id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17780 ChimeraX bug report submission chimerax-bug-report@… "{{{ The following bug report has been submitted: Platform: macOS-15.5-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. Fatal Python error: Segmentation fault Current thread 0x00000001f43d9f00 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop File ""/Applications/ChimeraX-1.9.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-1.9.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, 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""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/special\/_comb.cpython-311-darwin.so"", ""name"" : ""_comb.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 13130711040, ""size"" : 65536, ""uuid"" : ""04579fae-e25e-310b-9d9a-eb6567460a9a"", ""path"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/special\/_ellip_harm_2.cpython-311-darwin.so"", ""name"" : ""_ellip_harm_2.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 13610516480, ""size"" : 425984, ""uuid"" : ""790f202f-d1d8-3b1a-a2a4-6cedbfc5ae6f"", ""path"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/spatial\/_distance_pybind.cpython-311-darwin.so"", ""name"" : ""_distance_pybind.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 13633961984, ""size"" : 638976, ""uuid"" : ""1054ddef-4190-3041-95be-e16119344536"", ""path"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/spatial\/transform\/_rotation.cpython-311-darwin.so"", ""name"" : ""_rotation.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 13051740160, ""size"" : 32768, ""uuid"" : ""d08bc19e-a473-3d91-9401-19d68cabbac8"", ""path"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/optimize\/_direct.cpython-311-darwin.so"", ""name"" : ""_direct.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6545768448, ""size"" : 243284, ""uuid"" : ""60485b6f-67e5-38c1-aec9-efd6031ff166"", ""path"" : 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""CFBundleShortVersionString"" : ""6.9"", ""CFBundleIdentifier"" : ""com.apple.Foundation"", ""size"" : 14586624, ""uuid"" : ""e8f6a451-0acc-3e05-b18f-fec6618ce44a"", ""path"" : ""\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation"", ""name"" : ""Foundation"", ""CFBundleVersion"" : ""3502.1.401"" } ], ""sharedCache"" : { ""base"" : 6541377536, ""size"" : 5047205888, ""uuid"" : ""d7397d7f-8df9-3920-81a7-c0a144be9c51"" }, ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""c6fa742e92c9422c8ba77390c157418c29e1ebc8"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""654439cdafbf5b61207873a9"", ""factorPackIds"" : { }, ""deploymentId"" : 240000004 }, { ""rolloutId"" : ""66d35d7fe4d6bf7664f40ddf"", ""factorPackIds"" : { ""BLACKPEARL_SPARROW"" : ""67c7824a1baae429bb41b897"" }, ""deploymentId"" : 240000031 } ], ""experiments"" : [ { ""treatmentId"" : ""4cfb9672-7b7b-42d8-a7dc-b675ffa2f5dc"", ""experimentId"" : ""67f46877b1ea9f1f114b8d0b"", ""deploymentId"" : 400000001 } ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/sahtelis/Downloads/cryosparc_P2_J217_005_volume_map_sharp.mrc Opened cryosparc_P2_J217_005_volume_map_sharp.mrc as #1, grid size 384,384,384, pixel 0.828, shown at level 0.0432, step 2, values float32 > open /Users/sahtelis/Desktop/connexin- > str_analysis/cx45_hexamer_startingmodel_isolderelaxed.pdb Chain information for cx45_hexamer_startingmodel_isolderelaxed.pdb #2 --- Chain | Description A B C D E F | No description available > volume #1 level 0.04324 > volume flip #1 axis x Opened cryosparc_P2_J217_005_volume_map_sharp.mrc x flip as #3, grid size 384,384,384, pixel 0.828, shown at step 1, values float32 > close #1 > volume #3 level 0.1441 > volume #3 level 0.1 > volume #3 level 0.125 > surface dust #3 size 8.28 > hide atoms > show cartoons > transparency 50 > volume #3 level 0.1 > volume #3 level 0.15 > volume gaussian #2 sDev 1.2 > volume gaussian #3 sDev 1.2 Opened cryosparc_P2_J217_005_volume_map_sharp.mrc x flip gaussian as #1, grid size 384,384,384, pixel 0.828, shown at step 1, values float32 > volume #1 level 0.0956 > transparency #1.1 50 > volume #1 level 0.08253 > surface dust #1 size 8.28 > hide #!1 models > show #!1 models > help > cofr showPivot true > cofr centerOfView showPivot true > volume #1 level 0.071 > volume #1 level 0.07868 > volume #1 level 0.04716 > volume #1 level 0.06408 > volume #1 level 0.04793 > volume #1 level 0.06946 > for Unknown command: for > ~cofr > show #!3 models > hide #!1 models > show #!1 models > volume #1 level 0.125 > hide #!3 models > show #!3 models > hide #!1 models > volume #3 level 0.125 > hide #!3 models > show #!1 models > save /Users/sahtelis/Desktop/connexin-str_analysis/cx45map_20250521.cxs > includeMaps true > set bgColor gray > set bgColor black > set bgColor gray > set bgColor black > hide #!2 models > hide #!1 models > open 31495 fromDatabase emdb format ccp4 Summary of feedback from opening 31495 fetched from emdb --- notes | Fetching compressed map 31495 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-31495/map/emd_31495.map.gz Fetching map header 31495 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-31495/header/emd-31495.xml Opened emdb 31495 as #4, grid size 400,400,400, pixel 0.675, shown at level 0.032, step 2, values float32, fit PDB 7f92 > save /Users/sahtelis/Desktop/connexin-str_analysis/Cx43_gjc.mrc models #4 > volume #4 level 0.01019 > volume #4 level 0.02282 > surface dust #4 size 6.75 > volume #4 level 0.03143 > volume #4 level 0.01995 > volume #4 level 0.04348 > volume #4 level 0.02684 > cofr showPivot true > cofr centerOfView showPivot true > cofr centerOfView true Expected 3-tuple of numbers or a keyword > cofr centerOfView > cofr showPivot true > volume gaussian #4 sDev 2 Opened emdb 31495 gaussian as #5, grid size 400,400,400, pixel 0.675, shown at step 1, values float32 > volume #5 level 0.007418 > volume #5 level 0.009522 > volume #5 level 0.007328 > volume gaussian #4 sDev 1.5 Opened emdb 31495 gaussian as #6, grid size 400,400,400, pixel 0.675, shown at step 1, values float32 > volume #6 level 0.01301 > volume #6 level 0.01187 > volume #6 level 0.01171 > volume #6 level 0.003536 > close #5 > hide #!6 models > show #!4 models > volume #4 level 0.01708 > open /Users/sahtelis/Desktop/connexin-str_analysis/7z1t.pdb 7z1t.pdb title: CONNEXIN43 gap junction channel structure In digitonin [more info...] Chain information for 7z1t.pdb #5 --- Chain | Description | UniProt A B C D E F G H I J K L | gap junction α-1 protein | CXA1_HUMAN 1-382 > select add #5 18492 atoms, 19044 bonds, 12 pseudobonds, 2268 residues, 2 models selected > ui mousemode right ""move picked models"" > view matrix models #5,1,0,0,9.7007,0,1,0,0.82447,0,0,1,8.8541 > ui tool show ""Fit in Map"" > fitmap #5 inMap #4 Fit molecule 7z1t.pdb (#5) to map emdb 31495 (#4) using 18492 atoms average map value = 0.004396, steps = 92 shifted from previous position = 2.33 rotated from previous position = 2.86 degrees atoms outside contour = 14821, contour level = 0.01708 Position of 7z1t.pdb (#5) relative to emdb 31495 (#4) coordinates: Matrix rotation and translation 0.99911797 -0.03108315 -0.02823347 19.53107763 0.03183255 0.99914203 0.02649308 -6.01678294 0.02738576 -0.02736845 0.99925021 8.57024344 Axis -0.53988691 -0.55750536 0.63064245 Axis point 236.20196104 590.63542089 0.00000000 Rotation angle (degrees) 2.85922806 Shift along axis -1.78542516 > view matrix models > #5,0.99912,-0.031083,-0.028233,15.629,0.031833,0.99914,0.026493,1.1829,0.027386,-0.027368,0.99925,9.071 > fitmap #5 inMap #4 Fit molecule 7z1t.pdb (#5) to map emdb 31495 (#4) using 18492 atoms average map value = 0.00433, steps = 80 shifted from previous position = 1.61 rotated from previous position = 2.14 degrees atoms outside