id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20291 Crash moving tool window, Mac multiple displays P.Yu@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.3.1-arm64-arm-64bit ChimeraX Version: 1.11 (2025-12-17 06:45:39 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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memory 3152K 22 =========== ======= ======= TOTAL 7.9G 5935 TOTAL, minus reserved VM space 7.6G 5935 "", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""96d59f4ca9b550771864c02f2f59ae35c9f3a92a"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""67648e5334a82511f4acf879"", ""factorPackIds"" : { }, ""deploymentId"" : 240000008 }, { ""rolloutId"" : ""65a8173205d942272410674b"", ""factorPackIds"" : { ""SIRI_HOME_AUTOMATION_SERVER_FLOW_DEPRECATION"" : ""65d39fa4cb0e2417d11ce5f6"" }, ""deploymentId"" : 240000001 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260507_SA-F_B1_workflow5.cxs"" Opened cryosparc_P4_J216_class_03_00122_volume_sharp.mrc as #4, grid size 128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32 Opened cryosparc_P4_J216_class_04_00122_volume_sharp.mrc as #5, grid size 128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32 Opened CS_P4_J216_class_0_sharp_flip.mrc as #1, grid size 128,128,128, pixel 2.08, shown at level 0.185, step 1, values float32 Opened CS_P4_J216_class_1_sharp_flip.mrc as #2, grid size 128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32 Opened CS_P4_J216_class_2_sharp_flip.mrc as #3, grid size 128,128,128, pixel 2.08, shown at level 0.356, step 1, values float32 Opened CS_P4_J219_sharp_flip.mrc as #6, grid size 80,80,80, pixel 3.32, shown at level 1.17, step 1, values float32 Opened CS_P4_J244_sharp_flip.mrc as #7, grid size 80,80,80, pixel 3.32, shown at level 1.16, step 1, values float32 Opened cryosparc_P4_J242_class_00_00122_volume_sharp.mrc as #8, grid size 128,128,128, pixel 2.08, shown at level 0.221, step 1, values float32 Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #9, grid size 128,128,128, pixel 2.08, shown at level 0.146, step 1, values float32 Opened cryosparc_P4_J242_class_02_00122_volume_sharp.mrc as #10, grid size 128,128,128, pixel 2.08, shown at level 0.195, step 1, values float32 Opened cryosparc_P4_J242_class_03_00122_volume_sharp.mrc as #11, grid size 128,128,128, pixel 2.08, shown at level 0.15, step 1, values float32 Opened cryosparc_P4_J242_class_04_00122_volume_sharp.mrc as #12, grid size 128,128,128, pixel 2.08, shown at level 0.345, step 1, values float32 Opened cryosparc_P4_J117_class_00_00162_volume_sharp.mrc as #13, grid size 128,128,128, pixel 2.08, shown at level 0.163, step 1, values float32 Opened cryosparc_P4_J117_class_01_00162_volume_sharp.mrc as #14, grid size 128,128,128, pixel 2.08, shown at level 0.187, step 1, values float32 Opened CS_P4_J117_class_02_sharp_flip.mrc as #15, grid size 128,128,128, pixel 2.08, shown at level 0.335, step 1, values float32 Opened cryosparc_P4_J117_class_03_00162_volume_sharp.mrc as #16, grid size 128,128,128, pixel 2.08, shown at level 0.179, step 1, values float32 Opened cryosparc_P4_J117_class_04_00162_volume_sharp.mrc as #17, grid size 128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32 Opened CS_P4_J120_sharp_flip.mrc as #18, grid size 80,80,80, pixel 3.32, shown at level 1.29, step 1, values float32 Opened cryosparc_P4_J169_class_00_00182_volume_sharp.mrc as #19, grid size 128,128,128, pixel 2.08, shown at level 0.156, step 1, values float32 Opened cryosparc_P4_J169_class_01_00182_volume_sharp.mrc as #20, grid size 128,128,128, pixel 2.08, shown at level 0.198, step 1, values float32 Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #21, grid size 128,128,128, pixel 2.08, shown at level 0.248, step 1, values float32 Opened CS_P4_J169_class_03_sharp_flip.mrc as #22, grid size 128,128,128, pixel 2.08, shown at level 0.271, step 1, values float32 Opened cryosparc_P4_J169_class_04_00182_volume_sharp.mrc as #23, grid size 128,128,128, pixel 2.08, shown at level 0.2, step 1, values float32 Opened CS_P4_J176_NU_sharp_flip.mrc as #24, grid size 80,80,80, pixel 3.32, shown at level 1.6, step 1, values float32 Opened CS_P4_J255_sharp_flip.mrc as #25, grid size 80,80,80, pixel 3.32, shown at level 0.649, step 1, values float32 Opened CS_P4_J256_sharp_flip.mrc as #26, grid size 80,80,80, pixel 3.32, shown at level 1.01, step 1, values float32 Opened CS_P4_J257_sharp_flip.mrc as #27, grid size 80,80,80, pixel 3.32, shown at level 1.16, step 1, values float32 Opened CS_P4_J258_sharp_flip.mrc as #28, grid size 80,80,80, pixel 3.32, shown at level 0.533, step 1, values float32 Opened CS_P4_J259_sharp_flip.mrc as #29, grid size 80,80,80, pixel 3.32, shown at level 0.567, step 1, values float32 Opened CS_P4_J267_sharp_flip.mrc as #30, grid size 320,320,320, pixel 0.831, shown at level 0.134, step 1, values float32 Opened CS_P4_J277_sharp_flip.mrc as #31, grid size 320,320,320, pixel 0.831, shown at level 0.143, step 1, values float32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #32, grid size 320,320,320, pixel 0.831, shown at level 0.0548, step 2, values float32 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #33, grid size 320,320,320, pixel 0.831, shown at level 0.0508, step 2, values float32 Opened cryosparc_P4_J287_map_locres.mrc as #34, grid size 320,320,320, pixel 0.831, shown at level 3.78, step 2, values float32 Opened cryosparc_P4_J288_map_locres.mrc as #35, grid size 320,320,320, pixel 0.831, shown at level 3.77, step 2, values float32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #37, grid size 320,320,320, pixel 0.831, shown at level 0.065, step 1, values float32 Opened cryosparc_P4_J287_map_locres.mrc z flip as #38, grid size 320,320,320, pixel 0.831, shown at level 3.78, step 1, values float32 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc z flip as #39, grid size 320,320,320, pixel 0.831, shown at level 0.0664, step 1, values float32 Opened cryosparc_P4_J288_map_locres.mrc z flip as #40, grid size 320,320,320, pixel 0.831, shown at level 3.77, step 1, values float32 Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #42, grid size 128,128,128, pixel 2.08, shown at level 0.254, step 1, values float32 Opened CS_P4_J282_sharp_flip.mrc as #36, grid size 320,320,320, pixel 0.831, shown at level 0.0602, step 2, values float32 Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #43, grid size 128,128,128, pixel 2.08, shown at level 0.228, step 1, values float32 Opened CS_P4_J295_sharp_flip.mrc as #44, grid size 320,320,320, pixel 0.831, shown at level 0.0515, step 1, values float32 Opened CS_P4_J296_locres_flip.mrc as #45, grid size 320,320,320, pixel 0.831, shown at level 8.66, step 1, values float32 Opened CS_P4_J300_sharp_flip.mrc as #46, grid size 320,320,320, pixel 0.831, shown at level 0.0592, step 1, values float32 Opened CS_P4_J301_locres_flip.mrc as #47, grid size 320,320,320, pixel 0.831, shown at level 9.68, step 1, values float32 Opened CS_P4_J302_sharp_flip.mrc as #48, grid size 80,80,80, pixel 3.32, shown at level 0.612, step 1, values float32 Opened CS_P4_J303_sharp_flip.mrc as #49, grid size 80,80,80, pixel 3.32, shown at level 0.575, step 1, values float32 Opened CS_P4_J304_sharp_flip.mrc as #50, grid size 80,80,80, pixel 3.32, shown at level 1.95, step 1, values float32 Opened CS_P4_J305_sharp_flip.mrc as #51, grid size 80,80,80, pixel 3.32, shown at level 0.569, step 1, values float32 Opened CS_P4_J306_sharp_flip.mrc as #52, grid size 80,80,80, pixel 3.32, shown at level 1.03, step 1, values float32 Opened CS_P4_J307_sharp_flip.mrc as #53, grid size 80,80,80, pixel 3.32, shown at level 0.417, step 1, values float32 Opened CS_P4_J308_sharp_flip.mrc as #54, grid size 80,80,80, pixel 3.32, shown at level 0.487, step 1, values float32 Opened CS_P4_J309_sharp_flip.mrc as #55, grid size 80,80,80, pixel 3.32, shown at level 0.427, step 1, values float32 Opened CS_P4_J310_sharp_flip.mrc as #56, grid size 80,80,80, pixel 3.32, shown at level 0.719, step 1, values float32 Opened CS_P4_J311_sharp_flip.mrc as #57, grid size 80,80,80, pixel 3.32, shown at level 0.525, step 1, values float32 Opened CS_P4_J323_sharp_flip.mrc as #58, grid size 320,320,320, pixel 0.831, shown at level 0.0616, step 1, values float32 Opened CS_P4_J324_map_locres_flip.mrc as #59, grid size 320,320,320, pixel 0.831, shown at level 3.69, step 1, values float32 Opened CS_P4_J329_sharp_flip.mrc as #60, grid size 320,320,320, pixel 0.831, shown at level 0.0566, step 1, values float32 Opened CS_P4_J330_locres_flip.mrc as #61, grid size 320,320,320, pixel 0.831, shown at level 9.71, step 1, values float32 Opened CS_P4_J300_sharp_flip.mrc as #62, grid size 320,320,320, pixel 0.831, shown at level 0.0575, step 1, values float32 Opened CS_P4_J301_locres_flip.mrc as #63, grid size 320,320,320, pixel 0.831, shown at level 3.95, step 1, values float32 Log from Thu May 7 21:11:39 2026UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260507_SA-F_B1_workflow3.cxs"" Opened cryosparc_P4_J216_class_03_00122_volume_sharp.mrc as #4, grid size 128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32 Opened cryosparc_P4_J216_class_04_00122_volume_sharp.mrc as #5, grid size 128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32 Opened CS_P4_J216_class_0_sharp_flip.mrc as #1, grid size 128,128,128, pixel 2.08, shown at level 0.185, step 1, values float32 