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#17861 closed defect (can't reproduce)

Crash saving atomic session state

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

Description

The following bug report has been submitted:
Platform:        Linux-6.8.0-57-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x000073c573b02b80 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2000 in save_state
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 219 in take_snapshot
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 1417 in take_snapshot
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/session.py", line 296 in process
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/session.py", line 273 in discovery
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/session.py", line 636 in save
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/session.py", line 912 in save
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 95 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, 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, chimerax.surface._surface, chimerax.pdb_lib._load_libs, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, chimerax.connect_structure._cs, PIL._imagingmath, chimerax.atom_search.ast, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, lxml._elementpath, lxml.etree (total: 61)
===== Log before crash start =====
Startup Messages  
---  
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr
bundle with that from OME-Zarr bundle  
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /nfs-data/protein/regan/1.ssDNA_GNP/4.AuNP_DNA_CytC/1.seq2/sys_ed2.gro

Chain information for Gromacs Runs One Microsecond At Cannonball Speeds #1  
---  
Chain | Description  
? | No description available  
? | No description available  
  

> select :DA /3

9072 atoms, 9892 bonds, 288 residues, 1 model selected  

> select :DA & :3

2304 atoms, 2448 bonds, 72 residues, 1 model selected  

> swapna

Missing or invalid "residues" argument: empty atom specifier  

> swapna sel :DC

No connectivity template for residue ':DC'  

> swapna sel :C

No connectivity template for residue ':C'  

> swapna sel, C

Missing or invalid "residues" argument: only initial part "sel" of atom
specifier valid  

> swapna (:DC & :3)

Missing or invalid "resType" argument: Expected a text string  

> swapna (:DC & :3), C

Missing or invalid "residues" argument: invalid atom specifier  

> swapna (:DC & :3), DC

Missing or invalid "residues" argument: invalid atom specifier  

> swapna sel C

> select :DT & :5

2304 atoms, 2376 bonds, 72 residues, 1 model selected  

> swapna sel A

> select :DT & :8

2304 atoms, 2376 bonds, 72 residues, 1 model selected  

> swapna sel A

> select :DT & :10

2304 atoms, 2376 bonds, 72 residues, 1 model selected  

> swapna sel A

> nucleotides sel atoms

> style nucleic & sel stick

Changed 792 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 792 atom styles  

> select all

28612 atoms, 56575 bonds, 144 pseudobonds, 7244 residues, 2 models selected  

> nucleotides sel tube/slab shape muffler

> nucleotides sel atoms

> style nucleic & sel stick

Changed 20592 atom styles  

> save /nfs-
> data/protein/regan/1.ssDNA_GNP/4.AuNP_DNA_CytC/9.seq10/DNA_AuNP_CytC.pdb
> relModel #1

> close session

> open /nfs-
> data/protein/regan/1.ssDNA_GNP/4.AuNP_DNA_CytC/1.seq2/DualCoat_CytC_init.pdb

Summary of feedback from opening /nfs-
data/protein/regan/1.ssDNA_GNP/4.AuNP_DNA_CytC/1.seq2/DualCoat_CytC_init.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK THIS IS A SIMULATION BOX  
  
Duplicate atom serial number found: 9  
Duplicate atom serial number found: 10  
Duplicate atom serial number found: 11  
Duplicate atom serial number found: 12  
Duplicate atom serial number found: 13  
816 messages similar to the above omitted  
PDB SEQRES record for chain A is incomplete. Ignoring input sequence records
as basis for sequence.  
PDB SEQRES record for chain A is incomplete. Ignoring input sequence records
as basis for sequence.  
PDB SEQRES record for chain C is incomplete. Ignoring input sequence records
as basis for sequence.  
PDB SEQRES record for chain D is incomplete. Ignoring input sequence records
as basis for sequence.  
PDB SEQRES record for chain E is incomplete. Ignoring input sequence records
as basis for sequence.  
7 messages similar to the above omitted  
  
DualCoat_CytC_init.pdb title:  
Gromacs Runs One Microsecond At Cannonball Speeds [more info...]  
  
