Opened 21 months ago

Closed 21 months ago

#14646 closed defect (can't reproduce)

Crash cleaning up Collection pointers

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

Description 

The following bug report has been submitted:
Platform:        Linux-5.15.0-94-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.7.dev202305130100 (2023-05-13 01:00:26 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00007f537886d640 (most recent call first):
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 316 in wait
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 574 in wait
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 1297 in run
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f5379ffb640 (most recent call first):
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 910 in run
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f537a7fc640 (most recent call first):
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 910 in run
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f537affd640 (most recent call first):
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/selectors.py", line 416 in select
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/multiprocessing/connection.py", line 936 in wait
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 910 in run
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f537b7fe640 (most recent call first):
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 910 in run
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f537bfff640 (most recent call first):
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 910 in run
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f539cd80640 (most recent call first):
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 910 in run
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f539d581640 (most recent call first):
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 910 in run
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f539dd82640 (most recent call first):
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 910 in run
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f539e583640 (most recent call first):
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 910 in run
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f539ed84640 (most recent call first):
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 910 in run
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f539f585640 (most recent call first):
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 910 in run
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x00007f5430a1e740 (most recent call first):
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/weakref.py", line 576 in __init__
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/site-packages/chimerax/atomic/molarray.py", line 1604 in remove_deleted_pointers
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/site-packages/chimerax/atomic/molarray.py", line 123 in __init__
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/site-packages/chimerax/atomic/molarray.py", line 798 in __init__
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/site-packages/chimerax/atomic/ctypes_support.py", line 20 in atoms
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/site-packages/chimerax/atomic/molc.py", line 166 in get_prop
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/site-packages/chimerax/atomic/molobject.py", line 681 in __init__
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/site-packages/chimerax/atomic/molobject.py", line 2373 in 
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/site-packages/chimerax/atomic/molarray.py", line 1435 in 
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/site-packages/chimerax/atomic/molarray.py", line 1435 in __init__
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/site-packages/chimerax/addh/hbond.py", line 123 in add_hydrogens
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/site-packages/chimerax/addh/cmd.py", line 173 in hbond_add_hydrogens
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/site-packages/chimerax/addh/cmd.py", line 66 in cmd_addh
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/site-packages/chimerax/coulombic/coulombic.py", line 84 in assign_charges
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/site-packages/chimerax/coulombic/cmd.py", line 88 in cmd_coulombic
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38 in run
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py", line 513 in run
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py", line 570 in run_expanded_command
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py", line 61 in func_plus_tip
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py", line 327 in run
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py", line 408 in run_shortcut
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py", line 390 in try_shortcut
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py", line 1335 in run_provider
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/site-packages/chimerax/shortcuts/__init__.py", line 52 in run_provider
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/site-packages/chimerax/core/toolshed/__init__.py", line 1289 in run_provider
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/site-packages/chimerax/core/toolshed/info.py", line 386 in run_provider
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/site-packages/chimerax/toolbar/tool.py", line 205 in callback
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in 
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/runpy.py", line 87 in _run_code
  File "/share/sw/chimerax-2023.05.13/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== 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.dev202305130100 (2023-05-13)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/ksturm/Downloads/AF-Q38935-F1-model_v4.pdb

AF-Q38935-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for peptidyl-prolyl cis-trans isomerase
FKBP15-1 (Q38935) [more info...]  
  
Chain information for AF-Q38935-F1-model_v4.pdb #1  
---  
Chain | Description | UniProt  
A | peptidyl-prolyl cis-trans isomerase FKBP15-1 | FK151_ARATH 1-153  
  

> show surfaces

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for AF-Q38935-F1-model_v4.pdb_A SES surface #1.1: minimum,
-12.62, mean -0.11, maximum 15.22  
To also show corresponding color key, enter the above coulombic command and
add key true  

> close session

> open /home/ksturm/Downloads/AF-P93736-F1-model_v4.pdb

AF-P93736-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for valine--TRNA ligase, mitochondrial 1
(P93736) [more info...]  
  
Chain information for AF-P93736-F1-model_v4.pdb #1  
---  
Chain | Description | UniProt  
A | valine--TRNA ligase, mitochondrial 1 | SYVM1_ARATH 1-1108  
  

> show surfaces

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for AF-P93736-F1-model_v4.pdb_A SES surface #1.1: minimum,
-15.35, mean -1.21, maximum 11.69  
To also show corresponding color key, enter the above coulombic command and
add key true  

> close session

> alphafold fetch Q9MAB3

Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json  
Fetching compressed AlphaFold Q9MAB3 from
https://alphafold.ebi.ac.uk/files/AF-Q9MAB3-F1-model_v4.cif  
Chain information for AlphaFold Q9MAB3 #1  
---  
Chain | Description | UniProt  
A | Probable nucleolar protein 5-2 | NOP5B_ARATH 1-533  
  
Color AlphaFold Q9MAB3 by residue attribute pLDDT_score  

> show surfaces

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for AlphaFold Q9MAB3_A SES surface #1.1: minimum, -13.73,
mean 0.50, maximum 16.84  
To also show corresponding color key, enter the above coulombic command and
add key true  

