id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20294 Crash trying to render GUI with hundreds of sequence viewers chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-26.3.1-arm64-arm-64bit ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Aborted Current thread 0x00000001f0467100 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 414 in event_loop File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1064 in init File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1229 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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address space (unallocated) MALLOC_REALLOC (reserved) 3504K 1 reserved VM address space (unallocated) Mach message 64K 3 OpenGL GLSL 256K 3 PROTECTED_MEMORY 16K 1 STACK GUARD 656K 41 Stack 201.9M 42 Stack Guard 56.0M 1 VM_ALLOCATE 455.8M 458 VM_ALLOCATE (reserved) 160.0M 2 reserved VM address space (unallocated) __AUTH 5968K 657 __AUTH_CONST 90.5M 1043 __CTF 824 1 __DATA 43.9M 1177 __DATA_CONST 60.4M 1222 __DATA_DIRTY 8499K 900 __FONT_DATA 2352 1 __GLSLBUILTINS 5176K 1 __INFO_FILTER 8 1 __LINKEDIT 626.7M 175 __OBJC_RO 78.4M 1 __OBJC_RW 2571K 1 __TEXT 1.3G 1193 __TEXT (graphics) 232.6M 52 __TPRO_CONST 128K 2 dyld private memory 5840K 48 mapped file 680.7M 81 page table in kernel 11.9M 1 shared memory 3696K 25 =========== ======= ======= TOTAL 24.2G 8557 TOTAL, minus reserved VM space 23.8G 8557 "", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""ba8eb564385daa0cd4243ce662f2bf4fe72b83e5"", ""bug_type"" : ""309"", ""roots_installed"" : 0, ""trmStatus"" : 1, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""67648e5334a82511f4acf879"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000008 }, { ""rolloutId"" : ""67d07cd6a7affa169ae21f45"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000002 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/amy/Desktop/SPA > AAT_HNE/3C11_Fab_AAT_NE/3c11_aat_hen_csparc.cxs"" Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300, pixel 0.867, shown at level 0.0665, step 2, values float32 Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at level 0.0841, step 1, values float32 Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size 300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32 Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size 180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32 Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867, shown at level 0.0503, step 2, values float32 Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel 0.867, shown at level 0.0806, step 1, values float32 Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size 128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32 Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300, pixel 0.867, shown at level 0.0245, step 2, values float32 Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size 300,300,300, pixel 0.867, shown at level 0.0683, step 1, values float32 Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300, pixel 0.867, shown at level 0.0208, step 2, values float32 Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size 300,300,300, pixel 0.867, shown at level 0.0938, step 1, values float32 Opened J1122.mrc as #29, grid size 300,300,300, pixel 0.867, shown at level 0.071, step 2, values float32 Opened J1134.mrc as #34, grid size 300,300,300, pixel 0.867, shown at level 0.0707, step 2, values float32 Opened cryosparc_P483_molmap_of_combined_6A.mrc as #41, grid size 200,200,200, pixel 1, shown at level 0.293, step 1, values float32 Opened AATHNEcombined map 6 as #8, grid size 43,51,63, pixel 2, shown at level 0.366, step 1, values float32 Opened copy of copy of AATHNEcombined map 6 as #45, grid size 43,51,63, pixel 2, shown at level 0.354, step 1, values float32 Log from Thu Mar 12 17:49:41 2026UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/amy/Desktop/SPA AAT_HNE/csparc.cxs"" Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300, pixel 0.867, shown at level 0.0665, step 2, values float32 Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at level 0.0841, step 1, values float32 Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size 300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32 Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size 180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32 Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867, shown at level 0.0503, step 2, values float32 Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel 0.867, shown at level 0.0806, step 1, values float32 Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size 128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32 Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300, pixel 0.867, shown at level 0.0245, step 2, values float32 Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size 300,300,300, pixel 0.867, shown at level 0.0683, step 1, values float32 Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300, pixel 0.867, shown at level 0.0208, step 2, values float32 Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size 300,300,300, pixel 0.867, shown at level 0.0938, step 1, values float32 Opened J1122.mrc as #29, grid size 300,300,300, pixel 0.867, shown at level 0.071, step 2, values float32 Opened J1134.mrc as #34, grid size 300,300,300, pixel 0.867, shown at level 0.0707, step 2, values float32 Log from Wed Feb 11 13:24:40 2026UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. > open /Users/amy/Desktop/3C11_Fab_AAT_NE/csparc.cxs Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300, pixel 0.867, shown at level 0.0665, step 2, values float32 Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at level 0.0841, step 1, values float32 Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size 300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32 Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size 180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32 Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867, shown at level 0.0503, step 2, values float32 Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel 0.867, shown at level 0.0806, step 1, values float32 Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size 128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32 Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300, pixel 0.867, shown at level 0.0245, step 2, values float32 Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size 300,300,300, pixel 0.867, shown at level 0.0683, step 1, values float32 Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300, pixel 0.867, shown at level 0.0208, step 2, values float32 Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size 300,300,300, pixel 0.867, shown at level 0.0938, step 1, values float32 Opened J1122.mrc as #29, grid size 300,300,300, pixel 0.867, shown at level 0.071, step 2, values float32 Opened J1134.mrc as #34, grid size 300,300,300, pixel 0.867, shown at level 0.0707, step 2, values float32 Log from Sun Feb 1 23:24:08 2026UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. > open /Users/amy/Desktop/3C11_Fab_AAT_NE/csparc.cxs format session Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300, pixel 0.867, shown at level 0.0665, step 2, values float32 Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at level 0.0841, step 1, values float32 Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size 300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32 Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size 180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32 Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867, shown at level 0.0503, step 2, values float32 Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel 0.867, shown at level 