Opened 11 months ago

Closed 11 months ago

#16415 closed defect (duplicate)

Crash in garbage collection

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

Description 

The following bug report has been submitted:
Platform:        Linux-5.15.0-125-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
Last time you used ChimeraX it crashed.
Saving a large structure as mmcif from coot
Fatal Python error: Segmentation fault

Current thread 0x00007f9bb1e6b740 (most recent call first):
  Garbage-collecting
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in __iter__
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/mmcif/__init__.py", line 123 in save
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 101 in provider_save
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 86 in cmd_save
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 62 in display
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 138 in show_save_file_dialog
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 127 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, chimerax.pdb_lib._load_libs, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, openmm._openmm, openmm.app.internal.compiled, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.mmcif.mmcif_write (total: 54)
===== Log before crash start =====
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/alphafold/Downloads/cryosparc_P28_J1059_003_volume_map.mrc

Opened cryosparc_P28_J1059_003_volume_map.mrc as #1, grid size 400,400,400,
pixel 1.06, shown at level 0.0794, step 2, values float32  

> volume #1 step 1

> open
> /home/net/shared/scripts/processing_server/uploads/processing//wss205/241204_1226_job30_cryosparc_P28_J1059_003_volume_map_emready/job30_cryosparc_P28_J1059_003_volume_map_emready.mrc

Opened job30_cryosparc_P28_J1059_003_volume_map_emready.mrc as #2, grid size
400,400,400, pixel 1.06, shown at level 4.64, step 2, values float32  

> volume #2 step 1

> volume #1 level 0.06737

> save
> /home/alphafold/Downloads/cryosparc_P28_J1059_003_volume_map_emready.mrc
> models #2

> open /home/alphafold/Cryo-
> Em/Ribosome/coxiella/cryo/modelling/final_models/merge/merge_70S_protein_combine_50SDXT_fit50S_coot.cif

Summary of feedback from opening /home/alphafold/Cryo-
Em/Ribosome/coxiella/cryo/modelling/final_models/merge/merge_70S_protein_combine_50SDXT_fit50S_coot.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 19  
Unknown polymer entity '1' near line 110  
Unknown polymer entity '2' near line 1987  
Unknown polymer entity '3' near line 94555  
Unknown polymer entity '4' near line 95208  
Unknown polymer entity '5' near line 98205  
47 messages similar to the above omitted  
Unable to fetch template for 'ALAA': will connect using distance criteria  
Unable to fetch template for 'THRA': will connect using distance criteria  
Unable to fetch template for 'TYRA': will connect using distance criteria  
Unable to fetch template for 'META': will connect using distance criteria  
Unable to fetch template for 'ASNA': will connect using distance criteria  
27 messages similar to the above omitted  
Atom H is not in the residue template for GLN /A:7  
Atom H is not in the residue template for LYS /AD:3  
Atom H1 is not in the residue template for THR /AH:102  
Atom H1 is not in the residue template for ASP /AJ:82  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for merge_70S_protein_combine_50SDXT_fit50S_coot.cif #3  
---  
Chain | Description  
0 | No description available  
23 | No description available  
3 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
8 | No description available  
9 | No description available  
A | No description available  
AB | No description available  
AD | No description available  
AE | No description available  
AF | No description available  
AG | No description available  
AH | No description available  
AI | No description available  
AJ | No description available  
AK | No description available  
AL | No description available  
AM | No description available  
AN | No description available  
AO | No description available  
AP | No description available  
AQ | No description available  
AR | No description available  
AS | No description available  
AU | No description available  
AV | No description available  
AW | No description available  
AY | No description available  
F | No description available  
I | No description available  
L | No description available  
O | No description available  
P | No description available  
R | No description available  
U | No description available  
Y | No description available  
a | No description available  
c | No description available  
e | No description available  
h | No description available  
j | No description available  
l | No description available  
n | No description available  
p | No description available  
r | No description available  
t | No description available  
v | No description available  
y | No description available  
z | No description available  
  

> fitmap #3 inMap #2

Fit molecule merge_70S_protein_combine_50SDXT_fit50S_coot.cif (#3) to map
job30_cryosparc_P28_J1059_003_volume_map_emready.mrc (#2) using 238583 atoms  
average map value = 5.889, steps = 188  
shifted from previous position = 25.9  
rotated from previous position = 0.332 degrees  
atoms outside contour = 109431, contour level = 4.6369  
  
