Crash in find_clashing_atoms

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1160.88.1.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3 (2021-12-08 23:08:33 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 0x00007fce11cfd740 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/openmm/openmm.py", line 5145 in getState
  File "/home/uqnmodhi/.local/share/ChimeraX/1.3/site-packages/chimerax/isolde/openmm/openmm_interface.py", line 1627 in find_clashing_atoms
  File "/home/uqnmodhi/.local/share/ChimeraX/1.3/site-packages/chimerax/isolde/validation/clashes.py", line 72 in populate_clash_table
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in 
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 87 in _run_code
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/home/shared/JEV G3 SA14-14-2/Atomic model SA14-14-2 .cxs"

Opened SA14_final_postprocess_masked.mrc as #2, grid size 768,768,768, pixel
0.8, shown at level 0.016, step 1, values float32  
Restoring stepper: JEV3 SA14 homology EM all chain-
coot-0_real_space_refined_001.pdb  
opened ChimeraX session  

> ui tool show ISOLDE

> set selectionWidth 4

Done loading forcefield  
Opened SA14_final_postprocess_masked.mrc as #1.1.1.1, grid size 768,768,768,
pixel 0.8, shown at step 1, values float32  

> open "/home/shared/JEV G4/RealSpaceRefine_11/JEV G4 EM Atomic model fitted
> final DS_real_space_refined_011.pdb"

Chain information for JEV G4 EM Atomic model fitted final
DS_real_space_refined_011.pdb #2  
---  
Chain | Description  
A B C | No description available  
D E F | No description available  
  

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
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 JEV3 SA14 homology EM all chain-coot-0_real_space_refined_001.pdb,
chain A (#1.2) with JEV G4 EM Atomic model fitted final
DS_real_space_refined_011.pdb, chain A (#2), sequence alignment score = 2489.8  
RMSD between 476 pruned atom pairs is 0.726 angstroms; (across all 499 pairs:
1.014)  
  

> select #2

15882 atoms, 16170 bonds, 1707 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> matchmaker #2 to #1.2/C

Parameters  
---  
Chain pairing | bb  
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 JEV3 SA14 homology EM all chain-coot-0_real_space_refined_001.pdb,
chain C (#1.2) with JEV G4 EM Atomic model fitted final
DS_real_space_refined_011.pdb, chain A (#2), sequence alignment score = 2456.8  
RMSD between 483 pruned atom pairs is 0.668 angstroms; (across all 499 pairs:
0.885)  
  

> matchmaker #2 to #1.2/C

Parameters  
---  
Chain pairing | bb  
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 JEV3 SA14 homology EM all chain-coot-0_real_space_refined_001.pdb,
chain C (#1.2) with JEV G4 EM Atomic model fitted final
DS_real_space_refined_011.pdb, chain A (#2), sequence alignment score = 2456.8  
RMSD between 483 pruned atom pairs is 0.668 angstroms; (across all 499 pairs:
0.885)  
  

> select #2

15882 atoms, 16170 bonds, 1707 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 15882 atom styles  

> hide #2 models

ISOLDE: stopped sim  
Traceback (most recent call last):  
File "/home/uqnmodhi/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2749, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/uqnmodhi/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2784, in start_sim  
sm = self._sim_manager = Sim_Manager(self, self.selected_model, main_sel,  
File "/home/uqnmodhi/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 576, in __init__  
mobile_atoms = self.expand_mobile_selection(selected_atoms, expansion_mode)  
File "/home/uqnmodhi/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 971, in
expand_mobile_selection  
sel = selections.expand_selection_along_chains(core_atoms,  
File "/home/uqnmodhi/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/selections.py", line 39, in
expand_selection_along_chains  
raise TypeError('Selected atoms must all be in the same model!')  
TypeError: Selected atoms must all be in the same model!  
  
TypeError: Selected atoms must all be in the same model!  
  