0.0806, step 1, values float32 Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size 128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32 Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300, pixel 0.867, shown at level 0.0245, step 2, values float32 Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size 300,300,300, pixel 0.867, shown at level 0.0683, step 1, values float32 Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300, pixel 0.867, shown at level 0.0208, step 2, values float32 Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size 300,300,300, pixel 0.867, shown at level 0.0938, step 1, values float32 Opened J1122.mrc as #29, grid size 300,300,300, pixel 0.867, shown at level 0.071, step 2, values float32 Opened J1134.mrc as #34, grid size 300,300,300, pixel 0.867, shown at level 0.0707, step 2, values float32 Log from Tue Jan 6 13:31:49 2026UCSF ChimeraX version: 1.9rc202411230619 (2024-11-23) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/apple/Downloads/csparc.cxs Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300, pixel 0.867, shown at level 0.0665, step 2, values float32 Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at level 0.0841, step 1, values float32 Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size 300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32 Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size 180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32 Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867, shown at level 0.0503, step 2, values float32 Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel 0.867, shown at level 0.0806, step 1, values float32 Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size 128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32 Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300, pixel 0.867, shown at level 0.0245, step 2, values float32 Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size 300,300,300, pixel 0.867, shown at level 0.0683, step 1, values float32 Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300, pixel 0.867, shown at level 0.0208, step 2, values float32 Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size 300,300,300, pixel 0.867, shown at level 0.0938, step 1, values float32 Log from Wed Dec 31 02:28:23 2025UCSF ChimeraX version: 1.9rc202411230619 (2024-11-23) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/apple/Downloads/csparc.cxs Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300, pixel 0.867, shown at level 0.0665, step 2, values float32 Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at level 0.0841, step 1, values float32 Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size 300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32 Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size 180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32 Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867, shown at level 0.0503, step 2, values float32 Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel 0.867, shown at level 0.0806, step 1, values float32 Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size 128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32 Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300, pixel 0.867, shown at level 0.0245, step 2, values float32 Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size 300,300,300, pixel 0.867, shown at level 0.0683, step 1, values float32 Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300, pixel 0.867, shown at level 0.0208, step 2, values float32 Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size 300,300,300, pixel 0.867, shown at level 0.0938, step 1, values float32 Log from Wed Dec 10 00:50:43 2025UCSF ChimeraX version: 1.9rc202411230619 (2024-11-23) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/apple/Downloads/csparc.cxs Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300, pixel 0.867, shown at level 0.0665, step 2, values float32 Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at level 0.0841, step 1, values float32 Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size 300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32 Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size 180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32 Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867, shown at level 0.0503, step 2, values float32 Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel 0.867, shown at level 0.0806, step 1, values float32 Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size 128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32 Log from Fri Nov 28 18:17:17 2025UCSF ChimeraX version: 1.9rc202411230619 (2024-11-23) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/apple/Downloads/csparc.cxs Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300, pixel 0.867, shown at level 0.0665, step 2, values float32 Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at level 0.0841, step 1, values float32 Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size 300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32 Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size 180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32 Log from Tue Nov 25 15:20:48 2025 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9rc202411230619 (2024-11-23) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 1ezx format mmcif fromDatabase pdb 1ezx title: Crystal structure of A serpin:protease complex [more info...] Chain information for 1ezx #1 --- Chain | Description | UniProt A | ALPHA-1-ANTITRYPSIN | A1AT_HUMAN 24-358 B | ALPHA-1-ANTITRYPSIN | A1AT_HUMAN 359-394 C | TRYPSIN | TRY1_BOVIN 42-245 > open /Users/apple/Downloads/cryosparc_P371_J880_003_volume_map.mrc Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300, pixel 0.867, shown at level 0.0177, step 2, values float32 > volume #2 level 0.06652 > ui mousemode right ""translate selected models"" > select add #1 3984 atoms, 3982 bonds, 5 pseudobonds, 592 residues, 3 models selected > view matrix models #1,1,0,0,22.115,0,1,0,63.09,0,0,1,71.823 > view matrix models #1,1,0,0,69.177,0,1,0,79.741,0,0,1,64.119 > view matrix models #1,1,0,0,67.012,0,1,0,77.327,0,0,1,54.335 > view matrix models #1,1,0,0,68.613,0,1,0,71.318,0,0,1,51.449 > ui tool show ""Fit in Map"" > fitmap #1 inMap #2 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2) using 3984 atoms average map value = 0.0438, steps = 92 shifted from previous position = 3.55 rotated from previous position = 4.42 degrees atoms outside contour = 2880, contour level = 0.066523 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2) coordinates: Matrix rotation and translation 0.99872483 -0.00989522 0.04950557 63.11308004 0.00699761 0.99827076 0.05836545 67.58136236 -0.04999751 -0.05794461 0.99706703 56.37622316 Axis -0.75528783 0.64614759 0.10969770 Axis point 0.00000000 1024.64866555 -1103.37084637 Rotation angle (degrees) 4.41598404 Shift along axis 2.18333524 > view matrix models > #1,0.99872,-0.0098952,0.049506,62.468,0.0069976,0.99827,0.058365,78.039,-0.049998,-0.057945,0.99707,58.786 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.95028,-0.27274,-0.15028,221.56,0.30912,-0.88449,-0.34946,175.7,-0.037612,-0.37854,0.92482,78.268 > fitmap #1 inMap #2 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2) using 3984 atoms average map value = 0.04798, steps = 140 shifted from previous position = 7.9 rotated from previous position = 12.7 degrees atoms outside contour = 2817, contour level = 0.066523 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2) coordinates: Matrix rotation and translation -0.90965137 -0.21420693 -0.35587888 224.37202412 0.34819532 -0.86039384 -0.37213231 169.35532345 -0.22648268 -0.46242602 