id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17846 Crash on Mac waking from sleep guillermo.montoya@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.1.1-arm64-arm-64bit ChimeraX Version: 1.10.dev202412070146 (2024-12-07 01:46:57 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. Fatal Python error: Segmentation fault Current thread 0x00000001fbcfb840 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 335 in event_loop File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, 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Address size fault""},""pc"":{""value"":6823777740},""far"":{""value"":0}},""frames"":[{""imageOffset"":17868,""symbol"":""__psynch_cvwait"",""symbolLocation"":8,""imageIndex"":250},{""imageOffset"":30868,""symbol"":""_pthread_cond_wait"",""symbolLocation"":1204,""imageIndex"":251},{""imageOffset"":2118012,""imageIndex"":45},{""imageOffset"":2117824,""symbol"":""QWaitCondition::wait(QMutex*, 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Address size fault""},""pc"":{""value"":6824009960},""far"":{""value"":0}}},{""id"":11752627,""frames"":[{""imageOffset"":8424,""symbol"":""start_wqthread"",""symbolLocation"":0,""imageIndex"":251}],""threadState"":{""x"":[{""value"":13195620352},{""value"":158831},{""value"":13195083776},{""value"":0},{""value"":409604},{""value"":18446744073709551615},{""value"":0},{""value"":0},{""value"":0},{""value"":0},{""value"":0},{""value"":0},{""value"":0},{""value"":0},{""value"":0},{""value"":0},{""value"":0},{""value"":0},{""value"":0},{""value"":0},{""value"":0},{""value"":0},{""value"":0},{""value"":0},{""value"":0},{""value"":0},{""value"":0},{""value"":0},{""value"":0}],""flavor"":""ARM_THREAD_STATE64"",""lr"":{""value"":0},""cpsr"":{""value"":4096},""fp"":{""value"":0},""sp"":{""value"":13195620352},""esr"":{""value"":1442840704,""description"":"" Address size 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: 6819512320, ""size"" : 4753735680, ""uuid"" : ""f66bac4e-1e78-38af-b867-c1cf5daa0302"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=18.3G written=9509K(0%) resident=9509K(0%) swapped_out=0K(0%) unallocated=18.3G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 1584K 75 \nColorSync 640K 34 \nCoreAnimation 3904K 235 \nCoreGraphics 80K 5 \nCoreServices 624K 2 \nCoreUI image data 5728K 53 \nFoundation 64K 2 \nImage IO 16K 1 \nKernel Alloc Once 32K 1 \nMALLOC 17.4G 299 \nMALLOC guard page 288K 18 \nMach message 96K 5 \nOpenGL GLSL 384K 4 \nSTACK GUARD 608K 38 \nStack 192.8M 39 \nStack Guard 56.0M 1 \nVM_ALLOCATE 387.5M 369 \nVM_ALLOCATE (reserved) 224.0M 3 reserved VM address space (unallocated)\n__AUTH 5030K 660 \n__AUTH_CONST 69.6M 907 \n__CTF 824 1 \n__DATA 34.8M 1151 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2016-2024 Regents of the University of California. All rights reserved. > open /Users/gmontoya/Downloads/cas8_movment.cxs Opened halfcleaved_HNH_center_sharp.mrc as #13, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened post_HNH_cent_sharp.mrc as #5, grid size 420,420,420, pixel 0.725, shown at level 0.00328, step 2, values float32 Opened apo_HNH_cent_sharp.mrc as #9, grid size 420,420,420, pixel 0.725, shown at level 0.00199, step 2, values float32 Opened apo_HNH_cent_sharp.mrc zone as #21, grid size 420,420,420, pixel 0.725, shown at level 0.00199, step 2, values float32 Opened apo_HNH_in_sharp.mrc as #23, grid size 420,420,420, pixel 0.725, shown at level 0.00173, step 2, values float32 Opened apo_HNH_in_sharp.mrc zone as #24, grid size 420,420,420, pixel 0.725, shown at level 0.00173, step 2, values float32 Opened apo_HNH_out_sharp.mrc as #26, grid size 420,420,420, pixel 0.725, shown at level 0.00214, step 2, values float32 Opened apo_HNH_out_sharp.mrc zone as #27, grid size 420,420,420, pixel 0.725, shown at level 0.00214, step 2, values float32 Opened post_HNH_in_sharp.mrc as #2, grid size 420,420,420, pixel 0.725, shown at level 0.0257, step 2, values float32 Opened post_HNH_out_sharp.mrc as #6, grid size 420,420,420, pixel 0.725, shown at level 0.00342, step 2, values float32 Opened halfcleaved_HNH_in_sharp.mrc as #12, grid size 420,420,420, pixel 0.725, shown at level 0.00277, step 2, values float32 Opened halfcleaved_HNH_out_sharp.mrc as #16, grid size 420,420,420, pixel 0.725, shown at level 0.0029, step 2, values float32 Opened post_HNH_in_sharp.mrc zone as #17, grid size 420,420,420, pixel 0.725, shown at level 0.0257, step 2, values float32 Opened post_HNH_out_sharp.mrc zone as #18, grid size 420,420,420, pixel 0.725, shown at level 0.00342, step 2, values float32 Opened post_HNH_cent_sharp.mrc zone as #19, grid size 420,420,420, pixel 0.725, shown at level 0.00328, step 2, values float32 Opened halfcleaved_HNH_center.mrc zone as #20, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_in_sharp.mrc zone as #28, grid size 420,420,420, pixel 0.725, shown at level 0.00277, step 2, values float32 Opened halfcleaved_HNH_out_sharp.mrc zone as #29, grid size 420,420,420, pixel 0.725, shown at level 0.0029, step 2, values float32 Log from Wed May 28 12:25:00 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type > I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_movement.cxs"" Opened halfcleaved_HNH_center_sharp3Å.mrc as #13, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened post_HNH_cent_sharp.mrc as #5, grid size 420,420,420, pixel 0.725, shown at level 0.00328, step 2, values float32 Opened apo_HNH_cent_sharp.mrc as #9, grid size 420,420,420, pixel 0.725, shown at level 0.00199, step 2, values float32 Opened apo_HNH_cent_sharp.mrc zone as #10, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 2, values float32 Opened apo_HNH_cent_sharp.mrc zone as #21, grid size 420,420,420, pixel 0.725, shown at level 0.00199, step 2, values float32 Opened apo_HNH_in_sharp.mrc as #23, grid size 420,420,420, pixel 0.725, shown at level 0.00173, step 2, values float32 Opened apo_HNH_in_sharp.mrc zone as #24, grid size 420,420,420, pixel 0.725, shown at level 0.00173, step 2, values float32 Opened apo_HNH_out_sharp.mrc as #26, grid size 420,420,420, pixel 0.725, shown at level 0.00214, step 2, values float32 Opened apo_HNH_out_sharp.mrc zone as #27, grid size 420,420,420, pixel 0.725, shown at level 0.00214, step 2, values float32 Opened post_HNH_in_sharp.mrc as #2, grid size 420,420,420, pixel 0.725, shown at level 0.0257, step 2, values float32 Opened post_HNH_out_sharp.mrc as #6, grid size 420,420,420, pixel 0.725, shown at level 0.00342, step 2, values float32 Opened halfcleaved_HNH_in_sharp.mrc as #12, grid size 420,420,420, pixel 0.725, shown at level 0.00277, step 2, values float32 Opened halfcleaved_HNH_out_sharp.mrc as #16, grid size 420,420,420, pixel 0.725, shown at level 0.0029, step 2, values float32 Opened post_HNH_in_sharp.mrc zone as #17, grid size 420,420,420, pixel 0.725, shown at level 0.0257, step 2, values float32 Opened post_HNH_out_sharp.mrc zone as #18, grid size 420,420,420, pixel 0.725, shown at level 0.00342, step 2, values float32 Opened post_HNH_cent_sharp.mrc zone as #19, grid size 420,420,420, pixel 0.725, shown at level 0.00328, step 2, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #20, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_in_sharp.mrc zone as #28, grid size 420,420,420, pixel 0.725, shown at level 0.00277, step 2, values float32 Opened halfcleaved_HNH_out_sharp.mrc zone as #29, grid size 420,420,420, pixel 0.725, shown at level 0.0029, step 2, values float32 Log from Sat May 17 13:40:51 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type > I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_session.cxs"" Opened halfcleaved_HNH_center_sharp3Å.mrc as #13, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #40, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #39, grid size 420,420,420, pixel 0.725, shown at level 0.04, step 1, values float32 Log from Wed May 14 12:43:12 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type I-F_HNH/Manuscript/chimerax_session.cxs"" Opened halfcleaved_HNH_center_sharp3Å.mrc as #13, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 0 as #22.1, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 1 as #22.2, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 2 as #22.3, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 3 as #22.4, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 4 as #22.5, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 5 as #22.6, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 6 as #22.7, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 7 as #22.8, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 8 as #22.9, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 9 as #22.10, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_in_sharp.mrc as #9, grid size 420,420,420, pixel 0.725, shown at level 0.002, step 1, values float32 Opened halfcleaved_HNH_out_sharp.mrc as #10, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened halfcleaved_HNH_in_sharp.mrc 0 as #7.1, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_in_sharp.mrc 1 as #7.2, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_in_sharp.mrc 2 as #7.3, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_in_sharp.mrc 3 as #7.4, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_in_sharp.mrc 4 as #7.5, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_in_sharp.mrc 5 as #7.6, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_in_sharp.mrc 6 as #7.7, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_in_sharp.mrc 7 as #7.8, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_in_sharp.mrc 8 as #7.9, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_out_sharp.mrc 0 as #8.1, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened halfcleaved_HNH_out_sharp.mrc 1 as #8.2, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened halfcleaved_HNH_out_sharp.mrc 2 as #8.3, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened halfcleaved_HNH_out_sharp.mrc 3 as #8.4, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened halfcleaved_HNH_out_sharp.mrc 4 as #8.5, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened halfcleaved_HNH_out_sharp.mrc 5 as #8.6, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened halfcleaved_HNH_out_sharp.mrc 6 as #8.7, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened halfcleaved_HNH_out_sharp.mrc 7 as #8.8, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened halfcleaved_HNH_out_sharp.mrc 8 as #8.9, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened apo_HNH_cent_sharp.mrc as #17, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened apo_HNH_in_sharp.mrc as #18, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened apo_HNH_out_sharp.mrc as #19, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened post_HNH_cent_sharp.mrc as #24, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened post_HNH_in_sharp.mrc as #25, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened post_HNH_out_sharp.mrc as #26, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened apo_HNH_cent_sharp.mrc 0 as #27.1, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened apo_HNH_cent_sharp.mrc 1 as #27.2, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened apo_HNH_cent_sharp.mrc 2 as #27.3, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened apo_HNH_cent_sharp.mrc 3 as #27.4, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened apo_HNH_cent_sharp.mrc 4 as #27.5, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened apo_HNH_cent_sharp.mrc 5 as #27.6, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened apo_HNH_in_sharp.mrc 0 as #28.1, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened apo_HNH_in_sharp.mrc 1 as #28.2, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened apo_HNH_in_sharp.mrc 2 as #28.3, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened apo_HNH_in_sharp.mrc 3 as #28.4, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened apo_HNH_in_sharp.mrc 4 as #28.5, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened apo_HNH_in_sharp.mrc 5 as #28.6, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened apo_HNH_out_sharp.mrc 0 as #29.1, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened apo_HNH_out_sharp.mrc 1 as #29.2, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened apo_HNH_out_sharp.mrc 2 as #29.3, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened apo_HNH_out_sharp.mrc 3 as #29.4, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened apo_HNH_out_sharp.mrc 4 as #29.5, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened apo_HNH_out_sharp.mrc 5 as #29.6, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened post_HNH_cent_sharp.mrc 0 as #30.1, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened post_HNH_cent_sharp.mrc 1 as #30.2, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened post_HNH_cent_sharp.mrc 2 as #30.3, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened post_HNH_cent_sharp.mrc 3 as #30.4, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened post_HNH_cent_sharp.mrc 4 as #30.5, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened post_HNH_cent_sharp.mrc 5 as #30.6, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened post_HNH_cent_sharp.mrc 6 as #30.7, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened post_HNH_cent_sharp.mrc 7 as #30.8, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened post_HNH_in_sharp.mrc 0 as #31.1, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened post_HNH_in_sharp.mrc 1 as #31.2, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened post_HNH_in_sharp.mrc 2 as #31.3, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened post_HNH_in_sharp.mrc 3 as #31.4, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened post_HNH_in_sharp.mrc 4 as #31.5, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened post_HNH_in_sharp.mrc 5 as #31.6, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened post_HNH_in_sharp.mrc 6 as #31.7, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened post_HNH_in_sharp.mrc 7 as #31.8, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened post_HNH_out_sharp.mrc 0 as #33.1, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened post_HNH_out_sharp.mrc 1 as #33.2, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened post_HNH_out_sharp.mrc 2 as #33.3, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened post_HNH_out_sharp.mrc 3 as #33.4, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened post_HNH_out_sharp.mrc 4 as #33.5, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened post_HNH_out_sharp.mrc 5 as #33.6, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened post_HNH_out_sharp.mrc 6 as #33.7, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened post_HNH_out_sharp.mrc 7 as #33.8, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 1 0 as #34.1, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 1 1 as #34.2, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 1 2 as #34.3, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 1 3 as #34.4, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 1 4 as #34.5, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 1 5 as #34.6, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 1 6 as #34.7, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 1 7 as #34.8, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 1 8 as #34.9, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 1 9 as #34.10, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 1 10 as #34.11, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 1 11 as #34.12, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 1 12 as #34.13, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Log from Mon May 12 14:04:47 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type I-F_HNH/Manuscript/chimerax_session.cxs"" Opened halfcleaved_HNH_center_sharp3Å.mrc as #13, grid size 420,420,420, pixel 0.725, shown at level 0.03, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 0 as #22.1, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 1 as #22.2, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 2 as #22.3, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 3 as #22.4, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 4 as #22.5, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 5 as #22.6, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 6 as #22.7, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 7 as #22.8, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 8 as #22.9, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 9 as #22.10, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_in_sharp.mrc as #9, grid size 420,420,420, pixel 0.725, shown at level 0.00277, step 1, values float32 Opened halfcleaved_HNH_out_sharp.mrc as #10, grid size 420,420,420, pixel 0.725, shown at level 0.0029, step 1, values float32 Opened halfcleaved_HNH_in_sharp.mrc 0 as #7.1, grid size 420,420,420, pixel 0.725, shown at level 0.002, step 1, values float32 Opened halfcleaved_HNH_in_sharp.mrc 1 as #7.2, grid size 420,420,420, pixel 0.725, shown at level 0.002, step 1, values float32 Opened halfcleaved_HNH_in_sharp.mrc 2 as #7.3, grid size 420,420,420, pixel 0.725, shown at level 0.002, step 1, values float32 Opened halfcleaved_HNH_in_sharp.mrc 3 as #7.4, grid size 420,420,420, pixel 0.725, shown at level 0.002, step 1, values float32 Opened halfcleaved_HNH_in_sharp.mrc 4 as #7.5, grid size 420,420,420, pixel 0.725, shown at level 0.002, step 1, values float32 Opened halfcleaved_HNH_in_sharp.mrc 5 as #7.6, grid size 420,420,420, pixel 0.725, shown at level 0.002, step 1, values float32 Opened halfcleaved_HNH_in_sharp.mrc 6 as #7.7, grid size 420,420,420, pixel 0.725, shown at level 0.002, step 1, values float32 Opened halfcleaved_HNH_in_sharp.mrc 7 as #7.8, grid size 420,420,420, pixel 0.725, shown at level 0.002, step 1, values float32 Opened halfcleaved_HNH_in_sharp.mrc 8 as #7.9, grid size 420,420,420, pixel 0.725, shown at level 0.002, step 1, values float32 Opened halfcleaved_HNH_out_sharp.mrc 0 as #8.1, grid size 420,420,420, pixel 0.725, shown at level 0.002, step 1, values float32 Opened halfcleaved_HNH_out_sharp.mrc 1 as #8.2, grid size 420,420,420, pixel 0.725, shown at level 0.002, step 1, values float32 Opened halfcleaved_HNH_out_sharp.mrc 2 as #8.3, grid size 420,420,420, pixel 0.725, shown at level 0.002, step 1, values float32 Opened halfcleaved_HNH_out_sharp.mrc 3 as #8.4, grid size 420,420,420, pixel 0.725, shown at level 0.002, step 1, values float32 Opened halfcleaved_HNH_out_sharp.mrc 4 as #8.5, grid size 420,420,420, pixel 0.725, shown at level 0.002, step 1, values float32 Opened halfcleaved_HNH_out_sharp.mrc 5 as #8.6, grid size 420,420,420, pixel 0.725, shown at level 0.002, step 1, values float32 Opened halfcleaved_HNH_out_sharp.mrc 6 as #8.7, grid size 420,420,420, pixel 0.725, shown at level 0.002, step 1, values float32 Opened halfcleaved_HNH_out_sharp.mrc 7 as #8.8, grid size 420,420,420, pixel 0.725, shown at level 0.002, step 1, values float32 Opened halfcleaved_HNH_out_sharp.mrc 8 as #8.9, grid size 420,420,420, pixel 0.725, shown at level 0.002, step 1, values float32 Opened apo_HNH_cent_sharp.mrc as #17, grid size 420,420,420, pixel 0.725, shown at level 0.00199, step 1, values float32 Opened apo_HNH_in_sharp.mrc as #18, grid size 420,420,420, pixel 0.725, shown at level 0.00173, step 1, values float32 Opened apo_HNH_out_sharp.mrc as #19, grid size 420,420,420, pixel 0.725, shown at level 0.00214, step 1, values float32 Opened post_HNH_cent_sharp.mrc as #24, grid size 420,420,420, pixel 0.725, shown at level 0.00328, step 1, values float32 Opened post_HNH_in_sharp.mrc as #25, grid size 420,420,420, pixel 0.725, shown at level 0.0257, step 1, values float32 Opened post_HNH_out_sharp.mrc as #26, grid size 420,420,420, pixel 0.725, shown at level 0.00342, step 1, values float32 Opened apo_HNH_cent_sharp.mrc 0 as #27.1, grid size 420,420,420, pixel 0.725, shown at level 0.00199, step 1, values float32 Opened apo_HNH_cent_sharp.mrc 1 as #27.2, grid size 420,420,420, pixel 0.725, shown at level 0.00199, step 1, values float32 Opened apo_HNH_cent_sharp.mrc 2 as #27.3, grid size 420,420,420, pixel 0.725, shown at level 0.00199, step 1, values float32 Opened apo_HNH_cent_sharp.mrc 3 as #27.4, grid size 420,420,420, pixel 0.725, shown at level 0.00199, step 1, values float32 Opened apo_HNH_cent_sharp.mrc 4 as #27.5, grid size 420,420,420, pixel 0.725, shown at level 0.00199, step 1, values float32 Opened apo_HNH_cent_sharp.mrc 5 as #27.6, grid size 420,420,420, pixel 0.725, shown at level 0.00199, step 1, values float32 Opened apo_HNH_in_sharp.mrc 0 as #28.1, grid size 420,420,420, pixel 0.725, shown at level 0.00173, step 1, values float32 Opened apo_HNH_in_sharp.mrc 1 as #28.2, grid size 420,420,420, pixel 0.725, shown at level 0.00173, step 1, values float32 Opened apo_HNH_in_sharp.mrc 2 as #28.3, grid size 420,420,420, pixel 0.725, shown at level 0.00173, step 1, values float32 Opened apo_HNH_in_sharp.mrc 3 as #28.4, grid size 420,420,420, pixel 0.725, shown at level 0.00173, step 1, values float32 Opened apo_HNH_in_sharp.mrc 4 as #28.5, grid size 420,420,420, pixel 0.725, shown at level 0.00173, step 1, values float32 Opened apo_HNH_in_sharp.mrc 5 as #28.6, grid size 420,420,420, pixel 0.725, shown at level 0.00173, step 1, values float32 Opened apo_HNH_out_sharp.mrc 0 as #29.1, grid size 420,420,420, pixel 0.725, shown at level 0.00214, step 1, values float32 Opened apo_HNH_out_sharp.mrc 1 as #29.2, grid size 420,420,420, pixel 0.725, shown at level 0.00214, step 1, values float32 Opened apo_HNH_out_sharp.mrc 2 as #29.3, grid size 420,420,420, pixel 0.725, shown at level 0.00214, step 1, values float32 Opened apo_HNH_out_sharp.mrc 3 as #29.4, grid size 420,420,420, pixel 0.725, shown at level 0.00214, step 1, values float32 Opened apo_HNH_out_sharp.mrc 4 as #29.5, grid size 420,420,420, pixel 0.725, shown at level 0.00214, step 1, values float32 Opened apo_HNH_out_sharp.mrc 5 as #29.6, grid size 420,420,420, pixel 0.725, shown at level 0.00214, step 1, values float32 Opened post_HNH_cent_sharp.mrc 0 as #30.1, grid size 420,420,420, pixel 0.725, shown at level 0.00328, step 1, values float32 Opened post_HNH_cent_sharp.mrc 1 as #30.2, grid size 420,420,420, pixel 0.725, shown at level 0.00328, step 1, values float32 Opened post_HNH_cent_sharp.mrc 2 as #30.3, grid size 420,420,420, pixel 0.725, shown at level 0.00328, step 1, values float32 Opened post_HNH_cent_sharp.mrc 3 as #30.4, grid size 420,420,420, pixel 0.725, shown at level 0.00328, step 1, values float32 Opened post_HNH_cent_sharp.mrc 4 as #30.5, grid size 420,420,420, pixel 0.725, shown at level 0.00328, step 1, values float32 Opened post_HNH_cent_sharp.mrc 5 as #30.6, grid size 420,420,420, pixel 0.725, shown at level 0.00328, step 1, values float32 Opened post_HNH_cent_sharp.mrc 6 as #30.7, grid size 420,420,420, pixel 0.725, shown at level 0.00328, step 1, values float32 Opened post_HNH_cent_sharp.mrc 7 as #30.8, grid size 420,420,420, pixel 0.725, shown at level 0.00328, step 1, values float32 Opened post_HNH_in_sharp.mrc 0 as #31.1, grid size 420,420,420, pixel 0.725, shown at level 0.0257, step 1, values float32 Opened post_HNH_in_sharp.mrc 1 as #31.2, grid size 420,420,420, pixel 0.725, shown at level 0.07, step 1, values float32 Opened post_HNH_in_sharp.mrc 