contour = 14434, contour level = 0.01708 Position of 7z1t.pdb (#5) relative to emdb 31495 (#4) coordinates: Matrix rotation and translation 0.99863289 -0.03577737 -0.03810954 17.40615529 0.03809717 0.99734918 0.06199373 -2.68546053 0.03579054 -0.06336085 0.99734871 13.89840881 Axis -0.76812999 -0.45283441 0.45267793 Axis point 0.00000000 257.17370857 97.13848771 Rotation angle (degrees) 4.68038124 Shift along axis -5.86261816 > hide sel atoms > show sel cartoons > fitmap #5 inMap #4 Fit molecule 7z1t.pdb (#5) to map emdb 31495 (#4) using 18492 atoms average map value = 0.004331, steps = 64 shifted from previous position = 0.00482 rotated from previous position = 0.00986 degrees atoms outside contour = 14429, contour level = 0.01708 Position of 7z1t.pdb (#5) relative to emdb 31495 (#4) coordinates: Matrix rotation and translation 0.99863299 -0.03565402 -0.03822237 17.40426607 0.03797983 0.99735590 0.06195763 -2.66259565 0.03591227 -0.06332461 0.99734663 13.88063268 Axis -0.76795946 -0.45443307 0.45136332 Axis point 0.00000000 257.11406366 97.15205153 Rotation angle (degrees) 4.67871556 Shift along axis -5.89059084 > select subtract #5 Nothing selected > hide #!4 models > hide #!5 models > show #!1 models > show #!2 models > show #!3 models > hide #!1 models > volume #3 level 0.15 > show #!1 models > hide #!3 models > show #!6 models > hide #!6 models > volume #3 level 0.125 > volume #1 level 0.15 > volume #1 level 0.1 > volume #1 level 0.15 > volume #1 level 0.075 > surface dust #1 size 8.28 > volume #1 level 0.095 > show #!3 models > hide #!1 models > volume #3 level 0.15 > volume #3 color #88a9bf80 > volume #3 color #73aabf80 > volume #3 color #6c99bf80 > volume #3 color #97b0bf80 > volume #3 color #a9bbbf80 > volume #3 color #9ea8bf80 > volume #3 color #8bb2bf80 > volume #3 color #69b4bf80 > volume #3 color #55aebf80 > volume #3 color #70e5fc80 > volume #3 color #94f0fc80 > volume #3 color #adeafc80 > volume #3 color #8ee5fc80 > volume #3 color #8ee5fca3 > volume #3 color #86d9efa3 > volume #3 level 0.13 > volume #3 level 0.175 > volume #3 step 2 > volume #3 step 1 > show #!1 models > hide #!3 models > volume #3 level 0.095 > volume #1 level 0.1 > volume #1 level 0.125 > volume #1 level 0.1 > volume #1 level 0.125 > volume #3 level 0.125 > volume #3 level 0.15 > hide #!1 models > show #!3 models > volume #3 level 0.17 > volume #3 level 0.19 > volume #3 level 0.2 > volume #3 level 0.17 > surface dust #3 size 8.28 > surface dust #3 size 15 > surface dust #3 size 8 > surface dust #3 size 15 > surface dust #3 size 8 > surface dust #3 size 15 > surface dust #3 size 8 > surface dust #3 size 5 > surface dust #3 size 10 > surface dust #3 size 15 > surface dust #3 size 20 > surface dust #3 size 15 > surface dust #3 size 20 > surface dust #3 size 30 > surface dust #3 size 25 > surface dust #3 size 20 > surface dust #3 size 25 > surface dust #3 size 15 > surface dust #3 size 20 > show #!1 models > hide #!3 models > volume #1 level 0.15 > volume #1 level 0.1 > volume #1 level 0.13 > volume #1 level 0.12 > cofr centerOfView > cofr off Expected 3-tuple of numbers or a keyword > cofr showPivot false > volume #1 level 0.1 > volume #1 level 0.15 > volume #1 level 0.1 > volume #1 level 0.13 > volume #1 level 0.125 > volume #1 level 0.12 > volume #1 level 0.127 > volume #1 level 0.12 > save /Users/sahtelis/Desktop/connexin- > str_analysis/cx45_map_model_20250421_top.png width 1042 height 722 > supersample 3 transparentBackground true > save /Users/sahtelis/Desktop/connexin- > str_analysis/cx45_map_model_20250421_side.png width 1042 height 722 > supersample 3 transparentBackground true > hide #!1 models > show #!3 models > save /Users/sahtelis/Desktop/connexin-str_analysis/cx45map_20250521.cxs > includeMaps true > close session > open browser vseries true 'browser' has no suffix > open browser vseries 'browser' has no suffix > open browser 'browser' has no suffix > open browser Unknown command: vseries open browser > open > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_000.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_019.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_018.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_017.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_016.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_015.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_014.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_013.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_012.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_011.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_010.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_009.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_008.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_007.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_006.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_005.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_004.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_003.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_002.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_001.mrc > vseries Missing ""vseries"" keyword's argument > open > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_000.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_019.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_018.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_017.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_016.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_015.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_014.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_013.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_012.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_011.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_010.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_009.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_008.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_007.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_006.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_005.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_004.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_003.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_002.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_001.mrc > vseries true Opened map series J241_component_001_frame_000.mrc as #1, 20 images, grid size 384,384,384, pixel 0.828, shown at level 0.0406, step 2, values float32 > volume #1.1 level 0.15 > volume #1.1 level 0.1 > surface dust #1.1 size 8.28 > surface dust #1.1 size 10 > surface dust #1.1 size 11 > surface dust #1.1 size 12 > surface dust #1.1 size 15 > surface dust #1.1 size 13 > surface dust #1.1 size 12 > surface dust #1.1 size 10 > surface dust #1.1 size 8 > volume #1.1 level 0.09 > surface dust #1.1 size 8 > surface dust #1.1 size 10 > surface dust #1.1 size 8 > surface dust #1.1 size 9 > surface dust #1.1 size 5 > volume #1.1 level 0.1 > volume #1.1 level 0.15 > volume #1.1 level 0.1 > surface dust #1.1 size 5 > surface dust #1.1 size 0 > surface dust #1.1 size 2 > surface dust #1.1 size 5 > surface dust #1.1 size 7 > vseries play #1 loop true direction oscilate Invalid ""direction"" argument: Should be one of 'backward', 'forward', or 'oscillate' > vseries play #1 loop true direction oscillate pauseFrames frame 5 cache > frame 50 Invalid ""pauseFrames"" argument: Expected an integer > vseries play #1 loop true direction oscillate > vseries stop Missing or invalid ""series"" argument: empty atom specifier > Unknown command: vseries #1 stop > movie record > movie encode /Users/sahtelis/Desktop/movie1.mp4 framerate 25.0 Movie saved to /Users/sahtelis/Desktop/movie1.mp4 > movie record > movie encode /Users/sahtelis/Desktop/movie2.mp4 framerate 25.0 Error processing trigger ""new frame"": Movie encoding failed because no images were recorded. > pause Unknown command: vseries pause > vseries stop Missing or invalid ""series"" argument: empty atom specifier > vseries stop #1 > volume #1.1 level 0.125 > surface dust #1 10 Expected a keyword > surface dust #1.1 10 Expected a keyword > surface dust #1.1 size 10 > close #1 > open browser vseries true 'browser' has no suffix > open > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_000.