Opened 16 months ago

Closed 16 months ago

#15515 closed defect (can't reproduce)

Crash adding hydrogens for Dock Prep

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Editing Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-6.5.0-41-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x0000771cf4224640 (most recent call first):
 File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 324 in wait
 File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 622 in wait
 File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1392 in run
 File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
 File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x0000771db2c5cb80 (most recent call first):
 File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/widgets/item_chooser.py", line 167 in 
 File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/widgets/item_chooser.py", line 167 in _items_change
 File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/widgets/item_chooser.py", line 89 in _sleep_check
 File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/widgets/item_chooser.py", line 133 in get_value
 File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/widgets/item_chooser.py", line 130 in value
 File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/addh/tool.py", line 213 in structures
 File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/addh/tool.py", line 195 in add_h
 File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
 File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
 File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in 
 File "", line 88 in _run_code
 File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler (total: 49)
===== Log before crash start =====
> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  


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

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  

UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/nano/Documents/saturation_mutations/VEGF_PRO_17.pdb

Chain information for VEGF_PRO_17.pdb #1  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_PRO_21.pdb

Chain information for VEGF_PRO_21.pdb #2  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_PRO_25.pdb

Chain information for VEGF_PRO_25.pdb #3  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_PRO_63.pdb

Chain information for VEGF_PRO_63.pdb #4  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_PRO_64.pdb

Chain information for VEGF_PRO_64.pdb #5  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_PRO_86.pdb

Chain information for VEGF_PRO_86.pdb #6  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_SER_17.pdb

Chain information for VEGF_SER_17.pdb #7  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_SER_21.pdb

Chain information for VEGF_SER_21.pdb #8  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_SER_25.pdb

Chain information for VEGF_SER_25.pdb #9  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_SER_63.pdb

Chain information for VEGF_SER_63.pdb #10  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_SER_64.pdb

Chain information for VEGF_SER_64.pdb #11  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_SER_86.pdb

Chain information for VEGF_SER_86.pdb #12  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_THR_17.pdb

Chain information for VEGF_THR_17.pdb #13  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_THR_21.pdb

Chain information for VEGF_THR_21.pdb #14  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_THR_25.pdb

Chain information for VEGF_THR_25.pdb #15  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_THR_63.pdb

Chain information for VEGF_THR_63.pdb #16  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_THR_64.pdb

Chain information for VEGF_THR_64.pdb #17  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_THR_86.pdb

Chain information for VEGF_THR_86.pdb #18  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_TRP_17.pdb

Chain information for VEGF_TRP_17.pdb #19  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_TRP_21.pdb

Chain information for VEGF_TRP_21.pdb #20  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_TRP_25.pdb

Chain information for VEGF_TRP_25.pdb #21  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_TRP_63.pdb

Chain information for VEGF_TRP_63.pdb #22  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_TRP_64.pdb

Chain information for VEGF_TRP_64.pdb #23  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_TRP_86.pdb

Chain information for VEGF_TRP_86.pdb #24  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_TYR_17.pdb

Chain information for VEGF_TYR_17.pdb #25  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_TYR_21.pdb

Chain information for VEGF_TYR_21.pdb #26  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_TYR_25.pdb

Chain information for VEGF_TYR_25.pdb #27  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_TYR_63.pdb

Chain information for VEGF_TYR_63.pdb #28  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_TYR_64.pdb

Chain information for VEGF_TYR_64.pdb #29  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_TYR_86.pdb

Chain information for VEGF_TYR_86.pdb #30  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_VAL_17.pdb

Chain information for VEGF_VAL_17.pdb #31  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_VAL_21.pdb

Chain information for VEGF_VAL_21.pdb #32  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_VAL_25.pdb

Chain information for VEGF_VAL_25.pdb #33  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_VAL_63.pdb

Chain information for VEGF_VAL_63.pdb #34  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_VAL_64.pdb

Chain information for VEGF_VAL_64.pdb #35  
---  
Chain | Description  
A | No description available  


> open /home/nano/Documents/saturation_mutations/VEGF_VAL_86.pdb

Chain information for VEGF_VAL_86.pdb #36  
---  
Chain | Description  
A | No description available  





OpenGL version: 4.6 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2
OpenGL renderer: Mesa Intel(R) HD Graphics 4400 (HSW GT2)
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: LENOVO
Model: 20AMS2LK0C
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 4 Intel(R) Core(TM) i5-4300U CPU @ 1.90GHz
Cache Size: 3072 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           7.6Gi       2.7Gi       1.0Gi       493Mi       3.9Gi       4.1Gi
	Swap:          2.0Gi          0B       2.0Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation Haswell-ULT Integrated Graphics Controller [8086:0a16] (rev 0b)	
	Subsystem: Lenovo ThinkPad X240 [17aa:2214]	
	Kernel driver in use: i915

