id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18304 mshMIGPerform crash chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.5-arm64-arm-64bit ChimeraX Version: 1.10.dev202502120650 (2025-02-12 06:50:33 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x000000035f343000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031b80f000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031a803000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003197f7000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003187eb000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003177df000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003167d3000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003157c7000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003147bb000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003137af000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003127a3000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000311797000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031078b000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030f77f000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x000000020c7e9f00 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 339 in event_loop File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 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, psutil._psutil_osx, 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""663e65b4a1526e1ca0e288a1"" }, ""deploymentId"" : 240000002 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.10.dev202502120650 (2025-02-12) © 2016-2025 Regents of the University of California. All rights reserved. > open /Users/apple/Downloads/global_view_semiactive_map+model.cxs Opened semiactive_vop_max_EMReady.mrc as #2, grid size 420,420,420, pixel 0.95, shown at level 4.16, step 1, values float32 Opened semiactive_vop_max_EMReady.mrc gaussian as #3, grid size 420,420,420, pixel 0.95, shown at level 4, step 1, values float32 Opened semiactive_micelle_volumn.mrc as #1, grid size 420,420,420, pixel 0.95, shown at level 0.0353, step 1, values float32 Log from Tue Aug 27 10:53:52 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open > D:\\\Desktop\\\BTN_Coot_work\\\ChimeraX_working_folder_BTN\\\global_view_semiactive.cxs Opened semiactive_vop_max_EMReady.mrc as #2, grid size 420,420,420, pixel 0.95, shown at level 4.16, step 1, values float32 Opened semiactive_vop_max_EMReady.mrc gaussian as #3, grid size 420,420,420, pixel 0.95, shown at level 4, step 1, values float32 Opened semiactive_micelle_volumn.mrc as #1, grid size 420,420,420, pixel 0.95, shown at level 0.0353, step 1, values float32 Log from Wed Aug 7 13:00:59 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open > D:\\\Desktop\\\BTN_Coot_work\\\ChimeraX_working_folder_BTN\\\semiactive_global_view.cxs Opened semiactive_vop_max_EMReady.mrc as #2, grid size 420,420,420, pixel 0.95, shown at level 4.16, step 1, values float32 Opened semiactive_vop_max_EMReady.mrc gaussian as #3, grid size 420,420,420, pixel 0.95, shown at level 4, step 1, values float32 Log from Tue Aug 6 14:22:11 2024 Startup Messages --- note | available bundle cache has not been initialized yet 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 > D:/Desktop/BTN_Coot_work/final_semiactive_global/20240805_real_space_refined_007+HMBPP.pdb > D:/Desktop/BTN_Coot_work/final_semiactive_global/semiactive_vop_max_EMReady.mrc Chain information for 20240805_real_space_refined_007+HMBPP.pdb #1 --- Chain | Description A | No description available B | No description available E | No description available F | No description available Opened semiactive_vop_max_EMReady.mrc as #2, grid size 420,420,420, pixel 0.95, shown at level 0.115, step 2, values float32 > hide atoms > show cartoons > lighting soft > graphics silhouettes true > set bgColor white > select clear > volume #2 step 1 > volume #2 level 3.668 > volume #2 level 5.089 > hide #!2 models > select /A 3807 atoms, 3899 bonds, 2 pseudobonds, 480 residues, 2 models selected > ui tool show ""Color Actions"" > select all 13833 atoms, 14145 bonds, 16 pseudobonds, 1720 residues, 4 models selected > color sel bypolymer > select /A 3807 atoms, 3899 bonds, 2 pseudobonds, 480 residues, 2 models selected > color sel bypolymer > color (#!1 & sel) #d58fffff > select clear > select /B 2247 atoms, 2290 bonds, 1 