2 as #31.3, grid size 420,420,420, pixel 0.725, shown at level 0.0257, step 1, values float32 Opened post_HNH_in_sharp.mrc 3 as #31.4, grid size 420,420,420, pixel 0.725, shown at level 0.0257, step 1, values float32 Opened post_HNH_in_sharp.mrc 4 as #31.5, grid size 420,420,420, pixel 0.725, shown at level 0.0257, step 1, values float32 Opened post_HNH_in_sharp.mrc 5 as #31.6, grid size 420,420,420, pixel 0.725, shown at level 0.0257, step 1, values float32 Opened post_HNH_in_sharp.mrc 6 as #31.7, grid size 420,420,420, pixel 0.725, shown at level 0.0257, step 1, values float32 Opened post_HNH_in_sharp.mrc 7 as #31.8, grid size 420,420,420, pixel 0.725, shown at level 0.0257, step 1, values float32 Opened post_HNH_out_sharp.mrc 0 as #33.1, grid size 420,420,420, pixel 0.725, shown at level 0.00342, step 1, values float32 Opened post_HNH_out_sharp.mrc 1 as #33.2, grid size 420,420,420, pixel 0.725, shown at level 0.00342, step 1, values float32 Opened post_HNH_out_sharp.mrc 2 as #33.3, grid size 420,420,420, pixel 0.725, shown at level 0.00342, step 1, values float32 Opened post_HNH_out_sharp.mrc 3 as #33.4, grid size 420,420,420, pixel 0.725, shown at level 0.00342, step 1, values float32 Opened post_HNH_out_sharp.mrc 4 as #33.5, grid size 420,420,420, pixel 0.725, shown at level 0.00342, step 1, values float32 Opened post_HNH_out_sharp.mrc 5 as #33.6, grid size 420,420,420, pixel 0.725, shown at level 0.00342, step 1, values float32 Opened post_HNH_out_sharp.mrc 6 as #33.7, grid size 420,420,420, pixel 0.725, shown at level 0.00342, step 1, values float32 Opened post_HNH_out_sharp.mrc 7 as #33.8, grid size 420,420,420, pixel 0.725, shown at level 0.00342, step 1, values float32 Log from Thu May 1 15:38:06 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type I-F_HNH/Manuscript/chimerax_session.cxs"" Opened halfcleaved_HNH_center_sharp3Å.mrc as #13, grid size 420,420,420, pixel 0.725, shown at level 0.03, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 0 as #22.1, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 1 as #22.2, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 2 as #22.3, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 3 as #22.4, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 4 as #22.5, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 5 as #22.6, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 6 as #22.7, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 7 as #22.8, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 8 as #22.9, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 9 as #22.10, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Log from Fri Apr 25 19:29:02 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/zxc755/OneDrive - University of Copenhagen/Type > I-F_HNH/Manuscript/figures/chimera_session.cxs"" format session Opened halfcleaved_HNH_center_main_map_2p4Å.mrc as #4, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc as #13, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_in_sharp3Å.mrc as #14, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened post_HNH_in_sharp_4p5.mrc as #18, grid size 420,420,420, pixel 0.725, shown at level 0.0257, step 1, values float32 Opened post_HNH_cent_sharp.mrc as #19, grid size 420,420,420, pixel 0.725, shown at level 0.01, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 0 as #22.1, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 1 as #22.2, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 2 as #22.3, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 3 as #22.4, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 4 as #22.5, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 5 as #22.6, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 6 as #22.7, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 7 as #22.8, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 8 as #22.9, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 9 as #22.10, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 5 copy as #28, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 8 copy as #31, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 5 copy as #23, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 8 copy as #24, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened J620_abinitio_map.mrc as #29, grid size 128,128,128, pixel 2.38, shown at level 0.218, step 1, values float32 Opened half_hetref_J623_map.mrc as #30, grid size 128,128,128, pixel 2.38, shown at level 0.33, step 1, values float32 Log from Wed Apr 23 13:09:57 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/chimera_session.cxs"" Opened halfcleaved_HNH_center_main_map_2p4Å.mrc as #4, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc as #13, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_in_sharp3Å.mrc as #14, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened post_HNH_in_sharp_4p5.mrc as #18, grid size 420,420,420, pixel 0.725, shown at level 0.0257, step 1, values float32 Opened post_HNH_cent_sharp.mrc as #19, grid size 420,420,420, pixel 0.725, shown at level 0.01, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 0 as #22.1, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 1 as #22.2, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 2 as #22.3, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 3 as #22.4, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 4 as #22.5, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 5 as #22.6, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 6 as #22.7, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 7 as #22.8, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 8 as #22.9, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 9 as #22.10, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 5 copy as #28, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 8 copy as #31, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 5 copy as #23, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 8 copy as #24, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Log from Mon Mar 31 18:07:43 2025UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/chimera_session.cxs"" Opened halfcleaved_HNH_center_main_map_2p4Å.mrc as #4, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc as #13, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_in_sharp3Å.mrc as #14, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened post_HNH_in_sharp_4p5.mrc as #18, grid size 420,420,420, pixel 0.725, shown at level 0.0257, step 1, values float32 Opened post_HNH_cent_sharp.mrc as #19, grid size 420,420,420, pixel 0.725, shown at level 0.01, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 0 as #22.1, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 1 as #22.2, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 2 as #22.3, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 3 as #22.4, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 4 as #22.5, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 5 as #22.6, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 6 as #22.7, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 7 as #22.8, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 8 as #22.9, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 9 as #22.10, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 5 copy as #28, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 8 copy as #31, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 5 copy as #23, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc 8 copy as #24, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Log from Thu Mar 27 17:05:34 2025UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/chimera_session.cxs"" Opened halfcleaved_HNH_center_main_map_2p4Å.mrc as #4, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Opened halfcleaved_HNH_center_sharp3Å.mrc as #13, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened halfcleaved_HNH_in_sharp3Å.mrc as #14, grid size 420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32 Opened post_HNH_in_sharp_4p5.mrc as #18, grid size 420,420,420, pixel 0.725, shown at level 0.0257, step 1, values float32 Opened post_HNH_cent_sharp.mrc as #19, grid size 420,420,420, pixel 0.725, shown at level 0.01, step 1, values float32 Log from Wed Mar 26 12:19:53 2025UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/chimera_session.cxs"" Opened halfcleaved_HNH_center_main_map_2p4Å.mrc as #4, grid size 420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32 Log from Tue Mar 25 00:19:58 2025UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/chimera_session.cxs"" Opened halfcleaved_HNH_center_main_map_2p4Å.mrc as #4, grid size 420,420,420, pixel 0.725, shown at level 0.09, step 1, values float32 Log from Mon Mar 24 13:31:18 2025UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/chimera_session.cxs"" Opened halfcleaved_HNH_center_main_map_2p4Å.mrc as #4, grid size 420,420,420, pixel 0.725, shown at level 0.09, step 1, values float32 Log from Mon Mar 24 00:43:04 2025 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 1imp Summary of feedback from opening 1imp fetched from pdb --- note | Fetching compressed mmCIF 1imp from http://files.rcsb.org/download/1imp.cif 1imp title: Colicin E9 immunity protein IM9, NMR, 21 structures [more info...] Chain information for 1imp --- Chain | Description | UniProt 1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A 1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A 1.21/A | IM9 | IMM9_ECOLI 1-86 > hide #1.1 models > show #1.1 models > hide models > show #1.1 models > open 1fsj Summary of feedback from opening 1fsj fetched from pdb --- note | Fetching compressed mmCIF 1fsj from http://files.rcsb.org/download/1fsj.cif 1fsj title: Crystal structure of the E9 DNAse domain [more info...] Chain information for 1fsj #2 --- Chain | Description | UniProt B C D E | COLICIN E9 | CEA9_ECOLI 2-134 202-334 402-434 602-734 Non-standard residues in 1fsj #2 --- PO4 — phosphate ion ZN — zinc ion 1fsj mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 3| author_defined_assembly 4| author_defined_assembly > hide #!1 models Drag select of 49 atoms, 132 residues, 4 pseudobonds, 43 bonds > hide #2 cartoons > show sel cartoons Drag select of 60 atoms, 4 pseudobonds, 55 bonds > hide sel atoms Drag select of 141 atoms, 8 pseudobonds, 127 bonds > hide sel atoms > select clear > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type > I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_center_main_model_refined2.pdb"" Chain information for halfcleaved_HNH_center_main_model_refined2.pdb #3 --- Chain | Description Aa | No description available Ba | No description available Ca | No description available DA | No description available Da | No description available Db | No description available Dc | No description available Dd | No description available De | No description available Df | No description available EA | No description available FA | No description available > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type > I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_center_main_map_2p4Å.mrc"" Opened halfcleaved_HNH_center_main_map_2p4Å.mrc as #4, grid size 420,420,420, pixel 0.725, shown at level 0.0319, step 2, values float32 > volume #4 level 0.07 > volume #4 step 1 > hide #!4 models > style stick Changed 56061 atom styles > color #3/DA light gray > color #3/EA dim gray > color #3/FA dark red > color #3/Ca rebecca purple > color #3/Ba forest green > color #3/Da,Db,Dc,Dd,De,Df khaki > color #3/Aa steel blue > color #3/Aa:232-350 dark turquoise > hide #3 atoms > show #3 cartoons Drag select of 49 atoms, 132 residues, 4 pseudobonds, 43 bonds > ui mousemode right ""rotate selected models"" > view