Crash in garbage collection

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-6.5.0-15-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.7.dev202312142006 (2023-12-14 20:06:35 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00007fba90bf9640 (most recent call first):
  File "/app/lib/python3.11/threading.py", line 324 in wait
  File "/app/lib/python3.11/threading.py", line 622 in wait
  File "/app/lib/python3.11/threading.py", line 1392 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fba937fe640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fba93fff640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fbab0ff9640 (most recent call first):
  File "/app/lib/python3.11/selectors.py", line 415 in select
  File "/app/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/app/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/app/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fbab17fa640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fbab1ffb640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fbab27fc640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fbab2ffd640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fbab37fe640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fbab3fff640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fbad0ff9640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fbad17fa640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fbad1ffb640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fbad27fc640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fbad2ffd640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fbad37fe640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fbad3fff640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fbaf0ff9640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fbaf17fa640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fbaf1ffb640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fbaf27fc640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fbaf2ffd640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fbaf37fe640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fbaf3fff640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fbb10ff9640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fbb117fa640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fbb11ffb640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fbb127fc640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fbb12ffd640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fbb137fe640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fbb13fff640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fbb38ff9640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fbb397fa640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fbb39ffb640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fbb3a7fc640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007fbb3affd640 (most recent call first):
  File "/app/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/app/lib/python3.11/threading.py", line 975 in run
  File "/app/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/app/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00007fbbbc88a740 (most recent call first):
  Garbage-collecting
  File "/app/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in 
  File "/app/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in __iter__
  File "/app/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 907 in atomspec_atoms
  File "/app/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 627 in _add_model_parts
  File "/app/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 476 in _check
  File "/app/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 490 in _check
  File "/app/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 470 in find_matches
  File "/app/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 612 in find_matches
  File "/app/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 455 in find_matches
  File "/app/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1004 in find_matches
  File "/app/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1001 in evaluate
  File "/app/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1091 in evaluate
  File "/app/lib/python3.11/site-packages/chimerax/atomic/args.py", line 36 in parse
  File "/app/lib/python3.11/site-packages/chimerax/atomic/args.py", line 71 in parse
  File "/app/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2499 in _parse_arg
  File "/app/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2795 in _process_keyword_arguments
  File "/app/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2869 in run
  File "/app/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
  File "/app/lib/python3.11/site-packages/chimerax/match_maker/tool.py", line 303 in run_matchmaker
  File "/app/lib/python3.11/site-packages/chimerax/match_maker/tool.py", line 171 in 
  File "/app/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/app/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/app/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.surface._surface, 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.pdb_lib._load_libs, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (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  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.7.dev202312142006 (2023-12-14)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7MTS format mmcif fromDatabase pdb

7mts title:  
CryoEM Structure of mGlu2 - Gi Complex [more info...]  
  
Chain information for 7mts #1  
---  
Chain | Description | UniProt  
A B | Metabotropic glutamate receptor 2 | GRM2_HUMAN 18-872  
C | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN
1-354  
D | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
GBB1_HUMAN 2-340  
E | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
GBG2_HUMAN 1-71  
  
Non-standard residues in 7mts #1  
---  
GLU — glutamic acid  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
ZQY —
2-methoxy-6-propyl-N-(2-{4-[(1H-tetrazol-5-yl)methoxy]phenyl}ethyl)thieno[2,3-d]pyrimidin-4-amine  
  

> select :599,656,670,748,750,751,760,813,829,659,665,834,862,754,823

187 atoms, 166 bonds, 23 residues, 1 model selected  

> show sel atoms

> style sel sphere

Changed 187 atom styles  

> color sel red

> select all

16068 atoms, 16453 bonds, 9 pseudobonds, 2153 residues, 2 models selected  

> hide sel cartoons

> hide sel atoms

> show sel atoms

> style sel stick

Changed 16068 atom styles  

> show sel cartoons

> hide sel atoms

> select :599,656,670,748,750,751,760,813,829,659,665,834,862,754,823

187 atoms, 166 bonds, 23 residues, 1 model selected  

> show sel atoms

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> open 7EPA fromDatabase pdb format mmcif

7epa title:  
Cryo-EM structure of inactive mGlu2 homodimer [more info...]  
  