Opened CS_P4_J216_class_1_sharp_flip.mrc as #2, grid size 128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32 Opened CS_P4_J216_class_2_sharp_flip.mrc as #3, grid size 128,128,128, pixel 2.08, shown at level 0.356, step 1, values float32 Opened CS_P4_J219_sharp_flip.mrc as #6, grid size 80,80,80, pixel 3.32, shown at level 1.17, step 1, values float32 Opened CS_P4_J244_sharp_flip.mrc as #7, grid size 80,80,80, pixel 3.32, shown at level 1.16, step 1, values float32 Opened cryosparc_P4_J242_class_00_00122_volume_sharp.mrc as #8, grid size 128,128,128, pixel 2.08, shown at level 0.221, step 1, values float32 Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #9, grid size 128,128,128, pixel 2.08, shown at level 0.146, step 1, values float32 Opened cryosparc_P4_J242_class_02_00122_volume_sharp.mrc as #10, grid size 128,128,128, pixel 2.08, shown at level 0.195, step 1, values float32 Opened cryosparc_P4_J242_class_03_00122_volume_sharp.mrc as #11, grid size 128,128,128, pixel 2.08, shown at level 0.15, step 1, values float32 Opened cryosparc_P4_J242_class_04_00122_volume_sharp.mrc as #12, grid size 128,128,128, pixel 2.08, shown at level 0.345, step 1, values float32 Opened cryosparc_P4_J117_class_00_00162_volume_sharp.mrc as #13, grid size 128,128,128, pixel 2.08, shown at level 0.163, step 1, values float32 Opened cryosparc_P4_J117_class_01_00162_volume_sharp.mrc as #14, grid size 128,128,128, pixel 2.08, shown at level 0.187, step 1, values float32 Opened CS_P4_J117_class_02_sharp_flip.mrc as #15, grid size 128,128,128, pixel 2.08, shown at level 0.335, step 1, values float32 Opened cryosparc_P4_J117_class_03_00162_volume_sharp.mrc as #16, grid size 128,128,128, pixel 2.08, shown at level 0.179, step 1, values float32 Opened cryosparc_P4_J117_class_04_00162_volume_sharp.mrc as #17, grid size 128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32 Opened CS_P4_J120_sharp_flip.mrc as #18, grid size 80,80,80, pixel 3.32, shown at level 1.29, step 1, values float32 Opened cryosparc_P4_J169_class_00_00182_volume_sharp.mrc as #19, grid size 128,128,128, pixel 2.08, shown at level 0.156, step 1, values float32 Opened cryosparc_P4_J169_class_01_00182_volume_sharp.mrc as #20, grid size 128,128,128, pixel 2.08, shown at level 0.198, step 1, values float32 Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #21, grid size 128,128,128, pixel 2.08, shown at level 0.248, step 1, values float32 Opened CS_P4_J169_class_03_sharp_flip.mrc as #22, grid size 128,128,128, pixel 2.08, shown at level 0.271, step 1, values float32 Opened cryosparc_P4_J169_class_04_00182_volume_sharp.mrc as #23, grid size 128,128,128, pixel 2.08, shown at level 0.2, step 1, values float32 Opened CS_P4_J176_NU_sharp_flip.mrc as #24, grid size 80,80,80, pixel 3.32, shown at level 1.6, step 1, values float32 Opened CS_P4_J255_sharp_flip.mrc as #25, grid size 80,80,80, pixel 3.32, shown at level 0.649, step 1, values float32 Opened CS_P4_J256_sharp_flip.mrc as #26, grid size 80,80,80, pixel 3.32, shown at level 1.01, step 1, values float32 Opened CS_P4_J257_sharp_flip.mrc as #27, grid size 80,80,80, pixel 3.32, shown at level 1.16, step 1, values float32 Opened CS_P4_J258_sharp_flip.mrc as #28, grid size 80,80,80, pixel 3.32, shown at level 0.533, step 1, values float32 Opened CS_P4_J259_sharp_flip.mrc as #29, grid size 80,80,80, pixel 3.32, shown at level 0.567, step 1, values float32 Opened CS_P4_J267_sharp_flip.mrc as #30, grid size 320,320,320, pixel 0.831, shown at level 0.134, step 1, values float32 Opened CS_P4_J277_sharp_flip.mrc as #31, grid size 320,320,320, pixel 0.831, shown at level 0.143, step 1, values float32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #32, grid size 320,320,320, pixel 0.831, shown at level 0.0548, step 2, values float32 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #33, grid size 320,320,320, pixel 0.831, shown at level 0.0508, step 2, values float32 Opened cryosparc_P4_J287_map_locres.mrc as #34, grid size 320,320,320, pixel 0.831, shown at level 3.78, step 2, values float32 Opened cryosparc_P4_J288_map_locres.mrc as #35, grid size 320,320,320, pixel 0.831, shown at level 3.77, step 2, values float32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #37, grid size 320,320,320, pixel 0.831, shown at level 0.065, step 1, values float32 Opened cryosparc_P4_J287_map_locres.mrc z flip as #38, grid size 320,320,320, pixel 0.831, shown at level 3.78, step 1, values float32 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc z flip as #39, grid size 320,320,320, pixel 0.831, shown at level 0.0664, step 1, values float32 Opened cryosparc_P4_J288_map_locres.mrc z flip as #40, grid size 320,320,320, pixel 0.831, shown at level 3.77, step 1, values float32 Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #42, grid size 128,128,128, pixel 2.08, shown at level 0.254, step 1, values float32 Opened CS_P4_J282_sharp_flip.mrc as #36, grid size 320,320,320, pixel 0.831, shown at level 0.0602, step 2, values float32 Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #43, grid size 128,128,128, pixel 2.08, shown at level 0.228, step 1, values float32 Opened CS_P4_J295_sharp_flip.mrc as #44, grid size 320,320,320, pixel 0.831, shown at level 0.0515, step 1, values float32 Opened CS_P4_J296_locres_flip.mrc as #45, grid size 320,320,320, pixel 0.831, shown at level 8.66, step 1, values float32 Opened CS_P4_J300_sharp_flip.mrc as #46, grid size 320,320,320, pixel 0.831, shown at level 0.0592, step 1, values float32 Opened CS_P4_J301_locres_flip.mrc as #47, grid size 320,320,320, pixel 0.831, shown at level 9.68, step 1, values float32 Opened CS_P4_J302_sharp_flip.mrc as #48, grid size 80,80,80, pixel 3.32, shown at level 0.612, step 1, values float32 Opened CS_P4_J303_sharp_flip.mrc as #49, grid size 80,80,80, pixel 3.32, shown at level 0.575, step 1, values float32 Opened CS_P4_J304_sharp_flip.mrc as #50, grid size 80,80,80, pixel 3.32, shown at level 1.95, step 1, values float32 Opened CS_P4_J305_sharp_flip.mrc as #51, grid size 80,80,80, pixel 3.32, shown at level 0.569, step 1, values float32 Opened CS_P4_J306_sharp_flip.mrc as #52, grid size 80,80,80, pixel 3.32, shown at level 1.03, step 1, values float32 Opened CS_P4_J307_sharp_flip.mrc as #53, grid size 80,80,80, pixel 3.32, shown at level 0.417, step 1, values float32 Opened CS_P4_J308_sharp_flip.mrc as #54, grid size 80,80,80, pixel 3.32, shown at level 0.487, step 1, values float32 Opened CS_P4_J309_sharp_flip.mrc as #55, grid size 80,80,80, pixel 3.32, shown at level 0.427, step 1, values float32 Opened CS_P4_J310_sharp_flip.mrc as #56, grid size 80,80,80, pixel 3.32, shown at level 0.719, step 1, values float32 Opened CS_P4_J311_sharp_flip.mrc as #57, grid size 80,80,80, pixel 3.32, shown at level 0.525, step 1, values float32 Opened CS_P4_J323_sharp_flip.mrc as #58, grid size 320,320,320, pixel 0.831, shown at level 0.0616, step 1, values float32 Opened CS_P4_J324_map_locres_flip.mrc as #59, grid size 320,320,320, pixel 0.831, shown at level 3.69, step 1, values float32 Opened CS_P4_J329_sharp_flip.mrc as #60, grid size 320,320,320, pixel 0.831, shown at level 0.0566, step 1, values float32 Opened CS_P4_J330_locres_flip.mrc as #61, grid size 320,320,320, pixel 0.831, shown at level 9.71, step 1, values float32 Log from Thu May 7 15:58:17 2026UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260506_SA-F_B1_workflow.cxs"" Opened cryosparc_P4_J216_class_03_00122_volume_sharp.mrc as #4, grid size 128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32 Opened cryosparc_P4_J216_class_04_00122_volume_sharp.mrc as #5, grid size 128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32 Opened CS_P4_J216_class_0_sharp_flip.mrc as #1, grid size 128,128,128, pixel 2.08, shown at level 0.185, step 1, values float32 Opened CS_P4_J216_class_1_sharp_flip.mrc as #2, grid size 128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32 Opened CS_P4_J216_class_2_sharp_flip.mrc as #3, grid size 128,128,128, pixel 2.08, shown at level 0.356, step 1, values float32 Opened CS_P4_J219_sharp_flip.mrc as #6, grid size 80,80,80, pixel 3.32, shown at level 1.17, step 1, values float32 Opened CS_P4_J244_sharp_flip.mrc as #7, grid size 80,80,80, pixel 3.32, shown at level 1.16, step 1, values float32 Opened cryosparc_P4_J242_class_00_00122_volume_sharp.mrc as #8, grid size 128,128,128, pixel 2.08, shown at level 0.221, step 1, values float32 Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #9, grid size 128,128,128, pixel 2.08, shown at level 0.146, step 1, values float32 Opened cryosparc_P4_J242_class_02_00122_volume_sharp.mrc as #10, grid size 128,128,128, pixel 2.08, shown at level 0.195, step 1, values float32 Opened cryosparc_P4_J242_class_03_00122_volume_sharp.mrc as #11, grid size 128,128,128, pixel 2.08, shown at level 0.15, step 1, values float32 Opened cryosparc_P4_J242_class_04_00122_volume_sharp.mrc as #12, grid size 128,128,128, pixel 2.08, shown at level 0.345, step 1, values float32 Opened cryosparc_P4_J117_class_00_00162_volume_sharp.mrc as #13, grid size 128,128,128, pixel 2.08, shown at level 0.163, step 1, values float32 Opened cryosparc_P4_J117_class_01_00162_volume_sharp.mrc as #14, grid size 128,128,128, pixel 2.08, shown at level 0.187, step 1, values float32 Opened CS_P4_J117_class_02_sharp_flip.mrc as #15, grid size 128,128,128, pixel 2.08, shown at level 