id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15387 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.3.1-x86_64-i386-64bit 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 0x00000002046ab240 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py"", line 157 in asArray File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py"", line 146 in File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py"", line 145 in asArray File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py"", line 146 in File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py"", line 145 in asArray File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 2828 in set_matrix File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 817 in set_projection_matrix File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 725 in _use_shader File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 801 in _opengl_shader File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 698 in shader File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 818 in _draw_geometry File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 787 in draw_self File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 780 in draw File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 1567 in _draw_multiple File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 1554 in draw_opaque File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 258 in _draw_scene File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 188 in draw File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py"", line 288 in render File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py"", line 113 in _redraw File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 149 in invoke File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 248 in _activate File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 217 in activate File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 393 in activate_trigger File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 100 in draw_new_frame File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 150 in _redraw_timer_callback File ""/Applications/ChimeraX-1.7.1.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-1.7.1.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-1.7.1.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, 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, lxml._elementpath, lxml.etree, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.alignment_algs._sw (total: 56) 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], ""experiments"" : [ { ""treatmentId"" : ""2dffbe18-a39a-4f33-ada9-2cce30af39ca"", ""experimentId"" : ""6384d56b96e8d228551ec182"", ""deploymentId"" : 400000023 }, { ""treatmentId"" : ""3dff9c91-a8fb-424e-a656-c8d6e6037574"", ""experimentId"" : ""662152ede2d11d1408c4db33"", ""deploymentId"" : 400000014 } ] }, ""reportNotes"" : [ ""PC register does not match crashing frame (0x0 vs 0x7FF896AEEA78)"" ] } ===== Log before crash start ===== Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle > camera ortho > cofr centerOfView > mousemode rightMode zoom > mousemode alt rightMode ""contour level"" > mousemode alt leftMode ""translate selected models"" > mousemode shift leftMode ""rotate selected models"" > mousemode alt control leftMode ""pick blobs"" > alias cofron cofr centerofview showpivot true > alias cofroff cofr centerofview showpivot false > alias cootmode set bgColor black; surface cap false; surface style solid; > lighting flat; graphics silhouettes false; style stick; ~rib; color > ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style > solvent ball; size ballscale 0.2; size stickradius 0.07; transparency 70; > cofr centerofview; clip near -10 far 10 position cofr; color ##~num_residues > cornflower blue > alias cootmode_mesh surface cap false; surface style mesh; lighting flat; > graphics silhouettes false; style stick; ~rib; color ##num_residues gold; > color byhet ; disp; ~disp @H*; style solvent ball; style ions ball; size > ballscale 0.2; size stickradius 0.07; cofr centerofview; clip