id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15981 Crash on display change, Mac, Qt 6.6 chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.6.1-arm64-arm-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x0000000331c9b000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000330c8f000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000032fc83000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000032ec77000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000032dc6b000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000032cc5f000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000032bc53000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000032ac47000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000329c3b000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031d23f000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031c233000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031b227000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031a21b000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x0000000208034f40 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 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.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, 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model panel to edit those fields UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/sierkml/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/TAF/fold_2024_09_12_17_05_taf7_importin_alpha/fold_2024_09_12_17_05_taf7_importin_alpha_model_0.cif > /Users/sierkml/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/TAF/fold_2024_09_12_17_05_taf7_importin_alpha/fold_2024_09_12_17_05_taf7_importin_alpha_model_1.cif > /Users/sierkml/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/TAF/fold_2024_09_12_17_05_taf7_importin_alpha/fold_2024_09_12_17_05_taf7_importin_alpha_model_2.cif > /Users/sierkml/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/TAF/fold_2024_09_12_17_05_taf7_importin_alpha/fold_2024_09_12_17_05_taf7_importin_alpha_model_3.cif > /Users/sierkml/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/TAF/fold_2024_09_12_17_05_taf7_importin_alpha/fold_2024_09_12_17_05_taf7_importin_alpha_model_4.cif Chain information for fold_2024_09_12_17_05_taf7_importin_alpha_model_0.cif #1 --- Chain | Description A | . B | . Chain information for fold_2024_09_12_17_05_taf7_importin_alpha_model_1.cif #2 --- Chain | Description A | . B | . Chain information for fold_2024_09_12_17_05_taf7_importin_alpha_model_2.cif #3 --- Chain | Description A | . B | . Chain information for fold_2024_09_12_17_05_taf7_importin_alpha_model_3.cif #4 --- Chain | Description A | . B | . Chain information for fold_2024_09_12_17_05_taf7_importin_alpha_model_4.cif #5 --- Chain | Description A | . B | . > hide #2 models > hide #3 models > hide #4 models > hide #5 models > color #1 bychain > show #2 models > hide #2 models > show #3 models > hide #3 models > hide #1 models > show #2 models > color #2 bychain > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A #2/A #3/A #4/A #5/A Alignment identifier is 1 > select #1/A:142 #2/A:142 #3/A:142 #4/A:142 #5/A:142 40 atoms, 35 bonds, 5 residues, 5 models selected > select #1/A:142-158 #2/A:142-158 #3/A:142-158 #4/A:142-158 #5/A:142-158 780 atoms, 785 bonds, 85 residues, 5 models selected . [ID: 1] region 5 chains [142-158] RMSD: 41.287 > select #1/A:236 #2/A:236 #3/A:236 #4/A:236 #5/A:236 35 atoms, 30 bonds, 5 residues, 5 models selected > select #1/A:236-245 #2/A:236-245 #3/A:236-245 #4/A:236-245 #5/A:236-245 425 atoms, 425 bonds, 50 residues, 5 models selected . [ID: 1] region 5 chains [236-245] RMSD: 78.944 > select #1/A:336 #2/A:336 #3/A:336 #4/A:336 #5/A:336 40 atoms, 35 bonds, 5 residues, 5 models selected > select #1/A:336-345 #2/A:336-345 #3/A:336-345 #4/A:336-345 #5/A:336-345 390 atoms, 385 bonds, 50 residues, 5 models selected . [ID: 1] region 5 chains [336-345] RMSD: 81.323 > hide #2 models > show #3 models > color sel & #3 bychain > select > #1/A:22-33,37-41,116-130,138-140,143-146,152-157,160-175,186-195,214-227,248-308,312-347 > #2/A:22-33,37-41,116-130,138-140,143-146,152-157,160-175,186-195,214-227,248-308,312-347 > #3/A:22-33,37-41,116-130,138-140,143-146,152-157,160-175,186-195,214-227,248-308,312-347 > #4/A:22-33,37-41,116-130,138-140,143-146,152-157,160-175,186-195,214-227,248-308,312-347 > #5/A:22-33,37-41,116-130,138-140,143-146,152-157,160-175,186-195,214-227,248-308,312-347 7535 atoms, 7535 bonds, 910 residues, 5 models selected > select clear > color #3 bychain > hide #3 models > show #4 models > color #4 bychain > hide #4 models > show #5 models > color #5 bychain > hide #5 models > close > open /Users/sierkml/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/TAF/fold_2024_09_12_17_06_taf7_crm1/fold_2024_09_12_17_06_taf7_crm1_model_0.cif > /Users/sierkml/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/TAF/fold_2024_09_12_17_06_taf7_crm1/fold_2024_09_12_17_06_taf7_crm1_model_1.cif > /Users/sierkml/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/TAF/fold_2024_09_12_17_06_taf7_crm1/fold_2024_09_12_17_06_taf7_crm1_model_2.cif > /Users/sierkml/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/TAF/fold_2024_09_12_17_06_taf7_crm1/fold_2024_09_12_17_06_taf7_crm1_model_3.cif > /Users/sierkml/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/TAF/fold_2024_09_12_17_06_taf7_crm1/fold_2024_09_12_17_06_taf7_crm1_model_4.cif Chain information for fold_2024_09_12_17_06_taf7_crm1_model_0.cif #1 --- Chain | Description A | . B | . Chain information for fold_2024_09_12_17_06_taf7_crm1_model_1.cif #2 --- Chain | Description A | . B | . Chain information for fold_2024_09_12_17_06_taf7_crm1_model_2.cif #3 --- Chain | Description A | . B | . Chain information for fold_2024_09_12_17_06_taf7_crm1_model_3.cif #4 --- Chain | Description A | . B | . Chain information for fold_2024_09_12_17_06_taf7_crm1_model_4.cif #5 --- Chain | Description A | . B | . > hide #2 models > hide #3 models > hide #4 models > hide #5 models > color #1 bychain > hide #1 models > show #2 models > color #2 bychain > hide #2 models > show #3 models > color #3 bychain > hide #3 models > show #4 models > color #4 bychain > hide #4 models > show #5 models > color #5 bychain > hide #5 models > close #3 > close > open /Users/sierkml/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/TAF/TAF_models.cxs opened ChimeraX session > hide #3 models > select clear > color #2 bychain > show #!1 models > hide #!1 models > hide #1.1 models > hide #2 models > show #2 models > show #3 models > hide #3 models > show #3 models > hide #3 models > select #2/A:41 9 atoms, 8 bonds, 1 residue, 1 model selected > style sel stick Changed 9 atom styles > show sel atoms > color sel byhetero > color sel byelement > select #2/A:44 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > color sel byelement > label sel text ""{0.name} {0.number}{0.insertion_code}"" > select #2/A:45 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color sel byelement > label sel text ""{0.name} {0.number}{0.insertion_code}"" > select #2/B:5 23 atoms, 25 bonds, 1 residue, 1 model selected > select up 619 atoms, 690 bonds, 29 residues, 1 model selected > style sel stick Changed 619 atom styles > hide sel cartoons > show sel atoms > color sel byelement > hide sel atoms > show sel atoms > nucleotides sel atoms > select clear > select #2/A:46 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > color sel byelement > label sel text ""{0.name} {0.number}{0.insertion_code}"" > select #2/A:49 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > color sel byelement > label sel text ""{0.name} {0.number}{0.insertion_code}"" > select #2/A:50 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color sel byelement > label sel text ""{0.name} {0.number}{0.insertion_code}"" > select #2/A:51 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > color sel byelement > label sel text ""{0.name} {0.number}{0.insertion_code}"" > select #2/A:41@CB 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 1 model selected > label sel text ""{0.name} {0.number}{0.insertion_code}"" > select #2/A:52 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2/A:53 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color sel byelement > label sel text ""{0.name} {0.number}{0.insertion_code}"" > select #2/B:9@C1' 1 atom, 1 residue, 1 model selected > select up 20 atoms, 21 bonds, 1 residue, 1 model selected > label sel text ""{0.name} {0.number}{0.insertion_code}"" > select #2/B:8@C1' 1 atom, 1 residue, 1 model selected > select up 20 atoms, 21 bonds, 1 residue, 1 model selected > label sel text ""{0.name} {0.number}{0.insertion_code}"" > select #2/B:7@C3' 1 atom, 1 residue, 1 model selected > select up 20 atoms, 21 bonds, 1 residue, 1 model selected > label sel text ""{0.name} {0.number}{0.insertion_code}"" > select #2/A:54 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color sel byelement > label sel text ""{0.name} {0.number}{0.insertion_code}"" > select #2/A:55 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color sel byelement > label sel text ""{0.name} {0.number}{0.insertion_code}"" > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 1 model selected > select down 2 atoms, 1 bond, 1 residue, 1 model selected > select down 1 bond, 1 model selected > select down 1 bond, 1 model selected > select down 1 bond, 1 model selected > select clear > set bgColor white > save /Users/sierkml/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/TAF/TAF_models.cxs > save /Users/sierkml/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/TAF/TAR_RBD_interface_all.png width 1264 height > 758 supersample 3 > show #3 models > hide #3 models > show #3 models > hide #3 models > interfaces #!2 & ~solvent 1 buried areas: A B 658 > interfaces #!2 & ~solvent 1 buried areas: A B 658 > select #2/B:8@OP2 1 atom, 1 residue, 1 model selected > select #2/A:50@NZ 1 atom, 1 residue, 1 model selected > select #2/B:8@OP2 1 atom, 1 residue, 1 model selected > select #2/A:50@NZ 1 atom, 1 residue, 1 model selected > select add #2/B:8@OP2 2 atoms, 