File "/home/uqnmodhi/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/selections.py", line 39, in
expand_selection_along_chains  
raise TypeError('Selected atoms must all be in the same model!')  
  
See log for complete Python traceback.  
  

> select #1.2

25610 atoms, 25903 bonds, 1704 residues, 10 models selected  
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  
ISOLDE: started sim  

> volume #1.1.1.1 level 0.02515

> volume #1.1.1.1 level 0.01485

ISOLDE: paused sim  

> open "/home/shared/JEV G3 SA14-14-2/RealSpaceRefine_1/JEV3 SA14 homology EM
> all chain-coot-0_real_space_refined_001.pdb"

Chain information for JEV3 SA14 homology EM all chain-
coot-0_real_space_refined_001.pdb #3  
---  
Chain | Description  
A B C | No description available  
D E F | No description available  
  

> hide sel atoms

> show sel cartoons

> select #3

12885 atoms, 13178 bonds, 1704 residues, 1 model selected  

> style sel stick

Changed 12885 atom styles  

> hide sel atoms

> show sel cartoons

> open "/home/shared/JEV G3 SA14-14-2/SA14_final_postprocess_masked.mrc"

Opened SA14_final_postprocess_masked.mrc as #4, grid size 768,768,768, pixel
0.8, shown at step 1, values float32  

> volume #4 region 0,0,0,767,767,767 step 4

> volume #4 step 1

> volume #4 change image level -2.382e-06,0 level 0.02926,0.8 level 0.0845,1

> volume #4 level 0.01596

> close #1

Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/home/uqnmodhi/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1020, in
_sim_end_cb  
self._pr_sim_end_cb()  
File "/home/uqnmodhi/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1077, in
_pr_sim_end_cb  
restraints =
self.position_restraint_mgr.get_restraints(self.sim_construct.all_atoms)  
File "/home/uqnmodhi/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/molobject.py", line 2375, in get_restraints  
return self._get_restraints(atoms)  
File "/home/uqnmodhi/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/molobject.py", line 2328, in _get_restraints  
num = f(self._c_pointer, atoms._c_pointers, create, n, pointer(ret))  
AttributeError: 'PositionRestraintMgr' object has no attribute '_c_pointer'  
  
Error processing trigger "sim terminated":  
AttributeError: 'PositionRestraintMgr' object has no attribute '_c_pointer'  
  
File "/home/uqnmodhi/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/molobject.py", line 2328, in _get_restraints  
num = f(self._c_pointer, atoms._c_pointers, create, n, pointer(ret))  
  
See log for complete Python traceback.  
  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> ui tool show ISOLDE

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 63 residues in model #2 to IUPAC-IUB
standards.  
Chain information for JEV G4 EM Atomic model fitted final
DS_real_space_refined_011.pdb  
---  
Chain | Description  
1.2/A 1.2/B 1.2/C | No description available  
1.2/D 1.2/E 1.2/F | No description available  
  
Done loading forcefield  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 123 residues in model #3 to IUPAC-IUB
standards.  
Chain information for JEV3 SA14 homology EM all chain-
coot-0_real_space_refined_001.pdb  
---  
Chain | Description  
2.2/A 2.2/B 2.2/C | No description available  
2.2/D 2.2/E 2.2/F | No description available  
  
Opened SA14_final_postprocess_masked.mrc as #2.1.1.1, grid size 768,768,768,
pixel 0.8, shown at step 1, values float32  
ISOLDE: stopped sim  