near -10 far > 10 position cofr; color ##~num_residues #3d60ffff; transparency 50 > alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; > disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp > ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1 > alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp > @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius > 0.1 > alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000; > marker #10000 position cofr; sel ~sel; surface zone ##~num_residues > nearAtoms sel distance 15; close #10000 > alias map_unsphere surface unzone ##~num_residues > alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5; > lighting soft > alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker > #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel > distance 0; close #10000 > alias showmaps surface unzone ##~num_residues > alias caps_off surface cap false > alias caps_on surface cap true > alias selbetween ks ri > alias helix setattr $1 res is_helix true > alias strand setattr $1 res is_strand true > alias coil setattr $1 res is_strand false; setattr $1 res is_helix false > alias open_vseries ""open browse vseries true"" > buttonpanel Shortcuts rows 3 columns 4 > buttonpanel Shortcuts add Vol_Viewer command ""tool show 'Volume Viewer'"" > buttonpanel Shortcuts add Model_Panel command ""tool show Models"" > buttonpanel Shortcuts add Log command ""tool show Log"" > buttonpanel Shortcuts add default_disp command default_mol_display > buttonpanel Shortcuts add map_sphere command map_sphere_15 > buttonpanel Shortcuts add map_unsphere command map_unsphere > buttonpanel Shortcuts add cofron command cofron > buttonpanel Shortcuts add cofroff command cofroff > buttonpanel Shortcuts add cootmode command cootmode > buttonpanel Shortcuts add mark_cofr command ""marker #20000 position cofr"" > buttonpanel Shortcuts add hidemaps command hidemaps > buttonpanel Shortcuts add showmaps command showmaps 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 ""/Users/raop/Documents/Orexin/maps and models/three types of GPCR > ligands.pdb"" format pdb Summary of feedback from opening /Users/raop/Documents/Orexin/maps and models/three types of GPCR ligands.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 25 TYR A 39 1 15 Start residue of secondary structure not found: HELIX 2 2 GLN A 44 ARG A 73 1 30 Start residue of secondary structure not found: HELIX 3 3 HIS A 75 MET A 77 1 3 Start residue of secondary structure not found: HELIX 4 4 VAL A 80 CYS A 99 1 20 Start residue of secondary structure not found: HELIX 5 5 LEU A 100 THR A 109 1 10 41 messages similar to the above omitted End residue of secondary structure not found: HELIX 22 22 CYS B 12 HIS B 21 1 10 End residue of secondary structure not found: HELIX 23 23 ALA B 27 GLY B 29 1 3 Start residue of secondary structure not found: SHEET 1 1 1 MET A 183 SER A 187 0 Start residue of secondary structure not found: SHEET 2 2 1 SER A 200 GLU A 204 0 Start residue of secondary structure not found: HELIX 1 1 PRO A 25 TYR A 39 1 15 Start residue of secondary structure not found: HELIX 2 2 GLN A 44 ARG A 73 1 30 Start residue of secondary structure not found: HELIX 3 3 HIS A 75 MET A 77 1 3 8 messages similar to the above omitted End residue of secondary structure not found: HELIX 12 12 SER A 252 ARG A 256 1 5 Start residue of secondary structure not found: HELIX 13 13 ASN A 257 LYS A 259 1 3 Start residue of secondary structure not found: HELIX 14 14 PRO A 261 GLN A 270 1 10 Start residue of secondary structure not found: HELIX 15 15 GLY A 271 SER A 273 1 3 Start residue of secondary structure not found: HELIX 16 16 PRO A 278 LEU A 312 1 35 Start residue of secondary structure not found: HELIX 17 17 PRO A 313 ARG A 322 1 10 3 messages similar to the above omitted End residue of secondary structure not found: HELIX 21 21 ASP B 5 CYS B 7 1 3 Start residue of secondary structure not found: HELIX 22 22 CYS B 12 HIS B 21 1 10 Start residue of secondary structure not found: HELIX 23 23 ALA B 27 GLY B 29 1 3 Start residue of secondary structure not found: SHEET 1 1 1 MET