Chain information for DualCoat_CytC_init.pdb #1  
---  
Chain | Description  
0 1 2 3 4 5 6 7 8 9 B M N O P Q R S T U V W X Y Z a b c d e f g h i j k l n o
p q r s t u v w x y z | No description available  
A | No description available  
A C D E F G H I J K L | No description available  
  
Non-standard residues in DualCoat_CytC_init.pdb #1  
---  
AUS — (AUS)  
IAUM — (iaum)  
L3P — (L3P)  
  

> select protein

823 atoms, 839 bonds, 104 residues, 1 model selected  

> delete sel

> select :DA & :3

2304 atoms, 2448 bonds, 72 residues, 1 model selected  

> swapna sel C

> select :DT &:5

2304 atoms, 2376 bonds, 72 residues, 1 model selected  

> swapna sel A

> select :DT & :8

2304 atoms, 2376 bonds, 72 residues, 1 model selected  

> swapna sel A

> select :DT & :10

2304 atoms, 2376 bonds, 72 residues, 1 model selected  

> swapna sel A

> save /nfs-
> data/protein/regan/1.ssDNA_GNP/4.AuNP_DNA_CytC/9.seq10/DualCoat_AuNP.pdb
> relModel #1

> select :IAUM or :AUS

Expected a keyword  

> select :IAUM or :AU

Expected a keyword  

> select :IAUM

6276 atoms, 20255 pseudobonds, 6276 residues, 2 models selected  

> select :IAUM | :AUS

6348 atoms, 20516 pseudobonds, 6348 residues, 2 models selected  

> ui tool show "Build Structure"

> bond sel

Created 32850 bonds  

> bond sel

Created 0 bonds  

> save /nfs-
> data/protein/regan/1.ssDNA_GNP/4.AuNP_DNA_CytC/9.seq10/DualCoat_AuNP_goldbonds.pdb
> relModel #1

> close session

> open /nfs-data/protein/regan/1.ssDNA_GNP/4.AuNP_DNA_CytC/5.seq1/sys_ed2.gro

Chain information for Green Red Orange Magenta Azure Cyan Skyblue #1  
---  
Chain | Description  
? | No description available  
? | No description available  
  

> select :DG & :4

2376 atoms, 2520 bonds, 72 residues, 1 model selected  

> swapna sel A

> select :DC & :6

2160 atoms, 2232 bonds, 72 residues, 1 model selected  

> swapna sel T

> select :DC & :8

2160 atoms, 2232 bonds, 72 residues, 1 model selected  

> swapna sel A

> select :DA & :9

2304 atoms, 2448 bonds, 72 residues, 1 model selected  

> swapna sel T

> select :DT &:10

2304 atoms, 2376 bonds, 72 residues, 1 model selected  

> swapna sel A

> select :DA &:11

2304 atoms, 2448 bonds, 72 residues, 1 model selected  

> swapna sel C

> select :DT & :13

2304 atoms, 2376 bonds, 72 residues, 1 model selected  

> swapna sel C

> select :15 &DA

Expected a keyword  

> select :15 & :DA

2304 atoms, 2448 bonds, 72 residues, 1 model selected  

> swapna sel G

> save /nfs-
> data/protein/regan/1.ssDNA_GNP/4.AuNP_DNA_CytC/7.seq5/DNA_AuNP_CytC.pdb
> relModel #1

> close session

> open /nfs-
> data/protein/regan/1.ssDNA_GNP/4.AuNP_DNA_CytC/5.seq1/S1_AuNP_CytC_ed3.pdb

Summary of feedback from opening /nfs-
data/protein/regan/1.ssDNA_GNP/4.AuNP_DNA_CytC/5.seq1/S1_AuNP_CytC_ed3.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
1665 messages similar to the above omitted  
Ignored bad PDB record found on line 91687  
  