0.85724429 105.26930309 Axis -0.15458157 -0.22152447 0.96282472 Axis point 107.00674340 114.53127832 0.00000000 Rotation angle (degrees) 163.01876555 Shift along axis 29.15575838 > view matrix models > #1,-0.93537,-0.33888,0.10125,206.37,0.28885,-0.89713,-0.33425,173.15,0.2041,-0.2834,0.93703,61.97 > remove /C Unknown command: remove /C > delete /C > fitmap #1 inMap #2 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2) using 2975 atoms average map value = 0.05683, steps = 168 shifted from previous position = 10.2 rotated from previous position = 20.9 degrees atoms outside contour = 1876, contour level = 0.066523 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2) coordinates: Matrix rotation and translation -0.98775248 -0.03216686 0.15267718 185.97005837 0.01404291 -0.99287467 -0.11833294 193.09005228 0.15539570 -0.11473962 0.98116614 52.60294093 Axis 0.07739391 -0.05855237 0.99527976 Axis point 89.79478279 99.15188295 0.00000000 Rotation angle (degrees) 178.66978984 Shift along axis 55.44171271 > fitmap #1 inMap #2 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2) using 2975 atoms average map value = 0.05683, steps = 44 shifted from previous position = 0.00306 rotated from previous position = 0.00868 degrees atoms outside contour = 1876, contour level = 0.066523 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2) coordinates: Matrix rotation and translation -0.98775300 -0.03230499 0.15264466 185.98147456 0.01419042 -0.99287622 -0.11830233 193.08167122 0.15537901 -0.11468739 0.98117489 52.59959002 Axis 0.07738151 -0.05853153 0.99528195 Axis point 89.79393478 99.15365724 0.00000000 Rotation angle (degrees) 178.66156873 Shift along axis 55.44158488 Deleted lines to meet Trac size limit. Tom > hbonds #!39 reveal true The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: 8pi2 #35/A ARG 101 NE 13841 hydrogen bonds found > interfaces #!39 & ~solvent 5 buried areas: A C 2439, H L 1779, A H 684, A B 593, B L 433 > select #39/A:32@CB 1 atom, 1 residue, 1 model selected > select clear > select #39/H: 32 12 atoms, 12 bonds, 1 residue, 1 model selected > select #39/A: 32 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel byhetero > select #39/H: 28 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel byhetero > distance #39/A:32 #39/H:28 Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or one or more measurable objects and one or more atoms, got 16 atoms and 0 measurable objects > distance #39/A:32@OE1 #39/H:28@OG1 Distance between combined.pdb #39/A GLU 32 OE1 and /H THR 28 OG1: 3.567Å > select up 48 atoms, 49 bonds, 5 residues, 1 model selected > select up 1018 atoms, 1042 bonds, 134 residues, 1 model selected > select down 48 atoms, 49 bonds, 5 residues, 1 model selected > select down 7 atoms, 6 bonds, 1 residue, 1 model selected > select #39/A: 75 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel byhetero > select #39/H: 56 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel byhetero > distance #39/A:75@OE2 #39/H:56@OG Distance between combined.pdb #39/A GLU 75 OE2 and /H SER 56 OG: 2.495Å > select #39/A: 36 6 atoms, 5 bonds, 1 residue, 1 model selected > select #39/A: 306 8 atoms, 7 bonds, 1 residue, 1 model selected > select #39/A: 302 7 atoms, 6 bonds, 1 residue, 1 model selected > select #39/A: 2 Nothing selected > select #39/A: 32 9 atoms, 8 bonds, 1 residue, 1 model selected > select #39/A: 36 6 atoms, 5 bonds, 1 residue, 1 model selected > select add #39 7963 atoms, 7899 bonds, 1523 pseudobonds, 1256 residues, 4 models selected > select subtract #39 Nothing selected > select add #39 7963 atoms, 7899 bonds, 1523 pseudobonds, 1256 residues, 4 models selected > show sel cartoons > hide sel atoms > hide sel cartoons > show sel atoms > hide sel cartoons > hide sel atoms > show sel cartoons > ui tool show ""Show Sequence Viewer"" > sequence chain #4/H #6/H #17/H #24/H #33/H #39/H Alignment identifier is 1 > select clear > select #4/H:1 #6/H:1 #17/H:1 #24/H:1 #33/H:1 #39/H:1 30 atoms, 24 bonds, 6 residues, 6 models selected > select #4/H:1-169 #6/H:1-169 #17/H:1-169 #24/H:1-169 #33/H:1-169 #39/H:1-169 7686 atoms, 7878 bonds, 341 pseudobonds, 1020 residues, 13 models selected Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-171] RMSD: 42.741 > select #4/H:213 #6/H:213 #17/H:213 #24/H:213 #33/H:213 #39/H:213 72 atoms, 66 bonds, 6 residues, 6 models selected > select #4/H:151-213 #6/H:151-213 #17/H:151-213 #24/H:151-213 #33/H:151-213 > #39/H:151-213 2802 atoms, 2868 bonds, 149 pseudobonds, 378 residues, 7 models selected Fab 3C11 Heavy Chain [ID: 1] region 6 chains [153-215] RMSD: 64.253 > select #4/H:1-2 #6/H:1-2 #17/H:1-2 #24/H:1-2 #33/H:1-2 #39/H:1-2 72 atoms, 66 bonds, 12 residues, 6 models selected > select #4/H:1-146 #6/H:1-146 #17/H:1-146 #24/H:1-146 #33/H:1-146 #39/H:1-146 6678 atoms, 6828 bonds, 312 pseudobonds, 882 residues, 13 models selected Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-148] RMSD: 40.342 > select #4/H:1 #6/H:1 #17/H:1 #24/H:1 #33/H:1 #39/H:1 30 atoms, 24 bonds, 6 residues, 6 models selected > select #4/H:1-140 #6/H:1-140 #17/H:1-140 #24/H:1-140 #33/H:1-140 #39/H:1-140 6372 atoms, 6510 bonds, 303 pseudobonds, 846 residues, 13 models selected Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-142] RMSD: 39.273 > select #4/H:1-2 #6/H:1-2 #17/H:1-2 #24/H:1-2 #33/H:1-2 #39/H:1-2 72 atoms, 66 bonds, 12 residues, 6 models selected > select #4/H:1-132 #6/H:1-132 #17/H:1-132 #24/H:1-132 #33/H:1-132 #39/H:1-132 6108 atoms, 6252 bonds, 279 pseudobonds, 804 residues, 7 models selected Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-134] RMSD: 36.760 > select #4/H:1 #6/H:1 #17/H:1 #24/H:1 #33/H:1 #39/H:1 30 atoms, 24 bonds, 6 residues, 6 models selected > select #4/H:1-128 #6/H:1-128 #17/H:1-128 #24/H:1-128 #33/H:1-128 #39/H:1-128 5976 atoms, 6120 bonds, 277 pseudobonds, 780 residues, 7 models selected Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-130] RMSD: 33.946 > select #4/H:1-2 #6/H:1-2 #17/H:1-2 #24/H:1-2 #33/H:1-2 #39/H:1-2 72 atoms, 66 bonds, 12 residues, 6 models selected > select #4/H:1-94 #6/H:1-94 #17/H:1-94 #24/H:1-94 #33/H:1-94 #39/H:1-94 4548 atoms, 4644 bonds, 204 pseudobonds, 588 residues, 7 models selected Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-98] RMSD: 25.989 > select #4/H:1-101 #6/H:1-101 #17/H:1-101 #24/H:1-101 #33/H:1-101 #39/H:1-101 4806 atoms, 4908 bonds, 222 pseudobonds, 618 residues, 7 models selected Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-98] + 1 other block RMSD: 25.402 > select #4/H:1-106 #6/H:1-106 #17/H:1-106 #24/H:1-106 #33/H:1-106 #39/H:1-106 5058 atoms, 5178 bonds, 235 pseudobonds, 648 residues, 7 models selected Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-98] + 2 other blocks RMSD: 25.227 > select #4/H:1-111 #6/H:1-111 #17/H:1-111 #24/H:1-111 #33/H:1-111 #39/H:1-111 5274 atoms, 5394 bonds, 258 pseudobonds, 678 residues, 7 models selected Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-98] + 3 other blocks RMSD: 25.743 > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain #4/L #6/L #17/L #24/L #33/L #39/L Alignment identifier is 1 > select #4/L:2 #6/L:2 #17/L:2 #24/L:2 #33/L:2 #39/L:2 48 atoms, 42 bonds, 6 residues, 6 models selected > select #4/L:2-113 #6/L:2-113 #17/L:2-113 #24/L:2-113 #33/L:2-113 #39/L:2-113 4782 atoms, 4896 bonds, 292 pseudobonds, 636 residues, 13 models selected Fab 3C11 Light Chain [ID: 1] region 6 chains [1-113] RMSD: 28.868 > select #4/L:2-113 #6/L:2-113 #17/L:2-113 #24/L:2-113 #33/L:2-113 #39/L:2-113 4782 atoms, 4896 bonds, 292 pseudobonds, 636 residues, 13 models selected Fab 3C11 Light Chain [ID: 1] region 6 chains [1-113] + 1 other block RMSD: 30.988 > select clear > select #4/L:2-97 #6/L:2-97 #17/L:2-97 #24/L:2-97 #33/L:2-97 #39/L:2-97 4128 atoms, 4236 bonds, 234 pseudobonds, 