A 183 SER A 187 0 Start residue of secondary structure not found: SHEET 2 2 1 SER A 200 GLU A 204 0 Start residue of secondary structure not found: HELIX 1 1 PRO A 25 TYR A 39 1 15 8 messages similar to the above omitted End residue of secondary structure not found: HELIX 10 10 LEU A 210 TYR A 224 1 15 Start residue of secondary structure not found: HELIX 11 11 LEU A 225 TRP A 243 1 19 Start residue of secondary structure not found: HELIX 12 12 SER A 252 ARG A 256 1 5 Start residue of secondary structure not found: HELIX 13 13 ASN A 257 LYS A 259 1 3 Start residue of secondary structure not found: HELIX 14 14 PRO A 261 GLN A 270 1 10 Start residue of secondary structure not found: HELIX 15 15 GLY A 271 SER A 273 1 3 3 messages similar to the above omitted End residue of secondary structure not found: HELIX 19 19 ARG A 333 LEU A 361 1 29 Start residue of secondary structure not found: HELIX 20 20 GLY A 363 CYS A 376 1 14 Start residue of secondary structure not found: HELIX 21 21 ASP B 5 CYS B 7 1 3 Start residue of secondary structure not found: HELIX 22 22 CYS B 12 HIS B 21 1 10 Start residue of secondary structure not found: HELIX 23 23 ALA B 27 GLY B 29 1 3 Start residue of secondary structure not found: SHEET 1 1 1 MET A 183 SER A 187 0 1 messages similar to the above omitted Chain information for three types of GPCR ligands.pdb --- Chain | Description 1.1/A | No description available 1.2/A | No description available 1.3/A 1.3/F | No description available 1.4/A | No description available 1.5/A | No description available 1.1/B | No description available 1.3/B 1.3/C 1.3/D 1.3/J 1.3/N 1.3/O | No description available 1.4/B | No description available 1.4/C | No description available 1.3/E | No description available 1.4/E | No description available 1.3/G | No description available 1.3/H | No description available 1.3/I | No description available 1.3/K | No description available 1.3/L | No description available 1.4/L | No description available 1.3/M | No description available 1.3/P | No description available 1.3/Q | No description available 1.3/R | No description available 1.4/R | No description available > set bgColor white > select #1.1/A 2868 atoms, 2948 bonds, 357 residues, 1 model selected > open 2x6g 2x6g title: X-ray Structure of Macrophage Inflammatory Protein-1 α (D27A) [more info...] Chain information for 2x6g #2 --- Chain | Description | UniProt A B C D E F G H I J K L M N O P Q R | C-C MOTIF CHEMOKINE 3 | CCL3_HUMAN 1-70 2x6g mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 3| author_and_software_defined_assembly 4| author_and_software_defined_assembly 5| author_and_software_defined_assembly 6| author_and_software_defined_assembly 7| author_and_software_defined_assembly 8| author_and_software_defined_assembly 9| author_and_software_defined_assembly > close #1.1-2#1#1.3-5 > select /A 562 atoms, 532 bonds, 110 residues, 1 model selected > select ~sel 9029 atoms, 8860 bonds, 2 pseudobonds, 1497 residues, 2 models selected > hide sel cartoons > hide sel atoms > select /A 562 atoms, 532 bonds, 110 residues, 1 model selected > show sel cartoons > hide sel atoms > select /B 542 atoms, 526 bonds, 95 residues, 1 model selected > hide sel atoms > hide sel cartoons > show sel cartoons > hide #!2 models > show #!2 models > select add #2 9591 atoms, 9392 bonds, 2 pseudobonds, 1607 residues, 2 models selected > color (#!2 & sel) #fff2ffff > color (#!2 & sel) #fff0ffff > color (#!2 & sel) #ffdcffff > color (#!2 & sel) #ffc3ffff > color (#!2 & sel) #ffb5ffff > color (#!2 & sel) #ffafffff > color (#!2 & sel) #ffadffff > color (#!2 & sel) #ffabffff > color (#!2 & sel) #ffa7ffff > color (#!2 & sel) #ffa2ffff > color (#!2 & sel) #ff9cffff > color (#!2 & sel) #ef9cffff > color (#!2 & sel) #da9cffff > color (#!2 & sel) #c99cffff > color (#!2 & sel) #bf9cffff > color (#!2 & sel) #ba9cffff > color (#!2 & sel) #b89cffff > color (#!2 & sel) #b69cffff > color (#!2 & sel) #b49cffff > color (#!2 & sel) #b29cffff > color (#!2 & sel) #b19cffff > color (#!2 & sel) #af9cffff > color (#!2 & sel) #ac9cffff > color (#!2 & sel) #a99cffff > color (#!2 & sel) #a79cffff > color (#!2 & sel) #a59cffff > color (#!2 & sel) #a49cffff > color (#!2 & sel) #a09cffff > color (#!2 & sel) #999cffff > color (#!2 & sel) #919cffff > color (#!2 & sel) #8b9cffff > color (#!2 & sel) #889cffff > color (#!2 & sel) #859cffff > color (#!2 & sel) #849cffff > color (#!2 & sel) #829cffff > color (#!2 & sel) #809cffff > color (#!2 & sel) #899cffff > color (#!2 & sel) #8f9cffff > color (#!2 & sel) #949cffff > color (#!2 & sel) #969cffff > color (#!2 & sel) #968bffff > color (#!2 & sel) #9673ffff > color (#!2 & sel) #9665ffff > color (#!2 & sel) #965cffff > color (#!2 & sel) #9654ffff > color (#!2 & sel) #964effff > color (#!2 & sel) #964affff > color (#!2 & sel) #9647ffff > color (#!2 & sel) #9646ffff > color (#!2 & sel) #9645ffff > color (#!2 & sel) #9545ffff > color (#!2 & sel) #8545ffff > color (#!2 & sel) #7245ffff > color (#!2 & sel) #6845ffff > color (#!2 & sel) #6345ffff > color (#!2 & sel) #6045ffff > color (#!2 & sel) #5f45ffff > color (#!2 & sel) #5c45ffff > color (#!2 & sel) #5845ffff > color (#!2 & sel) #5445ffff > color (#!2 & sel) #5445f2ff > color (#!2 & sel) #5445e8ff > color (#!2 & sel) #5445e0ff > color (#!2 & sel) #5445d9ff > color (#!2 & sel) #5445d4ff > color (#!2 & sel) #5445d1ff > color (#!2 & sel) #5445cfff > color (#!2 & sel) #5445cbff > color (#!2 & sel) #5445c7ff > color (#!2 & sel) #5445c4ff > color (#!2 & sel) #5445c1ff > color (#!2 & sel) #5445beff > color (#!2 & sel) #5445bdff > color (#!2 & sel) #5445baff > color (#!2 & sel) #5445b8ff > color (#!2 & sel) #5445b5ff > color (#!2 & sel) #5445b4ff > color (#!2 & sel) #5445aeff > color (#!2 & sel) #5445a8ff > color (#!2 & sel) #5445a2ff > color (#!2 & sel) #54459bff > color (#!2 & sel) #544592ff > color (#!2 & sel) #54458bff > color (#!2 & sel) #544586ff > color (#!2 & sel) #544584ff > color (#!2 & sel) #544582ff > color (#!2 & sel) #544580ff > color (#!2 & sel) #544576ff > color (#!2 & sel) #544575ff > color (#!2 & sel) #544574ff > color (#!2 & sel) #544573ff > color (#!2 & sel) #544571ff > color (#!2 & sel) #54456cff > color (#!2 & sel) #544566ff > color (#!2 & sel) #544562ff > color (#!2 & sel) #54455fff > color (#!2 & sel) #54455eff > color (#!2 & sel) #54455cff > color (#!2 & sel) #544559ff > color (#!2 & sel) #544556ff > color (#!2 & sel) #544553ff > color (#!2 & sel) #544551ff > color (#!2 & sel) #544550ff > color (#!2 & sel) #54454fff > color (#!2 & sel) #544551ff > color (#!2 & sel) #544552ff > color (#!2 & sel) #544554ff > color (#!2 & sel) #544556ff > color (#!2 & sel) #544557ff > select clear > open 7o7f Summary of feedback from opening 7o7f fetched from pdb --- notes | Fetching compressed mmCIF 7o7f from http://files.rcsb.org/download/7o7f.cif Fetching CCD PCA from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/PCA/PCA.cif 7o7f title: Structural basis of the activation of the CC chemokine receptor 5 by a chemokine agonist [more info...] Chain information for 7o7f #1 --- Chain | Description | UniProt A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN 1-354 B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_BOVIN 1-340 C | C-C chemokine receptor type 5 | CCR5_HUMAN 1-352 F | Fab antibody fragment light chain | G | Guanine nucleotide-binding protein G(T) subunit gamma-T1 | GBG1_BOVIN 1-74 H | Fab antibody fragment heavy chain | I | C-C motif chemokine 5 | CCL5_HUMAN 0-68 > hide #!2 models > hide #!1 atoms > hide #!1 cartoons > show #!1 cartoons > show #!2 models > hide #!1 models > open 7wj5 Summary of feedback from opening 7wj5 fetched from pdb --- note | Fetching compressed mmCIF 7wj5 from http://files.rcsb.org/download/7wj5.cif 7wj5 title: Cryo-EM structure of human somatostatin receptor 2 complex with its agonist somatostatin delineates the ligand binding specificity [more info...] Chain information for 7wj5 #3 --- Chain | Description | UniProt A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN 1-354 B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340 C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71 E | Gai1 antibody (scfv16) | R | Soluble cytochrome b562,Somatostatin receptor type 2 | C562_ECOLX -105--1, SSR2_HUMAN 