0.335, step 1, values float32 Opened cryosparc_P4_J117_class_03_00162_volume_sharp.mrc as #16, grid size 128,128,128, pixel 2.08, shown at level 0.179, step 1, values float32 Opened cryosparc_P4_J117_class_04_00162_volume_sharp.mrc as #17, grid size 128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32 Opened CS_P4_J120_sharp_flip.mrc as #18, grid size 80,80,80, pixel 3.32, shown at level 1.29, step 1, values float32 Opened cryosparc_P4_J169_class_00_00182_volume_sharp.mrc as #19, grid size 128,128,128, pixel 2.08, shown at level 0.156, step 1, values float32 Opened cryosparc_P4_J169_class_01_00182_volume_sharp.mrc as #20, grid size 128,128,128, pixel 2.08, shown at level 0.198, step 1, values float32 Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #21, grid size 128,128,128, pixel 2.08, shown at level 0.248, step 1, values float32 Opened CS_P4_J169_class_03_sharp_flip.mrc as #22, grid size 128,128,128, pixel 2.08, shown at level 0.271, step 1, values float32 Opened cryosparc_P4_J169_class_04_00182_volume_sharp.mrc as #23, grid size 128,128,128, pixel 2.08, shown at level 0.2, step 1, values float32 Opened CS_P4_J176_NU_sharp_flip.mrc as #24, grid size 80,80,80, pixel 3.32, shown at level 1.6, step 1, values float32 Opened CS_P4_J255_sharp_flip.mrc as #25, grid size 80,80,80, pixel 3.32, shown at level 0.649, step 1, values float32 Opened CS_P4_J256_sharp_flip.mrc as #26, grid size 80,80,80, pixel 3.32, shown at level 1.01, step 1, values float32 Opened CS_P4_J257_sharp_flip.mrc as #27, grid size 80,80,80, pixel 3.32, shown at level 1.16, step 1, values float32 Opened CS_P4_J258_sharp_flip.mrc as #28, grid size 80,80,80, pixel 3.32, shown at level 0.533, step 1, values float32 Opened CS_P4_J259_sharp_flip.mrc as #29, grid size 80,80,80, pixel 3.32, shown at level 0.567, step 1, values float32 Opened CS_P4_J267_sharp_flip.mrc as #30, grid size 320,320,320, pixel 0.831, shown at level 0.134, step 1, values float32 Opened CS_P4_J277_sharp_flip.mrc as #31, grid size 320,320,320, pixel 0.831, shown at level 0.143, step 1, values float32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #32, grid size 320,320,320, pixel 0.831, shown at level 0.0548, step 2, values float32 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #33, grid size 320,320,320, pixel 0.831, shown at level 0.0508, step 2, values float32 Opened cryosparc_P4_J287_map_locres.mrc as #34, grid size 320,320,320, pixel 0.831, shown at level 3.78, step 2, values float32 Opened cryosparc_P4_J288_map_locres.mrc as #35, grid size 320,320,320, pixel 0.831, shown at level 3.77, step 2, values float32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #37, grid size 320,320,320, pixel 0.831, shown at level 0.065, step 1, values float32 Opened cryosparc_P4_J287_map_locres.mrc z flip as #38, grid size 320,320,320, pixel 0.831, shown at level 3.78, step 1, values float32 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc z flip as #39, grid size 320,320,320, pixel 0.831, shown at level 0.0664, step 1, values float32 Opened cryosparc_P4_J288_map_locres.mrc z flip as #40, grid size 320,320,320, pixel 0.831, shown at level 3.77, step 1, values float32 Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #42, grid size 128,128,128, pixel 2.08, shown at level 0.254, step 1, values float32 Opened CS_P4_J282_sharp_flip.mrc as #36, grid size 320,320,320, pixel 0.831, shown at level 0.0602, step 2, values float32 Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #43, grid size 128,128,128, pixel 2.08, shown at level 0.228, step 1, values float32 Opened CS_P4_J295_sharp_flip.mrc as #44, grid size 320,320,320, pixel 0.831, shown at level 0.0515, step 1, values float32 Opened CS_P4_J296_locres_flip.mrc as #45, grid size 320,320,320, pixel 0.831, shown at level 8.66, step 1, values float32 Opened CS_P4_J300_sharp_flip.mrc as #46, grid size 320,320,320, pixel 0.831, shown at level 0.0592, step 1, values float32 Opened CS_P4_J301_locres_flip.mrc as #47, grid size 320,320,320, pixel 0.831, shown at level 9.68, step 1, values float32 Opened CS_P4_J302_sharp_flip.mrc as #48, grid size 80,80,80, pixel 3.32, shown at level 0.612, step 1, values float32 Opened CS_P4_J303_sharp_flip.mrc as #49, grid size 80,80,80, pixel 3.32, shown at level 0.575, step 1, values float32 Opened CS_P4_J304_sharp_flip.mrc as #50, grid size 80,80,80, pixel 3.32, shown at level 1.95, step 1, values float32 Opened CS_P4_J305_sharp_flip.mrc as #51, grid size 80,80,80, pixel 3.32, shown at level 0.569, step 1, values float32 Opened CS_P4_J306_sharp_flip.mrc as #52, grid size 80,80,80, pixel 3.32, shown at level 1.03, step 1, values float32 Opened CS_P4_J307_sharp_flip.mrc as #53, grid size 80,80,80, pixel 3.32, shown at level 0.417, step 1, values float32 Opened CS_P4_J308_sharp_flip.mrc as #54, grid size 80,80,80, pixel 3.32, shown at level 0.487, step 1, values float32 Opened CS_P4_J309_sharp_flip.mrc as #55, grid size 80,80,80, pixel 3.32, shown at level 0.427, step 1, values float32 Opened CS_P4_J310_sharp_flip.mrc as #56, grid size 80,80,80, pixel 3.32, shown at level 0.719, step 1, values float32 Opened CS_P4_J311_sharp_flip.mrc as #57, grid size 80,80,80, pixel 3.32, shown at level 0.525, step 1, values float32 Log from Wed May 6 15:19:28 2026UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260505_SA-F_B1_workflow.cxs"" Opened cryosparc_P4_J216_class_03_00122_volume_sharp.mrc as #4, grid size 128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32 Opened cryosparc_P4_J216_class_04_00122_volume_sharp.mrc as #5, grid size 128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32 Opened CS_P4_J216_class_0_sharp_flip.mrc as #1, grid size 128,128,128, pixel 2.08, shown at level 0.185, step 1, values float32 Opened CS_P4_J216_class_1_sharp_flip.mrc as #2, grid size 128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32 Opened CS_P4_J216_class_2_sharp_flip.mrc as #3, grid size 128,128,128, pixel 2.08, shown at level 0.356, step 1, values float32 Opened CS_P4_J219_sharp_flip.mrc as #6, grid size 80,80,80, pixel 3.32, shown at level 1.17, step 1, values float32 Opened CS_P4_J244_sharp_flip.mrc as #7, grid size 80,80,80, pixel 3.32, shown at level 1.16, step 1, values float32 Opened cryosparc_P4_J242_class_00_00122_volume_sharp.mrc as #8, grid size 128,128,128, pixel 2.08, shown at level 0.221, step 1, values float32 Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #9, grid size 128,128,128, pixel 2.08, shown at level 0.146, step 1, values float32 Opened cryosparc_P4_J242_class_02_00122_volume_sharp.mrc as #10, grid size 128,128,128, pixel 2.08, shown at level 0.195, step 1, values float32 Opened cryosparc_P4_J242_class_03_00122_volume_sharp.mrc as #11, grid size 128,128,128, pixel 2.08, shown at level 0.15, step 1, values float32 Opened cryosparc_P4_J242_class_04_00122_volume_sharp.mrc as #12, grid size 128,128,128, pixel 2.08, shown at level 0.345, step 1, values float32 Opened cryosparc_P4_J117_class_00_00162_volume_sharp.mrc as #13, grid size 128,128,128, pixel 2.08, shown at level 0.163, step 1, values float32 Opened cryosparc_P4_J117_class_01_00162_volume_sharp.mrc as #14, grid size 128,128,128, pixel 2.08, shown at level 0.187, step 1, values float32 Opened CS_P4_J117_class_02_sharp_flip.mrc as #15, grid size 128,128,128, pixel 2.08, shown at level 0.335, step 1, values float32 Opened cryosparc_P4_J117_class_03_00162_volume_sharp.mrc as #16, grid size 128,128,128, pixel 2.08, shown at level 0.179, step 1, values float32 Opened cryosparc_P4_J117_class_04_00162_volume_sharp.mrc as #17, grid size 128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32 Opened CS_P4_J120_sharp_flip.mrc as #18, grid size 80,80,80, pixel 3.32, shown at level 1.29, step 1, values float32 Opened cryosparc_P4_J169_class_00_00182_volume_sharp.mrc as #19, grid size 128,128,128, pixel 2.08, shown at level 0.156, step 1, values float32 Opened cryosparc_P4_J169_class_01_00182_volume_sharp.mrc as #20, grid size 128,128,128, pixel 2.08, shown at level 0.198, step 1, values float32 Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #21, grid size 128,128,128, pixel 2.08, shown at level 0.248, step 1, values float32 Opened CS_P4_J169_class_03_sharp_flip.mrc as #22, grid size 128,128,128, pixel 2.08, shown at level 0.271, step 1, values float32 Opened cryosparc_P4_J169_class_04_00182_volume_sharp.mrc as #23, grid size 128,128,128, pixel 2.08, shown at level 0.2, step 1, values float32 Opened CS_P4_J176_NU_sharp_flip.mrc as #24, grid size 80,80,80, pixel 3.32, shown at level 1.6, step 1, values float32 Opened CS_P4_J255_sharp_flip.mrc as #25, grid size 80,80,80, pixel 3.32, shown at level 0.649, step 1, values float32 Opened CS_P4_J256_sharp_flip.mrc as #26, grid size 80,80,80, pixel 3.32, shown at level 1.01, step 1, values float32 Opened CS_P4_J257_sharp_flip.mrc as #27, grid size 80,80,80, pixel 3.32, shown at level 1.16, step 1, values float32 Opened CS_P4_J258_sharp_flip.mrc as #28, grid size 80,80,80, pixel 3.32, shown at level 0.533, step 1, values float32 Opened CS_P4_J259_sharp_flip.mrc as #29, grid size 80,80,80, pixel 3.32, shown at level 0.567, step 1, values float32 Opened CS_P4_J267_sharp_flip.mrc as #30, grid size 320,320,320, pixel 0.831, shown at level 0.134, step 1, values float32 Opened CS_P4_J277_sharp_flip.mrc as #31, grid size 320,320,320, pixel 0.831, shown at level 0.143, step 1, values