matrix models #2,1,0,0,82.662,0,1,0,181.25,0,0,1,114.9 > view matrix models > #2,1,0.0013443,-0.0025868,85.9,-0.0013444,1,-6.0428e-05,181.66,0.0025868,6.3905e-05,1,96.743 > mmaker sel to #3/Aa:230-350 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker halfcleaved_HNH_center_main_model_refined2.pdb, chain Aa (#3) with 1fsj, chain E (#2), sequence alignment score = 97 RMSD between 11 pruned atom pairs is 1.284 angstroms; (across all 97 pairs: 16.295) > color #2 yellow > color #2 byhetero > hide #!3 models > select subtract #2/E:700 1046 atoms, 43 bonds, 4 pseudobonds, 135 residues, 2 models selected > select subtract #2/E:701 1038 atoms, 39 bonds, 4 pseudobonds, 134 residues, 2 models selected > select subtract #2/E:702 1028 atoms, 32 bonds, 3 pseudobonds, 133 residues, 2 models selected > select subtract #2/E:703 1018 atoms, 25 bonds, 3 pseudobonds, 132 residues, 2 models selected > select subtract #2/E:719 1010 atoms, 25 bonds, 3 pseudobonds, 131 residues, 2 models selected > select subtract #2/E:720 999 atoms, 25 bonds, 3 pseudobonds, 130 residues, 2 models selected > select subtract #2/E:721 992 atoms, 25 bonds, 3 pseudobonds, 129 residues, 2 models selected > select subtract #2/E:722 985 atoms, 25 bonds, 3 pseudobonds, 128 residues, 2 models selected > select clear > select add #2/E:700 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #2/E:701 17 atoms, 15 bonds, 2 residues, 1 model selected > select add #2/E:702 27 atoms, 25 bonds, 3 residues, 1 model selected > select add #2/E:703 37 atoms, 35 bonds, 4 residues, 1 model selected > select add #2/E:719 45 atoms, 43 bonds, 5 residues, 1 model selected > select add #2/E:720 56 atoms, 53 bonds, 6 residues, 1 model selected > select add #2/E:721 63 atoms, 59 bonds, 7 residues, 1 model selected > select add #2/E:722 70 atoms, 65 bonds, 8 residues, 1 model selected > hide #!2 models > show #!3 models > mmaker sel to #3/Aa:300-325 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker halfcleaved_HNH_center_main_model_refined2.pdb, chain Aa (#3) with 1fsj, chain E (#2), sequence alignment score = 33.3 RMSD between 6 pruned atom pairs is 0.986 angstroms; (across all 8 pairs: 2.082) > show #!2 models > view matrix models > #2,0.97297,-0.22873,-0.031935,103.66,0.22967,0.94372,0.23802,167.46,-0.024305,-0.23892,0.97073,110.17 > view matrix models > #2,0.97551,-0.19874,-0.094297,106.33,0.21196,0.96388,0.16128,171.49,0.058839,-0.17731,0.98239,106.64 > view matrix models > #2,0.97749,-0.14562,0.15266,94.724,0.17631,0.96123,-0.21202,189.82,-0.11586,0.23416,0.96527,111.65 > select clear > select #2/E:702 10 atoms, 10 bonds, 1 residue, 1 model selected > view matrix models > #2,0.98567,-0.047376,0.16189,94.269,0.055707,0.99733,-0.047316,185.39,-0.15921,0.055656,0.98567,112.54 > select #2/E:700 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #2/E:701 17 atoms, 15 bonds, 2 residues, 1 model selected > select add #2/E:702 27 atoms, 25 bonds, 3 residues, 1 model selected > select add #2/E:703 37 atoms, 35 bonds, 4 residues, 1 model selected > select add #2/E:704 45 atoms, 42 bonds, 5 residues, 1 model selected > select add #2/E:706 52 atoms, 49 bonds, 6 residues, 1 model selected > select add #2/E:707 60 atoms, 56 bonds, 7 residues, 1 model selected > select add #2/E:708 66 atoms, 61 bonds, 8 residues, 1 model selected > select add #2/E:709 75 atoms, 69 bonds, 9 residues, 1 model selected > select add #2/E:710 79 atoms, 72 bonds, 10 residues, 1 model selected > mmaker sel to #3/Aa:300-314 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker halfcleaved_HNH_center_main_model_refined2.pdb, chain Aa (#3) with 1fsj, chain E (#2), sequence alignment score = 46.3 RMSD between 10 pruned atom pairs is 0.499 angstroms; (across all 10 pairs: 0.499) > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > select #3/Aa:280 11 atoms, 10 bonds, 1 residue, 1 model selected > show #3/Aa:305,280,328,304 > select #3/Aa:332 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > show #!4 models > transparency 50 > hide #!4 models > hide #!3 models > hide #!2 models > select clear > show #!3 models > show #!2 models > combine #2 > hide #!2 models > hide #!3 models > show #5 cartoons > select #5/C:273 7 atoms, 7 bonds, 1 residue, 1 model selected > select up 72 atoms, 72 bonds, 10 residues, 1 model selected > select up 1047 atoms, 1071 bonds, 132 residues, 1 model selected > delete sel > select #5/D:407 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #5/B:6 17 atoms, 15 bonds, 2 residues, 1 model selected > select up 86 atoms, 84 bonds, 10 residues, 1 model selected > select up 2111 atoms, 2159 bonds, 266 residues, 1 model selected > delete sel > save ""/Users/zxc755/OneDrive - University of Copenhagen/Type > I-F_HNH/Structure/1fsj_E9_nuclease_HNH_like.pdb"" models #5 > select #5/E:904@ZN 1 atom, 1 residue, 1 model selected > select up 3 atoms, 1 bond, 2 residues, 1 model selected > select up 6 atoms, 4 bonds, 2 residues, 1 model selected > select #5 1388 atoms, 1087 bonds, 7 pseudobonds, 457 residues, 2 models selected > select subtract #5/E:804@P 1387 atoms, 1083 bonds, 7 pseudobonds, 457 residues, 2 models selected > select subtract #5/E:804@O2 1386 atoms, 1083 bonds, 7 pseudobonds, 457 residues, 2 models selected > select subtract #5/E:804@O3 1385 atoms, 1083 bonds, 6 pseudobonds, 457 residues, 2 models selected > select subtract #5/E:804@O1 1384 atoms, 1083 bonds, 6 pseudobonds, 457 residues, 2 models selected > select subtract #5/E:804@O4 1383 atoms, 1083 bonds, 6 pseudobonds, 456 residues, 2 models selected > select subtract #5/E:904@ZN 1382 atoms, 1083 bonds, 3 pseudobonds, 455 residues, 2 models selected > delete sel > save ""/Users/zxc755/OneDrive - University of Copenhagen/Type > I-F_HNH/Structure/zn_phosphate_from_1fsj.pdb"" models #5 > hide #!5 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!2 models > hide #!2 models > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type > I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_center_main_model_refined_with_water.pdb"" Chain information for halfcleaved_HNH_center_main_model_refined_with_water.pdb #6 --- Chain | Description Aa | No description available Ba | No description available Ca | No description available DA | No description available Da | No description available Db | No description available Dc | No description available Dd | No description available De | No description available Df | No description available EA | No description available FA | No description available > style stick Changed 80248 atom styles > hide #6 atoms > show #6 cartoons > show #6/B atoms > show #6/D atoms > show #6/C atoms > show #6/A atoms > color #6/DA light gray > color #6/EA dim gray > color #6/FA dark red > color #6/Ca rebecca purple > color #6/Ba forest green > color #6/Da,Db,Dc,Dd,De,Df khaki > color #6/Aa steel blue > color #6/Aa:232-350 dark turquoise > color #6 byhetero > show #6/Aa:305,280,328 > show #6/Aa:304,280,328 > show #!5 models > hide #!5 models > show #!2 models > select #6/Aa:303 7 atoms, 6 bonds, 1 residue, 1 model selected > show #!3 models > hide #!3 models > show #!4 models > volume #4 level 0.09 > hide #!2 models > show #!2 models > hide #!4 models > select #6/Aa:332 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > lighting soft > lighting simple > lighting full > lighting soft > lighting simple > lighting soft > lighting simple > select #6/Aa:302 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #2/E:700 18 atoms, 16 bonds, 2 residues, 2 models selected > show sel atoms > select #2/E:723 7 atoms, 6 bonds, 1 residue, 1 model selected > select add #6/Aa:324 13 atoms, 11 bonds, 2 residues, 2 models selected > show sel atoms > open 1v14 Summary of feedback from opening 1v14 fetched from pdb --- note | Fetching compressed mmCIF 1v14 from http://files.rcsb.org/download/1v14.cif 1v14 title: Crystal Structure of the Colicin E9, mutant His103Ala, in complex with Mg+2 and dsDNA (resolution 2.9A) [more info...] Chain information for 1v14 #7 --- Chain | Description | UniProt A B C D | COLICIN E9 | CEA9_ECOLI 2-134 E F G H I J K L | 5'-D(*GP*CP*GP*AP*TP*CP*GP*CP)-3' | Non-standard residues in 1v14 #7 --- MG — magnesium ion 1v14 mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 3| author_and_software_defined_assembly 4| author_and_software_defined_assembly > hide #!2 models > hide #!6 models > view > select add #7 5341 atoms, 5524 bonds, 73 pseudobonds, 623 residues, 5 models selected > select clear > select add #7 5328 atoms, 5513 bonds, 73 pseudobonds, 621 residues, 3 models selected > hide sel atoms > show sel cartoons > select clear > select add #7/G:8 19 atoms, 20 bonds, 1 residue, 1 model selected > select add #7/H:12 40 atoms, 43 bonds, 2 residues, 1 model selected > select add #7/J:11 62 atoms, 67 bonds, 3 residues, 1 model selected > select add #7/I:8 81 atoms, 87 bonds, 4 residues, 1 model selected > select add #7/C:80 87 atoms, 92 bonds, 5 residues, 1 model selected > select add #7/B:123 94 atoms, 98 bonds, 6 residues, 1 model selected > select add #7/E:5 114 atoms, 119 bonds, 7 residues, 1 model selected > select add #7/F:12 135 atoms, 142 bonds, 8 residues, 1 model selected > select add #7/A:53 146 atoms, 153 bonds, 9 residues, 1 model selected > select up 1143 atoms, 1247 bonds, 77 residues, 1 model selected > select up 3979 atoms, 4147 bonds, 438 residues, 1 model selected > hide sel cartoons > select clear > select #7/D:100 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #7/D:101 17 atoms, 15 bonds, 2 residues, 1 model selected > select add #7/D:102 27 atoms, 25 bonds, 3 residues, 1 model selected > select add #7/D:103 32 atoms, 29 bonds, 4 residues, 1 model selected > select add #7/D:104 40 atoms, 36 bonds, 5 residues, 1 model selected > select add #7/D:105 49 atoms, 44 bonds, 6 residues, 1 model selected > select add #7/D:106 56 atoms, 51 bonds, 7 residues, 1 model selected > select add #7/D:107 64 atoms, 58 bonds, 8 residues, 1 model selected > show #!6 models > mmaker sel to #6/Aa:300-310 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker halfcleaved_HNH_center_main_model_refined_with_water.pdb, chain Aa (#6) with 1v14, chain D (#7), sequence alignment score = 23.8 RMSD between 8 pruned atom pairs is 0.406 angstroms; (across all 8 pairs: 0.406) > color #7 yellow > color #7 byhetero > select clear > select #7/K:6 19 atoms, 20 bonds, 1 residue, 1 model selected > show #!4 models > hide #!4 models > show #!4 models > show sel atoms > select #7/K:5 20 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > view sel > select #7/D:5 11 atoms, 10 bonds, 1 residue, 1 model selected > hide #!4 models > select #7/D:102 10 atoms, 10 bonds, 1 residue, 1 model selected > select add #7/D:6 18 atoms, 17 bonds, 2 residues, 1 model selected > select subtract #7/D:6 10 atoms, 10 bonds, 1 residue, 1 model selected > select add #7/D:5 21 atoms, 20 bonds, 2 residues, 1 model selected > select add #7/D:103 26 atoms, 24 bonds, 3 residues, 1 model selected > select add #7/D:100 35 atoms, 32 bonds, 4 residues, 1 model selected > select add #7/D:127 45 atoms, 42 bonds, 5 residues, 1 model selected > show sel atoms > style stick Changed 85576 atom styles > select add #7/K:4 66 atoms, 65 bonds, 6 residues, 1 model selected > select #7/K:5 20 atoms, 21 bonds, 1 residue, 1 model selected > select add #7/K:6 39 atoms, 41 bonds, 2 residues, 1 model selected > hide sel cartoons > select clear > show #!4 models > save ""/Users/zxc755/OneDrive - University of Copenhagen/Type > I-F_HNH/Structure/1v14_E9_nuclease_his103_mut_with_dsDNA.pdb"" models #7 > hide #!4 models > hide #!6 models > hide #!7 models > show #!7 models > show #7 cartoons > view > select #7/H:12 21 atoms, 23 bonds, 1 residue, 1 model selected > select