1-369 S | Somatostatin-14 (SST-14) | > show #!2-3 cartoons > hide #!2-3 atoms > ui mousemode right ""translate selected models"" > select #3/S 105 atoms, 110 bonds, 12 residues, 1 model selected > show sel atoms > style sel stick Changed 105 atom styles > color sel byhetero > ui tool show ""Show Sequence Viewer"" > sequence chain #3/S Alignment identifier is 3/S > select clear > select #3/S:3-10 75 atoms, 78 bonds, 8 residues, 1 model selected > select clear > close session > open ""/Users/raop/Documents/Orexin/maps and models/OX1R linker.pdb"" format > pdb Summary of feedback from opening /Users/raop/Documents/Orexin/maps and models/OX1R linker.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 25 TYR A 39 1 15 Start residue of secondary structure not found: HELIX 2 2 GLN A 44 ARG A 73 1 30 Start residue of secondary structure not found: HELIX 3 3 HIS A 75 MET A 77 1 3 Start residue of secondary structure not found: HELIX 4 4 VAL A 80 CYS A 99 1 20 Start residue of secondary structure not found: HELIX 5 5 LEU A 100 THR A 109 1 10 45 messages similar to the above omitted Chain information for OX1R linker.pdb --- Chain | Description 1.1/A | No description available 1.1/B | No description available 1.3/L | No description available 1.2/R | No description available 1.3/R | No description available > close session > open ""/Users/raop/Documents/Orexin/maps and models/OX1R.pdb"" format pdb Summary of feedback from opening /Users/raop/Documents/Orexin/maps and models/OX1R.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 25 TYR A 39 1 15 Start residue of secondary structure not found: HELIX 2 2 GLN A 44 ARG A 73 1 30 Start residue of secondary structure not found: HELIX 3 3 HIS A 75 MET A 77 1 3 Start residue of secondary structure not found: HELIX 4 4 VAL A 80 CYS A 99 1 20 Start residue of secondary structure not found: HELIX 5 5 LEU A 100 THR A 109 1 10 20 messages similar to the above omitted Chain information for OX1R.pdb --- Chain | Description 1.1/A | No description available 1.2/A | No description available 1.1/B | No description available > hide #1.2 models Drag select of 6 residues > delete atoms sel > delete bonds sel Drag select of 3 residues, 1 pseudobonds > delete atoms (#!1.1 & sel) > delete bonds (#!1.1 & sel) > select clear Drag select of 1 residues, 1 pseudobonds > delete atoms (#!1.1 & sel) > delete bonds (#!1.1 & sel) > close session > open ""/Users/raop/Documents/Orexin/maps and models/OX1R.pdb"" format pdb Summary of feedback from opening /Users/raop/Documents/Orexin/maps and models/OX1R.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 25 TYR A 39 1 15 Start residue of secondary structure not found: HELIX 2 2 GLN A 44 ARG A 73 1 30 Start residue of secondary structure not found: HELIX 3 3 HIS A 75 MET A 77 1 3 Start residue of secondary structure not found: HELIX 4 4 VAL A 80 CYS A 99 1 20 Start residue of secondary structure not found: HELIX 5 5 LEU A 100 THR A 109 1 10 20 messages similar to the above omitted Chain information for OX1R.pdb --- Chain | Description 1.1/A | No description available 1.2/A | No description available 1.1/B | No description available > hide #1.2 models > show #1.2 models > close #1.2 Drag select of 11 residues > select subtract /A:377 63 atoms, 10 residues, 1 model selected > delete atoms sel > delete bonds sel Drag select of 4 residues > select subtract /A:24 20 atoms, 3 residues, 1 model selected > delete atoms sel > delete bonds sel > ui tool show ""Color Actions"" > color bychain > lighting soft > graphics silhouettes true > select add /B:33 9 atoms, 8 bonds, 1 residue, 1 model selected > select add /B:32 16 atoms, 14 bonds, 2 residues, 1 model selected > select add /B:31 24 atoms, 21 bonds, 3 residues, 1 model selected > select add /A:119 30 atoms, 26 bonds, 4 residues, 1 model selected > select subtract /A:119 24 atoms, 21 bonds, 3 residues, 1 model selected > select add /B:30 32 atoms, 28 bonds, 4 residues, 1 model selected > select add /B:29 36 atoms, 31 bonds, 5 residues, 1 model selected > select add /B:28 41 atoms, 35 bonds, 6 residues, 1 model selected > select add /B:27 