Installed Packages:
   alabaster: 0.7.16
   appdirs: 1.4.4
   asttokens: 2.4.1
   Babel: 2.15.0
   beautifulsoup4: 4.12.3
   blockdiag: 3.0.0
   blosc2: 2.0.0
   build: 1.2.1
   certifi: 2024.6.2
   cftime: 1.6.4
   charset-normalizer: 3.3.2
   ChimeraX-AddCharge: 1.5.17
   ChimeraX-AddH: 2.2.6
   ChimeraX-AlignmentAlgorithms: 2.0.2
   ChimeraX-AlignmentHdrs: 3.5
   ChimeraX-AlignmentMatrices: 2.1
   ChimeraX-Alignments: 2.12.7
   ChimeraX-AlphaFold: 1.0
   ChimeraX-AltlocExplorer: 1.1.1
   ChimeraX-AmberInfo: 1.0
   ChimeraX-Arrays: 1.1
   ChimeraX-Atomic: 1.57.1
   ChimeraX-AtomicLibrary: 14.0.6
   ChimeraX-AtomSearch: 2.0.1
   ChimeraX-AxesPlanes: 2.4
   ChimeraX-BasicActions: 1.1.2
   ChimeraX-BILD: 1.0
   ChimeraX-BlastProtein: 2.4.6
   ChimeraX-BondRot: 2.0.4
   ChimeraX-BugReporter: 1.0.1
   ChimeraX-BuildStructure: 2.12.1
   ChimeraX-Bumps: 1.0
   ChimeraX-BundleBuilder: 1.2.7
   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: 2.2.4
   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: 1.8
   ChimeraX-CoreFormats: 1.2
   ChimeraX-coulombic: 1.4.3
   ChimeraX-Crosslinks: 1.0
   ChimeraX-Crystal: 1.0
   ChimeraX-CrystalContacts: 1.0.1
   ChimeraX-DataFormats: 1.2.3
   ChimeraX-Dicom: 1.2.4
   ChimeraX-DiffPlot: 1.0
   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: 1.1.1
   ChimeraX-Hbonds: 2.4
   ChimeraX-Help: 1.2.2
   ChimeraX-HKCage: 1.3
   ChimeraX-IHM: 1.1
   ChimeraX-ImageFormats: 1.2
   ChimeraX-IMOD: 1.0
   ChimeraX-IO: 1.0.1
   ChimeraX-ItemsInspection: 1.0.1
   ChimeraX-IUPAC: 1.0
   ChimeraX-Label: 1.1.10
   ChimeraX-LinuxSupport: 1.0.1
   ChimeraX-ListInfo: 1.2.2
   ChimeraX-Log: 1.1.6
   ChimeraX-LookingGlass: 1.1
   ChimeraX-Maestro: 1.9.1
   ChimeraX-Map: 1.2
   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: 2.1.3
   ChimeraX-MCopy: 1.0
   ChimeraX-MDcrds: 2.7.1
   ChimeraX-MedicalToolbar: 1.0.3
   ChimeraX-Meeting: 1.0.1
   ChimeraX-MLP: 1.1.1
   ChimeraX-mmCIF: 2.14.1
   ChimeraX-MMTF: 2.2
   ChimeraX-Modeller: 1.5.17
   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-Neuron: 1.0
   ChimeraX-Nifti: 1.2
   ChimeraX-NMRSTAR: 1.0.2
   ChimeraX-NRRD: 1.2
   ChimeraX-Nucleotides: 2.0.3
   ChimeraX-OpenCommand: 1.13.5
   ChimeraX-PDB: 2.7.5
   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: 1.1.1
   ChimeraX-PubChem: 2.2
   ChimeraX-ReadPbonds: 1.0.1
   ChimeraX-Registration: 1.1.2
   ChimeraX-RemoteControl: 1.0
   ChimeraX-RenderByAttr: 1.4.1
   ChimeraX-RenumberResidues: 1.1
   ChimeraX-ResidueFit: 1.0.1
   ChimeraX-RestServer: 1.2
   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: 3.0.15
   ChimeraX-SelInspector: 1.0
   ChimeraX-SeqView: 2.11.2
   ChimeraX-Shape: 1.0.1
   ChimeraX-Shell: 1.0.1
   ChimeraX-Shortcuts: 1.1.1
   ChimeraX-ShowSequences: 1.0.3
   ChimeraX-SideView: 1.0.1
   ChimeraX-Smiles: 2.1.2
   ChimeraX-SmoothLines: 1.0
   ChimeraX-SpaceNavigator: 1.0
   ChimeraX-StdCommands: 1.16.5
   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: 1.1.2
   ChimeraX-ToolshedUtils: 1.2.4
   ChimeraX-Topography: 1.0