540 residues, 13 models selected Fab 3C11 Light Chain [ID: 1] region 6 chains [1-97] RMSD: 25.885 > select #4/L:2-97,100-102 #6/L:2-97,100-102 #17/L:2-97,100-102 > #24/L:2-97,100-102 #33/L:2-97,100-102 #39/L:2-97,100-102 4200 atoms, 4302 bonds, 241 pseudobonds, 558 residues, 13 models selected Fab 3C11 Light Chain [ID: 1] region 6 chains [1-97] + 1 other block RMSD: 25.843 > select #4/L:2-102 #6/L:2-102 #17/L:2-102 #24/L:2-102 #33/L:2-102 #39/L:2-102 4308 atoms, 4422 bonds, 261 pseudobonds, 570 residues, 13 models selected Fab 3C11 Light Chain [ID: 1] region 6 chains [1-97] + 2 other blocks RMSD: 25.676 > select #4/L:2-102 #6/L:2-102 #17/L:2-102 #24/L:2-102 #33/L:2-102 #39/L:2-102 4308 atoms, 4422 bonds, 261 pseudobonds, 570 residues, 13 models selected Fab 3C11 Light Chain [ID: 1] region 6 chains [1-97] + 3 other blocks RMSD: 25.676 > select clear > select #4/L:80-84,122-128,184-188 #6/L:80-84,122-128,184-188 > #17/L:80-84,122-128,184-188 #24/L:80-84,122-128,184-188 > #33/L:80-84,122-128,184-188 #39/L:80-84,122-128,184-188 834 atoms, 828 bonds, 39 pseudobonds, 102 residues, 7 models selected > select > #4/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211 > #6/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211 > #17/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211 > #24/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211 > #33/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211 > #39/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211 4968 atoms, 4998 bonds, 292 pseudobonds, 636 residues, 7 models selected > select clear > select #4/L:2-102 #6/L:2-102 #17/L:2-102 #24/L:2-102 #33/L:2-102 #39/L:2-102 4308 atoms, 4422 bonds, 261 pseudobonds, 570 residues, 13 models selected Fab 3C11 Light Chain [ID: 1] region 6 chains [1-102] RMSD: 25.676 > select #4/L:2-107 #6/L:2-107 #17/L:2-107 #24/L:2-107 #33/L:2-107 #39/L:2-107 4530 atoms, 4644 bonds, 286 pseudobonds, 600 residues, 13 models selected Fab 3C11 Light Chain [ID: 1] region 6 chains [1-102] + 1 other block RMSD: 26.293 > open /Users/amy/Downloads/J1122_fit2.cif Summary of feedback from opening /Users/amy/Downloads/J1122_fit2.cif --- warnings | Missing entity information. Treating each chain as a separate entity. Missing or incorrect sequence information. Inferred polymer connectivity. Chain information for J1122_fit2.cif #49 --- Chain | Description Aa | No description available Ab | No description available Ac | No description available Ad | No description available Ae | No description available Ba | No description available Bb | No description available Bc | No description available Ca | No description available Cb | No description available Cc | No description available > open /Users/amy/Downloads/J1122_fit2_raw.cif Summary of feedback from opening /Users/amy/Downloads/J1122_fit2_raw.cif --- warnings | Missing entity information. Treating each chain as a separate entity. Missing or incorrect sequence information. Inferred polymer connectivity. Chain information for J1122_fit2_raw.cif #50 --- Chain | Description 0 5 BM CZ Co Cp Cy D4 DK DL DT DY DZ Dd Dk Do Dq EA U y | No description available 1 | No description available 2 A7 | No description available 3 t | No description available 4 x | No description available 6 | No description available 7 BF C5 Cj Cl Cn Cq D9 DP DQ Da Dm | No description available 8 | No description available 9 D8 | No description available A | No description available A0 | No description available A1 | No description available A2 | No description available A3 AR Al | No description available A4 | No description available A5 | No description available A6 | No description available A8 r | No description available A9 | No description available AA | No description available AB C7 | No description available AC u | No description available AD | No description available AE An BA | No description available AF | No description available AG | No description available AH | No description available AI | No description available AJ | No description available AK DO | No description available AL | No description available AM | No description available AN | No description available AO | No description available AP DD | No description available AQ | No description available AS | No description available AT | No description available AU | No description available AV | No description available AW | No description available AX | No description available AY | No description available AZ | No description available Aa | No description available Ab | No description available Ac | No description available Ad | No description available Ae | No description available Af | No description available Ag | No description available Ah | No description available Ai | No description available Aj Ch Cw | No description available Ak | No description available Am | No description available Ao | No description available Ap | No description available Aq | No description available Ar | No description available As | No description available At | No description available Au DS | No description available Av | No description available Aw Ck | No description available Ax Ci | No description available Ay | No description available Az | No description available B | No description available B0 | No description available B1 | No description available B2 | No description available B3 | No description available B4 | No description available B5 | No description available B6 | No description available B7 | No description available B8 | No description available B9 | No description available BB | No description available BC | No description available BD | No description available BE | No description available BG | No description available BH | No description available BI | No description available BJ | No description available BK | No description available BL | No description available BN | No description available BO | No description available BP | No description available BQ | No description available BR | No description available BS | No description available BT | No description available BU | No description available BV | No description available BW | No description available BX | No description available BY | No description available BZ | No description available Ba | No description available Bb | No description available Bc | No description available Bd | No description available Be | No description available Bf | No description available Bg | No description available Bh | No description available Bi | No description available Bj | No description available Bk | No description available Bl | No description available Bm | No description available Bn | No description available Bo DA DE DR Dh Dw Dz | No description available Bp | No description available Bq | No description available Br | No description available Bs | No description available Bt | No description available Bu | No description available Bv | No description available Bw | No description available Bx | No description available By | No description available Bz | No description available C | No description available C0 C1 C2 Cr Ct Cv Cx DF DU DW Dl Dr Ds Dx s | No description available C3 | No description available C4 D3 | No description available C6 D0 D5 | No description available C8 | No description available C9 DX | No description available CA | No description available CB | No description available CC | No description available CD | No description available CE | No description available CF | No description available CG | No description available CH | No description available CI | No description available CJ | No description available CK | No description available CL | No description available CM | No description available CN | No description available CO | No description available CP | No description available CQ | No description available