add #7/G:8 40 atoms, 43 bonds, 2 residues, 1 model selected > select add #7/F:13 60 atoms, 64 bonds, 3 residues, 1 model selected > select add #7/E:7 82 atoms, 88 bonds, 4 residues, 1 model selected > select add #7/A:102 92 atoms, 98 bonds, 5 residues, 1 model selected > select add #7/J:12 113 atoms, 121 bonds, 6 residues, 1 model selected > select add #7/I:7 135 atoms, 145 bonds, 7 residues, 1 model selected > select add #7/C:78 141 atoms, 150 bonds, 8 residues, 1 model selected > select up 956 atoms, 1055 bonds, 56 residues, 1 model selected > select up 2934 atoms, 3079 bonds, 306 residues, 1 model selected > select up 2956 atoms, 3079 bonds, 328 residues, 1 model selected > select up 5328 atoms, 5513 bonds, 621 residues, 1 model selected > select down 2956 atoms, 3079 bonds, 328 residues, 1 model selected > delete sel > select #7/B:89 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 42 atoms, 42 bonds, 5 residues, 1 model selected > select up 1045 atoms, 1068 bonds, 132 residues, 1 model selected > delete sel > save ""/Users/zxc755/OneDrive - University of Copenhagen/Type > I-F_HNH/Structure/1v14_E9_nuclease_his103_mut_with_dsDNA.pdb"" models #7 > hide #!7 models > open 1emv Summary of feedback from opening 1emv fetched from pdb --- note | Fetching compressed mmCIF 1emv from http://files.rcsb.org/download/1emv.cif 1emv title: Crystal structure of colicin E9 DNAse domain with its cognate immunity protein IM9 (1.7 angstroms) [more info...] Chain information for 1emv #8 --- Chain | Description | UniProt A | IMMUNITY PROTEIN IM9 | IMM9_ECOLI 1-86 B | COLICIN E9 | CEA9_ECOLI 2-134 Non-standard residues in 1emv #8 --- PO4 — phosphate ion > view > select #8/A:71 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 121 atoms, 123 bonds, 16 residues, 1 model selected > select up 651 atoms, 664 bonds, 83 residues, 1 model selected > delete sel > mmaker #8/B:100-110 to #6/Aa:300-310 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker halfcleaved_HNH_center_main_model_refined_with_water.pdb, chain Aa (#6) with 1emv, chain B (#8), sequence alignment score = 35.4 RMSD between 9 pruned atom pairs is 0.264 angstroms; (across all 9 pairs: 0.264) > view > show #!6 models > hide #!6 models > show #!6 models > hide #8 models > show #8 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > select #8/B:127 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > show #!6 models > hide #!6 models > show #!6 models > select #8/B:100 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > hide #8 models > hide #!6 models > show #!5 models > hide #!5 models > show #!2 models > show #!6 models > select #6/Aa:303 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select #2/E:704 8 atoms, 7 bonds, 1 residue, 1 model selected > select #6/Aa:306 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/E:706 7 atoms, 7 bonds, 1 residue, 1 model selected > select #6/Ba:128 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > show #!4 models > lighting simple > lighting soft > lighting simple > hide #!4 models > hide #!2 models > hide #!6 models > show #8 models > set chain Expected a keyword > set chain #8/B A Expected a keyword > set chain #8/B to A Expected a keyword > set chain A #8/B Expected a keyword > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type > I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_refined2.pdb"" Chain information for halfcleaved_HNH_center_main_model_refined2.pdb #9 --- Chain | Description 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 L | No description available > color #9/L light gray > color #9/K dim gray > color #9/J dark red > color #9/I rebecca purple > color #9/B forest green > color #9/C,D,E,F,G,H khaki > color #9/A steel blue > color #9/A:232-350 dark turquoise > style stick Changed 106889 atom styles > hide #9 atoms > show #9 cartoons > hide #!9 models > show #!3 models > hide #!3 models > show #!6 models > hide #!6 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #8 models > show #8 models > hide #8 models > show #8 models > hide #8 models [deleted to fit within ticket limits] > distance style radius 0.04 [Repeated 2 time(s)] > distance style radius 0.05 [Repeated 2 time(s)] > distance style radius 50 [Repeated 2 time(s)] > distance style radius 0.01 [Repeated 4 time(s)] > distance style radius 0.02 [Repeated 2 time(s)] > distance style radius 0.03 [Repeated 2 time(s)] > distance style radius 0.04 [Repeated 2 time(s)] > distance style radius 0.05 [Repeated 2 time(s)] > color #11 teal > select clear > show #!20 models > show #!19 models > show #!18 models > show #!16 models > select #32/A:47 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #32/A:48 14 atoms, 12 bonds, 2 residues, 1 model selected > select add #32/A:49 21 atoms, 19 bonds, 3 residues, 1 model selected > select add #32/A:50 25 atoms, 22 bonds, 4 residues, 1 model selected > select add #32/A:51 33 atoms, 29 bonds, 5 residues, 1 model selected > select add #32/A:52 41 atoms, 36 bonds, 6 residues, 1 model selected > select add #32/A:53 45 atoms, 39 bonds, 7 residues, 1 model selected > select add #32/A:54 50 atoms, 43 bonds, 8 residues, 1 model selected > select subtract #32/A:47 42 atoms, 36 bonds, 7 residues, 1 model selected > hide sel cartoons > select #32/A:78 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #32/A:77 15 atoms, 14 bonds, 2 residues, 1 model selected > select add #32/A:76 24 atoms, 22 bonds, 3 residues, 1 model selected > select add #32/A:75 33 atoms, 30 bonds, 4 residues, 1 model selected > select add #32/A:74 47 atoms, 45 bonds, 5 residues, 1 model selected > select add #32/A:73 51 atoms, 48 bonds, 6 residues, 1 model selected > select add #32/A:55 63 atoms, 60 bonds, 7 residues, 1 model selected > select add #32/A:56 71 atoms, 67 bonds, 8 residues, 1 model selected > select add #32/A:57 79 atoms, 74 bonds, 9 residues, 1 model selected > select add #32/A:58 87 atoms, 81 bonds, 10 residues, 1 model selected > select add #32/A:59 93 atoms, 86 bonds, 11 residues, 1 model selected > select add #32/A:60 99 atoms, 91 bonds, 12 residues, 1 model selected > select add #32/A:61 107 atoms, 98 bonds, 13 residues, 1 model selected > select add #32/A:62 115 atoms, 105 bonds, 14 residues, 1 model selected > select add #32/A:63 123 atoms, 112 bonds, 15 residues, 1 model selected > select add #32/A:64 129 atoms, 117 bonds, 16 residues, 1 model selected > select add #32/A:65 133 atoms, 120 bonds, 17 residues, 1 model selected > select add #32/A:66 145 atoms, 132 bonds, 18 residues, 1 model selected > select add #32/A:67 153 atoms, 139 bonds, 19 residues, 1 model selected > select add #32/A:68 161 atoms, 146 bonds, 20 residues, 1 model selected > select add #32/A:69 168 atoms, 152 bonds, 21 residues, 1 model selected > select add #32/A:70 173 atoms, 156 bonds, 22 residues, 1 model selected > select add #32/A:71 181 atoms, 163 bonds, 23 residues, 1 model selected > select add #32/A:72 186 atoms, 167 bonds, 24 residues, 1 model selected > hide sel cartoons > select #32/A:21 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #32/A:22 17 atoms, 15 bonds, 2 residues, 1 model selected > select add #32/A:23 29 atoms, 27 bonds, 3 residues, 1 model selected > select add #32/A:25 38 atoms, 35 bonds, 4 residues, 1 model selected > select add #32/A:24 46 atoms, 42 bonds, 5 residues, 1 model selected > select add #32/A:26 50 atoms, 45 bonds, 6 residues, 1 model selected > select add #32/A:27 58 atoms, 52 bonds, 7 residues, 1 model selected > select add #32/A:29 67 atoms, 60 bonds, 8 residues, 1 model selected > select add #32/A:28 78 atoms, 71 bonds, 9 residues, 1 model selected > hide sel cartoons > select add #32/A:30 84 atoms, 76 bonds, 10 residues, 1 model selected > select add #32/A:31 92 atoms, 83 bonds, 11 residues, 1 model selected > select add #32/A:32 100 atoms, 90 bonds, 12 residues, 1 model selected > select add #32/A:33 109 atoms, 98 bonds, 13 residues, 1 model selected > select add #32/A:34 117 atoms, 105 bonds, 14 residues, 1 model selected > select add #32/A:35 127 atoms, 115 bonds, 15 residues, 1 model selected > select subtract #32/A:35 117 atoms, 105 bonds, 14 residues, 1 model selected > select add #32/A:35 127 atoms, 115 bonds, 15 residues, 1 model selected > select add #32/A:36 135 atoms, 122 bonds, 16 residues, 1 model selected > select add #32/A:37 140 atoms, 126 bonds, 17 residues, 1 model selected > select add #32/A:38 147 atoms, 132 bonds, 18 residues, 1 model selected > select add #32/A:39 157 atoms, 142 bonds, 19 residues, 1 model selected > hide sel cartoons > select #32/A:47 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #32/A:41 13 atoms, 11 bonds, 2 residues, 1 model selected > select add #32/A:40 20 atoms, 17 bonds, 3 residues, 1 model selected > select add #32/A:79 28 atoms, 24 bonds, 4 residues, 1 model selected > select add #32/A:80 35 atoms, 30 bonds, 5 residues, 1 model selected > select add #32/A:81 42 atoms, 36 bonds, 6 residues, 1 model selected > select add #32/A:86 54 atoms, 48 bonds, 7 residues, 1 model selected > hide sel cartoons > select clear > select add #32/B:94 5 atoms, 4 bonds, 1 residue, 1 model selected > select add #32/B:90 14 atoms, 12 bonds, 2 residues, 1 model selected > select add #32/B:91 23 atoms, 20 bonds, 3 residues, 1 model selected > select add #32/B:92 31 atoms, 27 bonds, 4 residues, 1 model selected > select add #32/B:93 39 atoms, 34 bonds, 5 residues, 1 model selected > select add #32/B:97 47 atoms, 41 bonds, 6 residues, 1 model selected > select add #32/B:98 55 atoms, 48 bonds, 7 residues, 1 model selected > select add #32/B:99 64 atoms, 56 bonds, 8 residues, 1 model selected > select add #32/B:100 69 atoms, 60 bonds, 9 residues, 1 model selected > hide sel cartoons > turn y 45 > turn y -45 [Repeated 1 time(s)] > turn y 45 > turn y 10 > turn y -10 > turn y -20 [Repeated 2 time(s)] > turn y 40 > cd ""/Users/zxc755/Library/CloudStorage/OneDrive-UniversityofCopenhagen/Type > I-F_HNH/Manuscript/figures/structure/PAM"" Current working directory is: /Users/zxc755/Library/CloudStorage/OneDrive- UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/structure/PAM > save PAM_with_map.tif supersample 3 > turn y -40 > save PAM_with_map_rotate_40degree.tif supersample 3 > turn y 40 > close #1-10 > show #!12 models > hide #!12 models > close #12 > show #!14 models > hide #!14 models > close #14 > show #!15 models > hide #!15 models > show #!15 models > hide #!15 models > show #!39 models > hide #!39 models > show #!39 models > hide #!39 models > show #!40 models > hide #!40 models > close #39-40 > save PAM_session.cxs includeMaps true > select /A:85 9 atoms, 8 bonds, 1 residue, 1 model selected > select add /A:84 14 atoms, 12 bonds, 2 residues, 1 model selected > select add /A:83 22 atoms, 19 bonds, 3 residues, 1 model selected > select hid car Expected an objects specifier or a keyword > hide sel cartoons > show sel > show sel cartoons > hide sel cartoons > show sel cartoons > select /A:84@CB 1 atom, 1 residue, 1 model selected > hide sel > select clear > turn y 180 [Repeated 14 time(s)] > save PAM_with_map_front.tif supersample 3 > turn y 180 > save PAM_with_map_back.tif supersample 3 > hide #!18 models > hide #!19 models > hide #!20 models > hide #!16 models > hide #32 > show #32 cartoons > hide #32 & nucleic cartoons > show #32 & nucle Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show #32 & nucleic > color #32/L dark orange > color #32/K dim gray > color #32/J dark red > color #32/I rebecca purple > color #32/B forest green > color #32/C,D,E,F,G,H salmon > color #32/A steel blue > color #32/A:232-350 dark turquoise > color #32/O blue > color #32/M red > select /K:3@P 1 atom, 1 residue, 1 model selected > select add /K:2@O3' 2 atoms, 2 residues, 1 model