChimeraX-MouseModes: 1.2
   ChimeraX-Movie: 1.0
   ChimeraX-Neuron: 1.0
   ChimeraX-Nifti: 1.0
   ChimeraX-NRRD: 1.0
   ChimeraX-Nucleotides: 2.0.3
   ChimeraX-OpenCommand: 1.10.1
   ChimeraX-PDB: 2.7.2
   ChimeraX-PDBBio: 1.0
   ChimeraX-PDBLibrary: 1.0.2
   ChimeraX-PDBMatrices: 1.0
   ChimeraX-PickBlobs: 1.0.1
   ChimeraX-Positions: 1.0
   ChimeraX-PresetMgr: 1.1
   ChimeraX-PubChem: 2.1
   ChimeraX-ReadPbonds: 1.0.1
   ChimeraX-Registration: 1.1.1
   ChimeraX-RemoteControl: 1.0
   ChimeraX-RenderByAttr: 1.1
   ChimeraX-RenumberResidues: 1.1
   ChimeraX-ResidueFit: 1.0.1
   ChimeraX-RestServer: 1.1
   ChimeraX-RNALayout: 1.0
   ChimeraX-RotamerLibMgr: 3.0
   ChimeraX-RotamerLibsDunbrack: 2.0
   ChimeraX-RotamerLibsDynameomics: 2.0
   ChimeraX-RotamerLibsRichardson: 2.0
   ChimeraX-SaveCommand: 1.5.1
   ChimeraX-SchemeMgr: 1.0
   ChimeraX-SDF: 2.0.1
   ChimeraX-Segger: 1.0
   ChimeraX-Segment: 1.0.1
   ChimeraX-SelInspector: 1.0
   ChimeraX-SeqView: 2.8.3
   ChimeraX-Shape: 1.0.1
   ChimeraX-Shell: 1.0.1
   ChimeraX-Shortcuts: 1.1.1
   ChimeraX-ShowSequences: 1.0.1
   ChimeraX-SideView: 1.0.1
   ChimeraX-Smiles: 2.1
   ChimeraX-SmoothLines: 1.0
   ChimeraX-SpaceNavigator: 1.0
   ChimeraX-StdCommands: 1.10.3
   ChimeraX-STL: 1.0.1
   ChimeraX-Storm: 1.0
   ChimeraX-StructMeasure: 1.1.2
   ChimeraX-Struts: 1.0.1
   ChimeraX-Surface: 1.0.1
   ChimeraX-SwapAA: 2.0.1
   ChimeraX-SwapRes: 2.2.1
   ChimeraX-TapeMeasure: 1.0
   ChimeraX-Test: 1.0
   ChimeraX-Toolbar: 1.1.2
   ChimeraX-ToolshedUtils: 1.2.1
   ChimeraX-Topography: 1.0
   ChimeraX-Tug: 1.0.1
   ChimeraX-UI: 1.28.4
   ChimeraX-uniprot: 2.2.2
   ChimeraX-UnitCell: 1.0.1
   ChimeraX-ViewDockX: 1.2
   ChimeraX-VIPERdb: 1.0
   ChimeraX-Vive: 1.1
   ChimeraX-VolumeMenu: 1.0.1
   ChimeraX-VTK: 1.0
   ChimeraX-WavefrontOBJ: 1.0
   ChimeraX-WebCam: 1.0.2
   ChimeraX-WebServices: 1.1.1
   ChimeraX-Zone: 1.0.1
   colorama: 0.4.6
   comm: 0.1.3
   contourpy: 1.0.7
   cxservices: 1.2.2
   cycler: 0.11.0
   Cython: 0.29.33
   debugpy: 1.6.7
   decorator: 5.1.1
   distro: 1.7.0
   docutils: 0.19
   executing: 1.2.0
   filelock: 3.9.0
   fonttools: 4.39.3
   funcparserlib: 1.0.1
   grako: 3.16.5
   h5py: 3.8.0
   html2text: 2020.1.16
   idna: 3.4
   ihm: 0.35
   imagecodecs: 2022.9.26
   imagesize: 1.4.1
   importlib-metadata: 6.6.0
   ipykernel: 6.21.1
   ipython: 8.10.0
   ipython-genutils: 0.2.0
   ipywidgets: 8.0.6
   jedi: 0.18.2
   Jinja2: 3.1.2
   jupyter-client: 8.0.2
   jupyter-core: 5.3.0
   jupyterlab-widgets: 3.0.7
   kiwisolver: 1.4.4
   line-profiler: 4.0.2
   lxml: 4.9.2
   lz4: 4.3.2
   MarkupSafe: 2.1.2
   matplotlib: 3.6.3
   matplotlib-inline: 0.1.6
   msgpack: 1.0.4
   nest-asyncio: 1.5.6
   netCDF4: 1.6.2
   networkx: 2.8.8
   nibabel: 5.0.1
   nptyping: 2.5.0
   numexpr: 2.8.4
   numpy: 1.23.5
   openvr: 1.23.701
   packaging: 23.1
   ParmEd: 3.4.3
   parso: 0.8.3
   pep517: 0.13.0
   pexpect: 4.8.0
   pickleshare: 0.7.5
   Pillow: 9.3.0
   pip: 23.0
   pkginfo: 1.9.6
   platformdirs: 3.5.0
   prompt-toolkit: 3.0.38
   psutil: 5.9.4
   ptyprocess: 0.7.0
   pure-eval: 0.2.2
   pycollada: 0.7.2
   pydicom: 2.3.0
   Pygments: 2.14.0
   pynrrd: 1.0.0
   PyOpenGL: 3.1.5
   PyOpenGL-accelerate: 3.1.5
   pyparsing: 3.0.9
   pyproject-hooks: 1.0.0
   PyQt6-commercial: 6.4.2
   PyQt6-Qt6: 6.4.3
   PyQt6-sip: 13.4.1
   PyQt6-WebEngine-commercial: 6.4.0
   PyQt6-WebEngine-Qt6: 6.4.3
   python-dateutil: 2.8.2
   pytz: 2023.3
   pyzmq: 25.0.2
   qtconsole: 5.4.0
   QtPy: 2.3.1
   RandomWords: 0.4.0
   requests: 2.28.2
   scipy: 1.9.3
   setuptools: 67.4.0
   sfftk-rw: 0.7.3
   six: 1.16.0
   snowballstemmer: 2.2.0
   sortedcontainers: 2.4.0
   soupsieve: 2.4.1
   sphinx: 6.1.3
   sphinx-autodoc-typehints: 1.22
   sphinxcontrib-applehelp: 1.0.4
   sphinxcontrib-blockdiag: 3.0.0
   sphinxcontrib-devhelp: 1.0.2
   sphinxcontrib-htmlhelp: 2.0.1
   sphinxcontrib-jsmath: 1.0.1
   sphinxcontrib-qthelp: 1.0.3
   sphinxcontrib-serializinghtml: 1.1.5
   stack-data: 0.6.2
   tables: 3.7.0
   tcia-utils: 1.2.0
   tifffile: 2022.10.10
   tinyarray: 1.2.4
   tomli: 2.0.1
   tornado: 6.3.1
   traitlets: 5.9.0
   typing-extensions: 4.5.0
   tzdata: 2023.3
   urllib3: 1.26.15
   wcwidth: 0.2.6
   webcolors: 1.12
   wheel: 0.38.4
   wheel-filename: 1.4.1
   widgetsnbextension: 4.0.7
   zipp: 3.15.0

Change History (1)

comment:1 by Eric Pettersen, 12 months ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE: sim start: Error compiling kernel

Reported by Shanghua Fan

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