Position of merge_70S_protein_combine_50SDXT_fit50S_coot.cif (#3) relative to
job30_cryosparc_P28_J1059_003_volume_map_emready.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999182 0.00089218 0.00394580 17.22409547  
-0.00090849 0.99999104 0.00413496 -18.02625839  
-0.00394207 -0.00413851 0.99998367 -4.60534874  
Axis -0.71495553 0.68163445 -0.15560549  
Axis point 0.00000000 -2012.52171132 417.72459477  
Rotation angle (degrees) 0.33151510  
Shift along axis -23.88516347  
  

> save /home/alphafold/Cryo-
> Em/Ribosome/coxiella/cryo/modelling/final_models/merge/merge_70S_protein_combine_50SDXT_fit50S_coot_fit_J1059.cif
> relModel #3

Not saving entity_poly_seq for non-authoritative sequences  

> hide #!3 models

> open /home/alphafold/Cryo-
> Em/Ribosome/coxiella/cryo/modelling/final_models/merge/merge_70S_protein_combine_50SDXT_fit50S_coot_fit_J1059.cif

Summary of feedback from opening /home/alphafold/Cryo-
Em/Ribosome/coxiella/cryo/modelling/final_models/merge/merge_70S_protein_combine_50SDXT_fit50S_coot_fit_J1059.cif  
---  
warnings | Unknown polymer entity '1' near line 439  
Unknown polymer entity '2' near line 2316  
Unknown polymer entity '3' near line 94884  
Unknown polymer entity '4' near line 95537  
Unknown polymer entity '5' near line 98534  
46 messages similar to the above omitted  
Invalid residue range for struct_conf "HELX221": invalid entity "76", near
line 477844  
Invalid residue range for struct_conf "HELX222": invalid entity "76", near
line 477845  
Invalid residue range for struct_conf "HELX223": invalid entity "77", near
line 477846  
Invalid residue range for struct_conf "HELX224": invalid entity "78", near
line 477847  
Invalid residue range for struct_conf "HELX225": invalid entity "78", near
line 477848  
1 messages similar to the above omitted  
Atom H is not in the residue template for GLN /A:7  
Atom H is not in the residue template for LYS /AD:3  
Atom H1 is not in the residue template for THR /AH:102  
Atom H1 is not in the residue template for ASP /AJ:82  
Unable to fetch template for 'ALAA': will connect using distance criteria  
Unable to fetch template for 'PROP': will connect using distance criteria  
Unable to fetch template for 'A5': will connect using distance criteria  
Unable to fetch template for 'DXT2': will connect using distance criteria  
Unable to fetch template for 'THRA': will connect using distance criteria  
26 messages similar to the above omitted  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for
merge_70S_protein_combine_50SDXT_fit50S_coot_fit_J1059.cif #4  
---  
Chain | Description  
0 | No description available  
23 | No description available  
3 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
8 | No description available  
9 | No description available  
A | No description available  
AB | No description available  
AD | No description available  
AE | No description available  
AF | No description available  
AG | No description available  
AH | No description available  
AI | No description available  
AJ | No description available  
AK | No description available  
AL | No description available  
AM | No description available  
AN | No description available  
AO | No description available  
AP | No description available  
AQ | No description available  
AR | No description available  
AS | No description available  
AU | No description available  
AV | No description available  
AW | No description available  
AY | No description available  
F | No description available  
I | No description available  
L | No description available  
O | No description available  
P | No description available  
R | No description available  
U | No description available  
Y | No description available  
a | No description available  
c | No description available  
e | No description available  
h | No description available  
j | No description available  
l | No description available  
n | No description available  
p | No description available  
r | No description available  
t | No description available  
v | No description available  
y | No description available  
z | No description available  
  

> fitmap #4 inMap #1

Fit molecule merge_70S_protein_combine_50SDXT_fit50S_coot_fit_J1059.cif (#4)
to map cryosparc_P28_J1059_003_volume_map.mrc (#1) using 238583 atoms  
average map value = 0.08351, steps = 216  
shifted from previous position = 25.9  
rotated from previous position = 0.336 degrees  
atoms outside contour = 86262, contour level = 0.067366  
  