selected > select add /K:3@OP1 3 atoms, 2 residues, 1 model selected > select add /K:3@OP2 4 atoms, 2 residues, 1 model selected > select add /K:3@O5' 5 atoms, 2 residues, 1 model selected > color sel byhetero > select clear > color #32/a byhetero > select clear > show #32/a:319,328,280,304,305 > select /A:280@CB 1 atom, 1 residue, 1 model selected > select add /A:280@CG 2 atoms, 1 residue, 1 model selected > select add /A:280@CD 3 atoms, 1 residue, 1 model selected > select add /A:280@NE 4 atoms, 1 residue, 1 model selected > select add /A:280@CZ 5 atoms, 1 residue, 1 model selected > select add /A:280@NH1 6 atoms, 1 residue, 1 model selected > select add /A:280@NH2 7 atoms, 1 residue, 1 model selected > select add /A:305@CE1 8 atoms, 2 residues, 1 model selected > select add /A:305@NE2 9 atoms, 2 residues, 1 model selected > select add /A:305@CD2 10 atoms, 2 residues, 1 model selected > select add /A:305@CG 11 atoms, 2 residues, 1 model selected > select add /A:305@ND1 12 atoms, 2 residues, 1 model selected > select add /A:305@CB 13 atoms, 2 residues, 1 model selected > select add /A:319@ND2 14 atoms, 3 residues, 1 model selected > select add /A:319@OD1 15 atoms, 3 residues, 1 model selected > select add /A:319@CG 16 atoms, 3 residues, 1 model selected > select add /A:319@CB 17 atoms, 3 residues, 1 model selected > select add /A:304@ND1 18 atoms, 4 residues, 1 model selected > select add /A:304@CE1 19 atoms, 4 residues, 1 model selected > select add /A:304@NE2 20 atoms, 4 residues, 1 model selected > select add /A:304@CD2 21 atoms, 4 residues, 1 model selected > select add /A:304@CG 22 atoms, 4 residues, 1 model selected > select add /A:304@CB 23 atoms, 4 residues, 1 model selected > select add /A:328@NE2 24 atoms, 5 residues, 1 model selected > select add /A:328@CD2 25 atoms, 5 residues, 1 model selected > select add /A:328@CG 26 atoms, 5 residues, 1 model selected > select add /A:328@ND1 27 atoms, 5 residues, 1 model selected > select add /A:328@CE1 28 atoms, 5 residues, 1 model selected > select add /A:328@CB 29 atoms, 5 residues, 1 model selected > show #32/m,o > select add /M:2@MG 30 atoms, 6 residues, 1 model selected > volume zone #13 nearAtoms sel range 1 newMap true Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #1, grid size 420,420,420, pixel 0.725, shown at step 1, values float32 > transparency #1 90 > select /K:3@P 1 atom, 1 residue, 1 model selected > select add /K:3@OP2 2 atoms, 1 residue, 1 model selected > select add /K:3@OP1 3 atoms, 1 residue, 1 model selected > select add /K:3@O5' 4 atoms, 1 residue, 1 model selected > select add /K:2@O3' 5 atoms, 2 residues, 1 model selected > select add /K:2@C3' 6 atoms, 2 residues, 1 model selected > select add /K:2@C2' 7 atoms, 2 residues, 1 model selected > select add /K:2@C1' 8 atoms, 2 residues, 1 model selected > select add /K:2@O4' 9 atoms, 2 residues, 1 model selected > select add /K:2@C4' 10 atoms, 2 residues, 1 model selected > select add /K:2@C5' 11 atoms, 2 residues, 1 model selected > select add /K:2@O5' 12 atoms, 2 residues, 1 model selected > volume zone #13 nearAtoms sel range 1 newMap true Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #2, grid size 420,420,420, pixel 0.725, shown at step 1, values float32 > transparency #2 90 > select /O:1@O 1 atom, 1 residue, 1 model selected > volume zone #13 nearAtoms sel range 1 newMap true Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #3, grid size 420,420,420, pixel 0.725, shown at step 1, values float32 > transparency #3 90 > color #1 turquoise > color #2 dim gray > color #3 blue > select clear > hide #32/b-l cartoons > hide #32/j-l > show #32/k:1-3 > hide #32/a:1-232 cartoons > show #32/a:225-232 cartoons > select /A:232 12 atoms, 12 bonds, 1 residue, 1 model selected > select /A:231 9 atoms, 8 bonds, 1 residue, 1 model selected > select add /A:230 18 atoms, 16 bonds, 2 residues, 1 model selected > select add /A:229 26 atoms, 23 bonds, 3 residues, 1 model selected > select add /A:228 34 atoms, 30 bonds, 4 residues, 1 model selected > select add /A:226 43 atoms, 38 bonds, 5 residues, 1 model selected > select add /A:227 48 atoms, 42 bonds, 6 residues, 1 model selected > select add /A:225 53 atoms, 46 bonds, 7 residues, 1 model selected > hide sel cartoons > select clear > hide #32/a:324-350 cartoons > hide #32/a:282-301 cartoons > show #32/a:300-320 cartoons > show #32/a:300-330 cartoons > select add /A:301 12 atoms, 12 bonds, 1 residue, 1 model selected > select add /A:300 16 atoms, 15 bonds, 2 residues, 1 model selected > hide sel cartoons > select /A:278 8 atoms, 7 bonds, 1 residue, 1 model selected > hide #32/a:252-278 cartoons > hide #32/a:232-251 cartoons > hide #32/a:310-318 cartoons > select /A:306 8 atoms, 7 bonds, 1 residue, 1 model selected > select add /A:307 15 atoms, 13 bonds, 2 residues, 1 model selected > show sel > hide sel > select clear > graphics silhouettes false > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting soft > lighting full > lighting shadows false > lighting simple > lighting soft > lighting full > lighting flat > graphics silhouettes false > lighting soft > lighting full [Repeated 1 time(s)] > lighting soft > lighting full > lighting shadows false > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting simple > lighting shadows true > lighting shadows false > lighting soft > lighting full > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > graphics silhouettes false > lighting full > lighting flat > lighting simple > graphics silhouettes false > lighting soft > lighting flat > hide cd ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/structure/HNH"" Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > cd ""/Users/zxc755/Library/CloudStorage/OneDrive-UniversityofCopenhagen/Type > I-F_HNH/Manuscript/figures/structure/HNH"" Current working directory is: /Users/zxc755/Library/CloudStorage/OneDrive- UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/structure/HNH > select /A:307 7 atoms, 6 bonds, 1 residue, 1 model selected > select add /A:306 15 atoms, 13 bonds, 2 residues, 1 model selected > hide sel cartoons > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type > I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_center_refined.pdb"" Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive- UniversityofCopenhagen/Type I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_center_refined.pdb --- warning | Ignored bad PDB record found on line 59 SSBOND 1 CYS Aa 295 CYS Ca 140 Chain information for postcleavage_HNH_center_refined.pdb #4 --- Chain | Description 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 L | No description available > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type > I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/post_HNH_cent_sharp.mrc"" Opened post_HNH_cent_sharp.mrc as #5, grid size 420,420,420, pixel 0.725, shown at level 0.00328, step 2, values float32 > hide #!4 models > show #!4 models > hide #!5 models > hide #!4 models > style #4 stick Changed 23513 atom styles > hide #4 > show #4/a:279-330 cartoons Computing secondary structure > show #!4 models > hide #!4 models > show #!4 models > combine #4 > hide #!4 models > mmaker #6/a:232-350 to #32/a:232-350 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker halfcleaved_HNH_center_main_model_temp_editing.pdb, chain A (#32) with copy of postcleavage_HNH_center_refined.pdb, chain A (#6), sequence alignment score = 542.1 RMSD between 110 pruned atom pairs is 0.556 angstroms; (across all 111 pairs: 0.605) > show #6/A:280,319,328,304,305 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!6 models > save half_HNH_minimal_with_map.tif supersample 3 > show #!6 models > hide #!2 models > hide #!1 models > hide #!3 models > hide #32/k,m,o > hide #4,6/a:282-301 > hide #4,6/a:282-301 cartoons > select #6/A:307 7 atoms, 6 bonds, 1 residue, 1 model selected > select add #6/A:306 15 atoms, 13 bonds, 2 residues, 1 model selected > hide sel cartoons > select #6/A:318 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #6/A:317 17 atoms, 15 bonds, 2 residues, 1 model selected > select add #6/A:316 23 atoms, 20 bonds, 3 residues, 1 model selected > select add #6/A:315 31 atoms, 27 bonds, 4 residues, 1 model selected > select add #6/A:314 36 atoms, 31 bonds, 5 residues, 1 model selected > select add #6/A:313 40 atoms, 34 bonds, 6 residues, 1 model selected > select add #6/A:312 44 atoms, 37 bonds, 7 residues, 1 model selected > select add #6/A:311 53 atoms, 45 bonds, 8 residues, 1 model selected > select add #6/A:310 59 atoms, 50 bonds, 9 residues, 1 model selected > hide sel cartoons Drag select of 4 residues > hide sel cartoons > save minimal_HNH_superimposition.tif supersample 3 > color #4,6 salmon > save minimal_HNH_superimposition.tif supersample 3 > hide #!6 models > hide #!32 models > show #!4 models > show #4/a:280,319,328,304,305 > color #4/a byhetero > select clear > select #4/A:305@CE1 1 atom, 1 residue, 1 model selected > select add #4/A:305@ND1 2 atoms, 1 residue, 1 model selected > select add #4/A:305@CG 3 atoms, 1 residue, 1 model selected > select add #4/A:305@CD2 4 atoms, 1 residue, 1 model selected > select add #4/A:305@NE2 5 atoms, 1 residue, 1 model selected > select add #4/A:305@CB 6 atoms, 1 residue, 1 model selected > select add #4/A:319@ND2 7 atoms, 2 residues, 1 model selected > select add #4/A:319@OD1 8 atoms, 2 residues, 1 model selected > select add #4/A:319@CB 9 atoms, 2 residues, 1 model selected > select add #4/A:280@NE 10 atoms, 3 residues, 1 model selected > select add #4/A:280@CZ 11 atoms, 3 residues, 1 model selected > select add #4/A:280@NH1 12 atoms, 3 residues, 1 model selected > select add #4/A:280@NH2 13 atoms, 3 residues, 1 model selected > select add #4/A:280@CD 14 atoms, 3 residues, 1 model selected > select add #4/A:280@CG 15 atoms, 3 residues, 1 model selected > select add #4/A:280@CB 16 atoms, 3 residues, 1 model selected > select add #4/A:304@ND1 17 atoms, 4 residues, 1 model selected > select add #4/A:304@CE1 18 atoms, 4 residues, 1 model selected > select add #4/A:304@NE2 19 atoms, 4 residues, 1 model selected > select add #4/A:304@CD2 20 atoms, 4 residues, 1 model selected > select add #4/A:304@CG 21 atoms, 4 residues, 1 model selected > select add #4/A:304@CB 22 atoms, 4 residues, 1 model selected > select add #4/A:328@NE2 23 atoms, 5 residues, 1 model selected > select add #4/A:328@CD2 24 atoms, 5 residues, 1 model selected > select add #4/A:328@CG 25 atoms, 5 residues, 1 model selected > select add #4/A:328@CB 26 atoms, 5 residues, 1 model selected > select add #4/A:328@ND1 27 atoms, 5 residues, 1 model selected > select add #4/A:328@CE1 28 atoms, 5 residues, 1 model selected > volume zone #5 nearAtoms sel range 1 newMap true Opened post_HNH_cent_sharp.mrc zone as #7, grid size 420,420,420, pixel 0.725, shown at step 1, values float32 > close #7 > volume zone #5 nearAtoms sel range 1.5 newMap true Opened post_HNH_cent_sharp.mrc zone as #7, grid size 420,420,420, pixel 0.725, shown at step 1, values float32 > transparency #7 90 > volume #7 level 0.02 > volume #7 level 0.06 > volume #7 level 0.04 > volume #7 level 0.09 > color #7 salmon > color #7 charcoal Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #7 coal Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #7 dim gray > color #7 light slate gray > volume #7 level .03 > select clear > save post_HNH_minimal_with_map.tif supersample 3 > hide #!11 models > hide #!7 models > hide #!4 models > show #!32 models > show #!3 models > show #!2 models > show #!1 models > show #32/m,o > select clear > show #32/k:1-3 > select clear > save HNH_cat_session.cxs includeMaps true > show #32 cartoons > select #32/a:1-100 763 atoms, 777 bonds, 1 pseudobond, 98 residues, 