Crash writing mmCIF

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-4.18.0-425.19.2.el8_7.x86_64-x86_64-with-glibc2.28
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00007f55567fc700 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 316 in wait
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 574 in wait
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 1297 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x00007f56b5431740 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/atomic/ctypes_support.py", line 58 in residue_or_none
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/atomic/ctypes_support.py", line 60 in 
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/atomic/ctypes_support.py", line 60 in residues_or_nones
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/atomic/molc.py", line 166 in get_prop
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/mmcif/__init__.py", line 112 in save
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/save_command/cmd.py", line 90 in provider_save
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/save_command/cmd.py", line 75 in cmd_save
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
  File "/scratch/cs-bioinfo/tngu/6k_data/cif_box_crop.py", line 69 in main
  File "/scratch/cs-bioinfo/tngu/6k_data/cif_box_crop.py", line 72 in 
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/scripting.py", line 61 in _exec_python
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/scripting.py", line 84 in open_python_script
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/runscript.py", line 38 in runscript
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 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: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> runscript /scratch/cs-bioinfo/tngu/6k_data/cif_box_crop.py

> open 6gsm

Summary of feedback from opening 6gsm fetched from pdb  
---  
note | Fetching compressed mmCIF 6gsm from
http://files.rcsb.org/download/6gsm.cif  
  
6gsm title:  
Structure of a partial yeast 48S preinitiation complex in open conformation.
[more info...]  
  
Chain information for 6gsm #1  
---  
Chain | Description | UniProt  
1 | Met-tRNAi |  
2 | 18S ribosomal RNA |  
3 | mRNA (5'-R(P*AP*AP*U)-3') |  
A | 40S ribosomal protein S0 | RSSA_KLULA 2-209  
B | 40S ribosomal protein S1 | RS3A_KLULA 3-233  
C | KLLA0F09812p | Q6CKL3_KLULA 39-255  
D | KLLA0D08305p | Q6CRK7_KLULA 3-225  
E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261  
F | KLLA0D10659p | Q6CRA3_KLULA 22-227  
G | 40S ribosomal protein S6 | RS6_KLULA 1-226  
H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187  
I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201  
J | KLLA0E23673p | Q6CM18_KLULA 2-183  
K | KLLA0B08173p | Q6CVZ5_KLULA 1-96  
L | KLLA0A10483p | Q6CX80_KLULA 2-156  
M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134  
N | KLLA0F18040p | Q6CJK0_KLULA 2-151  
O | 40S ribosomal protein S14 | RS14_KLULA 11-137  
P | KLLA0F07843p | Q6CKV4_KLULA 13-131  
Q | 40S ribosomal protein S16 | RS16_KLULA 3-143  
R | KLLA0B01474p | Q6CWU3_KLULA 2-126  
S | KLLA0B01562p | Q6CWT9_KLULA 2-146  
T | KLLA0A07194p | Q6CXM0_KLULA 2-144  
U | KLLA0F25542p | Q6CIM1_KLULA 15-120  
V | 40S ribosomal protein S21 | RS21_KLULA 1-87  
W | 40S ribosomal protein S22 | RS22_KLULA 2-130  
X | KLLA0B11231p | F2Z602_KLULA 2-145  
Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135  
Z | KLLA0B06182p | Q6CW78_KLULA 36-105  
a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99  
b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82  
c | 40S ribosomal protein S28 | RS28_KLULA 6-67  
d | 40S ribosomal protein S29 | RS29_KLULA 4-56  
e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61  
f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150  
g | KLLA0E12277p | Q6CNI7_KLULA 3-326  
h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25  
i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115  
j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
3-265  
k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
90-519  
l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
127-270  
m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108  
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492  
p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737  
q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794  
r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96  
s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342  
  
Non-standard residues in 6gsm #1  
---  
7NO —
[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
(2~{S})-2-azanyl-4-methylsulfanyl-butanoate  
GCP — phosphomethylphosphonic acid guanylate ester  
MG — magnesium ion  
ZN — zinc ion  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc

Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
level 0.0673, step 2, values float32  

> volume #2 region 183,261,137,310,356,256

> open /scratch/cs-bioinfo/tngu/6k_data/select_box.py

executed select_box.py  

> selectbox #1 inMap #2

Selected 21277 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_Sample/0057_6gsm/0057_6gsm_G.cif #1
> selectedOnly true

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_Sample/0057_6gsm/0057_6gsm_G.mrc #2

