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Opened 15 months ago
Closed 15 months ago
#15666 closed defect (fixed)
Deleting chain B of 3h7s leads to a crash
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Greg Couch | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.9.dev202407240247 (2024-07-24 02:47:28 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
The following sequence causes a crash. The PDB 3h7s has something weird about it as evidenced by two chain Bs listed in the log when it is opened.
open 3h7s
delete /B
# In Python shell
m = session.models[0]
m.chains[1].existing_residues.ribbon_displays = True
Fatal Python error: Segmentation fault
Thread 0x000000035de13000 (most recent call first):
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 561 in select
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/asyncio/base_events.py", line 1884 in _run_once
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/asyncio/base_events.py", line 607 in run_forever
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tornado/platform/asyncio.py", line 205 in start
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ipykernel/iostream.py", line 92 in _thread_main
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000035ce07000 (most recent call first):
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 320 in wait
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/IPython/core/history.py", line 903 in run
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/IPython/core/history.py", line 61 in only_when_enabled
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/decorator.py", line 232 in fun
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001fa614c00 (most recent call first):
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 234 in set_prop
File "/var/folders/jb/f14hkn9s19l691b68w_lvm0w0000gn/T/ipykernel_75239/3694637564.py", line 1 in
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/IPython/core/interactiveshell.py", line 3577 in run_code
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/IPython/core/interactiveshell.py", line 3517 in run_ast_nodes
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/IPython/core/interactiveshell.py", line 3334 in run_cell_async
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/IPython/core/async_helpers.py", line 128 in _pseudo_sync_runner
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/IPython/core/interactiveshell.py", line 3130 in _run_cell
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/IPython/core/interactiveshell.py", line 3075 in run_cell
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ipykernel/zmqshell.py", line 549 in run_cell
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ipykernel/ipkernel.py", line 449 in do_execute
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ipykernel/kernelbase.py", line 778 in execute_request
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ipykernel/ipkernel.py", line 362 in execute_request
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ipykernel/inprocess/ipkernel.py", line 81 in execute_request
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ipykernel/kernelbase.py", line 437 in dispatch_shell
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/asyncio/events.py", line 80 in _run
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/asyncio/base_events.py", line 1922 in _run_once
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/asyncio/base_events.py", line 607 in run_forever
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/asyncio/base_events.py", line 640 in run_until_complete
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/jupyter_core/utils/__init__.py", line 165 in wrapped
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ipykernel/inprocess/client.py", line 195 in _dispatch_to_kernel
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ipykernel/inprocess/client.py", line 119 in execute
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/qtconsole/frontend_widget.py", line 288 in _execute
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/qtconsole/console_widget.py", line 680 in do_execute
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/qtconsole/history_console_widget.py", line 42 in do_execute
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/qtconsole/console_widget.py", line 605 in _trigger_is_complete_callback
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/qtconsole/console_widget.py", line 600 in _handle_is_complete_reply
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/qtconsole/base_frontend_mixin.py", line 138 in _dispatch
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/qtconsole/inprocess.py", line 46 in call_handlers
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/qtconsole/inprocess.py", line 42 in
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 329 in event_loop
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1037 in init
File "/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1200 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, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, lxml._elementpath, lxml.etree, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, zmq.backend.cython._zmq, tornado.speedups, psutil._psutil_osx, psutil._psutil_posix, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, PyQt6.QtSvg (total: 61)
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===== Log before crash start =====
UCSF ChimeraX version: 1.9.dev202407240247 (2024-07-24)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 3h7s
Summary of feedback from opening 3h7s fetched from pdb
---
warnings | Ignoring microheterogeneity for label_seq_id 63 in chain A
Ignoring microheterogeneity for label_seq_id 63 in chain B
3h7s title:
Crystal structures of K63-linked di- and tri-ubiquitin reveal a highly
extended chain architecture [more info...]