2 models selected > select #32/a:1-90 693 atoms, 706 bonds, 1 pseudobond, 88 residues, 2 models selected > select #32/a:1-80 608 atoms, 619 bonds, 78 residues, 1 model selected > select #32/a:1-40 309 atoms, 313 bonds, 38 residues, 1 model selected > select #32/a:1-30 229 atoms, 231 bonds, 28 residues, 1 model selected > select #32/a:1-35 272 atoms, 275 bonds, 33 residues, 1 model selected > select #32/a:80-150 584 atoms, 593 bonds, 1 pseudobond, 71 residues, 2 models selected > select #32/a:80-135 456 atoms, 461 bonds, 1 pseudobond, 56 residues, 2 models selected > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type I-F_HNH/Manuscript/apo_HNH_center_refined- > coot-0.pdb"" Chain information for apo_HNH_center_refined-coot-0.pdb #8 --- Chain | Description 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 > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type > I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_cent_sharp.mrc"" Opened apo_HNH_cent_sharp.mrc as #9, grid size 420,420,420, pixel 0.725, shown at level 0.00199, step 2, values float32 > hide #!1 models > hide #!2 models > hide #!3 models > hide #!32 models > style stick Changed 94148 atom styles > hide #8 > show #8 cartoons Computing secondary structure > transparency #9 90 > color #8/L dark orange > color #8/K dim gray > color #8/J dark red > color #8/I rebecca purple > color #8/B forest green > color #8/C,D,E,F,G,H salmon > color #8/A steel blue > color #8/A:232-350 dark turquoise > color #8/O blue > color #8/M red > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > volume zone #9 nearAtoms #8/A range 3 newMap true Opened apo_HNH_cent_sharp.mrc zone as #10, grid size 420,420,420, pixel 0.725, shown at step 1, values float32 > show #!9 models > hide #!9 models > hide #!10 models > show #!10 models > transparency #10 90 > volume #10 level 0.02 > hide #!10 models > show #!9 models > hide #!9 models > show #!9 models > show #!10 models > hide #!9 models > hide #8 cartoons > show #8/a cartoons > surface dust #10 size 5 > combine #8 > hide #!8 models > fitmap #12/A:232-350 inMap #9 Fit molecule copy of apo_HNH_center_refined-coot-0.pdb (#12) to map apo_HNH_cent_sharp.mrc (#9) using 897 atoms average map value = 0.1137, steps = 76 shifted from previous position = 1.81 rotated from previous position = 3.94 degrees atoms outside contour = 144, contour level = 0.0019908 Position of copy of apo_HNH_center_refined-coot-0.pdb (#12) relative to apo_HNH_cent_sharp.mrc (#9) coordinates: Matrix rotation and translation 0.99849050 0.04622093 0.02967081 -7.99164150 -0.04495289 0.99810294 -0.04206845 14.50694265 -0.03155897 0.04067116 0.99867407 0.51270662 Axis 0.60172121 0.44529167 -0.66305876 Axis point 301.29448148 199.80947793 0.00000000 Rotation angle (degrees) 3.94233491 Shift along axis 1.31112589 > save ""/Users/zxc755/OneDrive - University of Copenhagen/Type > I-F_HNH/Manuscript/apo_HNH_center_refined-coot-0_HNH_fit.pdb"" models #12 > fitmap #12/A:80-135 inMap #9 Fit molecule copy of apo_HNH_center_refined-coot-0.pdb (#12) to map apo_HNH_cent_sharp.mrc (#9) using 456 atoms average map value = 0.05565, steps = 96 shifted from previous position = 6.74 rotated from previous position = 5.58 degrees atoms outside contour = 120, contour level = 0.0019908 Position of copy of apo_HNH_center_refined-coot-0.pdb (#12) relative to apo_HNH_cent_sharp.mrc (#9) coordinates: Matrix rotation and translation 0.99481363 0.04551028 0.09096513 -18.50883752 -0.04872161 0.99825385 0.03339856 1.51076745 -0.08928631 -0.03765731 0.99529387 16.74468113 Axis -0.32980050 0.83662351 -0.43737025 Axis point 176.51077727 0.00000000 213.37405101 Rotation angle (degrees) 6.18421935 Shift along axis 0.04454214 > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > save ""/Users/zxc755/OneDrive - University of Copenhagen/Type > I-F_HNH/Manuscript/apo_HNH_center_refined-coot-0_N-ter_fit.pdb"" > hide #!12 models > show #!8 models > fitmap #8/A:80-135 inMap #9 Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map apo_HNH_cent_sharp.mrc (#9) using 456 atoms average map value = 0.05868, steps = 176 shifted from previous position = 2.5 rotated from previous position = 13.2 degrees atoms outside contour = 119, contour level = 0.0019908 Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to apo_HNH_cent_sharp.mrc (#9) coordinates: Matrix rotation and translation 0.97387880 0.10270175 -0.20251527 8.86888724 -0.10753121 0.99411722 -0.01296093 14.32149660 0.19999281 0.03439909 0.97919333 -23.07565390 Axis 0.10373066 -0.88159654 -0.46046443 Axis point 120.86155715 0.00000000 28.75781651 Rotation angle (degrees) 13.19604193 Shift along axis -1.08028845 > fitmap #8/A inMap #9 Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map apo_HNH_cent_sharp.mrc (#9) using 2728 atoms average map value = 0.05474, steps = 136 shifted from previous position = 1.91 rotated from previous position = 11.7 degrees atoms outside contour = 1271, contour level = 0.0019908 Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to apo_HNH_cent_sharp.mrc (#9) coordinates: Matrix rotation and translation 0.96863084 -0.03548685 -0.24595725 34.61064363 -0.01015117 0.98327484 -0.18184486 22.60765338 0.24829668 0.17863729 0.95207010 -47.86311464 Axis 0.58876206 -0.80724652 0.04137982 Axis point 214.60251744 0.00000000 112.99623949 Rotation angle (degrees) 17.82650237 Shift along axis 0.14691702 > show #!9 models > hide #!9 models > fitmap #8/A inMap #10 Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map apo_HNH_cent_sharp.mrc zone (#10) using 2728 atoms average map value = 0.04338, steps = 68 shifted from previous position = 0.747 rotated from previous position = 1.19 degrees atoms outside contour = 1886, contour level = 0.02 Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to apo_HNH_cent_sharp.mrc zone (#10) coordinates: Matrix rotation and translation 0.96913985 -0.02068010 -0.24564259 32.81429654 -0.02062424 0.98617920 -0.16439353 21.97080178 0.24564729 0.16438651 0.95531905 -46.25105779 Axis 0.55616727 -0.83107037 0.00009450 Axis point 207.83659879 0.00000000 107.50533490 Rotation angle (degrees) 17.19211508 Shift along axis -0.01341541 > select clear > select #8/A:231 9 atoms, 8 bonds, 1 residue, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.98518,0.053245,-0.16304,14.087,-0.04686,0.99799,0.042762,-2.3863,0.16499,-0.034489,0.98569,-19.98 > fitmap #8/A inMap #10 Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map apo_HNH_cent_sharp.mrc zone (#10) using 2728 atoms average map value = 0.1094, steps = 112 shifted from previous position = 5.82 rotated from previous position = 10.7 degrees atoms outside contour = 1095, contour level = 0.02 Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to apo_HNH_cent_sharp.mrc zone (#10) coordinates: Matrix rotation and translation 0.99997652 -0.00466439 0.00502091 0.20988985 0.00473618 0.99988534 -0.01438311 1.27122337 -0.00495325 0.01440656 0.99988395 -0.80414690 Axis 0.90290151 0.31280943 0.29482049 Axis point 0.00000000 63.62884067 80.26210486 Rotation angle (degrees) 0.91349740 Shift along axis 0.35008153 > fitmap #8/A:80-135 inMap #10 Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map apo_HNH_cent_sharp.mrc zone (#10) using 456 atoms average map value = 0.05864, steps = 96 shifted from previous position = 1.63 rotated from previous position = 12.7 degrees atoms outside contour = 227, contour level = 0.02 Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to apo_HNH_cent_sharp.mrc zone (#10) coordinates: Matrix rotation and translation 0.97694589 0.10504409 -0.18585603 6.38549743 -0.10761365 0.99418567 -0.00376302 13.31326798 0.18438012 0.02367691 0.98256978 -20.25353573 Axis 0.06413527 -0.86535176 -0.49704425 Axis point 114.59977050 0.00000000 20.50228547 Rotation angle (degrees) 12.35231087 Shift along axis -1.04422077 > fitmap #8/A:1-135 inMap #10 Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map apo_HNH_cent_sharp.mrc zone (#10) using 1057 atoms average map value = 0.07052, steps = 108 shifted from previous position = 2.65 rotated from previous position = 10.5 degrees atoms outside contour = 524, contour level = 0.02 Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to apo_HNH_cent_sharp.mrc zone (#10) coordinates: Matrix rotation and translation 0.99946033 0.02326146 -0.02319395 -0.64828860 -0.02335695 0.99971976 -0.00385462 3.15728544 0.02309779 0.00439427 0.99972355 -2.67969831 Axis 0.12457993 -0.69912699 -0.70406057 Axis point 122.81669961 28.56907646 0.00000000 Rotation angle (degrees) 1.89722763 Shift along axis -0.40143729 > fitmap #8/A:232-350 inMap #10 Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map apo_HNH_cent_sharp.mrc zone (#10) using 897 atoms average map value = 0.1135, steps = 88 shifted from previous position = 3.95 rotated from previous position = 3.77 degrees atoms outside contour = 263, contour level = 0.02 Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to apo_HNH_cent_sharp.mrc zone (#10) coordinates: Matrix rotation and translation 0.99894847 0.03136930 0.03343540 -6.87861474 -0.03015042 0.99888397 -0.03635608 10.87881307 -0.03453855 0.03530975 0.99877941 1.73316127 Axis 0.61586393 0.58413756 -0.52867281 Axis point 0.00000000 -57.34675321 281.67474684 Rotation angle (degrees) 3.33553382 Shift along axis 1.20215737 > save ""/Users/zxc755/OneDrive - University of Copenhagen/Type > I-F_HNH/Manuscript/apo_HNH_center_refined-coot-0_HNH_fit.pdb"" models #8 > hide #!10 models Drag select of 129 residues > show #!10 models > fitmap sel inMap #10 Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map apo_HNH_cent_sharp.mrc zone (#10) using 1033 atoms average map value = 0.06563, steps = 304 shifted from previous position = 5.04 rotated from previous position = 19.6 degrees atoms outside contour = 527, contour level = 0.02 Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to apo_HNH_cent_sharp.mrc zone (#10) coordinates: Matrix rotation and translation 0.97550451 -0.21809449 0.02873560 32.60163060 0.20802092 0.95705305 0.20193255 -41.53482359 -0.07154187 -0.19100851 0.97897779 42.51583633 Axis -0.66798838 0.17046879 0.72438382 Axis point 228.05641713 129.81114836 0.00000000 Rotation angle (degrees) 17.10493668 Shift along axis 1.93988222 > hide #!10 models Drag select of 92 residues > show #!10 models > fitmap #8/a inMap #10 Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map apo_HNH_cent_sharp.mrc zone (#10) using 2728 atoms average map value = 0.1094, steps = 152 shifted from previous position = 8.19 rotated from previous position = 17.4 degrees atoms outside contour = 1095, contour level = 0.02 Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to apo_HNH_cent_sharp.mrc zone (#10) coordinates: Matrix rotation and translation 0.99997611 -0.00472570 0.00504416 0.21355520 0.00479823 0.99988385 -0.01446572 1.27948594 -0.00497521 0.01448958 0.99988264 -0.80934348 Axis 0.90243179 0.31226729 0.29682657 Axis point 0.00000000 63.71907535 80.33882755 Rotation angle (degrees) 0.91923153 Shift along axis 0.35202596 > fitmap sel inMap #10 Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map apo_HNH_cent_sharp.mrc zone (#10) using 751 atoms average map value = 0.04893, steps = 116 shifted from previous position = 0.796 rotated from previous position = 3.08 degrees atoms outside contour = 429, contour level = 0.02 Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to apo_HNH_cent_sharp.mrc zone (#10) coordinates: Matrix rotation and translation 0.99892100 0.03260019 -0.03307674 -0.59088395 -0.03287494 0.99942906 -0.00779691 4.45668233 0.03280367 0.00887590 0.99942240 -4.33104269 Axis 0.17667979 -0.69812691 -0.69383217 Axis point 136.11302865 -0.00000000 -21.17869303 Rotation angle (degrees) 2.70443076 Shift along