> addh

Summary of feedback from adding hydrogens to multiple structures  
---  
notes | No usable SEQRES records for JEV G4 EM Atomic model fitted final
DS_real_space_refined_011.pdb (#1.2) chain A; guessing termini instead  
No usable SEQRES records for JEV G4 EM Atomic model fitted final
DS_real_space_refined_011.pdb (#1.2) chain B; guessing termini instead  
No usable SEQRES records for JEV G4 EM Atomic model fitted final
DS_real_space_refined_011.pdb (#1.2) chain C; guessing termini instead  
No usable SEQRES records for JEV G4 EM Atomic model fitted final
DS_real_space_refined_011.pdb (#1.2) chain D; guessing termini instead  
No usable SEQRES records for JEV G4 EM Atomic model fitted final
DS_real_space_refined_011.pdb (#1.2) chain E; guessing termini instead  
1 messages similar to the above omitted  
Chain-initial residues that are actual N termini: JEV G4 EM Atomic model
fitted final DS_real_space_refined_011.pdb #1.2/A PHE 1, JEV G4 EM Atomic
model fitted final DS_real_space_refined_011.pdb #1.2/B PHE 1, JEV G4 EM
Atomic model fitted final DS_real_space_refined_011.pdb #1.2/C PHE 1, JEV G4
EM Atomic model fitted final DS_real_space_refined_011.pdb #1.2/D THR 5, JEV
G4 EM Atomic model fitted final DS_real_space_refined_011.pdb #1.2/E THR 5,
JEV G4 EM Atomic model fitted final DS_real_space_refined_011.pdb #1.2/F THR 5  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: JEV G4 EM Atomic model fitted
final DS_real_space_refined_011.pdb #1.2/A ALA 500, JEV G4 EM Atomic model
fitted final DS_real_space_refined_011.pdb #1.2/B ALA 500, JEV G4 EM Atomic
model fitted final DS_real_space_refined_011.pdb #1.2/C ALA 500, JEV G4 EM
Atomic model fitted final DS_real_space_refined_011.pdb #1.2/D TYR 73, JEV G4
EM Atomic model fitted final DS_real_space_refined_011.pdb #1.2/E TYR 73, JEV
G4 EM Atomic model fitted final DS_real_space_refined_011.pdb #1.2/F TYR 73  
Chain-final residues that are not actual C termini:  
1191 hydrogen bonds  
No usable SEQRES records for JEV3 SA14 homology EM all chain-
coot-0_real_space_refined_001.pdb (#2.2) chain A; guessing termini instead  
No usable SEQRES records for JEV3 SA14 homology EM all chain-
coot-0_real_space_refined_001.pdb (#2.2) chain B; guessing termini instead  
No usable SEQRES records for JEV3 SA14 homology EM all chain-
coot-0_real_space_refined_001.pdb (#2.2) chain C; guessing termini instead  
No usable SEQRES records for JEV3 SA14 homology EM all chain-
coot-0_real_space_refined_001.pdb (#2.2) chain D; guessing termini instead  
No usable SEQRES records for JEV3 SA14 homology EM all chain-
coot-0_real_space_refined_001.pdb (#2.2) chain E; guessing termini instead  
1 messages similar to the above omitted  
Chain-initial residues that are actual N termini: JEV3 SA14 homology EM all
chain-coot-0_real_space_refined_001.pdb #2.2/A PHE 1, JEV3 SA14 homology EM
all chain-coot-0_real_space_refined_001.pdb #2.2/B PHE 1, JEV3 SA14 homology
EM all chain-coot-0_real_space_refined_001.pdb #2.2/C PHE 1, JEV3 SA14
homology EM all chain-coot-0_real_space_refined_001.pdb #2.2/D THR 1, JEV3
SA14 homology EM all chain-coot-0_real_space_refined_001.pdb #2.2/E THR 1,
JEV3 SA14 homology EM all chain-coot-0_real_space_refined_001.pdb #2.2/F THR 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: JEV3 SA14 homology EM all
chain-coot-0_real_space_refined_001.pdb #2.2/A HIS 499, JEV3 SA14 homology EM
all chain-coot-0_real_space_refined_001.pdb #2.2/B HIS 499, JEV3 SA14 homology
EM all chain-coot-0_real_space_refined_001.pdb #2.2/C HIS 499, JEV3 SA14
homology EM all chain-coot-0_real_space_refined_001.pdb #2.2/D TYR 69, JEV3
SA14 homology EM all chain-coot-0_real_space_refined_001.pdb #2.2/E TYR 69,
JEV3 SA14 homology EM all chain-coot-0_real_space_refined_001.pdb #2.2/F TYR
69  
Chain-final residues that are not actual C termini:  
1327 hydrogen bonds  
22626 hydrogens added  
  