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_019.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_018.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_017.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_016.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_015.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_014.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_013.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_012.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_011.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_010.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_009.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_008.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_007.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_006.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_005.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_004.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_003.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_002.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_001.mrc > vseries true Opened map series J241_component_002_frame_000.mrc as #1, 20 images, grid size 384,384,384, pixel 0.828, shown at level 0.0418, step 2, values float32 > volume #1.1 level 0.18 > volume #1.1 level 0.1 > volume #1.1 level 0.12 > surface dust #1.1 size 8.28 > volume #1.1 level 0.1 > volume #1.1 level 0.09 > volume #1.1 step 1 > volume #1.1 step 4 > volume #1.1 step 1 > volume #1.1 level 0.12 > volume #1.1 step 2 > volume #1.1 step 1 > volume #1.1 level 0.1 > volume #1.1 level 0.11 > volume #1.1 level 0.115 > volume #1.1 level 0.105 > vseries play #1 loop true direction oscillate pauseFrames frame 5 cache > frame 50 Invalid ""pauseFrames"" argument: Expected an integer > vseries play #1 loop true direction oscillate pauseFrames 5 cacheFrames 50 > vseries play #1 loop true direction oscillate pauseFrames 10 cacheFrames 50 > vseries play #1 loop true direction oscillate pauseFrames 2 cacheFrames 50 > vseries play #1 loop true direction oscillate pauseFrames 7 cacheFrames 50 > vseries play #1 loop true direction oscillate pauseFrames 5 cacheFrames 50 > vseries stop #1 > surface dust #1.7 size 8.28 > surface dust #1 size 10 > movie record > movie encode /Users/sahtelis/Desktop/movie2.mp4 framerate 25.0 Movie saved to /Users/sahtelis/Desktop/movie2.mp4 > close session > open > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_000.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_019.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_018.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_017.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_016.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_015.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_014.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_013.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_012.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_011.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_010.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_009.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_008.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_007.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_006.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_005.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_004.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_003.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_002.mrc > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_001.mrc > vseries true Opened map series J241_component_000_frame_000.mrc as #1, 20 images, grid size 384,384,384, pixel 0.828, shown at level 0.0404, step 2, values float32 > volume #1.1 level 0.125 > volume #1.1 step 1 > volume #1.1 level 0.15 > volume #1.1 level 0.1 > volume #1.1 level 0.09 > volume #1.1 level 0.17 > volume #1.1 level 0.125 > volume #1.1 step 2 > volume #1.1 step 1 > volume #1.1 step 2 > volume #1.1 step 1 > volume #1.1 step 2 > surface dust #1.1 size 8.28 > volume #1.1 level 0.1 > volume #1.1 level 0.11 > surface dust #1 size 12 > surface dust #1 size 8 > surface dust #1 size 7 > vseries play #1 loop true direction oscillate pauseFrames 5 cacheframe30 Expected a keyword > vseries play #1 loop true direction oscillate pauseFrames 5 cacheFrames 30 > vseries play #1 loop true direction oscillate pauseFrames 5 cacheFrames 50 > vseries play #1 loop true direction oscillate pauseFrames 5 cacheFrames 25 > vseries stop #1 > vseries play #1 loop true direction oscillate pauseFrames 5 cacheFrames 25 > vseries stop #1 > vseries play #1 loop true direction oscillate pauseFrames 5 cacheFrames 25 > movie record > movie encode /Users/sahtelis/Desktop/movie1.mp4 framerate 25.0 Movie saved to /Users/sahtelis/Desktop/movie1.mp4 > movie record > movie encode /Users/sahtelis/Desktop/movie1.mp4 framerate 25.0 Movie saved to /Users/sahtelis/Desktop/movie1.mp4 > vseries stop #1 > vseries play #1 loop true direction oscillate pauseFrames 10 cacheFrames 25 > vseries stop #1 > vseries play #1 loop true direction oscillate pauseFrames 2 cacheFrames 25 > vseries stop #1 > vseries play #1 loop true direction oscillate pauseFrames 5 cacheFrames 100 > vseries stop #1 > vseries play #1 loop true direction oscillate pauseFrames 5 cacheFrames 50 > vseries stop #1 > movie record supersample 3 size 1920 1080 Invalid ""size"" argument: Need exactly 2 ','-separated 2-tuple of integers > for i in range(1, 21): Unknown command: for i in range(1, 21): > set #1 index $i Unknown command: vseries set #1 index $i > wait 2 # Adjust to control speed (e.g., wait 2 = ~0.07 sec per frame at 30 > fps) Expected a keyword > movie stop No movie being recorded. > movie encode output cx45_vseries.mp4 bitrate 15000 No frames have been recorded > movie record supersample 3 size 1920 1080 Invalid ""size"" argument: Need exactly 2 ','-separated 2-tuple of integers > for i in range(1, 21): Unknown command: for i in range(1, 21): > set #1 index $i Unknown command: vseries set #1 index $i > wait 2 # Adjust to control speed (e.g., wait 2 = ~0.07 sec per frame at 30 > fps) Expected a keyword > movie stop No movie being recorded. > movie encode output cx45_vseries.mp4 bitrate 15000 No frames have been recorded > movie record supersample 3 size 1920 1080 Invalid ""size"" argument: Need exactly 2 ','-separated 2-tuple of integers > for i in range(1, 21): Unknown command: for i in range(1, 21): > hide #1.1-1.20 > show #1.