id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14409 Crash in garbage collection while showing alignment chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.0-x86_64-i386-64bit ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x000000031e0c0000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031d0bd000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031c0ba000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031a0b4000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031b0b7000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x0000000205059240 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/core/_internal.py"", line 255 in __init__ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py"", line 333 in pointer File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py"", line 251 in set_cvec_pointer File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 133 in __init__ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 807 in __init__ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 73 in _non_null_atoms File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py"", line 209 in get_prop File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py"", line 1933 in _colorize_label File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py"", line 2294 in _layout_line File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py"", line 2334 in layout_lines File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py"", line 1638 in __init__ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py"", line 1643 in __init__ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py"", line 1643 in __init__ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py"", line 1643 in __init__ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py"", line 1643 in __init__ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py"", line 1643 in __init__ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py"", line 1643 in __init__ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py"", line 1643 in __init__ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py"", line 1643 in __init__ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py"", line 783 in layout_alignment File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py"", line 205 in __init__ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/tool.py"", line 167 in _finalize_init File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/tool.py"", line 55 in __init__ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/tool.py"", line 928 in _start_seq_viewer File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/__init__.py"", line 48 in run_provider File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py"", line 1302 in run_provider File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py"", line 397 in run_provider File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/manager.py"", line 258 in new_alignment File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py"", line 241 in seqalign_chain File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/show_sequences/tool.py"", line 77 in show_seqs File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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, lxml._elementpath, lxml.etree, 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, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.mmcif.mmcif_write (total: 55) {""app_name"":""ChimeraX"",""timestamp"":""2024-01-18 16:33:36.00 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""reportNotes"" : [ ""PC register does not match crashing frame (0x0 vs 0x7FF89181AA78)"" ] } ===== Log before crash start ===== UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/yiyingli/Library/CloudStorage/OneDrive- > UCSanDiego/FtsH_1D/CryoEM_1D/TO SAVE DATA > W3/cryosparc_P3_J171_006_volume_map_sym_sharp.mrc"" format mrc Opened cryosparc_P3_J171_006_volume_map_sym_sharp.mrc as #1, grid size 448,448,448, pixel 0.86, shown at level 0.894, step 2, values float32 > open /Users/yiyingli/Library/CloudStorage/OneDrive- > UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/fresh_group1_assembly.cif Summary of feedback from opening /Users/yiyingli/Library/CloudStorage/OneDrive- UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/fresh_group1_assembly.cif --- warnings | Unknown polymer entity '1' near line 342 Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for fresh_group1_assembly.cif #2 --- Chain | Description K M O Q S U W Y a c e g i k m o q s u | No description available > hide atoms > show cartoons > hide #!1 models > ui tool show ""Change Chain IDs"" > changechains 2 1 Chain IDs of 68 residues changed > open formats Command Script --- File format| Short name(s)| Suffixes ChimeraX commands| cmd| .cxc Compiled Python code| compiled python| .pyc, .pyo Python code| python| .py Documentation --- File format| Short name(s)| Suffixes HTML| html| .html, .htm, .xhtml, .xht, .xml Generic 3D Objects --- File format| Short name(s)| Suffixes Chimera BILD object| bild| .bild, .bld COLLADA| collada| .dae Direction dependent resolution values| fsc| .dres glTF| gltf| .glb Interatomic pseudobonds| pseudobonds| .pb Marker model| markers| .cmm Model Positions| positions| .positions Mole tunnels| mole| .json NMR-STAR distance restraints*| nmrstr| .str