float32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #32, grid size 320,320,320, pixel 0.831, shown at level 0.0548, step 2, values float32 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #33, grid size 320,320,320, pixel 0.831, shown at level 0.0508, step 2, values float32 Opened cryosparc_P4_J287_map_locres.mrc as #34, grid size 320,320,320, pixel 0.831, shown at level 3.78, step 2, values float32 Opened cryosparc_P4_J288_map_locres.mrc as #35, grid size 320,320,320, pixel 0.831, shown at level 3.77, step 2, values float32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #37, grid size 320,320,320, pixel 0.831, shown at level 0.065, step 1, values float32 Opened cryosparc_P4_J287_map_locres.mrc z flip as #38, grid size 320,320,320, pixel 0.831, shown at level 3.78, step 1, values float32 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc z flip as #39, grid size 320,320,320, pixel 0.831, shown at level 0.0664, step 1, values float32 Opened cryosparc_P4_J288_map_locres.mrc z flip as #40, grid size 320,320,320, pixel 0.831, shown at level 3.77, step 1, values float32 Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #42, grid size 128,128,128, pixel 2.08, shown at level 0.254, step 1, values float32 Opened CS_P4_J282_sharp_flip.mrc as #36, grid size 320,320,320, pixel 0.831, shown at level 0.0602, step 2, values float32 Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #43, grid size 128,128,128, pixel 2.08, shown at level 0.228, step 1, values float32 Opened CS_P4_J295_sharp_flip.mrc as #44, grid size 320,320,320, pixel 0.831, shown at level 0.0515, step 1, values float32 Opened CS_P4_J296_locres_flip.mrc as #45, grid size 320,320,320, pixel 0.831, shown at level 8.66, step 1, values float32 Opened CS_P4_J300_sharp_flip.mrc as #46, grid size 320,320,320, pixel 0.831, shown at level 0.0592, step 1, values float32 Opened CS_P4_J301_locres_flip.mrc as #47, grid size 320,320,320, pixel 0.831, shown at level 9.68, step 1, values float32 Log from Tue May 5 09:31:57 2026UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260503_SA-F_B1_workflow4.cxs"" Opened cryosparc_P4_J216_class_03_00122_volume_sharp.mrc as #4, grid size 128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32 Opened cryosparc_P4_J216_class_04_00122_volume_sharp.mrc as #5, grid size 128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32 Opened CS_P4_J216_class_0_sharp_flip.mrc as #1, grid size 128,128,128, pixel 2.08, shown at level 0.185, step 1, values float32 Opened CS_P4_J216_class_1_sharp_flip.mrc as #2, grid size 128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32 Opened CS_P4_J216_class_2_sharp_flip.mrc as #3, grid size 128,128,128, pixel 2.08, shown at level 0.356, step 1, values float32 Opened CS_P4_J219_sharp_flip.mrc as #6, grid size 80,80,80, pixel 3.32, shown at level 1.17, step 1, values float32 Opened CS_P4_J244_sharp_flip.mrc as #7, grid size 80,80,80, pixel 3.32, shown at level 1.16, step 1, values float32 Opened cryosparc_P4_J242_class_00_00122_volume_sharp.mrc as #8, grid size 128,128,128, pixel 2.08, shown at level 0.221, step 1, values float32 Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #9, grid size 128,128,128, pixel 2.08, shown at level 0.146, step 1, values float32 Opened cryosparc_P4_J242_class_02_00122_volume_sharp.mrc as #10, grid size 128,128,128, pixel 2.08, shown at level 0.195, step 1, values float32 Opened cryosparc_P4_J242_class_03_00122_volume_sharp.mrc as #11, grid size 128,128,128, pixel 2.08, shown at level 0.15, step 1, values float32 Opened cryosparc_P4_J242_class_04_00122_volume_sharp.mrc as #12, grid size 128,128,128, pixel 2.08, shown at level 0.345, step 1, values float32 Opened cryosparc_P4_J117_class_00_00162_volume_sharp.mrc as #13, grid size 128,128,128, pixel 2.08, shown at level 0.163, step 1, values float32 Opened cryosparc_P4_J117_class_01_00162_volume_sharp.mrc as #14, grid size 128,128,128, pixel 2.08, shown at level 0.187, step 1, values float32 Opened CS_P4_J117_class_02_sharp_flip.mrc as #15, grid size 128,128,128, pixel 2.08, shown at level 0.335, step 1, values float32 Opened cryosparc_P4_J117_class_03_00162_volume_sharp.mrc as #16, grid size 128,128,128, pixel 2.08, shown at level 0.179, step 1, values float32 Opened cryosparc_P4_J117_class_04_00162_volume_sharp.mrc as #17, grid size 128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32 Opened CS_P4_J120_sharp_flip.mrc as #18, grid size 80,80,80, pixel 3.32, shown at level 1.29, step 1, values float32 Opened cryosparc_P4_J169_class_00_00182_volume_sharp.mrc as #19, grid size 128,128,128, pixel 2.08, shown at level 0.156, step 1, values float32 Opened cryosparc_P4_J169_class_01_00182_volume_sharp.mrc as #20, grid size 128,128,128, pixel 2.08, shown at level 0.198, step 1, values float32 Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #21, grid size 128,128,128, pixel 2.08, shown at level 0.248, step 1, values float32 Opened CS_P4_J169_class_03_sharp_flip.mrc as #22, grid size 128,128,128, pixel 2.08, shown at level 0.271, step 1, values float32 Opened cryosparc_P4_J169_class_04_00182_volume_sharp.mrc as #23, grid size 128,128,128, pixel 2.08, shown at level 0.2, step 1, values float32 Opened CS_P4_J176_NU_sharp_flip.mrc as #24, grid size 80,80,80, pixel 3.32, shown at level 1.6, step 1, values float32 Opened CS_P4_J255_sharp_flip.mrc as #25, grid size 80,80,80, pixel 3.32, shown at level 0.649, step 1, values float32 Opened CS_P4_J256_sharp_flip.mrc as #26, grid size 80,80,80, pixel 3.32, shown at level 1.01, step 1, values float32 Opened CS_P4_J257_sharp_flip.mrc as #27, grid size 80,80,80, pixel 3.32, shown at level 1.16, step 1, values float32 Opened CS_P4_J258_sharp_flip.mrc as #28, grid size 80,80,80, pixel 3.32, shown at level 0.533, step 1, values float32 Opened CS_P4_J259_sharp_flip.mrc as #29, grid size 80,80,80, pixel 3.32, shown at level 0.567, step 1, values float32 Opened CS_P4_J267_sharp_flip.mrc as #30, grid size 320,320,320, pixel 0.831, shown at level 0.134, step 1, values float32 Opened CS_P4_J277_sharp_flip.mrc as #31, grid size 320,320,320, pixel 0.831, shown at level 0.143, step 1, values float32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #32, grid size 320,320,320, pixel 0.831, shown at level 0.0548, step 2, values float32 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #33, grid size 320,320,320, pixel 0.831, shown at level 0.0508, step 2, values float32 Opened cryosparc_P4_J287_map_locres.mrc as #34, grid size 320,320,320, pixel 0.831, shown at level 3.78, step 2, values float32 Opened cryosparc_P4_J288_map_locres.mrc as #35, grid size 320,320,320, pixel 0.831, shown at level 3.77, step 2, values float32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #37, grid size 320,320,320, pixel 0.831, shown at level 0.065, step 1, values float32 Opened cryosparc_P4_J287_map_locres.mrc z flip as #38, grid size 320,320,320, pixel 0.831, shown at level 3.78, step 1, values float32 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc z flip as #39, grid size 320,320,320, pixel 0.831, shown at level 0.0664, step 1, values float32 Opened cryosparc_P4_J288_map_locres.mrc z flip as #40, grid size 320,320,320, pixel 0.831, shown at level 3.77, step 1, values float32 Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #42, grid size 128,128,128, pixel 2.08, shown at level 0.254, step 1, values float32 Opened CS_P4_J282_sharp_flip.mrc as #36, grid size 320,320,320, pixel 0.831, shown at level 0.0602, step 2, values float32 Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #43, grid size 128,128,128, pixel 2.08, shown at level 0.228, step 1, values float32 Log from Sun May 3 17:29:06 2026UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J216_class_00_00122_volume_sharp.mrc"" Opened cryosparc_P4_J216_class_00_00122_volume_sharp.mrc as #1, grid size 128,128,128, pixel 2.08, shown at level 0.204, step 1, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J216_class_01_00122_volume_sharp.mrc"" Opened cryosparc_P4_J216_class_01_00122_volume_sharp.mrc as #2, grid size 128,128,128, pixel 2.08, shown at level 0.218, step 1, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J216_class_02_00122_volume_sharp.mrc"" Opened cryosparc_P4_J216_class_02_00122_volume_sharp.mrc as #3, grid size 128,128,128, pixel 2.08, shown at level 0.263, step 1, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J216_class_03_00122_volume_sharp.mrc"" Opened cryosparc_P4_J216_class_03_00122_volume_sharp.mrc as #4, grid size 128,128,128, pixel 2.08, shown at level 0.199, step 1, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J216_class_04_00122_volume_sharp.mrc"" Opened cryosparc_P4_J216_class_04_00122_volume_sharp.mrc as #5, grid size 128,128,128, pixel 2.08, shown at level 0.235, step 1, values float32 > lighting soft > set bgColor white > hide #!5 models > hide #!4 models Deeleted thousands of lines to meet Trac size limit. Tom > view matrix models #43,1,0,0,-10.922,0,1,0,105.75,0,0,1,25.23 > ui mousemode right ""rotate selected models"" > view matrix models > #43,0.053361,-0.96815,-0.24461,270.41,-0.10024,-0.24891,0.96332,141.36,-0.99353,-0.026885,-0.11033,315.47 > ui mousemode right ""translate selected models"" > view matrix models > #43,0.053361,-0.96815,-0.24461,276.43,-0.10024,-0.24891,0.96332,50.344,-0.99353,-0.026885,-0.11033,257.37 > ui mousemode right ""rotate selected models"" > view matrix