$i Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > wait 2 > movie stop No movie being recorded. > movie encode output cx45_frames.mp4 bitrate 15000 No frames have been recorded > vseries save #1 ~/Desktop/test.cmap subregion 100,0,0,200,511,150 threshold > 140 valueType uint8 > open /Users/sahtelis/Desktop/test.cmap Opened map series test.cmap as #2, 20 images, grid size 101,512,151, pixel 0.828, shown at level 0.0002, step 1, values uint8 > select add #2 22 models selected > view clip false > close #2.1 > close #2 > vseries play #1 loop true direction oscillate pauseFrames 5 cacheFrames 50 > vseries play #1 loop true direction oscillate pauseFrames 5 cacheFrames 50 > record Expected a keyword > vseries play #1 loop true direction oscillate pauseFrames 5 cacheFrames 50 > recordmovie Expected a keyword > vseries stop #1 > vseries play #1 loop true direction oscillate pauseFrames 5 cacheFrames 50 > vseries play #1 loop false direction oscillate pauseFrames 5 cacheFrames 50 > vseries stop #1 > vseries play #1 loop false direction oscillate pauseFrames 5 cacheFrames 50 > lighting full > lighting soft > lighting simple > volume #1.1 color #82a9bf > volume #1.1 color #8cb6cf > transparency #1.1#!1 0 > vseries play #1 loop false direction oscillate pauseFrames 5 cacheFrames 50 > vseries play #1 loop true direction oscillate pauseFrames 5 cacheFrames 50 > movie record > turn y 2 180 > wait 180 > movie encode /Users/sahtelis/Desktop/movie1.mp4 Movie saved to /Users/sahtelis/Desktop/movie1.mp4 > vseries stop #1 > vseries play #1 loop true direction oscillate normalize true pauseFrames 5 > cacheFrames 50 > vseries stop #1 > vseries play #1 loop true direction oscillate normalize false pauseFrames 5 > cacheFrames 50 > vseries stop #1 > vseries play #1 loop true direction oscillate normalize true pauseFrames 5 > cacheFrames 50 > vseries stop #1 > vseries play #1 loop true direction oscillate normalize true pauseFrames 5 > cacheFrames 50 > vseries stop #1 > vseries slider #1 > vseries play #1 loop true direction oscillate normalize true pauseFrames 5 > cacheFrames 50 > vseries slider #1 > vseries stop #1 > movie record supersample 3 size 1920 1080 Invalid ""size"" argument: Need exactly 2 ','-separated 2-tuple of integers > movie record supersample 3 size 1920,1080 > vseries play #1 loop false direction forward normalize true pauseFrames 5 > cacheFrames 50 > wait 40 > movie stop > movie encode output cx45_vseries_play.mp4 bitrate 15000 Movie saved to cx45_vseries_play.mp4 > movie record supersample 3 size 1920,1080 > vseries play #1 loop false direction oscillate normalize true pauseFrames 5 > cacheFrames 50 > wait 80 # 40 forward + 40 backward Expected a keyword > wait 80 #1 40 forward + 40 backward Expected a keyword > wait 80 40 forward + 40 backward Expected a keyword > wait 80 > movie stop > movie encode output cx45_vseries_play2.mp4 bitrate 15000 Movie saved to cx45_vseries_play2.mp4 > vseries play #1 loop true direction oscillate pauseFrames 5 cacheFrames 50 > vseries stop #1 > record #1 loop true direction oscillate pauseframe 5 cacheframe 50 Unknown command: vseries record #1 loop true direction oscillate pauseframe 5 cacheframe 50 > movie record supersample 3 size 1920,1080 > set #1 index $i Unknown command: vseries set #1 index $i > hide #1.1-1.20 > movie record supersample 3 size 1920,1080 Already recording a movie > for i in range(1, 21): Unknown command: for i in range(1, 21): > show #1.$i Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > wait Unknown command: ui wait > wait 2 > hide #1.$i Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > movie stop > hide #1.1-1.20 > movie record supersample 3 size 1920,1080 > show #1.$i Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > movie stop > hide #1.1-1.20 > movie record supersample 3 size 1920,1080 > eval(""show #1.%d"" % i) Unknown command: eval(""show #1.%d"" % i) > show #1.1 > wait 2 > hide #1.1 > show #1.2 > wait 2 > hide #1.2 > show #1.3 > wait 2 > hide #1.3 > show #1.4 > wait 2 > hide #1.4 > show #1.5 > wait 2 > hide #1.5 > show #1.6 > wait 2 > hide #1.6 > show #1.7 > wait 2 > hide #1.7 > show #1.8 > wait 2 > hide #1.8 > show #1.9 > wait 2 > hide #1.9 > show #1.10 > wait 2 > hide #1.10 > show #1.11 > wait 2 > hide #1.11 > show #1.12 > wait 2 > hide #1.12 > show #1.13 > wait 2 > hide #1.13 > show #1.14 > wait 2 > hide #1.14 > show #1.15 > wait 2 > hide #1.15 > show #1.16 > wait 2 > hide #1.16 > show #1.17 > wait 2 > hide #1.17 > show #1.18 > wait 2 > hide #1.18 > show #1.19 > wait 2 > hide #1.19 > show #1.20 > wait 2 > hide #1.20 > movie stop > movie encode output cx45_frames_movie.mp4 bitrate 15000 Movie saved to cx45_frames_movie.mp4 > hide #1.1-1.20 > movie record supersample 3 size 1920,1080 > show #1.1 > wait; wait 2; hide #1.1 Unknown command: ui wait; wait 2; hide #1.1 > show #1.2 > wait; wait 2; hide #1.2 Unknown command: ui wait; wait 2; hide #1.2 > show #1.3 > wait; wait 2; hide #1.3 Unknown command: ui wait; wait 2; hide #1.3 > show #1.4 > wait; wait 2; hide #1.4 Unknown command: ui wait; wait 2; hide #1.4 > show #1.5 > wait; wait 2; hide #1.5 Unknown command: ui wait; wait 2; hide #1.5 > show #1.6 > wait; wait 2; hide #1.6 Unknown command: ui wait; wait 2; hide #1.6 > show #1.7 > wait; wait 2; hide #1.7 Unknown command: ui wait; wait 2; hide #1.7 > show #1.8 > wait; wait 2; hide #1.8 Unknown command: ui wait; wait 2; hide #1.8 > show #1.9 > wait; wait 2; hide #1.9 Unknown command: ui wait; wait 2; hide #1.9 > show #1.10 > wait; wait 2; hide #1.10 Unknown command: ui wait; wait 2; hide #1.10 > show #1.11 > wait; wait 2; hide #1.11 Unknown command: ui wait; wait 2; hide #1.11 > show #1.12 > wait; wait 2; hide #1.12 Unknown command: ui wait; wait 2; hide #1.12 > show #1.13 > wait; wait 2; hide #1.13 Unknown command: ui wait; wait 2; hide #1.13 > show #1.14 > wait; wait 2; hide #1.14 Unknown command: ui wait; wait 2; hide #1.14 > show #1.15 > wait; wait 2; hide #1.15 Unknown command: ui wait; wait 2; hide #1.15 > show #1.16 > wait; wait 2; hide #1.16 Unknown command: ui wait; wait 2; hide #1.16 > show #1.17 > wait; wait 2; hide #1.17 Unknown command: ui wait; wait 2; hide #1.17 > show #1.18 > wait; wait 2; hide #1.18 Unknown command: ui wait; wait 2; hide #1.18 > show #1.19 > wait; wait 2; hide #1.19 Unknown command: ui wait; wait 2; hide #1.19 > show #1.20 > wait; wait 2; hide #1.20 Unknown command: ui wait; wait 2; hide #1.20 > movie stop > movie encode output cx45_frames_movie.mp4 bitrate 15000 Movie encoding failed because no images were recorded. > movie record > movie encode /Users/sahtelis/Desktop/movie1.mp4 framerate 25.0 Movie saved to /Users/sahtelis/Desktop/movie1.mp4 > movie record > movie encode /Users/sahtelis/Desktop/movie2.mp4 framerate 25.0 Movie saved to /Users/sahtelis/Desktop/movie2.mp4 > movie record > movie encode /Users/sahtelis/Desktop/movie3.mp4 framerate 25.0 Movie saved to /Users/sahtelis/Desktop/movie3.mp4 > movie record > movie encode /Users/sahtelis/Desktop/movie3.mp4 framerate 50.0 Movie encoding failed because no images were recorded. > movie record > movie encode /Users/sahtelis/Desktop/movie4.mp4 framerate 25.0 Movie saved to /Users/sahtelis/Desktop/movie4.mp4 > movie record > movie encode /Users/sahtelis/Desktop/movie5.mp4 framerate 25.0 Movie saved to /Users/sahtelis/Desktop/movie5.mp4 > volume #1.1 step 1 > volume #1.1 level 0.1 > volume #1.1 level 0.11 > volume #1.1 level 0.1131 > movie record > movie encode /Users/sahtelis/Desktop/movie6.mp4 framerate 25.0 Movie saved to /Users/sahtelis/Desktop/movie6.mp4 > movie record > movie encode /Users/sahtelis/Desktop/movie7.mp4 framerate 25.0 Movie saved to /Users/sahtelis/Desktop/movie7.mp4 > view > ui tool show ""Side View"" > view > close session > open browse Unknown command: vseries open browse > browse open Unknown command: vseries browse open > open > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_000.mrc > vseries Missing ""vseries"" keyword's argument > open > /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_000.mrc > vseries true Opened J241_component_000_frame_000.mrc as #1, grid size 384,384,384, pixel 0.828, shown at level 0.0404, step 2, values float32 > volume #1 level 0.12 > volume #1 level 0.15 > volume #1 level 0.1 > surface dust #1 size 8.28 > close session > open /Users/sahtelis/Desktop/connexin-str_analysis/cx45map_20250521.cxs Opened cryosparc_P2_J217_005_volume_map_sharp.mrc x flip as #3, grid