2 residues, 1 model selected > ui tool show Distances > distance #2/A:50@NZ #2/B:8@OP2 Distance between fold_2024_08_06_16_17_taf7_rbd_tar_model_4.cif #2/A LYS 50 NZ and /B C 8 OP2: 2.632Å > select #2/A:44@NH1 1 atom, 1 residue, 1 model selected > select add #2/B:8@N4 2 atoms, 2 residues, 1 model selected > distance #2/A:44@NH1 #2/B:8@N4 Distance between fold_2024_08_06_16_17_taf7_rbd_tar_model_4.cif #2/A ARG 44 NH1 and /B C 8 N4: 4.177Å > save /Users/sierkml/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/TAF/TAR_RBD_Hbonds_1.png width 1264 height 758 > supersample 3 > select #2/B:8@C4 1 atom, 1 residue, 1 model selected > select add #2/A:48@CG 2 atoms, 2 residues, 1 model selected > distance #2/B:8@C4 #2/A:48@CG Distance between fold_2024_08_06_16_17_taf7_rbd_tar_model_4.cif #2/B C 8 C4 and /A PHE 48 CG: 9.308Å > ~distance #2/B:8@C4 #2/A:48@CG > select #2/B:19@OP1 1 atom, 1 residue, 1 model selected > select add #2/A:46@NH1 2 atoms, 2 residues, 1 model selected > distance #2/B:19@OP1 #2/A:46@NH1 Distance between fold_2024_08_06_16_17_taf7_rbd_tar_model_4.cif #2/B A 19 OP1 and /A ARG 46 NH1: 6.692Å > ~distance #2/B:19@OP1 #2/A:46@NH1 > select clear > select #2/A:53@NZ 1 atom, 1 residue, 1 model selected > select add #2/B:8@O2' 2 atoms, 2 residues, 1 model selected > distance #2/A:53@NZ #2/B:8@O2' Distance between fold_2024_08_06_16_17_taf7_rbd_tar_model_4.cif #2/A LYS 53 NZ and /B C 8 O2': 2.329Å > select #2/B:9@N3 1 atom, 1 residue, 1 model selected > view sel > cofr sel > ui tool show ""Side View"" > select #2/A:21 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #2/A:24 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #2/A:25 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #2/A:22 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #2/A:21 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:20 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:18 5 atoms, 4 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #2/A:47 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > color sel byelement > label sel text ""{0.name} {0.number}{0.insertion_code}"" > save /Users/sierkml/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/TAF/TAF_models.cxs > select #2/B:13@P 1 atom, 1 residue, 1 model selected > select up 20 atoms, 21 bonds, 1 residue, 1 model selected > select up 619 atoms, 690 bonds, 29 residues, 1 model selected > nucleotides sel stubs > nucleotides sel tube/slab shape box > nucleotides sel fill > style nucleic & sel stick Changed 619 atom styles > color sel bynucleotide > cartoon sel > save /Users/sierkml/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/TAF/TAR_bulge_RBD.png width 1264 height 758 > supersample 3 > hide #* target a > show sel target ab > undo > select #2/B 619 atoms, 690 bonds, 29 residues, 1 model selected > show sel target ab > cartoon hide sel > style sel ringFill off Changed 29 residue ring styles > color sel byelement > select #2/A:54 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #2/A:55 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #2/A:53 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #2/A:51 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select #2/A:49 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #2/A:50 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #2/A:44 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #2/A:45 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #2/A:47 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #2/A:41 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms ===== Log before crash end ===== Log: You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M2 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,9 Model Number: Z17G002HSLL/A Chip: Apple M2 Pro Total Number of Cores: 10 (6 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 10151.140.19 OS Loader Version: 10151.140.19 Software: System Software Overview: System Version: macOS 14.6.1 (23G93) Kernel Version: Darwin 23.6.0 Time since boot: 10 days, 3 hours, 58 minutes Graphics/Displays: Apple M2 Pro: Chipset Model: Apple M2 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: LF24T35: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 75.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal LF24T450F: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 75.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 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: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 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: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 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: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 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-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 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: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 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: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Window Toolkit duplicate all ChimeraX