46 atoms, 39 bonds, 7 residues, 1 model selected > select add /B:26 56 atoms, 49 bonds, 8 residues, 1 model selected > select add /B:25 64 atoms, 56 bonds, 9 residues, 1 model selected > select add /B:24 68 atoms, 59 bonds, 10 residues, 1 model selected > color sel lime > color sel #544557ff > color sel #544657ff > color sel #544c57ff > color sel #544f57ff > color sel #545e57ff > color sel #546657ff > color sel #547157ff > color sel #547c57ff > color sel #549257ff > color sel #549c57ff > color sel #54a457ff > color sel #54ac57ff > color sel #54b857ff > color sel #54bc57ff > color sel #54c057ff > color sel #54c357ff > color sel #54c657ff > color sel #54c957ff > color sel #54cc57ff > color sel #54ce57ff > select /B:19 8 atoms, 7 bonds, 1 residue, 1 model selected > select add /B:20 16 atoms, 14 bonds, 2 residues, 1 model selected > select /B:15 11 atoms, 10 bonds, 1 residue, 1 model selected > select add /B:16 19 atoms, 17 bonds, 2 residues, 1 model selected > select add /B:20 27 atoms, 24 bonds, 3 residues, 1 model selected > select add /B:19 35 atoms, 31 bonds, 4 residues, 1 model selected > color sel #54ce57ff > color sel #54cd57ff > color sel #54cc57ff > color sel #54cb57ff > color sel #54cc57ff > color sel #54cd57ff > color sel #54ce57ff > color sel #54cf57ff > color sel #54ce57ff > color sel #54cd57ff > color sel #54cc57ff > color sel #54cd57ff > color sel #54cb57ff > color sel #54cc57ff > color sel #54cd57ff > color sel #54cf57ff > select clear > select /B:33 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel hot pink > select clear > select /B:14 6 atoms, 5 bonds, 1 residue, 1 model selected > color #1.1 #7b688cff > color #1.1 #7bc28cff > color #1.1 #b9c28cff > color #1.1 #b9c2cdff > select clear > select /B 248 atoms, 252 bonds, 33 residues, 1 model selected > color sel cornflower blue > ui tool show ""Color Actions"" > color sel midnight blue > color sel maroon > select clear > select add /B:33 9 atoms, 8 bonds, 1 residue, 1 model selected > select add /B:32 16 atoms, 14 bonds, 2 residues, 1 model selected > select add /B:31 24 atoms, 21 bonds, 3 residues, 1 model selected > select add /B:30 32 atoms, 28 bonds, 4 residues, 1 model selected > select add /B:29 36 atoms, 31 bonds, 5 residues, 1 model selected > select add /B:26 46 atoms, 41 bonds, 6 residues, 1 model selected > select add /B:20 54 atoms, 48 bonds, 7 residues, 1 model selected > select add /B:19 62 atoms, 55 bonds, 8 residues, 1 model selected > color sel cornflower blue > ui tool show ""Color Actions"" > color sel dark slate blue > color sel medium slate blue > color sel steel blue > color sel dodger blue > color sel deep sky blue > color sel turquoise > color sel medium turquoise > select clear > select /B 248 atoms, 252 bonds, 33 residues, 1 model selected > ui tool show ""Color Actions"" > color sel medium turquoise > select subtract /B:33 239 atoms, 243 bonds, 32 residues, 1 model selected > select clear > select /B:33 9 atoms, 8 bonds, 1 residue, 1 model selected > select add /B:32 16 atoms, 14 bonds, 2 residues, 1 model selected > select add /B:31 24 atoms, 21 bonds, 3 residues, 1 model selected > select add /B:30 32 atoms, 28 bonds, 4 residues, 1 model selected > select add /B:29 36 atoms, 31 bonds, 5 residues, 1 model selected > select add /B:26 46 atoms, 41 bonds, 6 residues, 1 model selected > select add /B:20 54 atoms, 48 bonds, 7 residues, 1 model selected > select add /B:19 62 atoms, 55 bonds, 8 residues, 1 model selected > ui tool show ""Color Actions"" > color sel maroon > select clear > ui tool show ""Side View"" > ui tool show Matchmaker > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1.1/A > select /A:25 7 atoms, 7 bonds, 1 residue, 1 model selected > select /A:25-40 156 atoms, 162 bonds, 16 residues, 1 model selected ===== Log before crash end ===== Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle > camera ortho > cofr centerOfView > mousemode rightMode zoom > mousemode alt rightMode ""contour level"" > mousemode alt leftMode ""translate selected models"" > mousemode shift leftMode ""rotate selected models"" > mousemode alt control