size 384,384,384, pixel 0.828, shown at level 0.17, step 1, values float32 Opened cryosparc_P2_J217_005_volume_map_sharp.mrc x flip gaussian as #1, grid size 384,384,384, pixel 0.828, shown at level 0.12, step 1, values float32 Opened emdb 31495 as #4, grid size 400,400,400, pixel 0.675, shown at level 0.0171, step 2, values float32 Opened emdb 31495 gaussian as #6, grid size 400,400,400, pixel 0.675, shown at level 0.00354, step 1, values float32 opened ChimeraX session > movie record > turn y 2 180 > wait 180 > movie encode /Users/sahtelis/Desktop/movie1.mp4 Movie saved to /Users/sahtelis/Desktop/movie1.mp4 > show #!6 models > volume #6 level 0.009791 > hide #!6 models > show #!5 models > select add #5 18492 atoms, 19044 bonds, 12 pseudobonds, 2268 residues, 2 models selected > view matrix models > #5,0.99863,-0.035654,-0.038222,43.731,0.03798,0.99736,0.061958,18.394,0.035912,-0.063325,0.99735,-2.4187 > hide #!2 models > select subtract #5 Nothing selected > show #!1 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!3 models > volume #3 level 0.17 > volume #1 level 0.07947 > hide #!1 models > show #!3 models > volume #3 level 0.1182 > transparency #3,5 90 > transparency #3,5 20 > transparency #3,5 30 > volume gaussian #3 sDev 1 Opened cryosparc_P2_J217_005_volume_map_sharp.mrc x flip gaussian as #7, grid size 384,384,384, pixel 0.828, shown at step 1, values float32 > volume #7 level 0.1004 > volume #7 level 0.12 > surface dust #7 size 8.28 > volume #7 level 0.09955 > transparency #5,7 40 > hide #!5 models > volume #7 level 0.08023 > show #!5 models > volume #7 level 0.0825 > hide #!5 models > hide #!7 models > show #!6 models > show #!5 models > hide #!6 models > show #!4 models > hide #!5 models > hide #!4 models > show #!5 models > hide #!5 cartoons > show #!5 surfaces > hide #!5 surfaces > show #!5 atoms > hide #!5 atoms > style #!5 stick Changed 18492 atom styles > show #!5 cartoons > rainbow #!5 > undo > coulombic #!5 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 7z1t.pdb_A SES surface #5.2: minimum, -15.68, mean 0.27, maximum 14.86 Coulombic values for 7z1t.pdb_B SES surface #5.3: minimum, -13.61, mean 0.24, maximum 13.31 Coulombic values for 7z1t.pdb_C SES surface #5.4: minimum, -13.13, mean 0.24, maximum 13.52 Coulombic values for 7z1t.pdb_D SES surface #5.5: minimum, -13.79, mean 0.29, maximum 19.64 Coulombic values for 7z1t.pdb_E SES surface #5.6: minimum, -13.19, mean 0.25, maximum 14.62 Coulombic values for 7z1t.pdb_F SES surface #5.7: minimum, -13.54, mean 0.26, maximum 15.60 Coulombic values for 7z1t.pdb_G SES surface #5.8: minimum, -13.19, mean 0.27, maximum 16.26 Coulombic values for 7z1t.pdb_H SES surface #5.9: minimum, -13.15, mean 0.28, maximum 12.99 Coulombic values for 7z1t.pdb_I SES surface #5.10: minimum, -17.63, mean 0.28, maximum 14.83 Coulombic values for 7z1t.pdb_J SES surface #5.11: minimum, -17.52, mean 0.27, maximum 15.83 Coulombic values for 7z1t.pdb_K SES surface #5.12: minimum, -13.56, mean 0.28, maximum 15.36 Coulombic values for 7z1t.pdb_L SES surface #5.13: minimum, -16.14, mean 0.24, maximum 12.69 To also show corresponding color key, enter the above coulombic command and add key true > undo > hide #!5 surfaces Alignment identifier is 1 Alignment identifier is 2 > select #5/A-L:2 48 atoms, 36 bonds, 12 residues, 1 model selected > select #5/A-L:2-16 1344 atoms, 1356 bonds, 180 residues, 1 model selected > surface (#!5 & sel) > style (#!5 & sel) stick Changed 1344 atom styles > surface hidePatches (#!5 & sel) > style (#!5 & sel) stick Changed 1344 atom styles > surface style #5 dot > surface (#!5 & sel) > surface hidePatches (#!5 & sel) > surface (#!5 & sel) > surface style #5 dot > surface style #5 mesh > surface style #5 solid > transparency (#!5 & sel) 50 > select #5/A-L:2 48 atoms, 36 bonds, 12 residues, 1 model selected > select #5/A-L:2-17 1488 atoms, 1512 bonds, 192 residues, 1 model selected > ui tool show ""Selection Inspector"" > style sel ball Changed 1488 atom styles > surface hidePatches (#!5 & sel) > cartoon hide (#!5 & sel) > show (#!5 & sel) target ab > style (#!5 & sel) ball Changed 1488 atom styles > style (#!5 & sel) stick Changed 1488 atom styles > style (#!5 & sel) sphere Changed 1488 atom styles > style (#!5 & sel) ringFill thin Changed 192 residue ring styles > style (#!5 & sel) ringFill off Changed 192 residue ring styles > style (#!5 & sel) ball Changed 1488 atom styles > style (#!5 & sel) stick Changed 1488 atom styles > view sel > hide #* target a > show (#!5 & sel) target ab > hide (#!5 & sel) target a > cartoon style (#!5 & sel) modeHelix tube sides 20 > cartoon hide (#!5 & sel) > cartoon style (#!5 & sel) xsection oval modeHelix default > cartoon hide (#!5 & sel) > cartoon (#!5 & sel) > cartoon style (#!5 & sel & coil) xsection oval > cartoon style (#!5 & sel) xsection barbell modeHelix default > cartoon style (#!5 & sel) xsection oval modeHelix default > cartoon style (#!5 & sel) modeHelix tube sides 20 > select protein 34962 atoms, 35784 bonds, 18 pseudobonds, 3276 residues, 4 models selected > select clear > select #5/A-L:2-17 1488 atoms, 1512 bonds, 192 residues, 1 model selected > cartoon style (#!5 & sel & coil) xsection oval > cartoon style (#!5 & sel) xsection barbell modeHelix default > cartoon style (#!5 & sel) xsection rectangle modeHelix default > cartoon style (#!5 & sel) xsection oval modeHelix default > surface style #5 mesh > surface (#!5 & sel) > select ~sel 33474 atoms, 34260 bonds, 18 pseudobonds, 3084 residues, 14 models selected > undo > select clear > select #5/A-L:2-16 1344 atoms, 1356 bonds, 180 residues, 1 model selected > surface (#!5 & sel) > surface style #5 solid > color (#!5 & sel) red > color (#!5 & sel) lime > color (#!5 & sel) cyan > color (#!5 & sel) gray > select clear > transparency #5 10 > select clear > select #5/A-L:2-16 1344 atoms, 1356 bonds, 180 residues, 1 model selected > surface hidePatches (#!5 & sel) > select clear > show #!7 models > transparency #5,7 20 > volume #7 color #c0faffcc > volume #7 color #a6f2ffcc > volume #7 color #9dfff8cc Alignment identifier is 1 Alignment identifier is 2 > select clear > select #5/A-L:2-17 1488 atoms, 1512 bonds, 192 residues, 1 model selected > color (#!5 & sel) orange > select clear > select #5/A-L:2-17 1488 atoms, 1512 bonds, 192 residues, 1 model selected > color (#!5 & sel) orange red > select clear Drag select of 6 emdb 31495 gaussian > undo Drag select of 6 emdb 31495 gaussian > undo > hide #!5 models > show #!7 models > tile 2 models tiled > transparency #6-7 0 > volume #7 color #c9fbe7 > volume #7 color #adfbc8 > volume #7 color #a5fbd2 > volume #7 color #abfbf3 > volume #7 color #9feffb > lighting full > lighting simple > lighting soft > lighting flat > lighting full > lighting shadows false > graphics silhouettes false > lighting shadows true > view matrix models > #7,0.99342,-0.025082,0.11175,-4.22,-0.03759,0.85027,0.525,11.66,-0.10819,-0.52574,0.84373,48.43 > volume #6 level 0.009165 > volume gaussian #3 sDev 1.2 Opened cryosparc_P2_J217_005_volume_map_sharp.mrc x flip gaussian as #8, grid size 384,384,384, pixel 0.828, shown at step 1, values float32 > volume #8 level 0.08688 > select add #8 2 models selected > view matrix models #8,1,0,0,51.534,0,1,0,39.283,0,0,1,-27.73 > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.99936,-0.012202,0.033733,48.268,-0.0085695,0.83194,0.5548,-19.938,-0.034834,-0.55473,0.8313,92.511 > view matrix models > #8,0.99977,-0.018173,0.011388,52.668,0.010042,0.86588,0.50015,-19.678,-0.01895,-0.49992,0.86586,75.847 > ui mousemode right ""move picked models"" > view matrix models > #8,0.99846,-0.030417,0.046301,71.565,-0.0037266,0.79701,0.60395,-53.061,-0.055272,-0.6032,0.79567,124.56 > volume #8 level 0.07847 > surface dust #8 size 8.28 > select subtract #8 Nothing selected > volume #6 level 0.009556 > show #!3 models > show #!1 models > tile 5 models tiled > select add #6 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.99643,-0.036804,0.076014,128.36,0.0026097,0.91304,0.40786,261.2,-0.084415,-0.4062,0.90987,-73.946 > select subtract #6 Nothing selected > select add #1 2 models selected > view matrix models > #1,0.98773,-0.0064489,0.15604,33.423,-0.064652,0.89263,0.44612,97.527,-0.14217,-0.45074,0.88126,25.126 > select subtract #1 Nothing selected > select add #3 2 models selected > view matrix models > #3,0.98329,-0.012796,0.18159,-23.78,-0.094051,0.81838,0.56693,-45.095,-0.15587,-0.57454,0.8035,146.78 > select subtract #3 Nothing selected > tile 5 models tiled > transparency #1,3,6-8 0 > lighting full > hide #!1 models > show #!1 models > hide #!3 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > volume #7 level 0.08023 > volume gaussian #4 sDev 1.5 Opened emdb 31495 gaussian as #9, grid size 400,400,400, pixel 0.675, shown at step 1, values float32 > volume #9 level 0.008522 > select add #9 2 models selected > view matrix models > #9,0.8467,0.4658,-0.25716,-7.4711,-0.45329,0.88458,0.10977,61.957,0.27861,0.02362,0.96011,-35.416 > view matrix models > #9,0.90232,0.37633,-0.21022,-9.2384,-0.36837,0.92645,0.077404,49.209,0.22389,0.0075955,0.97459,-27.819 > ui mousemode right ""rotate selected models"" > view matrix models > #9,0.81074,0.5133,-0.28148,-5.7456,-0.49786,0.8575,0.12974,68.934,0.30796,0.034952,0.95076,-39.645 > view matrix models > #9,0.79247,0.53518,-0.29252,-4.743,-0.51825,0.84375,0.13967,72.204,0.32156,0.040918,0.946,-41.645 > hide #!6 models > close #9 > close #7 > hide #!1 models > show #!1 models > close #8 > volume gaussian #4 sDev 2 Opened emdb 31495 gaussian as #7, grid size 400,400,400, pixel 0.675, shown at step 1, values float32 > volume #7 level 0.007722 > select add #7 2 models selected > view matrix models > #7,0.70254,0.62659,-0.33737,1.113,-0.60233,0.77603,0.18702,86.302,0.379,0.071821,0.92261,-50.412 > view matrix models > #7,0.84957,0.46171,-0.25504,-7.5924,-0.44944,0.88674,0.10815,61.364,0.27609,0.022743,0.96086,-35.059 > ui mousemode right ""move picked models"" > view matrix models > #7,0.84957,0.46171,-0.25504,113.46,-0.44944,0.88674,0.10815,292.73,0.27609,0.022743,0.96086,-181.28 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.86188,0.50323,0.062579,63.318,-0.47261,0.75237,0.45889,266.64,0.18385,-0.42509,0.88629,-98.298 > select subtract #7 Nothing selected > tile 2 models tiled > volume #1 color #97b9fe > lighting full > select add #7 2 models selected > view matrix models > #7,0.85105,0.51632,0.095564,73.555,-0.5108,0.7719,0.37848,360.87,0.12165,-0.37092,0.92066,-112.53 > ui mousemode right ""move picked models"" > view matrix models > #7,0.85105,0.51632,0.095564,58.366,-0.5108,0.7719,0.37848,295.35,0.12165,-0.37092,0.92066,-76.808 > view matrix models > #7,0.85105,0.51632,0.095564,58.867,-0.5108,0.7719,0.37848,296.81,0.12165,-0.37092,0.92066,-77.626 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.85365,0.50785,0.11567,56.945,-0.50123,0.7406,0.44753,290.43,0.14161,-0.44001,0.88676,-66.418 > volume #7 level 0.0069 > select subtract #7 Nothing selected > close #7 > select add #6 2 models selected > view matrix models > #6,0.99449,0.027048,0.10126,112.8,-0.066163,0.91132,0.40635,261.24,-0.081293,-0.41081,0.90809,-67.508 > ui mousemode right ""move picked models"" > view matrix models > #6,0.99449,0.027048,0.10126,101.47,-0.066163,0.91132,0.40635,219.12,-0.081293,-0.41081,0.90809,-44.317 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.9921,0.023665,0.1232,99.293,-0.075799,0.89559,0.43838,218.22,-0.099958,-0.44426,0.89031,-34.882 > select subtract #6 Nothing selected > surface dust #1 size 8.28 > surface dust #6 size 6.75 > volume #1 level 0.0833 > select add #1 2 models selected > view matrix models > #1,0.98604,0.046183,0.15998,22.809,-0.12511,0.83948,0.52879,97.689,-0.10988,-0.54143,0.83354,44.946 > select subtract #1 Nothing selected > set bgColor gray > set bgColor #80808000 > open /Users/sahtelis/Downloads/emd_14452.map Opened emd_14452.map as #7, grid size 384,384,384, pixel 0.654, shown at level 0.00226, step 2, values float32 > open /Users/sahtelis/Downloads/emd_14455.map Opened emd_14455.map as #8, grid size 384,384,384, pixel 0.654, shown at level 0.00389, step 2, values float32 > open /Users/sahtelis/Downloads/emd_14456.map Opened emd_14456.map as #9, grid size 384,384,384, pixel 0.654, shown at level 0.00296, step 2, values float32 > open /Users/sahtelis/Downloads/emd_9116.map Opened emd_9116.map as #10, grid size 320,320,320, pixel 0.665, shown at level 0.0238, step 2, values float32 > open /Users/sahtelis/Downloads/emd_0826.map Opened emd_0826.map as #11, grid size 320,320,320, pixel 0.673, shown at level 0.0162, step 2, values float32 > tile 7 models tiled > hide #!6 models > show #!6 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > select add #7 2 models selected > color #7 #f77bb6ff models > view matrix models > #7,0.98363,0.0055776,0.1801,172.05,-0.064184,0.9448,0.32129,431.81,-0.16836,-0.32759,0.9297,-144.65 > volume #7 level 0.004092 > select subtract #7 Nothing selected > volume gaussian #7 sDev 2 Opened emd_14452.map gaussian as #12, grid size 384,384,384, pixel 0.654, shown at step 1, values float32 > volume #12 level 0.00227 > volume gaussian #7 sDev 1.5 Opened emd_14452.map gaussian as #13, grid size 384,384,384, pixel 0.654, shown at step 1, values float32 > close #12 > volume #13 level 0.002471 > show #!7 models > hide #!7 models > hide #!8 models > show #!8 models > select add #8 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.99511,0.068185,0.071465,232.86,-0.097711,0.78543,0.61119,73.863,-0.014457,-0.61518,0.78825,59.236 > select subtract #8 Nothing selected > volume #8 level 0.00631 > volume gaussian #8 sDev 1.5 Opened emd_14455.map gaussian as #12, grid size 384,384,384, pixel 0.654, shown at step 1, values float32 > hide #!12 models > show #!12 models > volume #12 level 0.004649 > hide #!9 models > show #!9 models > volume #9 level 0.005524 > select add #9 2 models selected > view matrix models > #9,0.99792,-0.056479,-0.030994,314.94,-0.0067944,0.38614,-0.92242,451.8,0.064065,0.92071,0.38495,-174.45 > view matrix models > #9,0.9663,-0.25737,0.004827,339.54,-0.21522,-0.81804,-0.53337,579.25,0.14122,0.51436,-0.84587,24.848 > view matrix models > #9,0.96561,-0.2584,0.028699,336.69,-0.20798,-0.83398,-0.5111,577.48,0.156,0.48756,-0.85904,28.048 > select subtract #9 Nothing selected > volume #9 level 0.005258 > volume #9 level 0.003842 > volume #9 level 0.00517 > volume gaussian #9 sDev 1.5 Opened emd_14456.map gaussian as #14, grid size 384,384,384, pixel 0.654, shown at step 1, values float32 > volume #14 level 0.003542 > select add #10 2 models selected > view matrix models > #10,0.93907,-0.16538,0.30134,368.57,0.09229,0.96577,0.24243,386.75,-0.33112,-0.19985,0.92218,-125.33 > volume gaussian #10 sDev 1.5 Opened emd_9116.map gaussian as #15, grid size 320,320,320, pixel 0.665, shown at step 1, values float32 > volume #15 level 0.01634 > view matrix models > #10,0.93907,-0.16538,0.30134,368.57,0.09229,0.96577,0.24243,386.75,-0.33112,-0.19985,0.92218,-125.33 > select add #15 4 models selected > view matrix models > #10,0.95661,-0.052457,0.28662,356.25,-0.022612,0.96733,0.25251,397.73,-0.2905,-0.24803,0.92417,-124.73,#15,0.98484,-0.1246,0.12069,378.58,0.070855,0.924,0.37577,379.29,-0.15834,-0.36152,0.91882,-126.15 > view matrix models > #10,0.95134,0.16204,0.26211,336.6,-0.23469,0.93221,0.27552,421.59,-0.19969,-0.32363,0.92487,-126.43,#15,0.98791,0.091283,0.12527,354.79,-0.13679,0.89352,0.42768,399.1,-0.072894,-0.43965,0.89521,-124.42 > view matrix models > #10,0.53428,-0.74217,0.40464,462.02,0.72956,0.64664,0.22273,354.99,-0.42696,0.17621,0.88694,-151.39,#15,0.54764,-0.80873,0.21459,487.9,0.79028,0.5842,0.18486,359.21,-0.27486,0.06835,0.95905,-163.77 > view matrix models > #10,0.5971,-0.69875,0.39398,451.85,0.67642,0.7026,0.22096,354.88,-0.4312,0.13456,0.89217,-147.07,#15,0.61041,-0.76649,0.19972,478.31,0.74073,0.6417,0.19885,356.87,-0.28058,0.026554,0.95946,-158.76 > view matrix models > #10,0.071132,-0.88378,0.46246,520.21,0.94417,0.20918,0.25453,375.32,-0.32169,0.41854,0.84932,-184.37,#15,0.091689,-0.94058,0.32696,538.48,0.98233,0.13924,0.12509,392.47,-0.16319,0.30971,0.93672,-198.96 > view matrix models > #10,0.39164,-0.8156,0.42592,482.74,0.82526,0.51607,0.2294,357.99,-0.4069,0.26165,0.8752,-161.37,#15,0.40607,-0.87934,0.24874,506.84,0.87838,0.45066,0.15919,366.77,-0.25208,0.15385,0.9554,-174.9 > view matrix models > #10,0.05033,-0.88421,0.46437,522.27,0.94792,0.18871,0.25658,376.88,-0.3145,0.42727,0.84766,-185.89,#15,0.14129,-0.93871,0.31442,534.34,0.9734,0.18959,0.12861,387.69,-0.18034,0.28789,0.94053,-195.22 > view clip false > view matrix models > #10,0.0057552,-0.89467,0.4467,530,0.90469,0.19497,0.37884,367.81,-0.42603,0.40195,0.81052,-167.38,#15,0.09464,-0.94839,0.30267,541.59,0.95051,0.17646,0.25573,378,-0.29594,0.26349,0.91815,-177.94 > select subtract #15 2 models selected > view matrix models > #10,0.0057552,-0.89467,0.4467,530,0.90469,0.19497,0.37884,367.81,-0.42603,0.40195,0.81052,-167.38 > hide #!15 models > hide #!14 models > hide #!13 models > hide #!12 models > hide #!11 models > show #!11 models > volume #11 level 0.03407 > view matrix models > #10,0.0057552,-0.89467,0.4467,530,0.90469,0.19497,0.37884,367.81,-0.42603,0.40195,0.81052,-167.38 > ui mousemode right ""move picked models"" > view matrix models > #11,0.9935,0.020734,0.1119,299.76,-0.00697,0.9925,-0.12202,334.12,-0.11359,0.12044,0.9862,-82.241 > view matrix models > #11,0.9935,0.020734,0.1119,225.16,-0.00697,0.9925,-0.12202,475.79,-0.11359,0.12044,0.9862,-110.02 > select add #11 4 models selected > view matrix models > #11,0.9935,0.020734,0.1119,214.38,-0.00697,0.9925,-0.12202,479.68,-0.11359,0.12044,0.9862,-107.11 > ui mousemode right ""rotate selected models"" > view matrix models > #10,-0.15789,-0.84389,0.51276,524.54,0.92257,-0.3112,-0.22809,590.23,0.35205,0.43704,0.82768,-263.93,#11,0.96122,-0.074588,0.2655,210.24,0.25572,0.6015,-0.75684,567.39,-0.10325,0.79538,0.59725,-135.63 > view matrix models > #10,0.16906,-0.9389,0.2998,544.43,0.24941,-0.25352,-0.93462,741.02,0.95353,0.23278,0.19131,-186.38,#11,0.99143,0.078188,-0.10466,233.62,-0.077078,-0.29676,-0.95184,722.65,-0.10548,0.95174,-0.28819,-49.158 > view matrix models > #10,0.23301,-0.96817,-0.091409,597.94,-0.59439,-0.067393,-0.80135,761.94,0.76968,0.24105,-0.59117,-64.491,#11,0.88531,-0.063107,-0.4607,301.71,-0.24508,-0.90529,-0.34696,735.86,-0.39517,0.42008,-0.81693,100.83 > view matrix models > #10,0.16904,-0.98414,-0.053825,604.39,-0.67894,-0.07668,-0.73018,764.24,0.71447,0.15997,-0.68114,-23.535,#11,0.91032,-0.10269,-0.40097,296.32,-0.21559,-0.94459,-0.24753,725.34,-0.35333,0.31178,-0.88202,115.56 > select subtract #11 2 models selected > volume #11 level 0.06705 > volume gaussian #11 sDev 1.5 Opened emd_0826.map gaussian as #16, grid size 320,320,320, pixel 0.673, shown at step 1, values float32 > volume #16 level 0.00762 > close #11 > close #10 > close #9 > close #8 > close #7 > show #!12 models > hide #!12 models > show #!12 models > hide #!6 models > show #!6 models > hide #!16 models > show #!16 models > show #!15 models > show #!14 models > show #!13 models > tile 7 models tiled > volume #16 color #91f762 > close #14 > tile 6 models tiled > hide #!16 models > show #!16 models > hide #!15 models > show #!15 models > hide #!13 models > show #!13 models > hide #!6 models > close #6 > close #4 > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!13 models > tile 4 models tiled > select add #12 2 models selected > view matrix models > #12,0.94659,-0.016676,0.322,103.7,-0.071205,0.96319,0.25921,311.1,-0.31447,-0.26829,0.91057,-45.418 > ui mousemode right ""move picked models"" > view matrix models > #12,0.94659,-0.016676,0.322,99.005,-0.071205,0.96319,0.25921,261.54,-0.31447,-0.26829,0.91057,-25.076 > select subtract #12 Nothing selected > select add #15 2 models selected > view matrix models > #15,0.18591,-0.97442,0.1263,456.2,0.93853,0.21416,0.27074,78.732,-0.29086,0.0682,0.95433,-35.489 > ui mousemode right ""rotate selected models"" > view matrix models > #15,0.1397,-0.95899,0.24663,446.68,0.87937,0.23465,0.4143,67.571,-0.45518,0.159,0.87609,-19.342 > ui mousemode right ""move picked models"" > view matrix models > #15,0.1397,-0.95899,0.24663,380.14,0.87937,0.23465,0.4143,84.864,-0.45518,0.159,0.87609,-5.0209 > select subtract #15 Nothing selected > select add #16 2 models selected > view matrix models > #16,0.75684,-0.12353,-0.64182,371.63,-0.27645,-0.95031,-0.14309,517.96,-0.59226,0.28573,-0.75339,115.59 > ui mousemode right ""rotate selected models"" > view matrix models > #16,0.97016,-0.06985,-0.23218,295.61,-0.14137,-0.94094,-0.30763,521.39,-0.19698,0.33128,-0.92274,87.666 > view matrix models > #16,0.95588,-0.089003,-0.27995,304.72,-0.16303,-0.9535,-0.25351,518.83,-0.24436,0.28796,-0.92594,97.801 > view matrix models > #16,0.95374,-0.078568,-0.2902,305.01,-0.16825,-0.93942,-0.29863,523.08,-0.24916,0.33364,-0.90918,91.464 > select subtract #16 Nothing selected > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!12 models > hide #!15 models > hide #!16 models > ui mousemode right ""move picked models"" > view #2 clip false No displayed objects specified. > select add #1 2 models selected > view #2 clip false No displayed objects specified. > view #1 clip false > select subtract #1 Nothing selected > volume #1 level 0.08482 > volume #1 level 0.07718 > show #!2 models > select add #2 16470 atoms, 16740 bonds, 6 pseudobonds, 1008 residues, 2 models selected > hide #!1 models > show #!1 models > view matrix models > #2,0.99706,-0.0055579,0.076461,43.4,0.00071027,0.998,0.063281,133.14,-0.07666,-0.06304,0.99506,-42.485 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.9773,-0.04743,0.2065,33.392,-0.0078424,0.96586,0.25896,109.82,-0.21173,-0.2547,0.94356,17.186 > view matrix models > #2,0.97873,-0.04646,0.19984,34.024,-0.0063833,0.96666,0.25599,109.91,-0.20507,-0.25182,0.9458,15.334 > view matrix models > #2,0.93521,-0.054235,0.34992,19.302,-0.027504,0.97409,0.22448,116.87,-0.35303,-0.21956,0.90948,39.132 > ui mousemode right ""move picked models"" > view matrix models > #1,0.046692,0.28593,-0.95711,310.46,0.40412,0.87084,0.27987,46.331,0.91351,-0.39985,-0.07489,3.8185 > view matrix models > #2,0.20307,0.20581,-0.95729,296.89,0.45813,0.84408,0.27865,46.929,0.86538,-0.49515,0.077114,17.619 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.90772,0.36596,-0.20523,332.64,0.41612,0.84787,-0.32858,145.39,0.053762,-0.38366,-0.92191,280.3 > view matrix models > #2,-0.90497,0.37688,-0.19744,329.28,0.42113,0.85955,-0.28952,136.79,0.060594,-0.34516,-0.93659,275.33 > ui tool show ""Fit in Map"" > fitmap #2 inMap #1 Fit molecule cx45_hexamer_startingmodel_isolderelaxed.pdb (#2) to map cryosparc_P2_J217_005_volume_map_sharp.mrc x flip gaussian (#1) using 16470 atoms average map value = 0.0483, steps = 60 shifted from previous position = 1.36 rotated from previous position = 3.57 degrees atoms outside contour = 12449, contour level = 0.077178 Position of cx45_hexamer_startingmodel_isolderelaxed.pdb (#2) relative to cryosparc_P2_J217_005_volume_map_sharp.mrc x flip gaussian (#1) coordinates: Matrix rotation and translation 0.99747380 -0.07098521 -0.00266685 12.07098320 0.07098654 