models > #43,0.25016,-0.91768,-0.30868,252.37,-0.0074281,-0.32063,0.94718,48.872,-0.96818,-0.23465,-0.087026,276.42 > ui mousemode right ""translate selected models"" > view matrix models > #43,0.25016,-0.91768,-0.30868,252.17,-0.0074281,-0.32063,0.94718,49.119,-0.96818,-0.23465,-0.087026,280.28 > view matrix models > #43,0.25016,-0.91768,-0.30868,245.18,-0.0074281,-0.32063,0.94718,41.479,-0.96818,-0.23465,-0.087026,278.46 > view matrix models > #43,0.25016,-0.91768,-0.30868,244.24,-0.0074281,-0.32063,0.94718,46.881,-0.96818,-0.23465,-0.087026,278.05 > select add #42 4 models selected > select subtract #43 2 models selected > view matrix models > #42,0.15189,-0.98482,-0.084022,248.26,-0.056394,-0.093504,0.99402,10.768,-0.98679,-0.14625,-0.069741,272.27 > select subtract #42 Nothing selected > color #36 #99BFE5 > hide #!42 models > select add #43 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #43,0.073784,-0.55439,0.82898,66.918,0.0052521,0.83145,0.55558,-43.45,-0.99726,-0.036639,0.064259,236.72 > ui mousemode right ""translate selected models"" > view matrix models > #43,0.073784,-0.55439,0.82898,82.905,0.0052521,0.83145,0.55558,-39.115,-0.99726,-0.036639,0.064259,236.78 > select subtract #43 Nothing selected > volume #36 level 0.0602 > select add #43 2 models selected > view matrix models > #43,0.073784,-0.55439,0.82898,84.941,0.0052521,0.83145,0.55558,-38.546,-0.99726,-0.036639,0.064259,236.53 > view matrix models > #43,0.073784,-0.55439,0.82898,84.833,0.0052521,0.83145,0.55558,-38.074,-0.99726,-0.036639,0.064259,236.34 > volume #43 level 0.1902 > color #43 #b2b2ff80 models > volume #43 level 0.2283 > select add #40 4 models selected > select subtract #40 2 models selected > select subtract #43 Nothing selected > color #43 #ffffb280 models > color #43 #b2b2ff80 models > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260503_SA-F_B1_workflow3.cxs"" > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_cryosparc_P4_J243_003_volume_map_35_TMD_regions_resampled.mrc"" Opened cryosparc_P4_cryosparc_P4_J243_003_volume_map_35_TMD_regions_resampled.mrc as #44, grid size 80,80,80, pixel 3.32, shown at level 0.324, step 1, values float32 > close #44 > save CS_P4_J282_show_mask_sharp.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260503_SA-F_B1_workflow4.cxs"" ——— End of log from Sun May 3 17:29:06 2026 ——— > view name session-start opened ChimeraX session > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J295_006_volume_map_sharp.mrc"" Opened cryosparc_P4_J295_006_volume_map_sharp.mrc as #44, grid size 320,320,320, pixel 0.831, shown at level 0.0361, step 2, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J296_map_locres.mrc"" Opened cryosparc_P4_J296_map_locres.mrc as #45, grid size 320,320,320, pixel 0.831, shown at level 8.66, step 2, values float32 > hide #!43 models > hide #!36 models > hide #!45 models > show #!45 models > hide #!45 models > volume flip #44 Opened cryosparc_P4_J295_006_volume_map_sharp.mrc z flip as #46, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > volume flip #45 Opened cryosparc_P4_J296_map_locres.mrc z flip as #47, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > close #45 > close #44 > rename #46 CS_P4_J295_sharp_flip id #44 > save CS_P4_J295_sharp_flip.mrc #44 > rename #47 CS_P4_J296_locres_flip id #45 > save CS_P4_J296_locres_flip.mrc #45 > ui tool show ""Surface Color"" > hide #!45 models > color sample #44.1 map #45 palette #ffb17f:#527dea:#99bfe5:#fff6c0:#f4fff3 > outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.132, maximum 48.35 > show #41 models > volume #44 level 0.0515 > color sample #44.1 map #45 palette > 1,#ffb17f:2,#527dea:3,#99bfe5:4,#fff6c0:5,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > color sample #44.1 map #45 palette > 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > color sample #44.1 map #45 palette > 2,#ffb17f:3,#527dea:4,#ffb17f:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > color sample #44.1 map #45 palette > 2,#527dea:3,#99bfe5:4,#ffb17f:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > key #527dea:2 #99bfe5:3 #ffb17f:4 #fff6c0:5 #f4fff3:6 showTool true > ui mousemode right ""color key"" > color sample #44.1 map #45 palette > 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#527dea outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > key #f4fff3:2 #fff6c0:3 #ffb17f:4 #99bfe5:5 #527dea:6 showTool true > ui mousemode right ""color key"" > color sample #44.1 map #45 palette > 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#527dd6 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > color sample #44.1 map #45 palette > 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#46a2de outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > color sample #44.1 map #45 palette > 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#4d8fde outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > color sample #44.1 map #45 palette > 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#94aec1 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > color sample #44.1 map #45 palette > 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#a78bc1 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > color sample #44.1 map #45 palette > 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#c1a77f outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > color sample #44.1 map #45 palette > 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#89b3c1 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > color sample #44.1 map #45 palette > 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > ui mousemode right ""color key"" > color sample #44.1 map #45 palette > 2,#ffb17f:3,#2c98ee:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > color sample #44.1 map #45 palette > 2,#ffb17f:3,#4979d3:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > save CS_P4_J295_locres_sharp.png supersample 3 transparentBackground true Cell requested for row 0 is out of bounds for table with 6 rows! Resizing table model. > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260505_SA-F_B1_workflow.cxs"" > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J300_005_volume_map_sharp.mrc"" Opened cryosparc_P4_J300_005_volume_map_sharp.mrc as #46, grid size 320,320,320, pixel 0.831, shown at level 0.0375, step 2, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J301_map_locres.mrc"" Opened cryosparc_P4_J301_map_locres.mrc as #47, grid size 320,320,320, pixel 0.831, shown at level 9.68, step 2, values float32 > hide #!44 models > hide #!47 models > volume flip #46 Opened cryosparc_P4_J300_005_volume_map_sharp.mrc z flip as #48, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > volume flip #47 Opened cryosparc_P4_J301_map_locres.mrc z flip as #49, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > close #46 > close #47 > rename #48 CS_P4_J300_sharp_flip id #46 > rename #49 CS_P4_J301_locres_flip id #47 > save CS_P4_J301_locres_flip.mrc #47 > save CS_P4_J300_sharp_flip.mrc #46 > color sample #46.1 map #47 palette > 2,#ffb17f:3,#4979d3:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.498, maximum 44.88 > hide #!47 models > volume #46 level 0.03399 > volume #46 level 0.06962 > volume #46 level 0.05919 > save CS_P4_J300_locres_sharp.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260505_SA-F_B1_workflow.cxs"" ——— End of log from Tue May 5 09:31:57 2026 ——— > view name session-start opened ChimeraX session > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J302_002_volume_map_sharp.mrc"" Opened cryosparc_P4_J302_002_volume_map_sharp.mrc as #48, grid size 80,80,80, pixel 3.32, shown at level 0.658, step 1, values float32 > select add #48 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #48,0.064602,0.97911,0.19278,-26.266,0.98732,-0.034646,-0.1549,22.036,-0.14498,0.20034,-0.96894,229.94 > volume flip #48 Opened cryosparc_P4_J302_002_volume_map_sharp.mrc z flip as #49, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #48 > rename #49 rename > rename #49 CS_P4_J302_sharp_flip id #48 > save CS_P4_J302_sharp_flip.mrc #48 > select add #48 2 models selected > view matrix models > #48,-0.56486,-0.82475,0.026783,324.58,0.77395,-0.54076,-0.32951,143.72,0.28625,-0.1654,0.94377,-52.222 > hide #41 models > hide #!46 models > show #!47 models > hide #!47 models > show #!45 models > hide #!45 models > show #!43 models > hide #!43 models > show #!39 models > ui mousemode right ""translate selected models"" > view matrix models > #48,-0.56486,-0.82475,0.026783,319.51,0.77395,-0.54076,-0.32951,139.04,0.28625,-0.1654,0.94377,-3.8614 > view matrix models > #48,-0.56486,-0.82475,0.026783,321.32,0.77395,-0.54076,-0.32951,140.03,0.28625,-0.1654,0.94377,-10.821 > fitmap $48 inmap #39 Missing or invalid ""atomsOrMap"" argument: invalid objects specifier > fitmap #48 inMap #39 Fit map CS_P4_J302_sharp_flip.mrc in map cryosparc_P4_J285_006_volume_map_sharp.mrc z flip using 5112 points correlation = 0.3608, correlation about mean = 0.02111, overlap = 103.8 steps = 76, shift = 4.71, angle = 3.71 degrees Position of CS_P4_J302_sharp_flip.mrc (#48) relative to cryosparc_P4_J285_006_volume_map_sharp.mrc z flip (#39) coordinates: Matrix rotation and translation -0.54436883 -0.83749052 0.04766738 317.13056079 0.79848148 -0.53475206 -0.27652762 129.04232256 0.25707950 -0.11247150 0.95982304 -11.58663120 Axis 0.09898047 -0.12634523 0.98703584 