CR | No description available CS | No description available CT | No description available CU | No description available CV | No description available CW | No description available CX | No description available CY | No description available Ca Cc D7 DV l | No description available Cb | No description available Cd Di Dt | No description available Ce Df | No description available Cf DJ Du | No description available Cg | No description available Cm | No description available Cs Dc | No description available Cu | No description available Cz DI | No description available D | No description available D1 DH | No description available D2 DB | No description available D6 | No description available DC Z | No description available DG | No description available DM | No description available DN | No description available Db | No description available De | No description available Dg | No description available Dj | No description available Dn | No description available Dp | No description available Dv | No description available Dy | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available V | No description available W p | No description available X | No description available Y | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available j | No description available k | No description available m | No description available n | No description available o | No description available q | No description available v | No description available w | No description available z | No description available > hide sel & #!39 atoms > show sel & #!39 cartoons > hide sel & #!39 surfaces > hide sel & #!39 atoms > hide sel & #!39 cartoons > show sel & #!39 cartoons > select add #33 6965 atoms, 7140 bonds, 287 pseudobonds, 922 residues, 14 models selected > select subtract #33 3775 atoms, 3870 bonds, 274 pseudobonds, 500 residues, 11 models selected > select clear > hide #50#!39,49 atoms > show #50#!39,49 cartoons Computing secondary structure > hide #!39 models > hide #50 models > show #50 models > hide #!49 models > show #50 atoms > style #50 stick Changed 9637 atom styles > hide #50 cartoons > hbonds #50 reveal true The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: 8pi2 #35/A ARG 101 NE 12126 hydrogen bonds found > select #29 2 models selected > select #29 2 models selected > select clear > select #50/H: 23 10 atoms, 10 bonds, 1 residue, 1 model selected > color sel byhetero > select #50/CR: 3 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel byhetero > distance #50/H:23@O 50£/CR:3@ND2 Expected a keyword > distance #50/H:23@O #50/CR:3@ND2 Distance between J1122_fit2_raw.cif #50/H HIS 23 O and /CR ASN 3 ND2: 2.742Å > show #!39 models > hide #50 models > show #!39 atoms > hide #!39 cartoons > show #50 models > hide #50 models > show #50 models > ui tool show ""Show Sequence Viewer"" > sequence chain #4/L #6/L #17/L #24/L #33/L #39/L Alignment identifier is 2 > hide #50 models > show #50 models > hide #50 models > select > #4/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211 > #6/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211 > #17/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211 > #24/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211 > #33/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211 > #39/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211 4968 atoms, 4998 bonds, 636 residues, 6 models selected > select clear > select #4/L:32-33 #6/L:32-33 #17/L:32-33 #24/L:32-33 #33/L:32-33 #39/L:32-33 96 atoms, 90 bonds, 12 residues, 6 models selected > select #4/L:32-33 #6/L:32-33 #17/L:32-33 #24/L:32-33 #33/L:32-33 #39/L:32-33 96 atoms, 90 bonds, 12 residues, 6 models selected Fab 3C11 Light Chain [ID: 2] region 6 chains [32-33] RMSD: 11.231 > show #50 models > select clear > select #4/L #6/L #17/L #24/L #33/L #39/L 9480 atoms, 9714 bonds, 6 pseudobonds, 1248 residues, 12 models selected Fab 3C11 Light Chain [ID: 2] region 6 chains [1-215] RMSD: 54.353 > save /Users/amy/Desktop/lightchain format fasta alignment 2 > select clear > hide #!39 models > hide #50 models > show #!49 models > hide #!49 cartoons > show #!49 atoms > hide #!49 cartoons > style #!49 stick Changed 1939 atom styles > hbonds #!49 reveal true The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: 8pi2 #35/A ARG 101 NE 3318 hydrogen bonds found > sequence chain > #1/A#5/A#16/A#19/A#23/A#26/A#31/A#32/A#37/A#42/C#43/C#44/C#39/A Alignment identifier is 3 > sequence chain > #1/B#5/B#16/B#19/B#23/B#26/B#31/B#32/B#37/B#42/B#43/B#44/B#39/C Alignment identifier is 4 > sequence chain #4/H#6/H#17/H#24/H#33/H#39/H Alignment identifier is 5 > sequence chain #4/L#6/L#17/L#24/L#33/L#39/L Alignment identifier is 6 > sequence chain #7/A#18/A#20/A#25/A#42/A#43/A#44/A Alignment identifier is 7 > sequence chain #19/C#26/C#32/C#30/B#37/C#57/C Alignment identifier is 8 > sequence chain #27/B#36/B#39/B Alignment identifier is 9 > sequence chain #35/A Alignment identifier is 35/A > sequence chain #36/A Alignment identifier is 36/A > sequence chain #38/A Alignment identifier is 38/A > sequence chain #38/B Alignment identifier is 38/B > sequence chain #38/H Alignment identifier is 38/H > sequence chain #38/L Alignment identifier is 38/L > sequence chain #40/Ba Alignment identifier is 40/Ba > sequence chain #40/Ca Alignment identifier is 40/Ca > sequence chain #40/Aa Alignment identifier is 40/Aa > sequence chain #40/Bb Alignment identifier is 40/Bb > sequence chain #40/Ab Alignment identifier is 40/Ab > sequence chain #40/Cb Alignment identifier is 40/Cb > sequence chain #40/Cc Alignment identifier is 40/Cc > sequence chain #40/Cd Alignment identifier is 40/Cd > sequence chain #46/A Alignment identifier is 46/A > sequence chain #46/B Alignment identifier is 46/B > sequence chain #46/C Alignment identifier is 46/C > sequence chain #46/D Alignment identifier is 46/D > sequence chain #46/E Alignment identifier is 46/E > sequence chain #46/F Alignment identifier is 46/F > sequence chain #46/G Alignment identifier is 46/G > sequence chain #46/H Alignment identifier is 46/H > sequence chain #46/I Alignment identifier is 46/I > sequence chain #46/J Alignment identifier is 46/J > sequence chain #46/K Alignment identifier is 46/K > sequence chain #46/L Alignment identifier is 46/L > sequence chain #46/M Alignment identifier is 46/M > sequence chain #46/N Alignment identifier is 46/N > sequence chain #46/O Alignment identifier is 46/O > sequence chain #46/P Alignment identifier is 46/P > sequence chain #46/Q Alignment identifier is 46/Q > sequence chain #46/R#50/j Alignment identifier is 10 > sequence chain #46/S,p,Bw,B3,C1,DW,Dj,Dy#50/Bo,DA,DE,DR,Dh,Dw,Dz Alignment identifier is 11 > sequence chain #46/T#50/Ag Alignment identifier is 12 > sequence chain #46/U Alignment identifier is 46/U > sequence chain #46/V,X,3 Alignment identifier is 13 > sequence chain #46/W,Dz,D2#50/Ay Alignment identifier is 14 > sequence chain #46/Y Alignment identifier is 46/Y > sequence chain #46/Z Alignment identifier is 46/Z > sequence chain #46/a Alignment identifier is 46/a > sequence chain #46/b,l,Av#50/a Alignment identifier is 15 > sequence chain #46/c Alignment identifier is 46/c > sequence chain #46/d Alignment identifier is 46/d > sequence chain #46/e,Bq#50/u,AC Alignment identifier is 16 > sequence chain #46/f Alignment identifier is 46/f > sequence chain #46/g,r,Az Alignment identifier is 17 > sequence chain > #46/h,o,Ay,BQ,Bl,Bm,CW,Ce,Cg,Cp,Cs,Cu,C8,DC,DH,DL,DN,Dg,Dh,Dk,Dq,Dt,D3,D5#50/U,y,0,5,BM,CZ,Co,Cp,Cy,DK,DL,DT,DY,DZ,Dd,Dk,Do,Dq,D4,EA Alignment identifier is 18 > sequence chain #46/i,y Alignment identifier is 19 > sequence chain > #46/j,CZ,Cz,DF,Da,De,Df,D6#50/7,BF,Cj,Cl,Cn,Cq,C5,DP,DQ,Da,Dm,D9 Alignment identifier is 20 > sequence chain #46/k,Ca Alignment identifier is 21 > sequence chain #46/m