Chain information for 7epa #2  
---  
Chain | Description | UniProt  
A B | Metabotropic glutamate receptor 2 | GRM2_HUMAN 19-825  
  

> select :599,656,670,748,750,751,760,813,829,659,665,834,862,754,823

287 atoms, 252 bonds, 39 residues, 2 models selected  

> color sel red

> show sel atoms

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> ui tool show Matchmaker

> matchmaker #2/A to #1/A pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7mts, chain A (#1) with 7epa, chain A (#2), sequence alignment
score = 3823.9  
RMSD between 88 pruned atom pairs is 1.399 angstroms; (across all 757 pairs:
8.930)  
  

> matchmaker #2/B to #1/A pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7mts, chain A (#1) with 7epa, chain B (#2), sequence alignment
score = 3822.1  
RMSD between 88 pruned atom pairs is 1.402 angstroms; (across all 757 pairs:
8.898)  
  

> undo

> close session

> open 7EPA format mmcif fromDatabase pdb

7epa title:  
Cryo-EM structure of inactive mGlu2 homodimer [more info...]  
  
Chain information for 7epa #1  
---  
Chain | Description | UniProt  
A B | Metabotropic glutamate receptor 2 | GRM2_HUMAN 19-825  
  

> open 7MTS fromDatabase pdb format mmcif

7mts title:  
CryoEM Structure of mGlu2 - Gi Complex [more info...]  
  
Chain information for 7mts #2  
---  
Chain | Description | UniProt  
A B | Metabotropic glutamate receptor 2 | GRM2_HUMAN 18-872  
C | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN
1-354  
D | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
GBB1_HUMAN 2-340  
E | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
GBG2_HUMAN 1-71  
  
Non-standard residues in 7mts #2  
---  
GLU — glutamic acid  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
ZQY —
2-methoxy-6-propyl-N-(2-{4-[(1H-tetrazol-5-yl)methoxy]phenyl}ethyl)thieno[2,3-d]pyrimidin-4-amine  
  

> hide cartoons

> show cartoons

> select all

26703 atoms, 27319 bonds, 11 pseudobonds, 3717 residues, 4 models selected  

> hide sel atoms

> select :599,656,670,748,750,751,760,813,829,659,665,834,862,754,823

287 atoms, 252 bonds, 39 residues, 2 models selected  

> select #1:599,656,670,748,750,751,760,813,829,659,665,834,862,754,823

100 atoms, 86 bonds, 16 residues, 1 model selected  

> color sel red

> show sel atoms

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> select #2:599,656,670,748,750,751,760,813,829,659,665,834,862,754,823

187 atoms, 166 bonds, 23 residues, 1 model selected  

> color sel forest green

> show sel atoms

> style sel stick

Changed 187 atom styles  

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> ui tool show Matchmaker


===== 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.dev202312142006 (2023-12-14)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 545.29.06
OpenGL renderer: NVIDIA RTX A4500/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: fr_FR.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=:99.0
Manufacturer: Dell Inc.
Model: Precision 3660
OS: Freedesktop SDK 22.08 Flatpak runtime
Architecture: 64bit ELF
Virtual Machine: detection failed
CPU: 32 13th Gen Intel(R) Core(TM) i9-13900
Cache Size: 36864 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            62Gi        18Gi        41Gi        54Mi       3.2Gi        43Gi
	Swap:          2.0Gi          0B       2.0Gi

Graphics:
	0000:01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA102GL [RTX A4500] [10de:2232] (rev a1)	
	Subsystem: Dell Device [1028:163c]	
	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-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.dev202312142006
    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
    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-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: 4.46.0
    funcparserlib: 2.0.0a0
    glfw: 2.6.3
    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: 5.5.0
    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
    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: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine: 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