Crash starting simulation

[morellth@…]

The following bug report has been submitted:
Platform:        Linux-6.1.6-arch1-3-x86_64-with-glibc2.36
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00007f556ce116c0 (most recent call first):
  File "/home/thomas/Downloads/chimerax-1.4/lib/python3.9/threading.py", line 316 in wait
  File "/home/thomas/Downloads/chimerax-1.4/lib/python3.9/threading.py", line 574 in wait
  File "/home/thomas/Downloads/chimerax-1.4/lib/python3.9/threading.py", line 1297 in run
  File "/home/thomas/Downloads/chimerax-1.4/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/home/thomas/Downloads/chimerax-1.4/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x00007f56d0680740 (most recent call first):
  File "/home/thomas/Downloads/chimerax-1.4/lib/python3.9/site-packages/openmm/openmm.py", line 5248 in __init__
  File "/home/thomas/Downloads/chimerax-1.4/lib/python3.9/site-packages/openmm/app/simulation.py", line 103 in __init__
  File "/home/thomas/.local/share/ChimeraX/1.4/site-packages/chimerax/isolde/openmm/openmm_interface.py", line 1582 in _prepare_sim
  File "/home/thomas/.local/share/ChimeraX/1.4/site-packages/chimerax/isolde/openmm/openmm_interface.py", line 1624 in start_sim
  File "/home/thomas/.local/share/ChimeraX/1.4/site-packages/chimerax/isolde/openmm/openmm_interface.py", line 677 in start_sim
  File "/home/thomas/.local/share/ChimeraX/1.4/site-packages/chimerax/isolde/isolde.py", line 893 in start_sim
  File "/home/thomas/.local/share/ChimeraX/1.4/site-packages/chimerax/isolde/cmd/cmd.py", line 111 in isolde_sim
  File "/home/thomas/Downloads/chimerax-1.4/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
  File "/home/thomas/Downloads/chimerax-1.4/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38 in run
  File "/home/thomas/.local/share/ChimeraX/1.4/site-packages/chimerax/isolde/toolbar.py", line 17 in toolbar_command
  File "/home/thomas/.local/share/ChimeraX/1.4/site-packages/chimerax/isolde/__init__.py", line 187 in run_provider
  File "/home/thomas/Downloads/chimerax-1.4/lib/python3.9/site-packages/chimerax/core/toolshed/__init__.py", line 1286 in run_provider
  File "/home/thomas/Downloads/chimerax-1.4/lib/python3.9/site-packages/chimerax/core/toolshed/info.py", line 386 in run_provider
  File "/home/thomas/Downloads/chimerax-1.4/lib/python3.9/site-packages/chimerax/toolbar/tool.py", line 205 in callback
  File "/home/thomas/Downloads/chimerax-1.4/lib/python3.9/site-packages/chimerax/ui/gui.py", line 318 in event_loop
  File "/home/thomas/Downloads/chimerax-1.4/lib/python3.9/site-packages/ChimeraX_main.py", line 870 in init
  File "/home/thomas/Downloads/chimerax-1.4/lib/python3.9/site-packages/ChimeraX_main.py", line 1021 in 
  File "/home/thomas/Downloads/chimerax-1.4/lib/python3.9/runpy.py", line 87 in _run_code
  File "/home/thomas/Downloads/chimerax-1.4/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/home/thomas/Studium/Master_1/X-Ray VTK/project/B34_refine_16.pdb"

Chain information for B34_refine_16.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open "/home/thomas/Studium/Master_1/X-Ray VTK/project/B34_refine_16.mtz"