Position of merge_70S_protein_combine_50SDXT_fit50S_coot_fit_J1059.cif (#4)
relative to cryosparc_P28_J1059_003_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999120 0.00077338 0.00412434 17.21743457  
-0.00079027 0.99999130 0.00409549 -18.03941434  
-0.00412114 -0.00409872 0.99998311 -4.58612127  
Axis -0.69860648 0.70297746 -0.13331048  
Axis point -1891.95877142 0.00000000 -96.73754064  
Rotation angle (degrees) 0.33602340  
Shift along axis -24.09813492  
  

> save /home/alphafold/Cryo-
> Em/Ribosome/coxiella/cryo/modelling/final_models/merge/merge_70S_protein_combine_50SDXT_fit50S_coot_fit_J1059.cif
> models #4

Not saving entity_poly_seq for non-authoritative sequences  

> close

> open /home/alphafold/Downloads/cryosparc_P28_J1058_005_volume_map_sharp.mrc

Opened cryosparc_P28_J1058_005_volume_map_sharp.mrc as #1, grid size
480,480,480, pixel 0.645, shown at level 0.107, step 2, values float32  

> open /home/alphafold/Cryo-
> Em/Ribosome/Ecoli/cryo/eBIC/models/7k00_fit_1058.cif

Summary of feedback from opening /home/alphafold/Cryo-
Em/Ribosome/Ecoli/cryo/eBIC/models/7k00_fit_1058.cif  
---  
warning | Skipping chem_comp category: Missing column 'type' near line 4142  
  
mmCIF parsing error: string outside of data block near line 4143  

> open /home/alphafold/Cryo-
> Em/Ribosome/Ecoli/cryo/eBIC/models/7k00_fit_1058.cif

Summary of feedback from opening /home/alphafold/Cryo-
Em/Ribosome/Ecoli/cryo/eBIC/models/7k00_fit_1058.cif  
---  
warning | Skipping chem_comp category: Missing column 'type' near line 4142  
  
mmCIF parsing error: string outside of data block near line 4143  

> open /home/alphafold/Cryo-
> Em/Ribosome/Ecoli/cryo/eBIC/models/7k00_fit_1058.pdb

Chain information for 7k00_fit_1058.pdb #2  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> view

> select /a:6060@MG

1 atom, 1 residue, 1 model selected  

> delete sel

> view

> hide #!2 models

> volume #1 step 1

> volume #1 level 0.06413

> show #!2 models

> select add #2

143421 atoms, 150201 bonds, 15102 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> select ::name="SPM"

14 atoms, 13 bonds, 1 residue, 1 model selected  

> hide #!1 models

> show sel atoms

> volume #1 color #4063bf68

> select /a:6223@N10

1 atom, 1 residue, 1 model selected  

> view sel

> select add #2

143421 atoms, 150201 bonds, 15102 residues, 1 model selected  

> show sel atoms

> select ::name="SPM"

14 atoms, 13 bonds, 1 residue, 1 model selected  

> delete sel

> select ::name="SPD"

150 atoms, 135 bonds, 15 residues, 1 model selected  

> delete sel

> ui tool show "Side View"

> save /home/alphafold/Cryo-
> Em/Ribosome/Ecoli/cryo/eBIC/models/7k00_fit_1058.cif relModel #2

Not saving entity_poly_seq for non-authoritative sequences  


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

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 535.183.01
OpenGL renderer: NVIDIA RTX A5000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_GB.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: To Be Filled By O.E.M.
Model: To Be Filled By O.E.M.
OS: Ubuntu 20.04 Focal Fossa
Architecture: 64bit ELF
Virtual Machine: none
CPU: 48 AMD Ryzen Threadripper 3960X 24-Core Processor
Cache Size: 512 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:          125Gi        67Gi       3.1Gi       393Mi        55Gi        56Gi
	Swap:          15Gi       3.8Gi        11Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:2231] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:147e]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    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: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    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: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.22.3
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7
    ChimeraX-CoreFormats: 1.2
    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: 1.1.3
    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-ISOLDE: 1.7
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    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: 1.1.4
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.13
    ChimeraX-ModelPanel: 1.4
    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: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.3
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PhenixUI: 1.2.2
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    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-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.3
    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: 2.2.2
    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: 1.33.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.0
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.0
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.5.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    Pillow: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    pprintpp: 0.4.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (2)

comment:1 by Eric Pettersen, 11 months ago

Component: Unassigned → Core
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in garbage collection

comment:2 by Eric Pettersen, 11 months ago

Resolution: → duplicate
Status: accepted → closed
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