id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18294 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.5-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 0x0000000322c47000 (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 0x0000000321c3b000 (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 0x00000003151fb000 (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 0x00000003141ef000 (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 0x00000003131e3000 (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 0x00000003121d7000 (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 0x00000003111cb000 (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 0x00000003101bf000 (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 0x000000030f1b3000 (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 0x000000030e1a7000 (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 0x000000030d19b000 (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 0x0000000209d15f00 (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, 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""com.apple.main-thread"" } }, ""logWritingSignature"" : ""28a1301702f38c27286f1eb97cf349d5fd0f202d"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""645eb1d0417dab722a215927"", ""factorPackIds"" : { }, ""deploymentId"" : 240000005 }, { ""rolloutId"" : ""63508950b3714d3622fc77f7"", ""factorPackIds"" : { ""SIRI_MEMORY_SYNC_CONFIG"" : ""6526e111d0c9ce2f459b54a8"" }, ""deploymentId"" : 240000015 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== 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 > /Users/mccaff0001/Downloads/cryosparc_P331_J208_003_volume_map_sharp.mrc Opened cryosparc_P331_J208_003_volume_map_sharp.mrc as #1, grid size 256,256,256, pixel 1.47, shown at level 0.155, step 1, values float32 > set bgColor white > lighting soft intensity 0.1 direction 0.577,-0.577,-0.577 color 100,100,100 > fillIntensity 0.5 fillDirection -0.81,-1,1 fillColor 100,100,100 > ambientIntensity 1.4 ambientColor 100,100,100 shadows true qualityOfShadows > finer depthBias 0.01 multiShadow 64 msMapSize 2000 msDepthBias 0.004 > moveWithCamera true > open > /Users/mccaff0001/Documents/PretzPaperFigs/pretzel1tetramer_flexfit_1.pdb Summary of feedback from opening /Users/mccaff0001/Documents/PretzPaperFigs/pretzel1tetramer_flexfit_1.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 54562 messages similar to the above omitted Chain information for pretzel1tetramer_flexfit_1.pdb #2 --- Chain | Description A B C D | No description available > open /Users/mccaff0001/Documents/PretzPaperFigs/pretzel1tetramer_flexfit.pdb Summary of feedback from opening /Users/mccaff0001/Documents/PretzPaperFigs/pretzel1tetramer_flexfit.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 GLU A 5 LEU A 13 1 9 Start residue of secondary structure not found: HELIX 2 2 LYS A 17 SER A 22 1 6 Start residue of secondary structure not found: HELIX 3 3 TYR A 29 THR A 42 1 14 Start residue of secondary structure not found: HELIX 4 4 ASP A 50 THR A 59 1 10 Start residue of secondary structure not found: HELIX 5 5 TYR A 69 LEU A 83 1 15 349 messages similar to the above omitted Chain information for pretzel1tetramer_flexfit.pdb --- Chain | Description 3.1/A 3.2/B 3.3/C 3.4/D | No description available > hide atoms > show cartoons > color #1 #b2b2b272 models > color #1 #b2b2b271 models > graphics silhouettes true > color #1 #b2b2b258 models > color #1 #b2b2b248 models > color #3.1 #7a81ffff > color #2 #d783ffff > open /Users/mccaff0001/Documents/PretzPaperFigs/structanalysis.cxs opened ChimeraX session > open /Users/mccaff0001/Documents/EMA2024poster/Posterstructs.cxs Opened cryosparc_P880_J41_004_volume_map_sharp.mrc as #5, grid size 360,360,360, pixel 1.34, shown at level 0.243, step 2, values float32 Opened cryosparc_P331_J208_003_volume_map_sharp.mrc as #6, grid size 256,256,256, pixel 1.47, shown at level 