pseudobond, 291 residues, 2 models selected > color (#!1 & sel) #f47f72ff > select /E 3901 atoms, 3993 bonds, 7 pseudobonds, 474 residues, 2 models selected > color (#!1 & sel) #fbb463ff > select /F 3863 atoms, 3949 bonds, 6 pseudobonds, 474 residues, 2 models selected > color (#!1 & sel) #fbf8b4ff > select clear > select /F 3863 atoms, 3949 bonds, 6 pseudobonds, 474 residues, 2 models selected > select clear > show #!2 models > ui tool show ""Color Zone"" > color zone #2 near #1 distance 5.7 > ui tool show ""Hide Dust"" > volume #2 level 4.157 > surface dust #2 size 5.7 > surface dust #2 size 9.18 > color zone #2 near #1 distance 11.38 > ui tool show ""Map Filter"" > volume gaussian #2 sDev 0.6 Opened semiactive_vop_max_EMReady.mrc gaussian as #3, grid size 420,420,420, pixel 0.95, shown at step 1, values float32 > volume #3 level 4.751 > surface dust #3 size 5.7 > volume #3 level 4.931 > surface dust #3 size 4.3 [Repeated 1 time(s)] > color zone #3 near #1 distance 5.7 > hide #!1 models > surface undust #3 > volume #3 level 3.981 > volume #3 level 4 > surface dust #3 size 5.55 > surface dust #3 size 5.36 > cd D:/Desktop/BTN_Coot_work/ChimeraX_working_folder_BTN Current working directory is: D:\Desktop\BTN_Coot_work\ChimeraX_working_folder_BTN > save > D:/Desktop/BTN_Coot_work/ChimeraX_working_folder_BTN/semiactive_global_view.cxs > includeMaps true ——— End of log from Tue Aug 6 14:22:11 2024 ——— opened ChimeraX session > open > D:/Desktop/BTN_Coot_work/final_semiactive_global/20240807_real_space_refined_011+HMBPP.pdb Chain information for 20240807_real_space_refined_011+HMBPP.pdb #4 --- Chain | Description A | No description available B | No description available E | No description available F | No description available > hide #!3 models > dssp > select #4/B:218 7 atoms, 7 bonds, 1 residue, 1 model selected > select #4/A:220 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > setattr /A:218-219 res ss_type 0 Assigning ss_type attribute to 4 items > setattr /B:218-219 res ss_type 0 Assigning ss_type attribute to 4 items > select #4/B:220 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > select #4/A:211 7 atoms, 7 bonds, 1 residue, 1 model selected > setattr /A:210-212 res ss_type 0 Assigning ss_type attribute to 6 items > select clear > select #4/B:149 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear > ui tool show ""Color Actions"" > color bypolymer > select clear [Repeated 6 time(s)] > dssp > select clear > hide #!4 atoms > show #!4 cartoons > select /A 7629 atoms, 7814 bonds, 4 pseudobonds, 961 residues, 4 models selected > ui tool show ""Color Actions"" > color (#!4 & sel) #d58fffff > select clear > select /A 7629 atoms, 7814 bonds, 4 pseudobonds, 961 residues, 4 models selected > color (#!4 & sel) #d7e9f8ff > color (#!4 & sel) #f0f0f0ff > color (#!4 & sel) #ffffffff > color (#!4 & sel) #bd92c8ff > color (#!4 & sel) #ffffffff > color (#!4 & sel) #948fe7ff > color (#!4 & sel) #ffffffff > color (#!4 & sel) #000000ff > color (#!4 & sel) #9d97f9ff > color (#!4 & sel) #a09bffff > color (#!4 & sel) #9f99fcff > color (#!4 & sel) #a19bffff > color (#!4 & sel) #000000ff > color (#!4 & sel) #ffffffff > color (#!4 & sel) #000000ff > color (#!4 & sel) #ffffffff > color (#!4 & sel) #7d78cfff > color (#!4 & sel) #958ff7ff > color (#!4 & sel) #958ff8ff > color (#!4 & sel) #948ef6ff > color (#!4 & sel) #928cf2ff > color (#!4 & sel) #958ff8ff > color (#!4 & sel) #9690fbff > color (#!4 & sel) #9892feff > color (#!4 & sel) #9791fcff > color (#!4 & sel) #9790fbff > color (#!4 & sel) #948ef7ff > color (#!4 & sel) #958ff8ff > color (#!4 & sel) #948df6ff > color (#!4 & sel) #928cf3ff > select clear > select /B 4494 atoms, 4582 bonds, 2 pseudobonds, 582 residues, 4 models selected > color (#!4 & sel) #f47f72ff > select clear > select /C 15 atoms, 14 bonds, 1 residue, 1 model selected > select /E 7802 atoms, 7988 bonds, 14 pseudobonds, 948 residues, 4 models selected > close #1 > select /C Nothing selected > select /E 3901 atoms, 3995 bonds, 7 pseudobonds, 474 residues, 2 models selected > color (#!4 & sel) #fbb463ff > select clear > select /F 3863 atoms, 3951 bonds, 6 pseudobonds, 474 residues, 2 models selected > color (#!4 & sel) #fbf8b4ff > select clear > select /A 3822 atoms, 3915 bonds, 2 pseudobonds, 481 residues, 2 models selected > ui tool show ""Color Actions"" > color (#!4 & sel) #d58fffff > select