> close session

> alphafold fetch Q48773

Fetching compressed AlphaFold Q48773 from
https://alphafold.ebi.ac.uk/files/AF-Q48773-F1-model_v4.cif  
Chain information for AlphaFold Q48773 #1  
---  
Chain | Description | UniProt  
A | Thiol-activated cytolysin | Q48773_LISMN 1-50  
  
Color AlphaFold Q48773 by residue attribute pLDDT_score  

> show surfaces

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for AlphaFold Q48773_A SES surface #1.1: minimum, -10.65,
mean -0.21, maximum 11.53  
To also show corresponding color key, enter the above coulombic command and
add key true  

> close session

> alphafold fetch P29517

Fetching compressed AlphaFold P29517 from
https://alphafold.ebi.ac.uk/files/AF-P29517-F1-model_v4.cif  
Chain information for AlphaFold P29517 #1  
---  
Chain | Description | UniProt  
A | Tubulin beta-9 chain | TBB9_ARATH 1-444  
  
Color AlphaFold P29517 by residue attribute pLDDT_score  

> show surfaces

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for AlphaFold P29517_A SES surface #1.1: minimum, -22.98,
mean -5.11, maximum 8.34  
To also show corresponding color key, enter the above coulombic command and
add key true  

> close session

> alphafold fetch Q94F40

Fetching compressed AlphaFold Q94F40 from
https://alphafold.ebi.ac.uk/files/AF-Q94F40-F1-model_v4.cif  
Chain information for AlphaFold Q94F40 #1  
---  
Chain | Description | UniProt  
A | GDSL esterase/lipase At1g28600 | GDL9_ARATH 1-393  
  
Color AlphaFold Q94F40 by residue attribute pLDDT_score  

> show surfaces

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for AlphaFold Q94F40_A SES surface #1.1: minimum, -17.77,
mean 0.22, maximum 15.82  
To also show corresponding color key, enter the above coulombic command and
add key true  

> close session

> alphafold fetch Q8SAB7

Fetching compressed AlphaFold Q8SAB7 from
https://alphafold.ebi.ac.uk/files/AF-Q8SAB7-F1-model_v4.cif  
Chain information for AlphaFold Q8SAB7 #1  
---  
Chain | Description | UniProt  
A | Guanine nucleotide exchange factor SPIKE 1 | SPK1_ARATH 1-1830  
  
Color AlphaFold Q8SAB7 by residue attribute pLDDT_score  

> show surfaces

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for AlphaFold Q8SAB7_A SES surface #1.1: minimum, -24.55,
mean -2.99, maximum 13.30  
To also show corresponding color key, enter the above coulombic command and
add key true  

> close session

> alphafold fetch Q96255

Fetching compressed AlphaFold Q96255 from
https://alphafold.ebi.ac.uk/files/AF-Q96255-F1-model_v4.cif  
Chain information for AlphaFold Q96255 #1  
---  
Chain | Description | UniProt  
A | Phosphoserine aminotransferase 1, chloroplastic | SERB1_ARATH 1-430  
  
Color AlphaFold Q96255 by residue attribute pLDDT_score  

> show surfaces

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for AlphaFold Q96255_A SES surface #1.1: minimum, -19.36,
mean -0.88, maximum 12.91  
To also show corresponding color key, enter the above coulombic command and
add key true  

> close session

> alphafold fetch Q9XEE2

Fetching compressed AlphaFold Q9XEE2 from
https://alphafold.ebi.ac.uk/files/AF-Q9XEE2-F1-model_v4.cif  
Chain information for AlphaFold Q9XEE2 #1  
---  
Chain | Description | UniProt  
A | Annexin D2 | ANXD2_ARATH 1-317  
  
Color AlphaFold Q9XEE2 by residue attribute pLDDT_score  

> show surfaces

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for AlphaFold Q9XEE2_A SES surface #1.1: minimum, -19.38,
mean -1.97, maximum 15.87  
To also show corresponding color key, enter the above coulombic command and
add key true  

> close session

> alphafold fetch Q96327

Fetching compressed AlphaFold Q96327 from
https://alphafold.ebi.ac.uk/files/AF-Q96327-F1-model_v4.cif  
Chain information for AlphaFold Q96327 #1  
---  
Chain | Description | UniProt  
A | ERBB-3 BINDING PROTEIN 1 | EBP1_ARATH 1-392  
  
Color AlphaFold Q96327 by residue attribute pLDDT_score  

> show surfaces

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for AlphaFold Q96327_A SES surface #1.1: minimum, -14.95,
mean -1.40, maximum 14.65  
To also show corresponding color key, enter the above coulombic command and
add key true  

> close session

> alphafold fetch Q9SGT7

Fetching compressed AlphaFold Q9SGT7 from
https://alphafold.ebi.ac.uk/files/AF-Q9SGT7-F1-model_v4.cif  
Chain information for AlphaFold Q9SGT7 #1  
---  
Chain | Description | UniProt  
A | At1g56110/T6H22_9 | Q9SGT7_ARATH 1-522  
  