0.155, step 1, values float32 opened ChimeraX session > open /Users/mccaff0001/Documents/PretzPaperFigs/structanalysis.cxs opened ChimeraX session > open > /Users/mccaff0001/Documents/PretzPaperFigs/Jul2025structurerendering.cxs Opened cryosparc_J244_3-29A_volume_map_sharp.mrc as #2, grid size 420,420,420, pixel 1.14, shown at level 0.279, step 1, values float32 Opened cryosparc_P331_J208_003_volume_map_sharp.mrc as #10, grid size 256,256,256, pixel 1.47, shown at level 0.155, step 1, values float32 opened ChimeraX session > hide #!10 models > show #!9 models > hide #!11 models > select add #9 72756 atoms, 74156 bonds, 40 pseudobonds, 8864 residues, 6 models selected > transparency 0 sel target c Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency sel 0 target c > select subtract #9 Nothing selected > show #!10 models > color #10 #a296a815 models > color #10 #a296a814 models > graphics silhouettes false > graphics silhouettes true > ui tool show ""Side View"" > graphics silhouettes width 2 > color #10 #a296a859 models > ui tool show ""Fit in Map"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select add #9 72756 atoms, 74156 bonds, 40 pseudobonds, 8864 residues, 6 models selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > fitmap sel inMap #10 Fit molecules pretzel1tetramer_flexfit.pdb (#9.1), pretzel1tetramer_flexfit.pdb (#9.2), pretzel1tetramer_flexfit.pdb (#9.3), pretzel1tetramer_flexfit.pdb (#9.4) to map cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) using 72756 atoms average map value = 0.1087, steps = 68 shifted from previous position = 3.34 rotated from previous position = 0.756 degrees atoms outside contour = 49876, contour level = 0.15536 Position of pretzel1tetramer_flexfit.pdb (#9.1) relative to cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) coordinates: Matrix rotation and translation 0.99682936 0.07775691 0.01688489 -33.02508314 -0.07737304 0.99675261 -0.02230855 22.17667973 -0.01856471 0.02093138 0.99960856 -3.50617310 Axis 0.26222078 0.21497770 -0.94075760 Axis point 270.06637423 433.73166700 0.00000000 Rotation angle (degrees) 4.72937574 Shift along axis -0.59391248 Position of pretzel1tetramer_flexfit.pdb (#9.2) relative to cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) coordinates: Matrix rotation and translation -0.99678828 0.07818631 0.01732188 363.73505443 -0.07733809 -0.99598125 0.04516848 384.19790383 0.02078383 0.04368377 0.99882922 -8.89086138 Axis -0.00954368 -0.02225331 -0.99970681 Axis point 189.39334630 185.11239622 0.00000000 Rotation angle (degrees) 175.53874086 Shift along axis -3.13278884 Position of pretzel1tetramer_flexfit.pdb (#9.3) relative to cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) coordinates: Matrix rotation and translation -0.99681676 0.07798291 -0.01658389 348.02558992 -0.07760709 -0.99673655 -0.02221279 391.34007402 -0.01826199 -0.02085505 0.99961574 10.48603193 Axis 0.00872553 0.01078432 -0.99990378 Axis point 181.68332105 188.94579438 0.00000000 Rotation angle (degrees) 175.53773625 Shift along axis -3.22797662 Position of pretzel1tetramer_flexfit.pdb (#9.4) relative to cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) coordinates: Matrix rotation and translation 0.99683792 0.07775582 -0.01637718 -4.63989303 -0.07695040 0.99601385 0.04511172 3.83788227 0.01981959 -0.04370884 0.99884772 1.67639540 Axis -0.48795644 -0.19885537 -0.84991473 Axis point 46.90616564 61.10264465 0.00000000 Rotation angle (degrees) 5.22187472 Shift along axis 0.07608901 > fitmap sel inMap #10 Fit molecules pretzel1tetramer_flexfit.pdb (#9.1), pretzel1tetramer_flexfit.pdb (#9.2), pretzel1tetramer_flexfit.pdb (#9.3), pretzel1tetramer_flexfit.pdb (#9.4) to map cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) using 72756 atoms average map value = 0.1087, steps = 48 shifted from previous position = 0.0271 rotated from previous position = 0.0106 degrees atoms outside contour = 