  
Cannot find LINK/SSBOND residue IAU (881 )  
Cannot find LINK/SSBOND residue IAU (1212 )  
Cannot find LINK/SSBOND residue IAU (1232 )  
Cannot find LINK/SSBOND residue IAU (1272 )  
Cannot find LINK/SSBOND residue IAU (16 )  
32460 messages similar to the above omitted  
  
Chain information for S1_AuNP_CytC_ed3.pdb #1  
---  
Chain | Description  
? | No description available  
0 1 2 3 4 5 6 7 8 9 K L M N O P Q R S T U V W X Y Z a b c d e f g h i j k l m
n o p q r s t u v w x y z | No description available  
A B C D E F G H I J | No description available  
  

> select protein

1672 atoms, 1688 bonds, 104 residues, 1 model selected  

> delete sel

> select :DG & :4

2376 atoms, 2520 bonds, 72 residues, 1 model selected  

> swapna sel A

> select :DC & :6

2160 atoms, 2232 bonds, 72 residues, 1 model selected  

> swapna sel T

> select :DC & :8

2160 atoms, 2232 bonds, 72 residues, 1 model selected  

> swapna sel A

> select :DA & :9

2304 atoms, 2448 bonds, 72 residues, 1 model selected  

> swapna sel T

> select :DT &:10

2304 atoms, 2376 bonds, 72 residues, 1 model selected  

> swapna sel A

> select :DA &:11

2304 atoms, 2448 bonds, 72 residues, 1 model selected  

> swapna sel C

> select :DT & :13

2304 atoms, 2376 bonds, 72 residues, 1 model selected  

> swapna sel C

> select :15 & :DA

2304 atoms, 2448 bonds, 72 residues, 1 model selected  

> swapna sel G

> save /nfs-
> data/protein/regan/1.ssDNA_GNP/4.AuNP_DNA_CytC/7.seq5/DualCoat_AuNP.pdb
> relModel #1

> close session

> open /nfs-
> data/protein/regan/1.ssDNA_GNP/4.AuNP_DNA_CytC/8.seq6/s6_ss_mod4.pdb

Chain information for s6_ss_mod4.pdb #1  
---  
Chain | Description  
? | No description available  
  

> close session

> open /nfs-
> data/protein/regan/1.ssDNA_GNP/4.AuNP_DNA_CytC/8.seq6/Top_row4-1.cxs

opened ChimeraX session  

> select add #1

717 atoms, 752 bonds, 42 residues, 2 models selected  

> select add #3

23400 atoms, 50924 bonds, 145 pseudobonds, 6964 residues, 3 models selected  

> select subtract #3

697 atoms, 752 bonds, 22 residues, 1 model selected  

> show #1 models

> hide #1 models

> show #1 models

> ui mousemode right select

> ~bond sel

> bond sel

Must specify two or more atoms  

> ~bond sel

> select add #1

697 atoms, 750 bonds, 22 residues, 1 model selected  

> ui mousemode right "translate selected atoms"

> combine #1 #3 name 4-2

> hide #!3 models

> hide #1 models

> select subtract #1

Nothing selected  

> ui mousemode right select

> select #4/?:3@P

20 atoms, 20 residues, 1 model selected  

> select add #4@@serial_number=31638

21 atoms, 21 residues, 1 model selected  

> bond sel

Created 1 bond  

> save /nfs-
> data/protein/regan/1.ssDNA_GNP/4.AuNP_DNA_CytC/8.seq6/Top_row4-2.cxs

> select add #1

718 atoms, 750 bonds, 43 residues, 2 models selected  

> show #1 models

> select add #4

24097 atoms, 51673 bonds, 145 pseudobonds, 6986 residues, 3 models selected  

> select subtract #4

697 atoms, 750 bonds, 22 residues, 1 model selected  

> ui mousemode right "translate selected atoms"