Color AlphaFold Q9SGT7 by residue attribute pLDDT_score  

> show surfaces

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for AlphaFold Q9SGT7_A SES surface #1.1: minimum, -18.08,
mean -0.35, maximum 17.58  
To also show corresponding color key, enter the above coulombic command and
add key true  

> close session

> alphafold fetch Q9SIZ2

Fetching compressed AlphaFold Q9SIZ2 from
https://alphafold.ebi.ac.uk/files/AF-Q9SIZ2-F1-model_v4.cif  
Chain information for AlphaFold Q9SIZ2 #1  
---  
Chain | Description | UniProt  
A | Eukaryotic translation initiation factor 2 subunit alpha homolog |
IF2AH_ARATH 1-344  
  
Color AlphaFold Q9SIZ2 by residue attribute pLDDT_score  

> show surfaces

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for AlphaFold Q9SIZ2_A SES surface #1.1: minimum, -29.97,
mean -2.25, maximum 11.37  
To also show corresponding color key, enter the above coulombic command and
add key true  

> close session

> alphafold fetch Q9SZN1

Fetching compressed AlphaFold Q9SZN1 from
https://alphafold.ebi.ac.uk/files/AF-Q9SZN1-F1-model_v4.cif  
Chain information for AlphaFold Q9SZN1 #1  
---  
Chain | Description | UniProt  
A | V-type proton ATPase subunit B2 | VATB2_ARATH 1-487  
  
Color AlphaFold Q9SZN1 by residue attribute pLDDT_score  

> show surfaces

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for AlphaFold Q9SZN1_A SES surface #1.1: minimum, -16.75,
mean -3.23, maximum 10.65  
To also show corresponding color key, enter the above coulombic command and
add key true  

> close session

> alphafold fetch Q9M084

Fetching compressed AlphaFold Q9M084 from
https://alphafold.ebi.ac.uk/files/AF-Q9M084-F1-model_v4.cif  
Chain information for AlphaFold Q9M084 #1  
---  
Chain | Description | UniProt  
A | Aspartate--tRNA ligase 2, cytoplasmic | SYDC2_ARATH 1-558  
  
Color AlphaFold Q9M084 by residue attribute pLDDT_score  

> show surfaces

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for AlphaFold Q9M084_A SES surface #1.1: minimum, -19.36,
mean -1.65, maximum 11.70  
To also show corresponding color key, enter the above coulombic command and
add key true  

> close session

> alphafold fetch Q9S775

Fetching compressed AlphaFold Q9S775 from
https://alphafold.ebi.ac.uk/files/AF-Q9S775-F1-model_v4.cif  
Chain information for AlphaFold Q9S775 #1  
---  
Chain | Description | UniProt  
A | CHD3-type chromatin-remodeling factor PICKLE | PKL_ARATH 1-1384  
  
Color AlphaFold Q9S775 by residue attribute pLDDT_score  

> show surfaces

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for AlphaFold Q9S775_A SES surface #1.1: minimum, -20.18,
mean -2.15, maximum 15.33  
To also show corresponding color key, enter the above coulombic command and
add key true  

> close session

> alphafold fetch O04658

Fetching compressed AlphaFold O04658 from
https://alphafold.ebi.ac.uk/files/AF-O04658-F1-model_v4.cif  
Chain information for AlphaFold O04658 #1  
---  
Chain | Description | UniProt  
A | Probable nucleolar protein 5-1 | NOP5A_ARATH 1-533  
  
Color AlphaFold O04658 by residue attribute pLDDT_score  

> show surfaces

> coulombic


===== 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.dev202305130100 (2023-05-13)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 470.223.02
OpenGL renderer: NVIDIA GeForce GTX 970/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=xubuntu
XDG_SESSION_DESKTOP=xubuntu
XDG_CURRENT_DESKTOP=XFCE
DISPLAY=:0.0
Manufacturer: ASUS
Model: All Series
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 Intel(R) Xeon(R) CPU E3-1246 v3 @ 3.50GHz
Cache Size: 8192 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi        14Gi       2.8Gi       491Mi        13Gi        15Gi
	Swap:           31Gi       2.0Mi        31Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GM204 [GeForce GTX 970] [10de:13c2] (rev a1)	
	Subsystem: ASUSTeK Computer Inc. GM204 [GeForce GTX 970] [1043:8508]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.11
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.45.5
    ChimeraX-AtomicLibrary: 10.0.6
    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: 2.10.2
    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: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.dev202305130100
    ChimeraX-CoreFormats: 1.1
    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: 1.1.2
    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: 1.2.1
    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-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    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
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.2
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    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: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.11.1
    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: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.2
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.4
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.1
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.2
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (2)

comment:1 by Eric Pettersen, 21 months ago

Cc: Eric Pettersen added
Component: Unassigned → Core
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash cleaning up Collection pointers

comment:2 by Tom Goddard, 21 months ago

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

This is a May 2023 ChimeraX 1.7 build, so most similar to ChimeraX 1.6.

It is in Coulombic. It crashed just making a class instance in the Python weakref module. So it seems likely to be the garbage collection crash or memory corruption.

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