49889, contour level = 0.15536 Position of pretzel1tetramer_flexfit.pdb (#9.1) relative to cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) coordinates: Matrix rotation and translation 0.99683971 0.07765722 0.01673204 -32.98005985 -0.07727702 0.99676060 -0.02228415 22.17316519 -0.01840836 0.02092072 0.99961168 -3.51982748 Axis 0.26242125 0.21343860 -0.94105210 Axis point 270.43732120 433.63280935 0.00000000 Rotation angle (degrees) 4.72191423 Shift along axis -0.60971825 Position of pretzel1tetramer_flexfit.pdb (#9.2) relative to cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) coordinates: Matrix rotation and translation -0.99678400 0.07827590 0.01716262 363.74588073 -0.07743406 -0.99597269 0.04519290 384.23265262 0.02063102 0.04371859 0.99883087 -8.85124017 Axis -0.00946555 -0.02226822 -0.99970722 Axis point 189.40784289 185.12070943 0.00000000 Rotation angle (degrees) 175.53340923 Shift along axis -3.15058120 Position of pretzel1tetramer_flexfit.pdb (#9.3) relative to cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) coordinates: Matrix rotation and translation -0.99680641 0.07808258 -0.01673676 348.03272064 -0.07770395 -0.99672948 -0.02219162 391.37374414 -0.01841480 -0.02082024 0.99961366 10.52305405 Axis 0.00880211 0.01077036 -0.99990326 Axis point 181.69777831 188.95401101 0.00000000 Rotation angle (degrees) 175.53208614 Shift along axis -3.24337881 Position of pretzel1tetramer_flexfit.pdb (#9.4) relative to cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) coordinates: Matrix rotation and translation 0.99684227 0.07766624 -0.01653643 -4.59389962 -0.07685350 0.99602037 0.04513288 3.83723220 0.01997592 -0.04371948 0.99884414 1.66756063 Axis -0.48834543 -0.20067721 -0.84926285 Axis point 46.93537934 60.69808257 0.00000000 Rotation angle (degrees) 5.21957720 Shift along axis 0.05716757 > select subtract #9 Nothing selected > select add #9 72756 atoms, 74156 bonds, 40 pseudobonds, 8864 residues, 6 models selected > fitmap sel inMap #10 Fit molecules pretzel1tetramer_flexfit.pdb (#9.1), pretzel1tetramer_flexfit.pdb (#9.2), pretzel1tetramer_flexfit.pdb (#9.3), pretzel1tetramer_flexfit.pdb (#9.4) to map cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) using 72756 atoms average map value = 0.1087, steps = 48 shifted from previous position = 0.0203 rotated from previous position = 0.0212 degrees atoms outside contour = 49884, contour level = 0.15536 Position of pretzel1tetramer_flexfit.pdb (#9.1) relative to cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) coordinates: Matrix rotation and translation 0.99682764 0.07787535 0.01643511 -32.96015739 -0.07750174 0.99674364 -0.02226226 22.20436317 -0.01811527 0.02091789 0.99961709 -3.56279832 Axis 0.26181669 0.20949129 -0.94210691 Axis point 270.02339677 432.15329709 0.00000000 Rotation angle (degrees) 4.73012785 Shift along axis -0.62136149 Position of pretzel1tetramer_flexfit.pdb (#9.2) relative to cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) coordinates: Matrix rotation and translation -0.99680738 0.07803906 0.01688110 363.84876696 -0.07720928 -0.99598915 0.04521467 384.17445465 0.02034191 0.04376694 0.99883468 -8.78762015 Axis -0.00932254 -0.02228556 -0.99970818 Axis point 189.43492039 185.11008032 0.00000000 Rotation angle (degrees) 175.54668182 Shift along axis -3.16847911 Position of pretzel1tetramer_flexfit.pdb (#9.3) relative to cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) coordinates: Matrix rotation and translation -0.99681844 0.07786442 -0.01703367 348.13155661 -0.07748017 -0.99674755 -0.02216221 391.31957812 -0.01870391 -0.02077192 0.99960930 10.58190162 Axis 0.00894879 0.01075081 -0.99990216 Axis point 181.72547125 188.94451160 0.00000000 Rotation angle (degrees) 175.54478163 Shift along axis -3.25850920 Position of pretzel1tetramer_flexfit.pdb (#9.4) relative to cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) coordinates: Matrix rotation and