   ChimeraX-ToQuest: 1.0
   ChimeraX-Tug: 1.0.1
   ChimeraX-UI: 1.39.1
   ChimeraX-uniprot: 2.3
   ChimeraX-UnitCell: 1.0.1
   ChimeraX-ViewDockX: 1.4.3
   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: 1.2.1
   cxservices: 1.2.2
   cycler: 0.12.1
   Cython: 3.0.10
   debugpy: 1.8.1
   decorator: 5.1.1
   distro: 1.9.0
   docutils: 0.20.1
   executing: 2.0.1
   filelock: 3.13.4
   fonttools: 4.53.0
   funcparserlib: 2.0.0a0
   glfw: 2.7.0
   grako: 3.16.5
   h5py: 3.11.0
   html2text: 2024.2.26
   idna: 3.7
   ihm: 1.0
   imagecodecs: 2024.1.1
   imagesize: 1.4.1
   ipykernel: 6.29.2
   ipython: 8.21.0
   ipywidgets: 8.1.3
   jedi: 0.19.1
   jinja2: 3.1.4
   jupyter-client: 8.6.0
   jupyter-core: 5.7.2
   jupyterlab-widgets: 3.0.11
   kiwisolver: 1.4.5
   line-profiler: 4.1.2
   lxml: 5.2.1
   lz4: 4.3.3
   MarkupSafe: 2.1.5
   matplotlib: 3.8.4
   matplotlib-inline: 0.1.7
   msgpack: 1.0.8
   nest-asyncio: 1.6.0
   netCDF4: 1.6.5
   networkx: 3.3
   nibabel: 5.2.0
   nptyping: 2.5.0
   numexpr: 2.10.0
   numpy: 1.26.4
   openvr: 1.26.701
   packaging: 24.1
   ParmEd: 4.2.2
   parso: 0.8.4
   pep517: 0.13.1
   pexpect: 4.9.0
   pillow: 10.3.0
   pip: 24.0
   pkginfo: 1.10.0
   platformdirs: 4.2.2
   prompt-toolkit: 3.0.47
   psutil: 5.9.8
   ptyprocess: 0.7.0
   pure-eval: 0.2.2
   py-cpuinfo: 9.0.0
   pycollada: 0.8
   pydicom: 2.4.4
   pygments: 2.17.2
   pynmrstar: 3.3.4
   pynrrd: 1.0.0
   PyOpenGL: 3.1.7
   PyOpenGL-accelerate: 3.1.7
   pyopenxr: 1.0.3401
   pyparsing: 3.1.2
   pyproject-hooks: 1.1.0
   PyQt6-commercial: 6.6.1
   PyQt6-Qt6: 6.6.3
   PyQt6-sip: 13.6.0
   PyQt6-WebEngine-commercial: 6.6.0
   PyQt6-WebEngine-Qt6: 6.6.3
   python-dateutil: 2.9.0.post0
   pytz: 2024.1
   pyzmq: 26.0.3
   qtconsole: 5.5.1
   QtPy: 2.4.1
   RandomWords: 0.4.0
   requests: 2.31.0
   scipy: 1.13.0
   setuptools: 69.5.1
   sfftk-rw: 0.8.1
   six: 1.16.0
   snowballstemmer: 2.2.0
   sortedcontainers: 2.4.0
   soupsieve: 2.5
   sphinx: 7.2.6
   sphinx-autodoc-typehints: 2.0.1
   sphinxcontrib-applehelp: 1.0.8
   sphinxcontrib-blockdiag: 3.0.0
   sphinxcontrib-devhelp: 1.0.6
   sphinxcontrib-htmlhelp: 2.0.5
   sphinxcontrib-jsmath: 1.0.1
   sphinxcontrib-qthelp: 1.0.7
   sphinxcontrib-serializinghtml: 1.1.10
   stack-data: 0.6.3
   superqt: 0.6.3
   tables: 3.8.0
   tcia-utils: 1.5.1
   tifffile: 2024.1.30
   tinyarray: 1.2.4
   tornado: 6.4.1
   traitlets: 5.14.2
   typing-extensions: 4.12.2
   tzdata: 2024.1
   urllib3: 2.2.1
   wcwidth: 0.2.13
   webcolors: 1.13
   wheel: 0.43.0
   wheel-filename: 1.4.1
   widgetsnbextension: 4.0.11

Change History (2)

comment:1 by Eric Pettersen, 16 months ago

Component: Unassigned → Structure Editing
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash adding hydrogens for Dock Prep

comment:2 by Eric Pettersen, 16 months ago

Resolution: → can't reproduce
Status: accepted → closed

The log doesn't show anything being opened before Dock Prep, yet Dock Prep doesn't do anything if nothing's open -- so I'm mystified.

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