0.99747719 0.00040881 -10.84033065 0.00263110 -0.00059709 0.99999636 -10.96426753 Axis -0.00708009 -0.03729010 0.99927940 Axis point 164.09589031 163.14848416 0.00000000 Rotation angle (degrees) 4.07355508 Shift along axis -10.63759339 > fitmap #2 inMap #1 Fit molecule cx45_hexamer_startingmodel_isolderelaxed.pdb (#2) to map cryosparc_P2_J217_005_volume_map_sharp.mrc x flip gaussian (#1) using 16470 atoms average map value = 0.0483, steps = 64 shifted from previous position = 0.00134 rotated from previous position = 0.00645 degrees atoms outside contour = 12446, contour level = 0.077178 Position of cx45_hexamer_startingmodel_isolderelaxed.pdb (#2) relative to cryosparc_P2_J217_005_volume_map_sharp.mrc x flip gaussian (#1) coordinates: Matrix rotation and translation 0.99746582 -0.07109717 -0.00266791 12.09011924 0.07109848 0.99746922 0.00040101 -10.85542717 0.00263265 -0.00058968 0.99999636 -10.96436038 Axis -0.00696204 -0.03724973 0.99928174 Axis point 164.06189377 163.16131742 0.00000000 Rotation angle (degrees) 4.07998058 Shift along axis -10.63629515 > show #!3 models > hide #!3 models > view matrix models > #2,0.58214,0.75996,0.28909,-41.72,-0.81284,0.53523,0.22983,305.43,0.019929,-0.36878,0.9293,2.0517 > fitmap #2 inMap #1 Fit molecule cx45_hexamer_startingmodel_isolderelaxed.pdb (#2) to map cryosparc_P2_J217_005_volume_map_sharp.mrc x flip gaussian (#1) using 16470 atoms average map value = 0.05138, steps = 104 shifted from previous position = 10.7 rotated from previous position = 9.49 degrees atoms outside contour = 12134, contour level = 0.077178 Position of cx45_hexamer_startingmodel_isolderelaxed.pdb (#2) relative to cryosparc_P2_J217_005_volume_map_sharp.mrc x flip gaussian (#1) coordinates: Matrix rotation and translation 0.99743047 0.07164049 -0.00029854 -10.94311791 -0.07164063 0.99743038 -0.00049075 11.77748300 0.00026261 0.00051087 0.99999983 10.32977683 Axis 0.00699041 -0.00391627 -0.99996790 Axis point 158.17955418 157.40401107 0.00000000 Rotation angle (degrees) 4.10835301 Shift along axis -10.45206592 > select subtract #2 Nothing selected > hide #!2 models > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > volume #3 level 0.1252 > volume #1 level 0.08129 > select add #1 2 models selected > select subtract #1 Nothing selected > save /Users/sahtelis/Downloads/cx45_NTD_pore.png width 954 height 637 > supersample 3 transparentBackground true > hide #!3 models > hide #!1 models > show #!12 models > view #12 clip false > save /Users/sahtelis/Downloads/cx43_NTD_pore.png width 867 height 637 > supersample 3 transparentBackground true > hide #!12 models > show #!13 models > close #13 > show #!15 models > view #15 clip false > save /Users/sahtelis/Downloads/cx46_NTD_pore.png width 867 height 637 > supersample 3 transparentBackground true > show #!16 models > hide #!15 models > view #16 clip false > color #16 #b9f2a7ff models > lighting full > surface dust #16 size 6.73 > volume #16 level 0.008334 > volume #16 level 0.006191 > volume #16 level 0.00762 > volume #16 level 0.008334 > save /Users/sahtelis/Downloads/cx31.3_NTD_pore.png width 867 height 637 > supersample 3 transparentBackground true > show #!15 models > hide #!16 models > view #15 clip false > save /Users/sahtelis/Downloads/cx46_NTD_pore.png width 867 height 637 > supersample 3 transparentBackground true > lighting full > hide #!15 models > show #!12 models > view #12 clip false > save /Users/sahtelis/Downloads/cx43_NTD_pore.png width 867 height 637 > supersample 3 transparentBackground true > hide #!12 models > show #!1 models > view #1 clip false > volume #1 level 0.0828 > save /Users/sahtelis/Downloads/cx45_NTD_pore.png width 867 height 637 > supersample 3 transparentBackground true > hide #!1 models > show #!16 models > view #16 clip false > ui mousemode right ""tape measure"" > marker segment #4 position 366.2,377.7,25.6 toPosition 381.1,376.4,21.94 > color yellow radius 0.1682 label 15.35 labelHeight 1.535 labelColor yellow > hide #!16 models > show #!15 models > close #4 > show #!12 models > show #!16 models > show #!3 models > hide #!3 models > show #!1 models > view clip false > ui mousemode right ""tape measure"" > ui mousemode right ""rotate slab"" > ui mousemode right ""tape measure"" > marker segment #4 position 370,370.3,31.76 toPosition 376.6,383.8,20.46 > color yellow radius 0.1682 label 18.79 labelHeight 1.879 labelColor yellow > marker segment #4 position 334.4,261.2,99.77 toPosition 322.8,275.2,94.87 > color yellow radius 0.1663 label 18.81 labelHeight 1.881 labelColor yellow > marker segment #4 position 199.4,288.3,83.42 toPosition 217.6,294.5,73.04 > color yellow radius 0.207 label 21.78 labelHeight 2.178 labelColor yellow > marker segment #4 position 254.2,422,41.15 toPosition 265.7,422.3,31.3 color > yellow radius 0.1635 label 15.16 labelHeight 1.516 labelColor yellow > close #4 > show #!2 models > hide #!12 models > hide #!15 models > hide #!16 models > view clip false > show #!3 models > hide #!1 models > hide #!2 models > hide #!3 models > show #!3 models > show #!2 models > view #3 clip false > show #!1 models > view #3 clip false > hide #!3 models > show #!3 models > hide #!2 models > hide #!1 models ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M3 OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac15,12 Model Number: MC8G4KS/A Chip: Apple M3 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: 4 days, 11 hours, 35 minutes Graphics/Displays: Apple M3: Chipset Model: Apple M3 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 autocommand: 2.2.2 babel: 2.16.0 backports.tarfile: 1.2.0 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: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 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-Clipper: 0.24.0 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: 1.9 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: 1.2.6 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-ISOLDE: 1.9 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 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: 2.1.6 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 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 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-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 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: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 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: 1.18.1 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 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: 1.41 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 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 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 importlib_metadata: 8.0.0 importlib_resources: 6.4.0 inflect: 7.3.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jaraco.context: 5.3.0 jaraco.functools: 4.0.1 jaraco.text: 3.12.1 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 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 more-itertools: 10.3.0 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 openvr: 1.26.701 ordered-set: 4.1.0 packaging: 23.2 packaging: 24.1 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 platformdirs: 4.2.2 prompt_toolkit: 3.0.48 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: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 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: 8.0.2 sphinx-autodoc-typehints: 2.2.3 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: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4.2 traitlets: 5.14.3 typeguard: 4.3.0 typing_extensions: 4.12.2 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 zipp: 3.19.2 }}} " defect new normal Unassigned