translation 0.99681908 0.07790308 -0.01681797 -4.57963907 -0.07707724 0.99600175 0.04516223 3.86217786 0.02026900 -0.04372229 0.99883812 1.63334870 Axis -0.48712221 -0.20325124 -0.84935321 Axis point 47.13203375 60.34467732 -0.00000000 Rotation angle (degrees) 5.23462021 Shift along axis 0.05856150 > fitmap sel inMap #10 Fit molecules pretzel1tetramer_flexfit.pdb (#9.1), pretzel1tetramer_flexfit.pdb (#9.2), pretzel1tetramer_flexfit.pdb (#9.3), pretzel1tetramer_flexfit.pdb (#9.4) to map cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) using 72756 atoms average map value = 0.1087, steps = 48 shifted from previous position = 0.0327 rotated from previous position = 0.0156 degrees atoms outside contour = 49871, contour level = 0.15536 Position of pretzel1tetramer_flexfit.pdb (#9.1) relative to cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) coordinates: Matrix rotation and translation 0.99682294 0.07787815 0.01670457 -33.01005736 -0.07749969 0.99674476 -0.02221949 22.18454624 -0.01838061 0.02085430 0.99961358 -3.52819453 Axis 0.26103605 0.21262338 -0.94162173 Axis point 269.65349060 432.93252118 0.00000000 Rotation angle (degrees) 4.73259318 Shift along axis -0.57763726 Position of pretzel1tetramer_flexfit.pdb (#9.2) relative to cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) coordinates: Matrix rotation and translation -0.99680164 0.07805369 0.01715016 363.79641279 -0.07721124 -0.99598705 0.04525741 384.15554048 0.02061385 0.04378847 0.99882816 -8.87542717 Axis -0.00945805 -0.02230170 -0.99970655 Axis point 189.41022499 185.10191268 0.00000000 Rotation angle (degrees) 175.54619765 Shift along axis -3.13530208 Position of pretzel1tetramer_flexfit.pdb (#9.3) relative to cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) coordinates: Matrix rotation and translation -0.99682323 0.07786166 -0.01676421 348.08440277 -0.07748380 -0.99674822 -0.02211953 391.30144718 -0.01843196 -0.02075031 0.99961480 10.49802432 Axis 0.00881320 0.01073470 -0.99990354 Axis point 181.70046898 188.93582213 0.00000000 Rotation angle (degrees) 175.54476280 Shift along axis -3.22877140 Position of pretzel1tetramer_flexfit.pdb (#9.4) relative to cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) coordinates: Matrix rotation and translation 0.99682473 0.07788845 -0.01654891 -4.62808742 -0.07707355 0.99600011 0.04520487 3.84266359 0.02000365 -0.04378585 0.99884068 1.66108761 Axis -0.48789582 -0.20040115 -0.84958640 Axis point 46.89857636 60.85081381 0.00000000 Rotation angle (degrees) 5.23255911 Shift along axis 0.07671290 > select subtract #9 Nothing selected > save /Users/mccaff0001/Documents/PretzPaperFigs/structinmap.png width 3000 > height 3916 supersample 3 transparentBackground true > close session > open /Users/mccaff0001/Downloads/I7MLD7/fold_2024_07_03_13_51_model_0.cif Chain information for fold_2024_07_03_13_51_model_0.cif #1 --- Chain | Description A | . > open /Users/mccaff0001/Downloads/I7MGF4_unrelaxed_model_1.pdb Chain information for I7MGF4_unrelaxed_model_1.pdb #2 --- Chain | Description A | No description available > open /Users/mccaff0001/Downloads/I7M9Z0_unrelaxed_model_1.pdb Chain information for I7M9Z0_unrelaxed_model_1.pdb #3 --- Chain | Description A | No description available > mmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_2024_07_03_13_51_model_0.cif, chain A (#1) with I7MGF4_unrelaxed_model_1.pdb, chain A (#2), sequence alignment score = 3662.9 RMSD between 500 pruned atom pairs is 1.171 angstroms; (across all 1805 pairs: 21.064) > mmaker #3 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_2024_07_03_13_51_model_0.cif, chain A (#1) with I7M9Z0_unrelaxed_model_1.pdb, chain A (#3), sequence alignment score = 4273.6 RMSD between 165 pruned atom pairs is 1.266 angstroms; (across all 2138 pairs: 22.020) ===== Log before crash end ===== Log: 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 /Users/mccaff0001/Downloads/DomainPDBs/CMAC_Domain1.pdb