> combine #1 #4 name 4-3

> hide #!4 models

> hide #1 models

> ui mousemode right select

> select #5/?:3@P

21 atoms, 21 residues, 1 model selected  

> select add #5@@serial_number=31995

22 atoms, 22 residues, 1 model selected  

> bond sel

Created 1 bond  

> show #1 models

> select add #5

24097 atoms, 51674 bonds, 145 pseudobonds, 6986 residues, 2 models selected  

> select subtract #5

Nothing selected  

> select add #1

697 atoms, 750 bonds, 22 residues, 1 model selected  

> ui mousemode right "translate selected atoms"

> combine #1 #5 name 4-4

> hide #!5 models

> hide #1 models

> ui mousemode right select

> select #6/?:3@P

22 atoms, 22 residues, 1 model selected  

> select add #6@@serial_number=32352

23 atoms, 23 residues, 1 model selected  

> bond sel

Created 1 bond  

> show #1 models

> select add #6

24794 atoms, 52425 bonds, 145 pseudobonds, 7008 residues, 2 models selected  

> select subtract #6

Nothing selected  

> select add #1

697 atoms, 750 bonds, 22 residues, 1 model selected  

> ui mousemode right "translate selected atoms"

> combine #1 #6 name 4-5

> hide #!6 models

> hide #1 models

> ui mousemode right select

> select #7/?:3@P

23 atoms, 23 residues, 1 model selected  

> select add #7@@serial_number=32709

24 atoms, 24 residues, 1 model selected  

> bond sel

Created 1 bond  

> show #1 models

> select add #1

721 atoms, 750 bonds, 46 residues, 2 models selected  

> select add #7

26188 atoms, 53926 bonds, 145 pseudobonds, 7052 residues, 3 models selected  

> select subtract #7

697 atoms, 750 bonds, 22 residues, 1 model selected  

> ui mousemode right "translate selected atoms"

> combine #1 #7 name 4-6

> hide #!7 models

> hide #1 models

> ui mousemode right select

Drag select of 1 atoms  

> select add #8@@serial_number=33066

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 0 bonds  

> close #8

> show #!7 models

> show #1 models

> select add #1

697 atoms, 750 bonds, 22 residues, 1 model selected  

> ui mousemode right "translate selected atoms"

> combine #1 #7 name 4-6

> hide #!7 models

> hide #1 models

> ui mousemode right select

> select #8/?:3@P

24 atoms, 24 residues, 1 model selected  

> select add #8@@serial_number=33066

25 atoms, 25 residues, 1 model selected  

> bond sel

Created 1 bond  

> close #3-7

> save /nfs-
> data/protein/regan/1.ssDNA_GNP/4.AuNP_DNA_CytC/8.seq6/Top_row4-6.cxs


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

Log:
Startup Messages  
---  
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr
bundle with that from OME-Zarr bundle  
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.6 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2
OpenGL renderer: Mesa Intel(R) UHD Graphics 770 (ADL-S GT1)
OpenGL vendor: Intel

Python: 3.11.2
Locale: en_US.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: Dell Inc.
Model: OptiPlex 7000
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700
Cache Size: 25600 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi       2.9Gi        24Gi       888Mi       3.3Gi        26Gi
	Swap:           13Gi       9.1Gi       4.9Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation AlderLake-S GT1 [8086:4680] (rev 0c)	
	Subsystem: Dell AlderLake-S GT1 [1028:0ac1]	
	Kernel driver in use: i915

Installed Packages:
    alabaster: 0.7.16
    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: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    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-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: 1.7.1
    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-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: 2.6.1
    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: 1.5.14
    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: 1.0.4
    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: 1.1.2
    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: 1.12.4
    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: 1.33.3
    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: 0.2.1
    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: 4.47.2
    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: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    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: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    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: 1.0.8
    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: 0.5.0
    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: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (2)

comment:1 by Eric Pettersen, 5 months ago

Component:	Unassigned → Sessions
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Crash saving atomic session state

comment:2 by Eric Pettersen, 5 months ago

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

Could be the garbage-collection bug that was fixed.

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