Axis point 124.28808276 149.04371086 0.00000000 Rotation angle (degrees) 124.03152255 Shift along axis 3.64942894 > ui mousemode right ""rotate selected models"" > view matrix models > #48,-0.38435,0.91427,-0.12797,86.018,-0.92117,-0.38898,-0.012326,307,-0.061046,0.11314,0.9917,-2.8083 > fitmap #48 inMap #39 Fit map CS_P4_J302_sharp_flip.mrc in map cryosparc_P4_J285_006_volume_map_sharp.mrc z flip using 5112 points correlation = 0.623, correlation about mean = 0.1973, overlap = 254 steps = 104, shift = 5.55, angle = 8.62 degrees Position of CS_P4_J302_sharp_flip.mrc (#48) relative to cryosparc_P4_J285_006_volume_map_sharp.mrc z flip (#39) coordinates: Matrix rotation and translation -0.49090927 0.85957769 -0.14189522 105.36638005 -0.85910240 -0.50468247 -0.08508012 328.20339808 -0.14474501 0.08013591 0.98621858 12.70754555 Axis 0.09568836 0.00165051 -0.99540997 Axis point 147.88121154 133.69042072 0.00000000 Rotation angle (degrees) 120.31054935 Shift along axis -2.02517664 > select subtract #48 Nothing selected > volume #48 level 0.8066 > hide #!48 models > show #!48 models > hide #!39 models > show #!40 models > hide #!40 models > show #!46 models > hide #!46 models > show #!46 models > hide #!46 models > volume #48 level 0.6121 > show #!24 models > hide #!24 models > color #48 #99BFE5 > hide #!48 models > show #!48 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J303_003_volume_map_sharp.mrc"" Opened cryosparc_P4_J303_003_volume_map_sharp.mrc as #49, grid size 80,80,80, pixel 3.32, shown at level 0.57, step 1, values float32 > select add #49 2 models selected > view matrix models > #49,0.53874,0.84077,0.053573,-61.438,0.83514,-0.54134,0.097405,87.116,0.1109,-0.0077344,-0.9938,260.56 > view matrix models > #49,0.53215,0.84494,0.053856,-61.154,0.83957,-0.53484,0.095262,85.896,0.10929,-0.0054773,-0.99399,260.49 > view matrix models > #49,-0.8763,-0.44891,0.17485,296.18,-0.45964,0.88777,-0.024369,82.131,-0.14428,-0.10172,-0.98429,307.41 > volume flip #49 Opened cryosparc_P4_J303_003_volume_map_sharp.mrc z flip as #50, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #49 > rename #50 CS_P4_J303_sharp_flip id #49 > save CS_P4_J303_sharp_flip.mrc #49 > select add #49 2 models selected > view matrix models > #49,-0.44927,0.88595,-0.11509,87.376,-0.86051,-0.46376,-0.21085,349.13,-0.24018,0.0043123,0.97072,61.749 > ui mousemode right ""translate selected models"" > view matrix models > #49,-0.44927,0.88595,-0.11509,93.572,-0.86051,-0.46376,-0.21085,352.06,-0.24018,0.0043123,0.97072,37.843 > fitmap #49 inMap 348 Invalid ""inMap"" argument: invalid density map specifier > fitmap #49 inMap #48 Fit map CS_P4_J303_sharp_flip.mrc in map CS_P4_J302_sharp_flip.mrc using 5118 points correlation = 0.8483, correlation about mean = 0.4386, overlap = 3011 steps = 68, shift = 10.7, angle = 7.19 degrees Position of CS_P4_J303_sharp_flip.mrc (#49) relative to CS_P4_J302_sharp_flip.mrc (#48) coordinates: Matrix rotation and translation 0.99996126 -0.00401528 0.00783497 -1.22617333 0.00399514 0.99998870 0.00258400 -1.26181412 -0.00784526 -0.00255260 0.99996598 1.34185977 Axis -0.28004899 0.85489100 0.43673098 Axis point 178.64594040 0.00000000 162.72002408 Rotation angle (degrees) 0.52546068 Shift along axis -0.14929320 > select subtract #49 Nothing selected > hide #!48 models > color #49 #FCEDFF > hide #!49 models > show #!49 models > volume #49 level 0.5753 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J304_002_volume_map_sharp.mrc"" Opened cryosparc_P4_J304_002_volume_map_sharp.mrc as #50, grid size 80,80,80, pixel 3.32, shown at level 1.66, step 1, values float32 > hide #!49 models > select add #50 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #50,0.25626,0.96633,0.023099,-33.544,0.9662,-0.25539,-0.035012,44.222,-0.027934,0.03129,-0.99912,256.23 > volume #50 level 2.579 > select subtract #50 Nothing selected > volume #50 level 1.975 > volume flip #50 Opened cryosparc_P4_J304_002_volume_map_sharp.mrc z flip as #51, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #50 > rename #51 CS_P4_J304_sharp_flip id #50 > save CS_P4_J304_sharp_flip.mrc #50 > select add #50 2 models selected > show #!49 models > view matrix models > #50,0.25432,0.96619,0.042346,-35.759,0.96711,-0.25431,-0.0057645,40.158,0.0051995,0.042419,-0.99909,250.22 > view matrix models > #50,-0.77557,0.61543,-0.14049,175.22,-0.61485,-0.78688,-0.052719,333.03,-0.143,0.045495,0.98868,11.993 > color #50 #FCEDFF > select subtract #50 Nothing selected > hide #!49 models > hide #!50 models > show #!50 models > volume #50 level 1.954 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J305_003_volume_map_sharp.mrc"" Opened cryosparc_P4_J305_003_volume_map_sharp.mrc as #51, grid size 80,80,80, pixel 3.32, shown at level 0.569, step 1, values float32 > hide #!50 models > select add #51 2 models selected > view matrix models > #51,-0.9391,-0.22026,0.26379,268.58,-0.1463,0.9508,0.27307,-8.1662,-0.31096,0.21785,-0.92512,264.01 > volume flip #51 Opened cryosparc_P4_J305_003_volume_map_sharp.mrc z flip as #52, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #51 > rename #52 CS_P4_J305_sharp_flip id #51 > save CS_P4_J305_sharp_flip.mrc #51 > color #51 #FCEDFF > show #!50 models > select add #51 2 models selected > view matrix models > #51,0.99548,-0.078687,0.053201,5.068,0.073705,0.99322,0.089881,-20.578,-0.059913,-0.085553,0.99453,15.159 > fitmap #51 inMap #50 Fit map CS_P4_J305_sharp_flip.mrc in map CS_P4_J304_sharp_flip.mrc using 5112 points correlation = 0.7769, correlation about mean = 0.3462, overlap = 4325 steps = 92, shift = 6.39, angle = 27.1 degrees Position of CS_P4_J305_sharp_flip.mrc (#51) relative to CS_P4_J304_sharp_flip.mrc (#50) coordinates: Matrix rotation and translation -0.48191930 -0.86211205 -0.15657780 337.25915719 0.86174903 -0.49867166 0.09335524 70.84333299 -0.15856359 -0.08994107 0.98324371 36.25215794 Axis -0.10573285 0.00114549 0.99439391 Axis point 149.95468753 133.49561797 0.00000000 Rotation angle (degrees) 119.91228641 Shift along axis 0.47070508 > select subtract #51 Nothing selected > hide #!50 models > hide #!51 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J306_002_volume_map_sharp.mrc"" Opened cryosparc_P4_J306_002_volume_map_sharp.mrc as #52, grid size 80,80,80, pixel 3.32, shown at level 0.89, step 1, values float32 > select add #52 2 models selected > view matrix models > #52,0.64736,0.71151,-0.27328,-15.881,0.69766,-0.69754,-0.16345,155.65,-0.30692,-0.084848,-0.94795,287.9 > volume flip #52 Opened cryosparc_P4_J306_002_volume_map_sharp.mrc z flip as #53, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #52 > select add #53 2 models selected > show #!51 models > view matrix models > #53,-0.54969,0.82414,-0.13652,114.28,-0.83504,-0.54665,0.062273,314.18,-0.023306,0.14823,0.98868,-59.023 > ui mousemode right ""translate selected models"" > view matrix models > #53,-0.54969,0.82414,-0.13652,112.71,-0.83504,-0.54665,0.062273,313.11,-0.023306,0.14823,0.98868,-22.329 > fitmap #53 inMap #51 Fit map cryosparc_P4_J306_002_volume_map_sharp.mrc z flip in map CS_P4_J305_sharp_flip.mrc using 5118 points correlation = 0.8696, correlation about mean = 0.2872, overlap = 4918 steps = 72, shift = 6.47, angle = 20.6 degrees Position of cryosparc_P4_J306_002_volume_map_sharp.mrc z flip (#53) relative to CS_P4_J305_sharp_flip.mrc (#51) coordinates: Matrix rotation and translation -0.48951817 0.85648171 -0.16374082 109.67271887 -0.85572951 -0.50794021 -0.09860917 331.28158536 -0.16762749 0.09184687 0.98156263 12.77250071 Axis 0.11055185 0.00225605 -0.99386780 Axis point 150.74970822 134.14339059 0.00000000 Rotation angle (degrees) 120.52723515 Shift along axis 0.17773418 > select subtract #53 Nothing selected > hide #!51 models > rename #53 CS_P4_J306_sharp_flip id #52 > save CS_P4_J306_sharp_flip.mrc #52 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J307_002_volume_map_sharp.mrc"" Opened cryosparc_P4_J307_002_volume_map_sharp.mrc as #53, grid size 80,80,80, pixel 3.32, shown at level 0.417, step 1, values float32 > hide #!52 models > select add #53 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #53,-0.97802,-0.15767,0.13647,275.15,-0.15325,0.98728,0.042392,17.478,-0.14141,0.020547,-0.98974,260.92 > volume flip #53 Opened cryosparc_P4_J307_002_volume_map_sharp.mrc z flip as #54, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #53 > select add #54 2 models selected > show #!51 models > view matrix models > #54,-0.83454,0.54308,0.09272,165.84,-0.53719,-0.83947,0.081916,314.21,0.12232,0.018554,0.99232,-51.868 > ui mousemode right ""translate selected models"" > view matrix models > #54,-0.83454,0.54308,0.09272,166.01,-0.53719,-0.83947,0.081916,312.6,0.12232,0.018554,0.99232,-21.112 > fitmap #54 inMap #51 Fit map cryosparc_P4_J307_002_volume_map_sharp.mrc z flip in map CS_P4_J305_sharp_flip.mrc using 5118 points correlation = 0.9157, correlation about mean = 0.3086, overlap = 1346 steps = 92, shift = 8.03, angle = 16.7 degrees Position of cryosparc_P4_J307_002_volume_map_sharp.mrc z flip (#54) relative to CS_P4_J305_sharp_flip.mrc (#51) coordinates: Matrix rotation and translation -0.49196091 0.85478647 -0.16527113 110.59805296 -0.85414546 -0.51062861 -0.09845785 330.98838770 -0.16855261 0.09272817 0.98132130 13.11747971 Axis 0.11118076 0.00190829 -0.99379837 Axis point 150.81392912 133.83273648 0.00000000 Rotation angle (degrees) 