Alignment identifier is 46/m > sequence chain #46/n Alignment identifier is 46/n > sequence chain > #46/q,AH,An,Cl,C0,C2,C9,DE,DS,Dv,Dw#50/s,Cr,Ct,Cv,Cx,C0,C1,C2,DF,DU,DW,Dl,Dr,Ds,Dx Alignment identifier is 22 > sequence chain #46/s Alignment identifier is 46/s > sequence chain #46/t Alignment identifier is 46/t > sequence chain #46/u Alignment identifier is 46/u > sequence chain #46/v Alignment identifier is 46/v > sequence chain #46/w Alignment identifier is 46/w > sequence chain #46/x Alignment identifier is 46/x > sequence chain #46/z,AF#50/6 Alignment identifier is 23 > sequence chain #46/0 Alignment identifier is 46/0 > sequence chain #46/1 Alignment identifier is 46/1 > sequence chain #46/2 Alignment identifier is 46/2 > sequence chain #46/4 Alignment identifier is 46/4 > sequence chain #46/5 Alignment identifier is 46/5 > sequence chain #46/6 Alignment identifier is 46/6 > sequence chain #46/7 Alignment identifier is 46/7 > sequence chain #46/8 Alignment identifier is 46/8 > sequence chain #46/9 Alignment identifier is 46/9 > sequence chain #46/AA Alignment identifier is 46/AA > sequence chain #46/AB Alignment identifier is 46/AB > sequence chain #46/AC Alignment identifier is 46/AC > sequence chain #46/AD Alignment identifier is 46/AD > sequence chain #46/AE#50/AZ Alignment identifier is 24 > sequence chain #46/AG Alignment identifier is 46/AG > sequence chain #46/AI,CY#50/Cf,DJ,Du Alignment identifier is 25 > sequence chain #46/AJ Alignment identifier is 46/AJ > sequence chain #46/AK Alignment identifier is 46/AK > sequence chain #46/AL Alignment identifier is 46/AL > sequence chain #46/AM Alignment identifier is 46/AM > sequence chain #46/AN Alignment identifier is 46/AN > sequence chain #46/AO Alignment identifier is 46/AO > sequence chain #46/AP Alignment identifier is 46/AP > sequence chain #46/AQ Alignment identifier is 46/AQ > sequence chain #46/AR Alignment identifier is 46/AR > sequence chain #46/AS Alignment identifier is 46/AS > sequence chain #46/AT Alignment identifier is 46/AT > sequence chain #46/AU Alignment identifier is 46/AU > sequence chain #46/AV Alignment identifier is 46/AV > sequence chain #46/AW Alignment identifier is 46/AW > sequence chain #46/AX Alignment identifier is 46/AX > sequence chain #46/AY Alignment identifier is 46/AY > sequence chain #46/AZ Alignment identifier is 46/AZ > sequence chain #46/Aa Alignment identifier is 46/Aa > sequence chain #46/Ab Alignment identifier is 46/Ab > sequence chain #46/Ac Alignment identifier is 46/Ac > sequence chain #46/Ad Alignment identifier is 46/Ad > sequence chain #46/Ae Alignment identifier is 46/Ae > sequence chain #46/Af Alignment identifier is 46/Af > sequence chain #46/Ag Alignment identifier is 46/Ag > sequence chain #46/Ah Alignment identifier is 46/Ah > sequence chain #46/Ai Alignment identifier is 46/Ai > sequence chain #46/Aj Alignment identifier is 46/Aj > sequence chain #46/Ak Alignment identifier is 46/Ak > sequence chain #46/Al,Cr,Cx,DP#50/Cm Alignment identifier is 26 > sequence chain #46/Am#50/C4,D3 Alignment identifier is 27 > sequence chain #46/Ao Alignment identifier is 46/Ao > sequence chain #46/Ap Alignment identifier is 46/Ap > sequence chain #46/Aq Alignment identifier is 46/Aq > sequence chain #46/Ar Alignment identifier is 46/Ar > sequence chain #46/As Alignment identifier is 46/As > sequence chain #46/At Alignment identifier is 46/At > sequence chain #46/Au Alignment identifier is 46/Au > sequence chain #46/Aw Alignment identifier is 46/Aw > sequence chain #46/Ax Alignment identifier is 46/Ax > sequence chain #46/A0 Alignment identifier is 46/A0 > sequence chain #46/A1 Alignment identifier is 46/A1 > sequence chain #46/A2#50/AR,Al,A3 Alignment identifier is 28 > sequence chain #46/A3 Alignment identifier is 46/A3 > sequence chain #46/A4#50/A1 Alignment identifier is 29 > sequence chain #46/A5 Alignment identifier is 46/A5 > sequence chain #46/A6#50/v Alignment identifier is 30 > sequence chain #46/A7 Alignment identifier is 46/A7 > sequence chain #46/A8 Alignment identifier is 46/A8 > sequence chain #46/A9 Alignment identifier is 46/A9 > sequence chain #46/BA Alignment identifier is 46/BA > sequence chain #46/BB Alignment identifier is 46/BB > sequence chain #46/BC Alignment identifier is 46/BC > sequence chain #46/BD Alignment identifier is 46/BD > sequence chain #46/BE Alignment identifier is 46/BE > sequence chain #46/BF Alignment identifier is 46/BF > sequence chain #46/BG Alignment identifier is 46/BG > sequence chain #46/BH Alignment identifier is 46/BH > sequence chain #46/BI Alignment identifier is 46/BI > sequence chain #46/BJ Alignment identifier is 46/BJ > sequence chain #46/BK Alignment identifier is 46/BK > sequence chain #46/BL Alignment identifier is 46/BL > sequence chain #46/BM Alignment identifier is 46/BM > sequence chain #46/BN Alignment identifier is 46/BN > sequence chain #46/BO Alignment identifier is 46/BO > sequence chain #46/BP Alignment identifier is 46/BP > sequence chain #46/BR Alignment identifier is 46/BR > sequence chain #46/BS Alignment identifier is 46/BS > sequence chain #46/BT,Dp,D4#50/DH,D1 Alignment identifier is 31 > sequence chain #46/BU Alignment identifier is 46/BU > sequence chain #46/BV Alignment identifier is 46/BV > sequence chain #46/BW Alignment identifier is 46/BW > sequence chain #46/BX Alignment identifier is 46/BX > sequence chain #46/BY Alignment identifier is 46/BY > sequence chain #46/BZ Alignment identifier is 46/BZ > sequence chain #46/Ba Alignment identifier is 46/Ba > sequence chain #46/Bb Alignment identifier is 46/Bb > sequence chain #46/Bc Alignment identifier is 46/Bc > sequence chain #46/Bd Alignment identifier is 46/Bd > sequence chain #46/Be Alignment identifier is 46/Be > sequence chain #46/Bf Alignment identifier is 46/Bf > sequence chain #46/Bg Alignment identifier is 46/Bg > sequence chain #46/Bh Alignment identifier is 46/Bh > sequence chain #46/Bi Alignment identifier is 46/Bi > sequence chain #46/Bj Alignment identifier is 46/Bj > sequence chain #46/Bk Alignment identifier is 46/Bk > sequence chain #46/Bn Alignment identifier is 46/Bn > sequence chain #46/Bo Alignment identifier is 46/Bo > sequence chain #46/Bp Alignment identifier is 46/Bp > sequence chain #46/Br Alignment identifier is 46/Br > sequence chain #46/Bs Alignment identifier is 46/Bs > sequence chain #46/Bt Alignment identifier is 46/Bt > sequence chain #46/Bu Alignment identifier is 46/Bu > sequence chain #46/Bv Alignment identifier is 46/Bv > sequence chain #46/Bx Alignment identifier is 46/Bx > sequence chain #46/By Alignment identifier is 46/By > sequence chain #46/Bz Alignment identifier is 46/Bz > sequence chain #46/B0,Ck#50/C3 Alignment identifier is 32 > sequence chain #46/B1 Alignment identifier is 46/B1 > sequence chain #46/B2 Alignment identifier is 46/B2 > sequence chain #46/B4 Alignment identifier is 46/B4 > sequence chain #46/B5 Alignment identifier is 46/B5 > sequence chain #46/B6 Alignment identifier is 46/B6 > sequence chain #46/B7 Alignment identifier is 46/B7 > sequence chain #46/B8 Alignment identifier is 46/B8 > sequence chain #46/B9 Alignment identifier is 46/B9 > sequence chain #46/CA Alignment identifier is 46/CA > sequence chain #46/CB Alignment identifier is 46/CB > sequence chain #46/CC Alignment identifier is 46/CC > sequence chain #46/CD Alignment identifier is 46/CD > sequence chain #46/CE Alignment identifier is 46/CE > sequence chain #46/CF Alignment identifier is 46/CF > sequence chain #46/CG Alignment identifier is 46/CG > sequence chain #46/CH Alignment identifier is 46/CH > sequence chain #46/CI Alignment identifier is 46/CI > sequence chain #46/CJ Alignment identifier is 46/CJ > sequence chain #46/CK Alignment identifier is 46/CK > sequence chain #46/CL Alignment identifier is 46/CL > sequence chain #46/CM Alignment identifier is 46/CM > sequence chain #46/CN Alignment identifier is 46/CN > sequence chain #46/CO Alignment identifier is 46/CO > sequence chain #46/CP Alignment identifier is 46/CP > sequence chain #46/CQ Alignment identifier is 46/CQ > sequence chain #46/CR Alignment identifier is 46/CR > sequence chain #46/CS Alignment identifier is 46/CS > sequence chain #46/CT Alignment identifier is 46/CT > sequence chain #46/CU Alignment identifier is 46/CU > sequence chain #46/CV#50/DM Alignment identifier is 33 > sequence chain #46/CX Alignment identifier is 46/CX > sequence chain #46/Cb,DA,Ds#50/Cs,Dc Alignment identifier is 34 > sequence chain #46/Cc Alignment identifier is 46/Cc > sequence chain #46/Cd Alignment identifier is 46/Cd > sequence chain #46/Cf,Dm Alignment identifier is 35 > sequence chain #46/Ch Alignment identifier is 46/Ch > sequence chain #46/Ci,DQ#50/Ce,Df Alignment identifier is 36 > sequence chain #46/Cj#50/Db Alignment identifier is 37 > sequence chain #46/Cm#50/l,Ca,Cc,DV,D7 Alignment identifier is 38 > sequence chain #46/Cn#50/Ax,Ci Alignment identifier is 39 > sequence chain #46/Co,DB,Dd Alignment identifier is 40 > sequence chain #46/Cq,Dr#50/t,3 Alignment identifier is 41 > sequence chain #46/Ct,DM#50/Dv Alignment identifier is 42 > sequence chain #46/Cv,C6,D0#50/Cu Alignment identifier is 43 > sequence chain #46/Cw Alignment identifier is 46/Cw > sequence chain #46/Cy Alignment identifier is 46/Cy > sequence chain #46/C3 Alignment identifier is 46/C3 > sequence chain #46/C4 Alignment identifier is 46/C4 > sequence chain #46/C5#50/AB,C7 Alignment identifier is 44 > sequence chain #46/C7 Alignment identifier is 46/C7 > sequence chain #46/DD Alignment identifier is 46/DD > sequence chain #46/DG#50/Aj,Ch,Cw Alignment identifier is 45 > sequence chain #46/DI Alignment identifier is 46/DI > sequence chain #46/DJ Alignment identifier is 46/DJ > sequence chain #46/DK Alignment identifier is 46/DK > sequence chain #46/DO#50/Cd,Di,Dt Alignment identifier is 46 > sequence chain #46/DR Alignment identifier is 46/DR > sequence chain #46/DT#50/Ap Alignment identifier is 47 > sequence chain #46/DU Alignment identifier is 46/DU > sequence chain #46/DV#50/W,p Alignment identifier is 48 > sequence chain #46/DX,Db#50/DN Alignment identifier is 49 > sequence chain #46/DY#50/9,D8 Alignment identifier is 50 > sequence chain #46/DZ#50/C9,DX Alignment identifier is 51 > sequence chain #46/Dc#50/n Alignment identifier is 52 > sequence chain #46/Di,Dl,Do#50/AI Alignment identifier is 53 > sequence chain #46/Dn Alignment identifier is 46/Dn > sequence chain #46/Du Alignment identifier is 46/Du > sequence chain #46/Dx Alignment identifier is 46/Dx > sequence chain #46/D1 Alignment identifier is 46/D1 > sequence chain #46/D7 Alignment identifier is 46/D7 > sequence chain #49/Aa Alignment identifier is 49/Aa > sequence chain #49/Ab Alignment identifier is 49/Ab > sequence chain #49/Ca Alignment identifier is 49/Ca > sequence chain #49/Ba Alignment identifier is 49/Ba > sequence chain #49/Bb Alignment identifier is 49/Bb > sequence chain #49/Ac Alignment identifier is 49/Ac > sequence chain #49/Cb Alignment identifier is 49/Cb > sequence chain #49/Cc Alignment identifier is 49/Cc > sequence chain #49/Bc Alignment identifier is 49/Bc > sequence chain #49/Ad Alignment identifier is 49/Ad > sequence chain #49/Ae Alignment identifier is 49/Ae > sequence chain #50/A Alignment identifier is 50/A > sequence chain #50/B Alignment identifier is 50/B > sequence chain #50/C Alignment identifier is 50/C > sequence chain #50/D Alignment identifier is 50/D > sequence chain #50/E Alignment identifier is 50/E > sequence chain #50/F Alignment identifier is 50/F > sequence chain #50/G Alignment identifier is 50/G > sequence chain #50/H Alignment identifier is 50/H > sequence chain #50/I Alignment identifier is 50/I > sequence chain #50/J Alignment identifier is 50/J > sequence chain #50/K Alignment identifier is 50/K > sequence chain #50/L Alignment identifier is 50/L > sequence chain #50/M Alignment identifier is 50/M > sequence chain #50/N Alignment identifier is 50/N > sequence chain #50/O Alignment identifier is 50/O > sequence chain #50/P Alignment identifier is 50/P > sequence chain #50/Q Alignment identifier is 50/Q > sequence chain #50/R Alignment identifier is 50/R > sequence chain #50/S Alignment identifier is 50/S > sequence chain #50/T Alignment identifier is 50/T > sequence chain #50/V Alignment identifier is 50/V > sequence chain #50/X Alignment identifier is 50/X > sequence chain #50/Y Alignment identifier is 50/Y > sequence chain #50/Z,DC Alignment identifier is 54 > sequence chain #50/b Alignment identifier is 50/b > sequence chain #50/c Alignment identifier is 50/c > sequence chain #50/d Alignment identifier is 50/d > sequence chain #50/e Alignment identifier is 50/e > sequence chain #50/f Alignment identifier is 50/f > sequence chain #50/g Alignment identifier is 50/g > sequence chain #50/h Alignment identifier is 50/h > sequence chain #50/i Alignment identifier is 50/i > sequence chain #50/k Alignment identifier is 50/k > sequence chain #50/m Alignment identifier is 50/m > sequence chain #50/o Alignment identifier is 50/o > sequence chain #50/q Alignment identifier is 50/q > sequence chain #50/r,A8 Alignment identifier is 55 > sequence chain #50/w Alignment identifier is 50/w > sequence chain #50/x,4 Alignment identifier is 56 > sequence chain #50/z Alignment identifier is 50/z > sequence chain #50/1 Alignment identifier is 50/1 > sequence chain #50/2,A7 Alignment identifier is 57 > sequence chain #50/8 Alignment identifier is 50/8 > sequence chain #50/AA Alignment identifier is 50/AA > sequence chain #50/AD Alignment identifier is 50/AD > sequence chain #50/AE,An,BA Alignment identifier is 58 > sequence chain #50/AF Alignment identifier is 50/AF > sequence chain #50/AG Alignment identifier is 50/AG > sequence chain #50/AH Alignment identifier is 50/AH > sequence chain #50/AJ Alignment identifier is 50/AJ > sequence chain #50/AK,DO Alignment identifier is 59 > sequence chain #50/AL Alignment identifier is 50/AL > sequence chain #50/AM Alignment identifier is 50/AM > sequence chain #50/AN Alignment identifier is 50/AN > sequence chain #50/AO Alignment identifier is 50/AO > sequence chain #50/AP,DD Alignment identifier is 60 > sequence chain #50/AQ Alignment identifier is 50/AQ > sequence chain #50/AS Alignment identifier is 50/AS > sequence chain #50/AT Alignment identifier is 50/AT > sequence chain #50/AU Alignment identifier is 50/AU > sequence chain #50/AV Alignment identifier is 50/AV > sequence chain #50/AW Alignment identifier is 50/AW > sequence chain #50/AX Alignment identifier is 50/AX > sequence chain #50/AY Alignment identifier is 50/AY > sequence chain #50/Aa Alignment identifier is 50/Aa > sequence chain #50/Ab Alignment identifier is 50/Ab > sequence chain #50/Ac Alignment identifier is 50/Ac > sequence chain #50/Ad Alignment identifier is 50/Ad > sequence chain #50/Ae Alignment identifier is 50/Ae > sequence chain #50/Af Alignment identifier is 50/Af > sequence chain #50/Ah Alignment identifier is 50/Ah > sequence chain #50/Ai Alignment identifier is 50/Ai > sequence chain #50/Ak Alignment identifier is 50/Ak > sequence chain #50/Am Alignment identifier is 50/Am > sequence chain #50/Ao Alignment identifier is 50/Ao > sequence chain #50/Aq Alignment identifier is 50/Aq > sequence chain #50/Ar Alignment identifier is 50/Ar > sequence chain #50/As Alignment identifier is 50/As > sequence chain #50/At Alignment identifier is 50/At > sequence chain #50/Au,DS Alignment identifier is 61 > sequence chain #50/Av Alignment identifier is 50/Av > sequence chain #50/Aw,Ck Alignment identifier is 62 > sequence chain #50/Az Alignment