Crash opening mmCIF

[r.xie@…]

The following bug report has been submitted:
Platform:        Linux-6.5.0-41-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x00007761d3ec6b80 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/mmcif/__init__.py", line 54 in open
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 484 in remember_data_format
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 513 in collated_open
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 213 in provider_open
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 131 in cmd_open
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 1979 in _open_dropped_file
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 614 in dropEvent
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, lxml._elementpath, lxml.etree, chimerax.map._map, chimerax.surface._surface, 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, PIL._imagingmath (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  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /mnt/DATA/ren/Input_ntps/uniprot_unique/val_pdb/2X1V_final.cif

Summary of feedback from opening
/mnt/DATA/ren/Input_ntps/uniprot_unique/val_pdb/2X1V_final.cif  
---  
warnings | Unknown polymer entity '1 1' near line 185  
Unknown polymer entity '1 2' near line 244  
Unknown polymer entity '1 3' near line 330  
Unknown polymer entity '1 4' near line 411  
Unknown polymer entity '1 5' near line 488  
4 messages similar to the above omitted  
Skipping atom "CB" near line 859: missing coordinates  
Unknown polymer entity '1 10' near line 885  
Unknown polymer entity '1 11' near line 962  
Unknown polymer entity '1 12' near line 1046  
Skipping atom "CD" near line 1061: missing coordinates  
Skipping atom "CE" near line 1062: missing coordinates  
Skipping atom "NZ" near line 1063: missing coordinates  
Unknown polymer entity '1 13' near line 1121  
Skipping atom "O" near line 1242: missing coordinates  
Skipping atom "O" near line 1244: missing coordinates  
Skipping atom "O" near line 1267: missing coordinates  
Skipping atom "O" near line 1334: missing coordinates  
Skipping atom "O" near line 1335: missing coordinates  
1 messages similar to the above omitted  
Unable to fetch template for 'GDP': will connect using distance criteria  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for 2X1V_final.cif #1  
---  
Chain | Description  
A | No description available  
  