120.70607669 Shift along axis -0.10813355 > select subtract #54 Nothing selected > rename #54 CS_P4_J307_sharp_flip id #53 > save CS_P4_J307_sharp_flip.mrc #53 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J308_003_volume_map_sharp.mrc"" Opened cryosparc_P4_J308_003_volume_map_sharp.mrc as #54, grid size 80,80,80, pixel 3.32, shown at level 0.487, step 1, values float32 > hide #!51 models > hide #!53 models > select add #54 2 models selected > view matrix models #54,1,0,0,-2.2085,0,1,0,5.106,0,0,1,17.329 > ui mousemode right ""rotate selected models"" > view matrix models > #54,-0.97907,-0.098429,0.17813,263.99,-0.078474,0.99017,0.11581,3.2524,-0.18778,0.099408,-0.97717,270.12 > volume flip #54 Opened cryosparc_P4_J308_003_volume_map_sharp.mrc z flip as #55, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #54 > select add #55 2 models selected > show #!53 models > view matrix models > #55,-0.032009,-0.99944,0.0094019,279.03,0.99475,-0.030941,0.097574,-4.0943,-0.097229,0.012476,0.99518,-8.8511 > ui mousemode right ""translate selected models"" > view matrix models > #55,-0.032009,-0.99944,0.0094019,275.5,0.99475,-0.030941,0.097574,4.3503,-0.097229,0.012476,0.99518,10.879 > fitmap #55 inMap #53 Fit map cryosparc_P4_J308_003_volume_map_sharp.mrc z flip in map CS_P4_J307_sharp_flip.mrc using 5116 points correlation = 0.9635, correlation about mean = 0.3444, overlap = 1309 steps = 80, shift = 11, angle = 8.02 degrees Position of cryosparc_P4_J308_003_volume_map_sharp.mrc z flip (#55) relative to CS_P4_J307_sharp_flip.mrc (#53) coordinates: Matrix rotation and translation -0.47079667 0.87008681 -0.14594324 102.09450866 -0.87101131 -0.48471046 -0.07996914 326.37268834 -0.14032031 0.08946901 0.98605553 9.07494900 Axis 0.09685875 -0.00321433 -0.99529295 Axis point 148.07793015 132.95152312 0.00000000 Rotation angle (degrees) 118.99450917 Shift along axis -0.19255539 > select subtract #55 Nothing selected > hide #!53 models > color #55 #fcedffff models > rename #55 CS_P4_J308_sharp_flip id #54 > save CS_P4_J308_sharp_flip.mrc #54 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J309_002_volume_map_sharp.mrc"" Opened cryosparc_P4_J309_002_volume_map_sharp.mrc as #55, grid size 80,80,80, pixel 3.32, shown at level 0.427, step 1, values float32 > hide #!54 models > select add #55 2 models selected > show #!54 models > ui mousemode right ""rotate selected models"" > view matrix models > #55,0.72482,-0.68817,-0.032661,133.9,-0.68882,-0.72298,-0.053201,331.74,0.012998,0.061058,-0.99805,234.36 > hide #!54 models > view matrix models > #55,-0.98503,0.14104,0.099091,242.98,0.14443,0.98912,0.027904,-21.89,-0.094078,0.041798,-0.99469,251.29 > volume flip #55 Opened cryosparc_P4_J309_002_volume_map_sharp.mrc z flip as #56, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #55 > select add #56 2 models selected > show #!54 models > view matrix models > #56,-0.63923,0.76709,0.054278,117.91,-0.76391,-0.64153,0.069883,315.42,0.088428,0.0032076,0.99608,-48.086 > ui mousemode right ""translate selected models"" > view matrix models > #56,-0.63923,0.76709,0.054278,118.17,-0.76391,-0.64153,0.069883,313.6,0.088428,0.0032076,0.99608,-18.356 > fitmap #56 inMap #54 Fit map cryosparc_P4_J309_002_volume_map_sharp.mrc z flip in map CS_P4_J308_sharp_flip.mrc using 5111 points correlation = 0.9585, correlation about mean = 0.3571, overlap = 1283 steps = 104, shift = 10.8, angle = 17.1 degrees Position of cryosparc_P4_J309_002_volume_map_sharp.mrc z flip (#56) relative to CS_P4_J308_sharp_flip.mrc (#54) coordinates: Matrix rotation and translation -0.48831434 -0.86312376 -0.12871093 333.56502617 0.86459679 -0.49852007 0.06285020 75.43057430 -0.11841248 -0.08059241 0.98968852 28.18171624 Axis -0.08273806 -0.00594017 0.99655362 Axis point 146.06051902 134.60897835 0.00000000 Rotation angle (degrees) 119.90563147 Shift along axis 0.03799683 > select subtract #56 Nothing selected > hide #!54 models > hide #!56 models > show #!56 models > color #56 #fcedffff models > rename #56 CS_P4_J309_sharp_flip id #55 > save CS_P4_J309_sharp_flip.mrc #55 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J310_003_volume_map_sharp.mrc"" Opened cryosparc_P4_J310_003_volume_map_sharp.mrc as #56, grid size 80,80,80, pixel 3.32, shown at level 0.683, step 1, values float32 > volume flip #56 Opened cryosparc_P4_J310_003_volume_map_sharp.mrc z flip as #57, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #56 > fitmap #56 inMap #52 No atoms or maps for #56 > fitmap #57 inMap #52 Fit map cryosparc_P4_J310_003_volume_map_sharp.mrc z flip in map CS_P4_J306_sharp_flip.mrc using 5115 points correlation = 0.769, correlation about mean = 0.3701, overlap = 4288 steps = 88, shift = 5.42, angle = 22.7 degrees Position of cryosparc_P4_J310_003_volume_map_sharp.mrc z flip (#57) relative to CS_P4_J306_sharp_flip.mrc (#52) coordinates: Matrix rotation and translation -0.48166864 -0.85899522 -0.17355843 339.66736714 0.86194402 -0.50013127 0.08319372 72.72621082 -0.15826501 -0.10952585 0.98130335 38.95738038 Axis -0.11128512 -0.00883113 0.99374928 Axis point 150.89500052 135.18260516 0.00000000 Rotation angle (degrees) 120.01642768 Shift along axis 0.27169032 > hide #!55 models > show #!52 models > color #57 #fcedffff models > hide #!52 models > save #57 CS_P4_J310_sharp_flip id #56 Cannot determine format for '#57' > rename #57 CS_P4_J310_sharp_flip id #56 > save CS_P4_J310_sharp_flip.mrc #56 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J311_004_volume_map_sharp.mrc"" Opened cryosparc_P4_J311_004_volume_map_sharp.mrc as #57, grid size 80,80,80, pixel 3.32, shown at level 0.525, step 1, values float32 > volume flip #57 Opened cryosparc_P4_J311_004_volume_map_sharp.mrc z flip as #58, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #57 > color #58 #fcedffff models > rename #58 CS_P4_J311_sharp_flip id #57 > save CS_P4_J311_sharp_flip.mrc #57 > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260506_SA-F_B1_workflow.cxs"" > view P1 > hide #!57 models > hide #!56 models > show #!47 models > hide #!47 models > show #!48 models > save CS_P4_J302_NU_sharp.png supersample 3 transparentBackground true > hide #!48 models > show #!49 models > save CS_P4_J303_NU_sharp.png supersample 3 transparentBackground true > hide #!49 models > show #!50 models > save CS_P4_J304_NU_sharp.png supersample 3 transparentBackground true > hide #!50 models > show #!51 models > save CS_P4_J305_NU_sharp.png supersample 3 transparentBackground true > hide #!51 models > show #!52 models > volume #52 level 1.034 > save CS_P4_J306_NU_sharp.png supersample 3 transparentBackground true > hide #!52 models > show #!53 models > color #53 #fcedffff models > save CS_P4_J307_NU_sharp.png supersample 3 transparentBackground true > hide #!53 models > show #!54 models > save CS_P4_J308_NU_sharp.png supersample 3 transparentBackground true > hide #!54 models > show #!55 models > save CS_P4_J309_NU_sharp.png supersample 3 transparentBackground true > hide #!55 models > show #!56 models > volume #56 level 0.7192 > save CS_P4_J310_NU_sharp.png supersample 3 transparentBackground true > hide #!56 models > show #!57 models > save CS_P4_J311_NU_sharp.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260506_SA-F_B1_workflow.cxs"" ——— End of log from Wed May 6 15:19:28 2026 ——— > view name session-start opened ChimeraX session > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J323_006_volume_map_sharp.mrc"" Opened cryosparc_P4_J323_006_volume_map_sharp.mrc as #58, grid size 320,320,320, pixel 0.831, shown at level 0.0345, step 2, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J324_map_locres.mrc"" Opened cryosparc_P4_J324_map_locres.mrc as #59, grid size 320,320,320, pixel 0.831, shown at level 8.89, step 2, values float32 > hide #!57 models > hide #!58 models > show #!58 models > hide #!59 models > show #!59 models > volume flip #58 Opened cryosparc_P4_J323_006_volume_map_sharp.mrc z flip as #60, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > volume flip #59 Opened cryosparc_P4_J324_map_locres.mrc z flip as #61, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > close #58 > close #59 > rename #60 CS_P4_J323_sharp_flip #58 Expected a keyword > rename #60 CS_P4_J323_sharp_flip id #58 > save CS_P4_J323_sharp_flip.mrc #58 > rename CS_P4_J324_map_locres_flip id #59 Missing or invalid ""models"" argument: invalid models specifier > rename #61 CS_P4_J324_map_locres_flip id #59 > save CS_P4_J324_map_locres_flip.mrc #59 > hide #!58 models > show #!58 models > hide #!59 models > volume #59 level 9.377 > hide #!59 models > volume #58 level 0.05889 > show #!59 models > volume #59 level 3.695 > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260507_SA-F_B1_workflow.cxs"" > ui tool show ""Surface Color"" > hide #!58 models > show #!58 models > hide #!59 models > color radial #58.1 palette #ffb17f:#4979d3:#99bfe5:#fff6c0:#f4fff3 > color sample #58.1 map #59 palette > 166.9,#ffb17f:198,#4979d3:229.1,#99bfe5:260.3,#fff6c0:291.4,#f4fff3 > outsideColor #808080 Map values for surface ""surface"": minimum 2.944, mean 3.552, maximum 44.59 > color sample #58.1 map #59 palette > 2,#ffb17f:3,#4979d3:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 2.944, mean 3.552, maximum 44.59 > show #!59 models > hide #!58 models > hide #!59 models > show #!59 models > show #!58 models > hide #!59 models > show #!59 models > hide #!59 models > volume #58 level 0.0634 > volume #58 level 0.04264 > volume #58 level 0.07693 > volume #58 level 0.06069 > volume #58 level 0.07152 > volume #58 level 0.05889 > volume #58 level 0.05167 > volume #58 level 0.06159 > key #ffb17f:2 #4979d3:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > ui mousemode right ""color key"" > key pos 0.82265,0.196044 size 0.0692066,0.202924 > ui mousemode right translate > ui mousemode right ""color key"" > key pos 0.802943,0.231339 size 0.039822,0.144632 > key #ffb17f:2 #4979d3:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > key pos 0.836801,0.165731 size 0.0516869,0.238605 > show #41 models > key pos 0.820538,0.190547 size 0.0458442,0.242723 > save CS_P4_J323_sharp_flip.