> close session

> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_Sample/0057_6gsm/0057_6gsm_G.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_Sample/0057_6gsm/0057_6gsm_G.cif  
---  
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 52598  
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
52599  
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
52600  
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
52601  
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
52602  
111 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
52851  
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
52852  
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
52853  
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
52854  
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
52855  
139 messages similar to the above omitted  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:48  
Atom C5' has no neighbors to form bonds with according to residue template for
G /2:48  
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:220  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:307  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:376  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:410  
Atom O5' has no neighbors to form bonds with according to residue template for
C /2:410  
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:469  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:472  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:511  
Atom C5' has no neighbors to form bonds with according to residue template for
A /2:511  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:637  
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:837  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:858  
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:1662  
Atom ND1 has no neighbors to form bonds with according to residue template for
HIS /H:122  
Atom N has no neighbors to form bonds with according to residue template for
LYS /H:124  
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /H:124  
Atom O has no neighbors to form bonds with according to residue template for
ALA /J:55  
Atom CB has no neighbors to form bonds with according to residue template for
ALA /J:55  
Atom N has no neighbors to form bonds with according to residue template for
LYS /J:65  
Atom O has no neighbors to form bonds with according to residue template for
ARG /J:107  
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /J:129  
Atom CD has no neighbors to form bonds with according to residue template for
LYS /J:175  
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /J:175  
Atom N has no neighbors to form bonds with according to residue template for
ALA /J:177  
Atom CB has no neighbors to form bonds with according to residue template for
ALA /J:177  
Atom N has no neighbors to form bonds with according to residue template for
TYR /L:93  
Atom CB has no neighbors to form bonds with according to residue template for
TYR /L:93  
Atom CB has no neighbors to form bonds with according to residue template for
ARG /L:103  
Atom CD has no neighbors to form bonds with according to residue template for
ARG /L:103  
Atom CB has no neighbors to form bonds with according to residue template for
ASN /W:80  
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /W:80  
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /W:105  
Atom N has no neighbors to form bonds with according to residue template for
LYS /W:124  
Atom CD has no neighbors to form bonds with according to residue template for
LYS /W:124  
Atom O has no neighbors to form bonds with according to residue template for
LYS /p:711  
Atom CB has no neighbors to form bonds with according to residue template for
LYS /p:711  
Atom N has no neighbors to form bonds with according to residue template for
VAL /q:191  
Atom O has no neighbors to form bonds with according to residue template for
LYS /q:203  
Atom CB has no neighbors to form bonds with according to residue template for
LYS /q:203  
Atom O has no neighbors to form bonds with according to residue template for
LYS /q:204  
  
Chain information for 0057_6gsm_G.cif #1  
---  
Chain | Description  
2 | 18S ribosomal RNA  
E | 40S ribosomal protein S4  
G | 40S ribosomal protein S6  
H | 40S ribosomal protein S7  
I | 40S ribosomal protein S8  
J | KLLA0E23673p  
L | KLLA0A10483p  
N | KLLA0F18040p  
W | 40S ribosomal protein S22  
Y | 40S ribosomal protein S24  
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a  
p | Eukaryotic translation initiation factor 3 subunit B  
q | Eukaryotic translation initiation factor 3 subunit C  
s | Eukaryotic translation initiation factor 3 subunit I  
  

> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_Sample/0057_6gsm/0057_6gsm_G.mrc

Opened 0057_6gsm_G.mrc as #2, grid size 128,96,120, pixel 1, shown at level
0.137, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_G.cif (#1) to map 0057_6gsm_G.mrc (#2) using 21277
atoms  
average map value = 0.08241, steps = 52  
shifted from previous position = 0.565  
rotated from previous position = 0.0908 degrees  
atoms outside contour = 19986, contour level = 0.13743  
  
Position of 0057_6gsm_G.cif (#1) relative to 0057_6gsm_G.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999988 0.00036109 0.00033554 -0.46287238  
-0.00036159 0.99999880 0.00150641 -0.65958073  
-0.00033500 -0.00150654 0.99999881 0.32002281  
Axis -0.95041723 0.21151699 -0.22796416  
Axis point 0.00000000 246.46942257 469.98187871  
Rotation angle (degrees) 0.09081766  
Shift along axis 0.22745563  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_Sample/0057_6gsm/0057_6gsm_G_fitted.cif #1


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

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.5 (Core Profile) Mesa 22.3.0
OpenGL renderer: llvmpipe (LLVM 15.0.0, 256 bits)
OpenGL vendor: Mesa/X.org

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=xfce
XDG_SESSION_DESKTOP=
XDG_CURRENT_DESKTOP=XFCE
DISPLAY=:1006.0
Manufacturer: Dell Inc.
Model: PowerEdge R640
OS: Rocky Linux 8.8 Green Obsidian
Architecture: 64bit 
Virtual Machine: none
CPU: 80 Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz
Cache Size: 28160 KB
Memory:
	MemTotal:       196640872 kB
	MemFree:        39525448 kB
	MemAvailable:   160145432 kB

Graphics:
	unknown

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: 1.5.9.1
    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: 1.43.10
    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: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    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: 1.6.1
    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: 1.1.1
    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: 1.1.1
    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: 2.0.12
    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: 1.10.1
    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-QScore: 1.0
    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: 1.10.3
    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: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 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
    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: 4.39.3
    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: 3.5.0
    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
    torch: 1.13.1+cu117
    torchaudio: 0.13.1+cu117
    torchvision: 0.14.1+cu117
    tornado: 6.3.1
    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

[pett]

Best guess is trying to get a property of a bad/dead residue. Probably not enough info to reproduce.