> close #1

> open /mnt/DATA/ren/Input_ntps/uniprot_unique/val_pdb/2A5J_final.cif

Summary of feedback from opening
/mnt/DATA/ren/Input_ntps/uniprot_unique/val_pdb/2A5J_final.cif  
---  
warnings | Skipping atom "CD1" near line 258: missing coordinates  
Skipping atom "CG" near line 268: missing coordinates  
Skipping atom "OD1" near line 269: missing coordinates  
Skipping atom "OD2" near line 270: missing coordinates  
Skipping atom "CG2" near line 508: missing coordinates  
26 messages similar to the above omitted  
Unknown polymer entity '1 1' near line 778  
Skipping atom "N" near line 778: missing coordinates  
Skipping atom "CA" near line 779: missing coordinates  
Skipping atom "C" near line 780: missing coordinates  
Skipping atom "O" near line 781: missing coordinates  
Skipping atom "CB" near line 782: missing coordinates  
575 messages similar to the above omitted  
Bad residue range for struct_conf "STRN4" near line 3278  
Bad residue range for struct_conf "HELX_RH_AL_P3" near line 3280  
Bad residue range for struct_conf "HELX_RH_AL_P4" near line 3282  
Bad residue range for struct_conf "STRN5" near line 3285  
Bad residue range for struct_conf "HELX_RH_3T_P2" near line 3287  
3 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "A D" near line 2918  
Invalid sheet range for struct_sheet_range "A E" near line 2919  
Invalid sheet range for struct_sheet_range "A F" near line 2921  
Unable to connect ASP /A:92 and TYR /A:91  
Unable to connect ASP /A:92 and ILE /A:93  
Expected gap or linking atoms for ILE /A:93 and THR /A:94  
Unable to connect ILE /A:93 and THR /A:94  
Unable to connect ARG /A:95 and THR /A:94  
Unable to connect ARG /A:96 and GLU /A:97  
Expected gap or linking atoms for GLU /A:97 and THR /A:98  
Unable to connect GLU /A:97 and THR /A:98  
Unable to connect PHE /A:99 and THR /A:98  
Unable to connect PHE /A:99 and ASN /A:100  
Expected gap or linking atoms for ASN /A:100 and HIS /A:101  
Unable to connect ASN /A:100 and HIS /A:101  
Expected gap or linking atoms for HIS /A:101 and LEU /A:102  
Unable to connect HIS /A:101 and LEU /A:102  
Unable to connect THR /A:103 and LEU /A:102  
Unable to connect THR /A:103 and SER /A:104  
Unable to connect TRP /A:105 and SER /A:104  
Unable to connect TRP /A:105 and LEU /A:106  
Expected gap or linking atoms for LEU /A:106 and GLU /A:107  
Unable to connect LEU /A:106 and GLU /A:107  
Unable to connect ASP /A:108 and GLU /A:107  
Unable to connect ASP /A:108 and ALA /A:109  
Unable to connect ARG /A:110 and ALA /A:109  
Unable to connect ARG /A:110 and GLN /A:111  
Unable to connect HIS /A:112 and GLN /A:111  
Unable to connect SER /A:114 and SER /A:115  
Expected gap or linking atoms for SER /A:115 and ASN /A:116  
Unable to connect SER /A:115 and ASN /A:116  
Expected gap or linking atoms for ASN /A:116 and MET /A:117  
Unable to connect ASN /A:116 and MET /A:117  
Expected gap or linking atoms for MET /A:117 and VAL /A:118  
Unable to connect MET /A:117 and VAL /A:118  
Expected gap or linking atoms for VAL /A:118 and ILE /A:119  
Unable to connect VAL /A:118 and ILE /A:119  
Expected gap or linking atoms for ILE /A:119 and MET /A:120  
Unable to connect ILE /A:119 and MET /A:120  
Expected gap or linking atoms for MET /A:120 and LEU /A:121  
Unable to connect MET /A:120 and LEU /A:121  
Expected gap or linking atoms for LEU /A:121 and ILE /A:122  
Unable to connect LEU /A:121 and ILE /A:122  
Expected gap or linking atoms for ILE /A:122 and GLY /A:123  
Unable to connect ILE /A:122 and GLY /A:123  
Unable to connect ASN /A:124 and GLY /A:123  
Unable to connect LYS /A:125 and SER /A:126  
Unable to connect ASP /A:127 and SER /A:126  
Unable to connect GLU /A:129 and SER /A:130  
Unable to connect ARG /A:131 and SER /A:130  
Expected gap or linking atom in ILE /A:149 for LEU /A:148  
Unable to connect LEU /A:148 and ILE /A:149  
Unable to connect PHE /A:150 and ILE /A:149  
Unable to connect PHE /A:150 and MET /A:151  
Expected gap or linking atoms for MET /A:151 and GLU /A:152  
Unable to connect MET /A:151 and GLU /A:152  
Expected gap or linking atoms for GLU /A:152 and THR /A:153  
Unable to connect GLU /A:152 and THR /A:153  
Unable to connect SER /A:154 and THR /A:153  
Unable to connect CYS /A:159 and ASN /A:160  
Unable to connect VAL /A:161 and ASN /A:160  
Expected gap or linking atom in GLU /A:163 for GLU /A:162  
Unable to connect GLU /A:162 and GLU /A:163  
Expected gap or linking atoms for GLU /A:163 and ALA /A:164  
Unable to connect GLU /A:163 and ALA /A:164  
Expected gap or linking atom in ALA /A:164 for PHE /A:165  
Unable to connect PHE /A:165 and ALA /A:164  
Unable to connect ILE /A:166 and ASN /A:167  
Expected gap or linking atoms for ASN /A:167 and THR /A:168  
Unable to connect ASN /A:167 and THR /A:168  
Unable to connect ALA /A:169 and THR /A:168  
Unable to connect ALA /A:169 and LYS /A:170  
Expected gap or linking atoms for LYS /A:170 and GLU /A:171  
Unable to connect LYS /A:170 and GLU /A:171  
Expected gap or linking atoms for GLU /A:171 and ILE /A:172  
Unable to connect GLU /A:171 and ILE /A:172  
Expected gap or linking atoms for ILE /A:172 and TYR /A:173  
Unable to connect ILE /A:172 and TYR /A:173  
Unable to connect ARG /A:174 and TYR /A:173  
Unable to connect ARG /A:174 and LYS /A:175  
Unable to connect ILE /A:176 and LYS /A:175  
Unable to connect ILE /A:176 and GLN /A:177  
Unable to connect GLN /A:178 and GLN /A:177  
Skipping residue with duplicate label_seq_id 90 in chain A  
Unable to connect GLN /A:178 and GLY /A:179  
Unable to connect VAL /A:90 and GLY /A:179  
Atom N has no neighbors to form bonds with according to residue template for
LEU /A:88  
Atom O has no neighbors to form bonds with according to residue template for
LEU /A:88  
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /A:128  
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /A:128  
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /A:134  
Atom N has no neighbors to form bonds with according to residue template for
ILE /A:166  
Unable to fetch template for 'MG': will connect using distance criteria  
Unable to fetch template for 'GDP': will connect using distance criteria  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
2A5J_final.cif title:  
? [more info...]  
  