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260507_SA-F_B1_workflow1.cxs"" > color sample #58.1 map #59 palette > 2,#ffb17f:3,#169bd3:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 2.944, mean 3.532, maximum 44.61 > color sample #58.1 map #59 palette > 2,#ffb17f:3,#46c7f6:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 2.944, mean 3.532, maximum 44.61 > color sample #58.1 map #59 palette > 2,#ffb17f:3,#11b6e1:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 2.944, mean 3.532, maximum 44.61 > key #ffb17f:2 #11b6e1:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > ui mousemode right ""color key"" > color sample #58.1 map #59 palette > 2,#ffb17f:3,#11b6e1:4,#99bfe5:5,#fff6c0:6,#ffb17f outsideColor #808080 Map values for surface ""surface"": minimum 2.944, mean 3.532, maximum 44.61 > key #ffb17f:2 #11b6e1:3 #99bfe5:4 #fff6c0:5 #ffb17f:6 showTool true > color sample #58.1 map #59 palette > 2,#13097f:3,#11b6e1:4,#99bfe5:5,#fff6c0:6,#ffb17f outsideColor #808080 Map values for surface ""surface"": minimum 2.944, mean 3.532, maximum 44.61 > key #13097f:2 #11b6e1:3 #99bfe5:4 #fff6c0:5 #ffb17f:6 showTool true > save CS_P4_J323_sharp_flip2.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260507_SA-F_B1_workflow2.cxs"" > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J329_005_volume_map_sharp.mrc"" Opened cryosparc_P4_J329_005_volume_map_sharp.mrc as #60, grid size 320,320,320, pixel 0.831, shown at level 0.0384, step 2, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J330_map_locres.mrc"" Opened cryosparc_P4_J330_map_locres.mrc as #61, grid size 320,320,320, pixel 0.831, shown at level 9.71, step 2, values float32 > hide #!58 models > hide #!60 models > show #!60 models > hide #!61 models > volume flip #60 Opened cryosparc_P4_J329_005_volume_map_sharp.mrc z flip as #62, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > volume flip #61 Opened cryosparc_P4_J330_map_locres.mrc z flip as #63, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > close #60 > close #61 > rename #62 CS_P4_J329_sharp_flip id #60 > save CS_P4_J329_sharp_flip.mrc #60 > rename #63 rename > rename #63 CS_P4_J330_locres_flip id #61 > save CS_P4_J330_locres_flip.mrc #61 > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260507_SA-F_B1_workflow3.cxs"" > hide #!61 models > color sample #58.1 map #59 palette > 2,#13097f:3,#11b6e1:4,#99bfe5:5,#fff6c0:6,#ffb17f outsideColor #808080 Map values for surface ""surface"": minimum 2.944, mean 3.532, maximum 44.61 > color sample #60.1 map #61 palette > 2,#13097f:3,#11b6e1:4,#99bfe5:5,#fff6c0:6,#ffb17f outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.466, maximum 46.71 > volume #60 level 0.06443 > key #13097f:2 #11b6e1:3 #99bfe5:4 #fff6c0:5 #ffb17f:6 showTool true > ui mousemode right ""color key"" > volume #60 level 0.05663 > save CS_P4_J329_locres_sharp.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260507_SA-F_B1_workflow3.cxs"" ——— End of log from Thu May 7 15:58:17 2026 ——— > view name session-start opened ChimeraX session > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J300_005_volume_map_sharp.mrc"" Opened cryosparc_P4_J300_005_volume_map_sharp.mrc as #62, grid size 320,320,320, pixel 0.831, shown at level 0.0375, step 2, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J301_map_locres.mrc"" Opened cryosparc_P4_J301_map_locres.mrc as #63, grid size 320,320,320, pixel 0.831, shown at level 9.68, step 2, values float32 > hide #!60 models > hide #!63 models > volume flip #62 Opened cryosparc_P4_J300_005_volume_map_sharp.mrc z flip as #64, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > volume flip #63 Opened cryosparc_P4_J301_map_locres.mrc z flip as #65, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > close #62 > close #63 > rename #64 CS_P4_J300_sharp_flip id #62 > save CS_P4_J300_sharp_flip.mrc #62 > rename #65 CS_P4_J301_locres_flip id #63 > save CS_P4_J301_locres_flip.mrc #63 > show #!46 models > show #!47 models > hide #!47 models > hide #!46 models > hide #!63 models > show #!63 models > volume #63 level 3.952 > hide #!63 models > volume #62 level 0.0392 > ui tool show ""Surface Color"" > color sample #62.1 map #63 palette #13097f:#11b6e1:#99bfe5:#fff6c0:#ffb17f > outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.383, maximum 43.37 > color sample #62.1 map #63 palette > 2,#13097f:3,#11b6e1:4,#99bfe5:5,#fff6c0:6,#ffb17f outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.383, maximum 43.37 > show #!63 models > hide #!63 models > hide #!62 models > show #!62 models > volume #62 level 0.06614 > volume #62 level 0.05745 > save CS_P4_J300_locres_sharp.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260507_SA-F_B1_workflow4.cxs"" > open /Users/peiyuyu/Downloads/cryosparc_P7_J110_004_volume_map_sharp.mrc Opened cryosparc_P7_J110_004_volume_map_sharp.mrc as #64, grid size 160,160,160, pixel 1.66, shown at level 0.28, step 1, values float32 > hide #!62 models > close #64 > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260507_SA-F_B1_workflow5.cxs"" ——— End of log from Thu May 7 21:11:39 2026 ——— > view name session-start opened ChimeraX session Failed to send bug report. Bug report server www.rbvi.ucsf.edu is unavailable [Repeated 1 time(s)] OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M4 Pro OpenGL vendor: Apple Python: 3.11.9 Locale: UTF-8 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac16,8 Model Number: MX2F3D/A Chip: Apple M4 Pro Total Number of Cores: 14 (10 performance and 4 efficiency) Memory: 24 GB System Firmware Version: 11881.81.4 OS Loader Version: 11881.81.4 Software: System Software Overview: System Version: macOS 15.3.1 (24D70) Kernel Version: Darwin 24.3.0 Time since boot: 29天16小時42分鐘 Graphics/Displays: Apple M4 Pro: Chipset Model: Apple M4 Pro Type: GPU Bus: Built-In Total Number of Cores: 20 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal LEN T22i-10: 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: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.12.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.4 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.1.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.61.4 ChimeraX-AtomicLibrary: 14.2.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.0 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.11 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 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: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.7.3 ChimeraX-Label: 1.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 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: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.1.0 ChimeraX-MDcrds: 2.17.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 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: 1.0.1 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: 1.15.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.11 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.4.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.5 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.3 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 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: 1.49.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.5.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.19 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.61.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.3.0 ipykernel: 6.30.1 ipython: 9.5.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.8 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.25.1 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.0 narwhals: 2.17.0 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 2.4.2 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.5 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.1 plotly: 6.5.2 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.5 pydantic-settings: 2.12.0 pydantic_core: 2.41.5 pydicom: 2.4.4 Pygments: 2.18.0 pyKVFinder: 0.9.0 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.2.5 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.21 pytz: 2025.2 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.0.0 roman-numerals-py: 4.0.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 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 sse-starlette: 3.0.4 stack-data: 0.6.3 starlette: 0.50.0 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tomlkit: 0.14.0 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 tzdata: 2025.3 urllib3: 2.6.2 uvicorn: 0.38.0 wcwidth: 0.2.14 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0 }}} " defect closed normal Window Toolkit duplicate all ChimeraX