STL (3D printing)| stl| .stl STORM microscopy| storm| .storm SWC neuron traces| swc| .swc VTK PolyData| vtk| .vtk Wavefront OBJ| obj| .obj *Not installed; click on link to install Geometric Model --- File format| Short name(s)| Suffixes ArtiaX geometric model*| geomodel| .axm *Not installed; click on link to install Higher-Order Structure --- File format| Short name(s)| Suffixes Integrative/Hybrid Models| ihm| .ihm Image --- File format| Short name(s)| Suffixes photo| photo| .jpg Medical Imaging --- File format| Short name(s)| Suffixes DICOM| dicom| .dcm Molecular Structure --- File format| Short name(s)| Suffixes Amber SQM output file*| sqmout| .sqmout AutoDock PDBQT| pdbqt| .pdbqt Formatted Checkpoint file*| fchk| .fchk Gaussian input file*| com| .com, .gjf Gaussian output file*| log| .log Gromos87 structure| gro| .gro Macromolecular Transmission| mmtf| .mmtf Maestro| schrodinger maestro| .mae, .maegz mmCIF| mmcif| .cif, .mmcif MOL/SDF| sdf| .sdf, .mol Mol2| mol2| .mol2 NBO input file*| nbo47| .47 NBO output file*| nbo31| .31 ORCA output file*| out| .out PDB| pdb| .pdb, .pdb1, .ent, .pqr PSF| psf| .psf Psi4 output file*| dat| .dat, .out Q-Chem output file*| qout| .qout, .out, .dat RMF*| rmf| .rmf, .rmf3 Small Molecule CIF| corecif or smallcif| .cif SwissDock| swissdock| .pdb VIPERdb| viperdb| .vdb XYZ coordinate file*| xyz| .xyz ZDOCK| zdock| .pdb *Not installed; click on link to install Molecular Trajectory --- File format| Short name(s)| Suffixes Amber netCDF format| amber| .nc DCD trajectory format| dcd| .dcd Gromacs trr format| trr| .trr Gromacs xtc format| xtc| .xtc XYZ trajectory file*| allxyz| .allxyz *Not installed; click on link to install Particle List --- File format| Short name(s)| Suffixes Artiatomi particle lists*| motl or motivelist| .em Dynamo particle table*| dynamo or tbl| .tbl IMOD model2point output*| coords or model2point| .coords PEET model/csv*| peet| .mod RELION star files*| star or relion| .star TSV particle lists*| generic_particles| .tsv *Not installed; click on link to install Sequence --- File format| Short name(s)| Suffixes Clustal ALN sequence| aln or clustal| .aln, .clustal, .clustalw, .clustalx FASTA sequence| fasta| .fa, .fasta, .afasta, .afa HSSP sequence| hssp| .hssp MSF sequence| msf| .msf Pfam sequence| pfam| .selex, .slx, .pfam PIR sequence| pir| .ali, .pir RSF sequence| rsf| .rsf Stockholm sequence| stockholm| .sth, .sto Session --- File format| Short name(s)| Suffixes ChimeraX session| session| .cxs Structure Analysis --- File format| Short name(s)| Suffixes Attributes| defattr| .defattr Structure Factors --- File format| Short name(s)| Suffixes MTZ*| mtz| .mtz *Not installed; click on link to install Volume Data --- File format| Short name(s)| Suffixes Amira mesh| amira| .am APBS potential| apbs| .dx BRIX density map| brix| .brix CCP4 density map| ccp4| .ccp4, .map Chimera map| cmap| .cmap, .cmp CNS or XPLOR density map| xplor| .cns, .xplor DelPhi or GRASP potential| delphi| .phi DeltaVision map| dv| .dv DOCK scoring grid| dock| .bmp, .cnt, .nrg DSN6 density map| dsn6| .omap EMAN HDF map| emanhdf| .hdf, .hdf5, .h5 EMDB SFF| sff| .sff, .hff Gaussian cube grid| cube| .cube, .cub gOpenMol grid| gopenmol| .plt HDF map| hdf| Image stack| images| .tif, .tiff, .png, .pgm IMAGIC density map| imagic| .hed, .img Imaris map| ims| .ims IMOD map| imodmap| .rec IMOD model| imod| .imod, .mod MacMolPlt grid| macmolplt| .mmp MRC density map| mrc| .mrc NetCDF map| netcdfmap| .nc NIfTI| nifti| .nii, .nii.gz NRRD| nrrd| .nrrd Priism microscope image| priism| .xyzw, .xyzt PROFEC free energy grid| profec| .profec Purdue image format| pif| .pif Segger segmentation| segger| .seg SITUS map file| situs| .sit, .situs SPIDER volume data| spider| .spi, .vol TOM toolbox EM density map| tom_em| .em UHBD grid, binary| uhbd| .grd Database| Formats ---|--- alphafold| mmcif ccd| ccd cellpack| cellpack cod| cod eds| ccp4 edsdiff| ccp4 emdb| ccp4 emdb_china| ccp4 emdb_europe| ccp4 emdb_fits| ccp4 emdb_japan| ccp4 emdb_us| ccp4 esmfold| pdb iupac| iupac pcod| pcod pdb| mmcif, mmtf, pdb pdb_nmr| nmrstr pdbdev| ihm pdbe| mmcif, pdb pdbe_bio| mmcif pdbj| mmcif, pdb pubchem| sdf rcsb_bio| mmcif smiles| smiles uniprot| uniprot > log metadata #2 No models had metadata > log chains #2 Chain information for fresh_group1_assembly.cif #2 --- Chain | Description K M O Q S U W Y a c e g i k m o q s u | No description available > select /K:156-605 3131 atoms, 3173 bonds, 403 residues, 1 model selected > show #!1 models > hide #!1 models > changechains #2/K A Proposed chain ID change would produce multiple residues with the samechain- ID/number/insertion-code combo (A/800/) > select ::name=""HOH"" 2040 atoms, 2040 residues, 1 model selected > delete sel > show #!1 models > view orient > save /Users/yiyingli/Library/CloudStorage/OneDrive- > UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/fresh_group1_assembly2.cif relModel > #2 Not saving entity_poly_seq for non-authoritative sequences > open /Users/yiyingli/Library/CloudStorage/OneDrive- > UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/fresh_group1_assembly2.cif Summary of feedback from opening /Users/yiyingli/Library/CloudStorage/OneDrive- UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/fresh_group1_assembly2.cif --- warnings | Unknown polymer entity '1' near line 281 Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for fresh_group1_assembly2.cif #3 --- Chain | Description K M O Q S U W Y a c e g i k m o q s u | No description available > hide #!2 models > hide atoms > show cartoons > volume #1 level 2 > volume #1 step 1 > hide #!3 models > close #2 > log metadata #3 No models had metadata > log chains #3 Chain information for fresh_group1_assembly2.cif #3 --- Chain | Description K M O Q S U W Y a c e g i k m o q s u | No description available > open ""/Users/yiyingli/Library/CloudStorage/OneDrive- > UCSanDiego/FtsH_1D/CryoEM_1D/CryoEM > final/ATP_C1_class1/helix_ATP_C1_refined.pdb"" Summary of feedback from opening /Users/yiyingli/Library/CloudStorage/OneDrive- UCSanDiego/FtsH_1D/CryoEM_1D/CryoEM final/ATP_C1_class1/helix_ATP_C1_refined.pdb --- warnings | Ignored bad PDB record found on line 20 Ignored bad PDB record found on line 21 GEOMETRY RESTRAINTS LIBRARY: CDL v1.2 Ignored bad PDB record found on line 22 DEVIATIONS FROM IDEAL VALUES. Ignored bad PDB record found on line 23 BOND : 0.007 0.097 96540 Ignored bad PDB record found on line 24 ANGLE : 0.891 19.396 130620 18 messages similar to the above omitted Chain information for helix_ATP_C1_refined.pdb #2 --- Chain | Description 1 3 5 7 A C E G I K M O Q S U W Y a c e g i k m o q s u w y | No description available > close #2 > log metadata #3 No models had metadata > log chains #3 Chain information for fresh_group1_assembly2.cif #3 --- Chain | Description K M O Q S U W Y a c e g i k m o q s u | No description available > open /Users/yiyingli/Library/CloudStorage/OneDrive- > UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/fresh_group1_assembly_rename.cif Summary of feedback from opening /Users/yiyingli/Library/CloudStorage/OneDrive- UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/fresh_group1_assembly_rename.cif --- warning | Unknown polymer entity '1' near line 27 > log metadata #3 No models had metadata > log chains #3 Chain information for fresh_group1_assembly2.cif #3 --- Chain | Description K M O Q S U W Y a c e g i k m o q s u | No description available > log metadata #2 The model has no metadata > log chains #2 > hide #2 models > show #2 models > open /Users/yiyingli/Library/CloudStorage/OneDrive- > UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/fresh_group1_assembly_rename2.cif Summary of feedback from opening /Users/yiyingli/Library/CloudStorage/OneDrive- UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/fresh_group1_assembly_rename2.cif --- warning | Unknown polymer entity '1' near line 27 > log metadata #4 The model has no metadata > log chains #4 > open /Users/yiyingli/Library/CloudStorage/OneDrive- > UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/fresh_group1_assembly3.cif Summary of feedback from opening /Users/yiyingli/Library/CloudStorage/OneDrive- UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/fresh_group1_assembly3.cif --- warning | Unknown polymer entity '1' near line 27 > close #4 > close #2 > close #5 > log metadata #3 No models had metadata > log chains #3 Chain information for fresh_group1_assembly2.cif #3 --- Chain | Description K M O Q S U W Y a c e g i k m o q s u | No description available > select /K:156-605 3131 atoms, 3173 bonds, 403 residues, 1 model selected > show #!3 models > open /Users/yiyingli/Library/CloudStorage/OneDrive- > UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/fresh_group1_assembly3.cif Summary of feedback from opening /Users/yiyingli/Library/CloudStorage/OneDrive- UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/fresh_group1_assembly3.cif --- warning | Unknown polymer entity '1' near line 27 > ui tool show ""Show Sequence Viewer"" > sequence chain #3/K Alignment identifier is 3/K > sequence chain #3/M Alignment identifier is 3/M > sequence chain #3/O Alignment identifier is 3/O > sequence chain #3/Q Alignment identifier is 3/Q > sequence chain #3/S Alignment identifier is 3/S > sequence chain #3/U Alignment identifier is 3/U ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 86 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: Mac Model Identifier: Mac14,2 Model Number: FLY13LL/A Chip: Unknown Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 10151.1.1 OS Loader Version: 10151.1.1 Software: System Software Overview: System Version: macOS 14.0 (23A344) Kernel Version: Darwin 23.0.0 Time since boot: 21 hours, 14 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL U2414H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 50.00Hz Mirror: Off Online: Yes Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 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: 2022.12.7 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 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-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 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.0 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: 5.5.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 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: 21.3 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-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 setuptools-scm: 7.0.5 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 }}} " defect closed normal Core can't reproduce Tom Goddard all ChimeraX