ISOLDE: started sim  

> select clear

Traceback (most recent call last):  
File "/home/uqnmodhi/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 1932, in _apply_register_shift  
rs = self._register_shifter = Protein_Register_Shifter(self.session, self,
sel)  
File "/home/uqnmodhi/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/manipulations/register_shift.py", line 131, in
__init__  
nspl = self.n_spline = interpolate.splprep(ncoords.transpose(), u=u_vals)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/scipy/interpolate/fitpack.py", line 155, in splprep  
res = _impl.splprep(x, w, u, ub, ue, k, task, s, t, full_output, nest, per,  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/scipy/interpolate/_fitpack_impl.py", line 264, in splprep  
raise TypeError('m > k must hold')  
TypeError: m > k must hold  
  
TypeError: m > k must hold  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/scipy/interpolate/_fitpack_impl.py", line 264, in splprep  
raise TypeError('m > k must hold')  
  
See log for complete Python traceback.  
  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  

No rotamer preview selected! Ignoring command.  

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: resumed sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
ISOLDE: started sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
ISOLDE: started sim  

> select #1.2.1

1 model selected  

> select #1.2.1

1 model selected  

> select #1.2.2

1 model selected  

> select #1.2.3

2 models selected  

> select #1.2.2

1 model selected  

> select #1.2.1

1 model selected  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> hide #!2 models

> show #!2 models

> hide #!1 models

> select #2.1

5 models selected  

> select #2.2

25610 atoms, 25903 bonds, 1704 residues, 11 models selected  

> select #2.3

1 model selected  

> select #2.2

25610 atoms, 25903 bonds, 1704 residues, 11 models selected  
ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
ISOLDE: started sim  


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

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/home/shared/JEV G3 SA14-14-2/SA14_final_postprocess_masked.mrc"

Opened SA14_final_postprocess_masked.mrc as #1, grid size 768,768,768, pixel
0.8, shown at step 1, values float32  

> volume #1 region 0,0,0,767,767,767 step 4

[Repeated 1 time(s)]

> open "/home/shared/JEV G3 SA14-14-2/RealSpaceRefine_1/JEV3 SA14 homology EM
> all chain-coot-0_real_space_refined_001.pdb"

Chain information for JEV3 SA14 homology EM all chain-
coot-0_real_space_refined_001.pdb #2  
---  
Chain | Description  
A B C | No description available  
D E F | No description available  
  

> hide atoms

> show cartoons




OpenGL version: 3.3.0 NVIDIA 525.105.17
OpenGL renderer: NVIDIA GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision 7920 Tower
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 Intel(R) Xeon(R) Silver 4110 CPU @ 2.10GHz
Cache Size: 11264 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           250G         25G        165G         47M         59G        224G
	Swap:          4.0G          0B        4.0G

Graphics:
	0000:17:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU102 [GeForce RTX 2080 Ti] [10de:1e04] (rev a1)	
	Subsystem: Gigabyte Technology Co., Ltd Device [1458:37c4]	
	Kernel driver in use: nvidia
Locale: ('en_AU', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

[Eric Pettersen]

There were various errors before the crash, and the version is 1.3, so maybe already fixed....

[Tristan Croll]

Yeah, those should all be fixed. They hit a couple of the old classics: closing the model while a simulation was running caused the first set of tracebacks, and the segmentation fault in find_clashing atoms would occur if the user killed the simulation while the minimiser was still churning (code would try to get forces from an already-deleted OpenMM context).