identifier is 50/Az > sequence chain #50/A0 Alignment identifier is 50/A0 > sequence chain #50/A2 Alignment identifier is 50/A2 > sequence chain #50/A4 Alignment identifier is 50/A4 > sequence chain #50/A5 Alignment identifier is 50/A5 > sequence chain #50/A6 Alignment identifier is 50/A6 > sequence chain #50/A9 Alignment identifier is 50/A9 > sequence chain #50/BB Alignment identifier is 50/BB > sequence chain #50/BC Alignment identifier is 50/BC > sequence chain #50/BD Alignment identifier is 50/BD > sequence chain #50/BE Alignment identifier is 50/BE > sequence chain #50/BG Alignment identifier is 50/BG > sequence chain #50/BH Alignment identifier is 50/BH > sequence chain #50/BI Alignment identifier is 50/BI > sequence chain #50/BJ Alignment identifier is 50/BJ > sequence chain #50/BK Alignment identifier is 50/BK > sequence chain #50/BL Alignment identifier is 50/BL > sequence chain #50/BN Alignment identifier is 50/BN > sequence chain #50/BO Alignment identifier is 50/BO > sequence chain #50/BP Alignment identifier is 50/BP > sequence chain #50/BQ Alignment identifier is 50/BQ > sequence chain #50/BR Alignment identifier is 50/BR > sequence chain #50/BS Alignment identifier is 50/BS > sequence chain #50/BT Alignment identifier is 50/BT > sequence chain #50/BU Alignment identifier is 50/BU > sequence chain #50/BV Alignment identifier is 50/BV > sequence chain #50/BW Alignment identifier is 50/BW > sequence chain #50/BX Alignment identifier is 50/BX > sequence chain #50/BY Alignment identifier is 50/BY > sequence chain #50/BZ Alignment identifier is 50/BZ > sequence chain #50/Ba Alignment identifier is 50/Ba > sequence chain #50/Bb Alignment identifier is 50/Bb > sequence chain #50/Bc Alignment identifier is 50/Bc > sequence chain #50/Bd Alignment identifier is 50/Bd > sequence chain #50/Be Alignment identifier is 50/Be > sequence chain #50/Bf Alignment identifier is 50/Bf > sequence chain #50/Bg Alignment identifier is 50/Bg > sequence chain #50/Bh Alignment identifier is 50/Bh > sequence chain #50/Bi Alignment identifier is 50/Bi > sequence chain #50/Bj Alignment identifier is 50/Bj > sequence chain #50/Bk Alignment identifier is 50/Bk > sequence chain #50/Bl Alignment identifier is 50/Bl > sequence chain #50/Bm Alignment identifier is 50/Bm > sequence chain #50/Bn Alignment identifier is 50/Bn > sequence chain #50/Bp Alignment identifier is 50/Bp > sequence chain #50/Bq Alignment identifier is 50/Bq > sequence chain #50/Br Alignment identifier is 50/Br > sequence chain #50/Bs Alignment identifier is 50/Bs > sequence chain #50/Bt Alignment identifier is 50/Bt > sequence chain #50/Bu Alignment identifier is 50/Bu > sequence chain #50/Bv Alignment identifier is 50/Bv > sequence chain #50/Bw Alignment identifier is 50/Bw > sequence chain #50/Bx Alignment identifier is 50/Bx > sequence chain #50/By Alignment identifier is 50/By > sequence chain #50/Bz Alignment identifier is 50/Bz > sequence chain #50/B0 Alignment identifier is 50/B0 > sequence chain #50/B1 Alignment identifier is 50/B1 > sequence chain #50/B2 Alignment identifier is 50/B2 > sequence chain #50/B3 Alignment identifier is 50/B3 > sequence chain #50/B4 Alignment identifier is 50/B4 > sequence chain #50/B5 Alignment identifier is 50/B5 > sequence chain #50/B6 Alignment identifier is 50/B6 > sequence chain #50/B7 Alignment identifier is 50/B7 > sequence chain #50/B8 Alignment identifier is 50/B8 > sequence chain #50/B9 Alignment identifier is 50/B9 > sequence chain #50/CA Alignment identifier is 50/CA > sequence chain #50/CB Alignment identifier is 50/CB > sequence chain #50/CC Alignment identifier is 50/CC > sequence chain #50/CD Alignment identifier is 50/CD > sequence chain #50/CE Alignment identifier is 50/CE > sequence chain #50/CF Alignment identifier is 50/CF > sequence chain #50/CG Alignment identifier is 50/CG > sequence chain #50/CH Alignment identifier is 50/CH > sequence chain #50/CI Alignment identifier is 50/CI > sequence chain #50/CJ Alignment identifier is 50/CJ > sequence chain #50/CK Alignment identifier is 50/CK > sequence chain #50/CL Alignment identifier is 50/CL > sequence chain #50/CM Alignment identifier is 50/CM > sequence chain #50/CN Alignment identifier is 50/CN > sequence chain #50/CO Alignment identifier is 50/CO > sequence chain #50/CP Alignment identifier is 50/CP > sequence chain #50/CQ Alignment identifier is 50/CQ > sequence chain #50/CR Alignment identifier is 50/CR > sequence chain #50/CS Alignment identifier is 50/CS > sequence chain #50/CT Alignment identifier is 50/CT > sequence chain #50/CU Alignment identifier is 50/CU > sequence chain #50/CV Alignment identifier is 50/CV > sequence chain #50/CW Alignment identifier is 50/CW > sequence chain #50/CX Alignment identifier is 50/CX > sequence chain #50/CY Alignment identifier is 50/CY > sequence chain #50/Cb Alignment identifier is 50/Cb > sequence chain #50/Cg Alignment identifier is 50/Cg > sequence chain #50/Cz,DI Alignment identifier is 63 > sequence chain #50/C6,D0,D5 Alignment identifier is 64 > sequence chain #50/C8 Alignment identifier is 50/C8 > sequence chain #50/DB,D2 Alignment identifier is 65 > sequence chain #50/DG Alignment identifier is 50/DG > sequence chain #50/De Alignment identifier is 50/De > sequence chain #50/Dg Alignment identifier is 50/Dg > sequence chain #50/Dj Alignment identifier is 50/Dj > sequence chain #50/Dn Alignment identifier is 50/Dn > sequence chain #50/Dp Alignment identifier is 50/Dp > sequence chain #50/Dy Alignment identifier is 50/Dy > sequence chain #50/D6 Alignment identifier is 50/D6 ===== Log before crash end ===== OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M5 OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.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: Mac17,2 Model Number: MDE64B/A Chip: Apple M5 Total Number of Cores: 10 (4 Super and 6 Efficiency) Memory: 24 GB System Firmware Version: 13822.81.10 OS Loader Version: 13822.81.10 Software: System Software Overview: System Version: macOS 26.3.1 (a) (25D771280a) Kernel Version: Darwin 25.3.0 Time since boot: 8天23分钟 Graphics/Displays: Apple M5: Chipset Model: Apple M5 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 4 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 DELL P2314H: 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: 4.12.1 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-ArtiaX: 0.6.0 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-Clipper: 0.26.1 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: 1.11.1 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-ISOLDE: 1.11.1 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: 2.7.12 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: 7.13.1 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 geomdl: 5.4.0 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: 4.26.0 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 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: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 pandas: 3.0.1 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 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 pyarrow: 23.0.1 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 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 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 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: 4.1.0 roman-numerals-py: 4.1.0 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: 2.8.3 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: 3.2.0 stack-data: 0.6.3 starfile: 0.5.13 starlette: 0.52.1 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 urllib3: 2.6.3 uvicorn: 0.40.0 wcwidth: 0.3.2 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0 }}} " defect closed normal Sequence can't reproduce all ChimeraX