Chain information for 3h7s #1
---
Chain | Description | UniProt
A B | Ubiquitin | UBIQ_HUMAN 1-76
B | Ubiquitin | UBIQ_HUMAN 1-76
Non-standard residues in 3h7s #1
---
ZN — zinc ion
3h7s mmCIF Assemblies
---
1| author_defined_assembly
2| software_defined_assembly
3| software_defined_assembly
19 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show Shell
> delete /B
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.9.dev202407240247 (2024-07-24)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.0, Qt 6.7.1
Qt runtime version: 6.7.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac Studio
Model Identifier: Mac14,14
Model Number: Z1800003VLL/A
Chip: Apple M2 Ultra
Total Number of Cores: 24 (16 performance and 8 efficiency)
Memory: 64 GB
System Firmware Version: 10151.121.1
OS Loader Version: 10151.121.1
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 36 days, 19 hours, 13 minutes
Graphics/Displays:
Apple M2 Ultra:
Chipset Model: Apple M2 Ultra
Type: GPU
Bus: Built-In
Total Number of Cores: 60
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
PHL 278B1:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
biopython: 1.83
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
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: 2.14
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.3
ChimeraX-AtomicLibrary: 14.1.1
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: 2.13
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-Clipper: 0.23.0
ChimeraX-clix: 0.1.4
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: 1.9.dev202407240247
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-DeepMutationalScan: 1.0
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-Foldseek: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.3
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.3
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-ListInfo: 1.2.2
ChimeraX-Log: 1.1.7
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-maskChains: 1.1
ChimeraX-MatchMaker: 2.1.5
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-NIHPresets: 1.1.19
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
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: 1.4.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3
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: 3.1.5
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.13
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.3
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: 1.18
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: 1.39.8
ChimeraX-uniprot: 2.3.1
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: 1.8.2
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.1
fsspec: 2024.3.1
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: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.3
jedi: 0.19.1
Jinja2: 3.1.4
joblib: 1.4.2
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
llvmlite: 0.42.0
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
mpmath: 1.3.0
mrcfile: 1.5.0
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numba: 0.59.1
numexpr: 2.10.1
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.1.2
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt_toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.17.2
pynmrstar: 3.3.4
pynndescent: 0.5.12
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: 6.7.0
PyQt6-Qt6: 6.7.2
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.2
PyQt6-WebEngineSubwheel-Qt6: 6.7.2
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.2
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.32.3
scikit-learn: 1.4.2
scipy: 1.13.0
setuptools: 70.3.0
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
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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: 2.0.6
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.8
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
sympy: 1.12
tables: 3.8.0
tcia_utils: 1.5.1
threadpoolctl: 3.5.0
tifffile: 2024.1.30
tinyarray: 1.2.4
torch: 2.3.0
tornado: 6.4.1
tqdm: 4.66.4
traitlets: 5.14.2
typing_extensions: 4.12.2
tzdata: 2024.1
umap-learn: 0.5.6
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wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (9)
comment:1 by , 15 months ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Deleting chain B of 3h7s leads to a crash |
comment:2 by , 15 months ago
| Status: | assigned → accepted |
|---|
comment:4 by , 15 months ago
| Cc: | added; removed |
|---|---|
| Owner: | changed from to |
| Status: | accepted → assigned |
When opened, the mmCIF version of 3h7s has two copies of chain B.
comment:6 by , 15 months ago
The mmCIF reader does not explicitly create any chains -- there are no calls to structure->new_chain(). set_input_seq() is only called twice after the inter-residue bonds are created for that sequence. At the end of that process, I expect that structure->chains_made() will return false. But it first returns true after connecting the 60th residue pair of the second sequence. Still digging....
comment:7 by , 15 months ago
| Cc: | added; removed |
|---|---|
| Owner: | changed from to |
| Status: | accepted → assigned |
The extra chain is being made when the microheterogeneous residue is deleted from the set of residues that were read in: structure->delete_residue(r) when structure->chains_made() is False. Not sure why it doesn't happen the first time, but it does explain why it is chain B.
comment:8 by , 15 months ago
The following patch appears to fix the bug, but I don't know if it is the right fix:
--- a/src/bundles/atomic_lib/atomic_cpp/atomstruct_cpp/Structure.cpp
+++ b/src/bundles/atomic_lib/atomic_cpp/atomstruct_cpp/Structure.cpp
@@ -922,7 +922,7 @@ Structure::_delete_atoms(const std::set<Atom*>& atoms, bool verify)
}
}
if (res_removals.size() > 0) {
- if (_chains != nullptr) {
+ if (chains_made() && _chains != nullptr) {
std::map<Chain*, std::set<Residue*>> chain_res_removals;
for (auto r: res_removals)
if (r->chain() != nullptr) {
comment:9 by , 15 months ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Fixed. Fix: https://github.com/RBVI/ChimeraX/commit/2aadd4b85b1492407f314215517f5a4916082991
Greg's suggested fix was correct, but since chains_made() being true guarantees that _chains is not null, the '&&' part of the test was unneeded.
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This is a simplified version of a crash in my Foldseek tool opening hit 3h7s, ticket #15665.