Chain information for 2A5J_final.cif #1  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in 2A5J_final.cif #1  
---  
ALA — alanine  
ARG — arginine  
ASN — asparagine  
ASP — asparticacid  
CYS — cysteine  
GDP — guanosine-5'-diphosphate  
GLN — glutamine  
GLU — glutamicacid  
GLY — glycine  
HIS — histidine  
ILE — isoleucine  
LEU — leucine  
LYS — lysine  
MET — methionine  
MG — magnesium ion  
PHE — phenylalanine  
PRO — proline  
SER — serine  
THR — threonine  
TRP — tryptophan  
TYR — tyrosine  
VAL — valine  
  

> close #1

> open /mnt/DATA/ren/Input_ntps/uniprot_unique/val_pdb/4XUS_final.cif


===== 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: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /mnt/DATA/ren/Input_ntps/uniprot_unique/val_pdb/5C2O_final.cif

Summary of feedback from opening
/mnt/DATA/ren/Input_ntps/uniprot_unique/val_pdb/5C2O_final.cif  
---  
warnings | Unknown polymer entity '1 1' near line 293  
Unknown polymer entity '1 2' near line 370  
Unknown polymer entity '1 3' near line 443  
Unknown polymer entity '1 4' near line 518  
Unknown polymer entity '1 5' near line 589  
9 messages similar to the above omitted  
Missing second residue in struct_conn "metalc1"  
Missing second residue in struct_conn "metalc2"  
Missing second residue in struct_conn "metalc3"  
Missing second residue in struct_conn "metalc5"  
Missing second residue in struct_conn "metalc6"  
9 messages similar to the above omitted  
Unable to fetch template for 'ZN': will connect using distance criteria  
Unable to fetch template for 'MG': will connect using distance criteria  
Unable to fetch template for 'TTP': will connect using distance criteria  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for 5C2O_final.cif #1  
---  
Chain | Description  
A B | No description available  
  

> close #1




OpenGL version: 3.3.0 NVIDIA 535.183.01
OpenGL renderer: NVIDIA GeForce RTX 3090/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: bluechip Computer AG
Model: bluechip BUSINESSline individu
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 32 AMD Ryzen 9 5950X 16-Core Processor
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            62Gi       8.3Gi        12Gi       151Mi        41Gi        53Gi
	Swap:             0B          0B          0B

Graphics:
	08:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA102 [GeForce RTX 3090] [10de:2204] (rev a1)	
	Subsystem: ASUSTeK Computer Inc. GA102 [GeForce RTX 3090] [1043:87b3]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.22.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.3.2
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

[pett]

Reported by Ren Xie

[Greg Couch]

Hello, please try opening the problem mmCIF file with ChimeraX 1.8. If that solves the problem, then please let us know. If that doesn't solve the problem then please send me the mmCIF file that caused the problem, so I can reproduce it the bug. If you need to keep the data private, then send it to me directly at gregc@….

[Greg Couch]

Any news? Does ChimeraX 1.8 fix the problem?

[Greg Couch]

No response from bug submitter. Need problematic mmCIF file to reproduce bug.