Summary of feedback from opening /home/thomas/Studium/Master_1/X-Ray
VTK/project/B34_refine_16.mtz  
---  
warning | WARNING: multiple experimental reflection datasets found:  
(Original-experimental-data-mapped-to-asu) I-obs, SIGI-obs,  
(Experimental-data-used-in-refinement) F-obs-filtered, SIGF-obs-filtered  
Automatically choosing "(Experimental-data-used-in-refinement) F-obs-filtered,
SIGF-obs-filtered".  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 70,64,64, pixel
0.378,0.387,0.381, shown at level 0.0138, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 70,64,64, pixel
0.378,0.387,0.381, shown at level -0.008,0.008, step 1, values float32  
Opened (LIVE) 2mFo-DFc_smooth_22 as #1.1.1.4, grid size 70,64,64, pixel
0.378,0.387,0.381, shown at level 0.00551, step 1, values float32  
Opened (STATIC) (Model-structure-factors-(all-solvent-and-scales-included))
F-model, PHIF-model as #1.1.1.5, grid size 70,64,64, pixel 0.378,0.387,0.381,
shown at level -0.64,0.64, step 1, values float32  
Opened (STATIC) (Fourier-map-coefficients) 2FOFCWT, PH2FOFCWT as #1.1.1.6,
grid size 70,64,64, pixel 0.378,0.387,0.381, shown at level 0.646, step 1,
values float32  
Opened (STATIC) (Fourier-map-coefficients) 2FOFCWT_no_fill, PH2FOFCWT_no_fill
as #1.1.1.7, grid size 70,64,64, pixel 0.378,0.387,0.381, shown at level
0.646, step 1, values float32  
Opened (STATIC) (Fourier-map-coefficients) FOFCWT, PHFOFCWT as #1.1.1.8, grid
size 70,64,64, pixel 0.378,0.387,0.381, shown at level -0.543,0.543, step 1,
values float32  
Chain information for B34_refine_16.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
  
Opened crystallographic dataset from /home/thomas/Studium/Master_1/X-Ray
VTK/project/B34_refine_16.mtz  
Found experimental reflection data:  
(Experimental-data-used-in-refinement) F-obs-filtered, SIGF-obs-filtered  
Rwork: 27283106491966814492465885433823232.0000; Rfree:
30228496750988344076122435679682560.0000  
Generated maps:  
Reflection Data  
(LIVE) 2mFo-DFc  
(LIVE) mFo-DFc  
(LIVE) 2mFo-DFc_smooth_22  
(STATIC) (Model-structure-factors-(all-solvent-and-scales-included)) F-model,
PHIF-model  
(STATIC) (Fourier-map-coefficients) 2FOFCWT, PH2FOFCWT  
(STATIC) (Fourier-map-coefficients) 2FOFCWT_no_fill, PH2FOFCWT_no_fill  
(STATIC) (Fourier-map-coefficients) FOFCWT, PHFOFCWT  
Any unwanted maps may be safely closed via the Model panel.  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 34 residues in model #1.2 to IUPAC-IUB
standards.  
Cached rota8000-val data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-leu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ile data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-pro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-phe data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-tyr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-trp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ser data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-thr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-cys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-met data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-lys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-his data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-arg data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asn data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-gln data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-glu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-cispro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-transpro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-gly-sym data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-prepro-noGP data not found. Regenerating from text file. This
is normal if running ISOLDE for the first time  
Cached rama8000-ileval-nopreP data not found. Regenerating from text file.
This is normal if running ISOLDE for the first time  
Cached rama8000-general-noGPIVpreP data not found. Regenerating from text
file. This is normal if running ISOLDE for the first time  
Opened (LIVE) MDFF potential as #1.1.1.9, grid size 70,64,64, pixel
0.378,0.387,0.381, shown at level 0.418, step 1, values float32  
Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.  
Done loading forcefield  

> select clear

> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  

> st /A:30

> isolde sim start sel

Loading residue template for EOH from internal database  
Updating bulk solvent parameters...  
ISOLDE: stopped sim  