Chain information for CMAC_Domain1.pdb #1 --- Chain | Description A | No description available > open /Users/mccaff0001/Downloads/DomainPDBs/CMAC_Domain2.pdb Chain information for CMAC_Domain2.pdb #2 --- Chain | Description A | No description available > open /Users/mccaff0001/Downloads/DomainPDBs/CMAC_Domain3.pdb Chain information for CMAC_Domain3.pdb #3 --- Chain | Description A | No description available > open /Users/mccaff0001/Downloads/DomainPDBs/CMAC_Domain4.pdb Chain information for CMAC_Domain4.pdb #4 --- Chain | Description A | No description available > open /Users/mccaff0001/Downloads/DomainPDBs/CMAC_Domain5.pdb Chain information for CMAC_Domain5.pdb #5 --- Chain | Description A | No description available > open /Users/mccaff0001/Downloads/DomainPDBs/CMAC_Domain6.pdb Chain information for CMAC_Domain6.pdb #6 --- Chain | Description A | No description available > open /Users/mccaff0001/Downloads/DomainPDBs/CMAC_Domain7.pdb Chain information for CMAC_Domain7.pdb #7 --- Chain | Description A | No description available > open /Users/mccaff0001/Downloads/DomainPDBs/CMAC_Domain8.pdb Chain information for CMAC_Domain8.pdb #8 --- Chain | Description A | No description available > open /Users/mccaff0001/Downloads/DomainPDBs/CMAC_Domain9.pdb Chain information for CMAC_Domain9.pdb #9 --- Chain | Description A | No description available > open /Users/mccaff0001/Downloads/DomainPDBs/CMAC_Domain10.pdb Chain information for CMAC_Domain10.pdb #10 --- Chain | Description A | No description available > open /Users/mccaff0001/Downloads/DomainPDBs/CMAC_Domain11.pdb Chain information for CMAC_Domain11.pdb #11 --- Chain | Description A | No description available > open /Users/mccaff0001/Downloads/DomainPDBs/CMAC_Domain12.pdb Chain information for CMAC_Domain12.pdb #12 --- Chain | Description A | No description available > open /Users/mccaff0001/Downloads/DomainPDBs/CMAC_Domain13.pdb Chain information for CMAC_Domain13.pdb #13 --- Chain | Description A | No description available > open /Users/mccaff0001/Downloads/DomainPDBs/CMAC_Domain14.pdb Chain information for CMAC_Domain14.pdb #14 --- Chain | Description A | No description available > open /Users/mccaff0001/Downloads/DomainPDBs/CMAC_Domain15.pdb Chain information for CMAC_Domain15.pdb #15 --- Chain | Description A | No description available > set bgColor white > lighting soft intensity 0.1 direction 0.577,-0.577,-0.577 color 100,100,100 > fillIntensity 0.5 fillDirection -0.81,-1,1 fillColor 100,100,100 > ambientIntensity 1.4 ambientColor 100,100,100 shadows true qualityOfShadows > finer depthBias 0.01 multiShadow 64 msMapSize 2000 msDepthBias 0.004 > moveWithCamera true > select add #8 834 atoms, 848 bonds, 104 residues, 1 model selected > hide #7 models > hide #6 models > hide #5 models > hide #4 models > hide #3 models > hide #2 models > hide #1 models > hide #9 models > hide #10 models > hide #11 models > hide #12 models > hide #13 models > hide #14 models > hide #15 models OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.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: Mac14,7 Model Number: Z16S000YASM/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 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: 20 days, 15 hours, 37 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal 24B1W: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.16 annotated-types: 0.7.0 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-ArtiaX: 0.6.0 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 geomdl: 5.3.1 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 pandas: 2.2.3 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 pyarrow: 19.0.1 pycollada: 0.8 pydantic: 2.11.3 pydantic-core: 2.33.1 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 starfile: 0.5.12 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 typing-inspection: 0.4.0 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