clear > show #!3 models > hide #!3 models > show #!3 models > ui tool show ""Hide Dust"" > ui tool show ""Color Zone"" > surface dust #3 size 5.36 > ui tool show ""Surface Zone"" > surface zone #3 nearAtoms #4 distance 5.7 > surface zone #3 nearAtoms #4 distance 6.6 [Repeated 1 time(s)] > surface dust #3 size 5.36 > surface dust #3 size 5.28 [Repeated 1 time(s)] > color zone #3 near #4 distance 5.7 [Repeated 4 time(s)] > open > D:/Desktop/BTN_Coot_work/final_semiactive_global/semiactive_micelle_volumn.mrc Opened semiactive_micelle_volumn.mrc as #1, grid size 420,420,420, pixel 0.95, shown at level 0.0177, step 2, values float32 > volume #1 step 1 > volume #1 level 0.0341 > volume #1 level 0.03527 > surface dust #1 size 5.7 > select #1 2 models selected > transparency #1.1 70 > select clear [Repeated 2 time(s)] > hide #!1 models > show #!1 models > hide #!3 models > select /A 3822 atoms, 3915 bonds, 2 pseudobonds, 481 residues, 2 models selected > ui tool show ""Color Actions"" > color (#!4 & sel) #b177d5ff > color (#!4 & sel) #9b68baff > color (#!4 & sel) #a871caff > color (#!4 & sel) #9262afff > color (#!4 & sel) #a26dc3ff > color (#!4 & sel) #b97cdeff > color (#!4 & sel) #b87cddff > color (#!4 & sel) #b97cdeff > color (#!4 & sel) #c786efff > color (#!4 & sel) #d28dfcff > color (#!4 & sel) #d48fffff > color (#!4 & sel) #d38efeff > color (#!4 & sel) #bf81e6ff > color (#!4 & sel) #b47ad9ff > color (#!4 & sel) #b479d8ff > color (#!4 & sel) #a16dc2ff > color (#!4 & sel) #9a68b9ff > color (#!4 & sel) #9c69bcff > color (#!4 & sel) #bc7fe2ff > color (#!4 & sel) #d38efeff > color (#!4 & sel) #d48fffff > color (#!4 & sel) #d38efeff > color (#!4 & sel) #b77bdcff > color (#!4 & sel) #a972cbff > color (#!4 & sel) #a871caff > color (#!4 & sel) #9a68b9ff > color (#!4 & sel) #9c69bcff > color (#!4 & sel) #b47ad9ff > color (#!4 & sel) #c887f1ff > color (#!4 & sel) #d48fffff > color (#!4 & sel) #d38efeff > color (#!4 & sel) #bb7ee1ff > color (#!4 & sel) #a972cbff > color (#!4 & sel) #a871caff > color (#!4 & sel) #ab74ceff > color (#!4 & sel) #be80e5ff > color (#!4 & sel) #d48fffff > color (#!4 & sel) #d38efeff > color (#!4 & sel) #cc89f5ff > color (#!4 & sel) #9c69bcff > color (#!4 & sel) #9363b1ff > color (#!4 & sel) #9665b4ff > color (#!4 & sel) #ad75d0ff > color (#!4 & sel) #be80e5ff > color (#!4 & sel) #d48fffff > color (#!4 & sel) #110b14ff > color (#!4 & sel) #a670c8ff > select /B 2247 atoms, 2292 bonds, 1 pseudobond, 291 residues, 2 models selected > color (#!4 & sel) #f47f72ff > color (#!4 & sel) #140a09ff > color (#!4 & sel) #c8685dff > select clear > select /E 3901 atoms, 3995 bonds, 7 pseudobonds, 474 residues, 2 models selected > color (#!4 & sel) #fbb463ff > color (#!4 & sel) #fbb46314 > color (#!4 & sel) #fbb463c8 > color (#!4 & sel) #fbb46302 > color (#!4 & sel) #fbb46319 > color (#!4 & sel) #fbb463ff > color (#!4 & sel) #140e08ff > color (#!4 & sel) #c88e4fff > select clear > select /F 3863 atoms, 3951 bonds, 6 pseudobonds, 474 residues, 2 models selected > color (#!4 & sel) #fbf8b4ff > color (#!4 & sel) #14140eff > color (#!4 & sel) #c8c590ff > select clear > color zone #3 near #4 distance 5.7 > show #!3 models > hide #!3 models > undo [Repeated 9 time(s)] > select /A 3822 atoms, 3915 bonds, 2 pseudobonds, 481 residues, 2 models selected > color (#!4 & sel) #d58fffff > select /B 2247 atoms, 2292 bonds, 1 pseudobond, 291 residues, 2 models selected > color (#!4 & sel) #f47f72ff > select /C Nothing selected > select /E 3901 atoms, 3995 bonds, 7 pseudobonds, 474 residues, 2 models selected > color (#!4 & sel) #fbb463ff > select clear > color zone #3 near #4 distance 5.7 > show #!3 models > hide #!1 models > show #!1 models > hide #!4 models > save > D:/Desktop/BTN_Coot_work/ChimeraX_working_folder_BTN/semiactive_global_view.cxs > includeMaps true ——— End of log from Wed Aug 7 13:00:59 2024 ——— opened ChimeraX session > ui tool show ""Side View"" > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > select #3 2 models selected > transparency #3.1 80 > select clear > select #3 2 models selected > transparency #3.1 70 > select clear > lighting soft > lighting simple > lighting soft > graphics silhouettes false > graphics silhouettes true > hide #!1 models > show #!1 models > hide #!1 models > select /A:501 15 atoms, 14 bonds, 1 residue, 1 model selected > show sel atoms > color sel lime > color sel byhetero > show sel surfaces > hide sel surfaces > select clear > select #3 3 models selected > transparency #3.1 70 > select clear > lighting soft > graphics silhouettes false > graphics silhouettes true > select clear > save > D:/Desktop/BTN_Coot_work/ChimeraX_working_folder_BTN/figure/20240827_active_global_volumn+model.tif > width 1469 height 999 supersample 3 > save > D:/Desktop/BTN_Coot_work/ChimeraX_working_folder_BTN/figure/20240827_semiactive_global_volumn+model.tif > width 1469 height 999 supersample 3 > lighting full > lighting soft > lighting flat > lighting soft > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting soft [Repeated 2 time(s)] > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > select #3 4 models selected > transparency #3.1 50 > transparency #3.1 70 > select clear > select #3 4 models selected > select clear > graphics silhouettes true width 2 > graphics silhouettes true width 1 > save > D:/Desktop/BTN_Coot_work/ChimeraX_working_folder_BTN/global_view_semiactive_map+model.cxs > includeMaps true ——— End of log from Tue Aug 27 10:53:52 2024 ——— > view name session-start opened ChimeraX session > show #!2 models > show #!1 models ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.10.dev202502120650 (2025-02-12) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M4 OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac16,1 Model Number: MW2V3CH/A Chip: Apple M4 Total Number of Cores: 10 (4 performance and 6 efficiency) Memory: 16 GB System Firmware Version: 11881.121.1 OS Loader Version: 11881.121.1 Software: System Software Overview: System Version: macOS 15.5 (24F74) Kernel Version: Darwin 24.5.0 Time since boot: 3天22小时16分钟 Graphics/Displays: Apple M4: Chipset Model: Apple M4 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Q24E11: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 100.00Hz 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: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 anyio: 4.8.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.2.0 babel: 2.17.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.1 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.19.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.0.1 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.5 ChimeraX-AtomicLibrary: 14.1.13 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 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: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10.dev202502120650 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.7 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: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.5.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 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: 2.1.7 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 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-MutationScores: 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: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.7 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: 1.1.2 ChimeraX-ProfileGrids: 1.0.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 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: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 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: 2.5.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.43 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 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: 1.3.1 coverage: 7.6.12 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.12 decorator: 5.1.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.15.4 fonttools: 4.56.0 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.0.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.5 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.8 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.6 pluggy: 1.5.0 prompt_toolkit: 3.0.50 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.1 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.3.4 pytest-cov: 6.0.0 python-dateutil: 2.9.0.post0 pytz: 2025.1 pyzmq: 26.2.1 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.1.3 sphinx-autodoc-typehints: 3.0.1 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2025.1 urllib3: 2.3.0 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.13 }}} " defect closed normal Platform duplicate all ChimeraX