> addh #1.2

Summary of feedback from adding hydrogens to B34_refine_16.pdb #1.2  
---  
warning | Not adding hydrogens to /B ASP 71 CB because it is missing heavy-
atom bond partners  
notes | No usable SEQRES records for B34_refine_16.pdb (#1.2) chain A;
guessing termini instead  
No usable SEQRES records for B34_refine_16.pdb (#1.2) chain B; guessing
termini instead  
Chain-initial residues that are actual N termini: /A LEU 4, /B LEU 7  
Chain-initial residues that are not actual N termini: /A SER 137, /A ARG 186,
/B GLY 20, /B ARG 70, /B GLY 73, /B LEU 96, /B GLY 146, /B VAL 158  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A GLY 231, /A ILE 133, /A
LEU 181, /B VAL 228, /B LEU 17, /B ASP 67, /B ASP 71, /B LYS 88, /B MET 143,
/B ALA 155  
362 hydrogen bonds  
Adding 'H' to /A SER 137  
Adding 'H' to /A ARG 186  
Adding 'H' to /B GLY 20  
Adding 'H' to /B ARG 70  
Adding 'H' to /B GLY 73  
3 messages similar to the above omitted  
/A GLY 231 is not terminus, removing H atom from 'C'  
/B VAL 228 is not terminus, removing H atom from 'C'  
/B LYS 88 is not terminus, removing H atom from 'C'  
/B LYS 88 is not terminus, removing H atom from 'C'  
3273 hydrogens added  
  
Loading residue template for ACT from internal database  

> isolde sim start sel

Updating bulk solvent parameters...  
ISOLDE: stopped sim  
Fetching CCD EOH from http://ligand-expo.rcsb.org/reports/E/EOH/EOH.cif  

> delete sel

> st /A:30

> isolde sim start sel


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.6 (Core Profile) Mesa 22.3.3
OpenGL renderer: AMD Radeon Vega 8 Graphics (raven, LLVM 15.0.7, DRM 3.49, 6.1.6-arch1-3)
OpenGL vendor: AMD

Python: 3.9.11
Locale: en_GB.UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: xcb

XDG_SESSION_TYPE=tty
DESKTOP_SESSION=
XDG_SESSION_DESKTOP=
XDG_CURRENT_DESKTOP=
DISPLAY=:0
Manufacturer: Acer
Model: Nitro AN515-42
OS: Arch Linux rolling n/a
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 AMD Ryzen 5 2500U with Radeon Vega Mobile Gfx
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            14Gi       1.1Gi        12Gi        43Mi       1.0Gi        13Gi
	Swap:          3.0Gi          0B       3.0Gi

Graphics:
	04:00.0 VGA compatible controller [0300]: Advanced Micro Devices, Inc. [AMD/ATI] Raven Ridge [Radeon Vega Series / Radeon Vega Mobile Series] [1002:15dd] (rev c4)	
	Subsystem: Acer Incorporated [ALI] Device [1025:125c]	
	Kernel driver in use: amdgpu

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.18.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.4
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    distro: 1.6.0
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
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[pett]

Reported by Thomas Morell

[Tristan Croll]

Hmm... hard to say exactly what's gone wrong here. My first guess is it's an OpenCL driver issue - could you check and see if you're using the latest official manufacturer's driver for your GPU? I'm afraid that is a somewhat underpowered GPU for running MD simulations, and not one I have a lot of experience with. If it's crashing every time, it *might* be possible to get a better idea of where things are going wrong by starting ChimeraX with:

gdb chimerax

... then triggering the crash by trying to start a simulation, and in the terminal window you launched from, do:

bt

... and copy/paste the result here.

Oh, and I'd recommend updating to ChimeraX 1.5 and the corresponding latest ISOLDE version.

[Tristan Croll]

... oh, wait. Missed that at first glance: something has gone *horribly* wrong with the structure factor calculations:

Rwork: 27283106491966814492465885433823232.0000; Rfree:
30228496750988344076122435679682560.0000  

Would it be possible to share the model and MTZ file (either here or directly to me at tcroll@…) so I can investigate? I will make sure to keep them confidential.

[Tristan Croll]

So it turns out that now I'm working for a private company rather than a university, the rules I need to operate by have changed - these days I *can't* ask for (or accept) models or data for debugging unless they're already public domain. That being said, I'd very much appreciate your help getting to the bottom of this. To rule out something specific to your hardware or OS (from the looks of it you're using the "Generic Linux" ChimeraX build), is there any other machine you could try it out on to see if it still crashes in the same way?