leftMode ""pick blobs"" > alias cofron cofr centerofview showpivot true > alias cofroff cofr centerofview showpivot false > alias cootmode set bgColor black; surface cap false; surface style solid; > lighting flat; graphics silhouettes false; style stick; ~rib; color > ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style > solvent ball; size ballscale 0.2; size stickradius 0.07; transparency 70; > cofr centerofview; clip near -10 far 10 position cofr; color ##~num_residues > cornflower blue > alias cootmode_mesh surface cap false; surface style mesh; lighting flat; > graphics silhouettes false; style stick; ~rib; color ##num_residues gold; > color byhet ; disp; ~disp @H*; style solvent ball; style ions ball; size > ballscale 0.2; size stickradius 0.07; cofr centerofview; clip near -10 far > 10 position cofr; color ##~num_residues #3d60ffff; transparency 50 > alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; > disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp > ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1 > alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp > @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius > 0.1 > alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000; > marker #10000 position cofr; sel ~sel; surface zone ##~num_residues > nearAtoms sel distance 15; close #10000 > alias map_unsphere surface unzone ##~num_residues > alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5; > lighting soft > alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker > #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel > distance 0; close #10000 > alias showmaps surface unzone ##~num_residues > alias caps_off surface cap false > alias caps_on surface cap true > alias selbetween ks ri > alias helix setattr $1 res is_helix true > alias strand setattr $1 res is_strand true > alias coil setattr $1 res is_strand false; setattr $1 res is_helix false > alias open_vseries ""open browse vseries true"" > buttonpanel Shortcuts rows 3 columns 4 > buttonpanel Shortcuts add Vol_Viewer command ""tool show 'Volume Viewer'"" > buttonpanel Shortcuts add Model_Panel command ""tool show Models"" > buttonpanel Shortcuts add Log command ""tool show Log"" > buttonpanel Shortcuts add default_disp command default_mol_display > buttonpanel Shortcuts add map_sphere command map_sphere_15 > buttonpanel Shortcuts add map_unsphere command map_unsphere > buttonpanel Shortcuts add cofron command cofron > buttonpanel Shortcuts add cofroff command cofroff > buttonpanel Shortcuts add cootmode command cootmode > buttonpanel Shortcuts add mark_cofr command ""marker #20000 position cofr"" > buttonpanel Shortcuts add hidemaps command hidemaps > buttonpanel Shortcuts add showmaps command showmaps 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 OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M2 Pro 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: Mac14,10 Model Number: Z1740017JLL/A Chip: Unknown Total Number of Cores: 12 (8 performance and 4 efficiency) Memory: 32 GB System Firmware Version: 10151.81.1 OS Loader Version: 10151.81.1 Software: System Software Overview: System Version: macOS 14.3.1 (23D60) Kernel Version: Darwin 23.3.0 Time since boot: 31 days, 1 hour, 15 minutes Graphics/Displays: Apple M2 Pro: Chipset Model: Apple M2 Pro Type: GPU Bus: Built-In Total Number of Cores: 19 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: DELL U2723QE: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL U2723QE: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Installed Packages: alabaster: 0.7.16 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: 2.12.2 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-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-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 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: 21.3 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: 23.0 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: 1.0.8 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 }}} " defect closed normal Core duplicate Tom Goddard all ChimeraX