axis -0.21071038 > save ""/Users/zxc755/OneDrive - University of Copenhagen/Type > I-F_HNH/Manuscript/apo_HNH_center_refined-coot-0_N-ter_fit.pdb"" models #8 > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!10 models > fitmap sel inMap #9 Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map apo_HNH_cent_sharp.mrc (#9) using 751 atoms average map value = 0.04893, steps = 64 shifted from previous position = 0.00612 rotated from previous position = 0.0147 degrees atoms outside contour = 222, contour level = 0.0019908 Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to apo_HNH_cent_sharp.mrc (#9) coordinates: Matrix rotation and translation 0.99891180 0.03266370 -0.03329126 -0.57577626 -0.03294448 0.99942580 -0.00792044 4.48398773 0.03301344 0.00900858 0.99941431 -4.37110048 Axis 0.17857319 -0.69940507 -0.69205792 Axis point 136.52172827 0.00000000 -20.61037254 Rotation angle (degrees) 2.71688308 Shift along axis -0.21388724 Drag select of 2 residues, 9 apo_HNH_cent_sharp.mrc > hide #!9 models Drag select of 92 residues > show #!9 models > view matrix models > #8,0.99891,0.032664,-0.033291,-3.0428,-0.032944,0.99943,-0.0079204,1.8123,0.033013,0.0090086,0.99941,-4.4427 > fitmap sel inMap #9 Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map apo_HNH_cent_sharp.mrc (#9) using 751 atoms average map value = 0.04941, steps = 112 shifted from previous position = 1.87 rotated from previous position = 13.6 degrees atoms outside contour = 241, contour level = 0.0019908 Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to apo_HNH_cent_sharp.mrc (#9) coordinates: Matrix rotation and translation 0.99824896 -0.04930729 -0.03267722 10.31067123 0.05510661 0.97598361 0.21075875 -27.44944198 0.02150049 -0.21219043 0.97699179 35.29516095 Axis -0.96343154 -0.12341082 0.23784331 Axis point 0.00000000 148.42617946 146.07203449 Rotation angle (degrees) 12.67975067 Shift along axis 1.84865039 > view matrix models > #8,0.99825,-0.049307,-0.032677,9.4603,0.055107,0.97598,0.21076,-22.821,0.0215,-0.21219,0.97699,34.178 > fitmap sel inMap #9 Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map apo_HNH_cent_sharp.mrc (#9) using 751 atoms average map value = 0.0484, steps = 320 shifted from previous position = 4.25 rotated from previous position = 13 degrees atoms outside contour = 234, contour level = 0.0019908 Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to apo_HNH_cent_sharp.mrc (#9) coordinates: Matrix rotation and translation 0.97609557 0.09991348 -0.19301485 8.78155338 -0.06675455 0.98296459 0.17124380 -9.35267581 0.20683633 -0.15426570 0.96613706 4.94968795 Axis -0.60072274 -0.73791918 -0.30758327 Axis point -16.25369823 0.00000000 47.83281120 Rotation angle (degrees) 15.71970747 Shift along axis 0.10379886 > view matrix models > #8,0.94061,-0.031443,-0.33802,47.216,-0.0044741,0.99447,-0.10496,14.912,0.33945,0.10024,0.93527,-47.508 > fitmap sel inMap #9 Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map apo_HNH_cent_sharp.mrc (#9) using 751 atoms average map value = 0.04895, steps = 140 shifted from previous position = 4.05 rotated from previous position = 13.8 degrees atoms outside contour = 235, contour level = 0.0019908 Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to apo_HNH_cent_sharp.mrc (#9) coordinates: Matrix rotation and translation 0.98211439 0.09352479 -0.16341495 5.31498086 -0.09144608 0.99560485 0.02021373 8.63776478 0.16458720 -0.00490854 0.98635032 -14.18520647 Axis -0.06656667 -0.86911010 -0.49011888 Axis point 90.73511369 0.00000000 22.22348540 Rotation angle (degrees) 10.87692740 Shift along axis -0.90853175 > view matrix models > #8,0.98211,0.093525,-0.16341,-3.653,-0.091446,0.9956,0.020214,15.181,0.16459,-0.0049085,0.98635,-17.989 > fitmap sel inMap #9 Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map apo_HNH_cent_sharp.mrc (#9) using 751 atoms average map value = 0.04278, steps = 204 shifted from previous position = 11.5 rotated from previous position = 49.1 degrees atoms outside contour = 286, contour level = 0.0019908 Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to apo_HNH_cent_sharp.mrc (#9) coordinates: Matrix rotation and translation 0.51617442 0.50434421 -0.69224337 52.94424808 -0.36241786 0.86093017 0.35700496 22.73796343 0.77602659 0.06660453 0.62717348 -56.46806541 Axis -0.16790288 -0.84892009 -0.50114200 Axis point 81.93964639 0.00000000 19.23832231 Rotation angle (degrees) 59.85838174 Shift along axis 0.10631310 > view matrix models > #8,0.75563,0.53552,0.37715,-102.7,-0.65339,0.65658,0.37681,98.385,-0.045843,-0.53116,0.84603,110.59 > fitmap sel inMap #9 Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map apo_HNH_cent_sharp.mrc (#9) using 751 atoms average map value = 0.02767, steps = 144 shifted from previous position = 7.5 rotated from previous position = 13 degrees atoms outside contour = 399, contour level = 0.0019908 Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to apo_HNH_cent_sharp.mrc (#9) coordinates: Matrix rotation and translation 0.84445830 0.49866537 0.19550710 -85.59391132 -0.52302025 0.68898866 0.50174140 57.10323282 0.11549889 -0.52595387 0.84263428 92.00315528 Axis -0.70809886 0.05512697 -0.70395811 Axis point 0.00000000 175.17228734 -5.33803959 Rotation angle (degrees) 46.52479336 Shift along axis -1.00948880 > view matrix models > #8,0.22325,-0.12434,0.9668,1.3433,-0.96716,-0.1519,0.2038,273.03,0.12152,-0.98054,-0.15417,271.04 > fitmap sel inMap #9 Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map apo_HNH_cent_sharp.mrc (#9) using 751 atoms average map value = 0.02054, steps = 72 shifted from previous position = 0.557 rotated from previous position = 6.62 degrees atoms outside contour = 451, contour level = 0.0019908 Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to apo_HNH_cent_sharp.mrc (#9) coordinates: Matrix rotation and translation 0.32093819 -0.07334501 0.94425589 -15.53284174 -0.93429007 -0.18794079 0.30295267 264.15586909 0.15524413 -0.97943798 -0.12884289 264.10267667 Axis -0.73936752 0.45490792 -0.49638136 Axis point 0.00000000 230.80804800 33.94290972 Rotation angle (degrees) 119.86266478 Shift along axis 0.55543077 > view matrix models > #8,0.51797,0.29889,0.80148,-77.363,-0.84718,0.3088,0.43234,159.71,-0.11827,-0.90294,0.41316,217.23 > fitmap sel inMap #9 Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map apo_HNH_cent_sharp.mrc (#9) using 751 atoms average map value = 0.03756, steps = 156 shifted from previous position = 8.79 rotated from previous position = 28.4 degrees atoms outside contour = 345, contour level = 0.0019908 Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to apo_HNH_cent_sharp.mrc (#9) coordinates: Matrix rotation and translation 0.82035985 0.09006159 0.56471110 -54.91363732 -0.57114524 0.17797173 0.80132339 101.29105575 -0.02833415 -0.97990559 0.19743911 248.32489572 Axis -0.89491213 0.29795349 -0.33219874 Axis point 0.00000000 193.91338679 71.34026782 Rotation angle (degrees) 84.38258802 Shift along axis -3.17031318 > fitmap #8/a:1-232 inMap #9 Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map apo_HNH_cent_sharp.mrc (#9) using 1843 atoms average map value = 0.07444, steps = 132 shifted from previous position = 5.34 rotated from previous position = 8.06 degrees atoms outside contour = 740, contour level = 0.0019908 Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to apo_HNH_cent_sharp.mrc (#9) coordinates: Matrix rotation and translation 0.85556495 0.03689190 0.51637932 -43.24932520 -0.51768413 0.06757577 0.85289897 100.05195461 -0.00342966 -0.99703184 0.07691381 261.90564432 Axis -0.92496541 0.25990449 -0.27728802 Axis point 0.00000000 184.53788363 82.42044866 Rotation angle (degrees) 89.99843794 Shift along axis -6.61521397 > fitmap #8/a:1-232 inMap #10 Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map apo_HNH_cent_sharp.mrc zone (#10) using 1843 atoms average map value = 0.04496, steps = 204 shifted from previous position = 3.49 rotated from previous position = 15.1 degrees atoms outside contour = 1324, contour level = 0.02 Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to apo_HNH_cent_sharp.mrc zone (#10) coordinates: Matrix rotation and translation 0.85917065 0.12276216 0.49674464 -53.18821240 -0.50867642 0.31010579 0.80317040 65.81149160 -0.05544446 -0.94274272 0.32888002 229.17603074 Axis -0.90136454 0.28507929 -0.32599351 Axis point 0.00000000 186.58673918 75.48977018 Rotation angle (degrees) 75.57702649 Shift along axis -8.00643664 > view matrix models > #8,0.85917,0.12276,0.49674,-64.07,-0.50868,0.31011,0.80317,70.614,-0.055444,-0.94274,0.32888,227.33 > fitmap #8/a:1-232 inMap #10 Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map apo_HNH_cent_sharp.mrc zone (#10) using 1843 atoms average map value = 0.03523, steps = 100 shifted from previous position = 1.41 rotated from previous position = 6.44 degrees atoms outside contour = 1400, contour level = 0.02 Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to apo_HNH_cent_sharp.mrc zone (#10) coordinates: Matrix rotation and translation 0.80480185 0.18549600 0.56381310 -75.67146644 -0.59351183 0.26133077 0.76121609 93.91370671 -0.00613918 -0.94725786 0.32041356 222.16366887 Axis -0.87065314 0.29045262 -0.39698914 Axis point 0.00000000 190.88011217 63.74735928 Rotation angle (degrees) 78.85614004 Shift along axis 4.96451775 > view matrix models > #8,0.95413,0.18283,0.2371,-44.561,-0.29249,0.73836,0.60767,1.8038,-0.063966,-0.64915,0.75797,133.99 > fitmap #8/a:1-232 inMap #10 Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map apo_HNH_cent_sharp.mrc zone (#10) using 1843 atoms average map value = 0.04793, steps = 112 shifted from previous position = 1.31 rotated from previous position = 8.5 degrees atoms outside contour = 1301, contour level = 0.02 Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to apo_HNH_cent_sharp.mrc zone (#10) coordinates: Matrix rotation and translation 0.93571186 0.27776002 0.21746882 -53.80939596 -0.35134002 0.78914218 0.50380035 13.01747719 -0.03167822 -0.54781747 0.83599791 104.83057724 Axis -0.84096032 0.19923852 -0.50308027 Axis point 0.00000000 173.44882492 44.82069031 Rotation angle (degrees) 38.70040585 Shift along axis -4.89304496 > view matrix models > #8,-0.34192,-0.82356,0.4526,255.51,0.043806,-0.49507,-0.86775,319.8,0.93871,-0.27688,0.20535,9.9731 > fitmap #8/a:1-232 inMap #10 Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map apo_HNH_cent_sharp.mrc zone (#10) using 1843 atoms average map value = 0.01904, steps = 240 shifted from previous position = 15.2 rotated from previous position = 14.3 degrees atoms outside contour = 1658, contour level = 0.02 Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to apo_HNH_cent_sharp.mrc zone (#10) coordinates: Matrix rotation and translation -0.25816560 -0.79737188 0.54548016 216.97863355 0.22288946 -0.59854746 -0.76945515 298.39643581 0.94003766 -0.07706507 0.33225015 -41.78946055 Axis 0.53482557 -0.30476959 0.78808445 Axis point 53.68514190 192.65985646 0.00000000 Rotation angle (degrees) 139.66131452 Shift along axis -7.83006181 > hide #!8 models > show #!10 models > hide #!10 models > show #!10 models > hide #!9 models > show #!8 models > view matrix models > #8,0.99221,0.12413,0.010984,-16.454,-0.11883,0.91586,0.38351,-21.706,0.037546,-0.38183,0.92347,54.561 > fitmap #8/a:1-232 inMap #10 Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map apo_HNH_cent_sharp.mrc zone (#10) using 1843 atoms average map value = 0.1142, steps = 192 shifted from previous position = 7.86 rotated from previous position = 24.2 degrees atoms outside contour = 781, contour level = 0.02 Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to apo_HNH_cent_sharp.mrc zone (#10) coordinates: Matrix rotation and translation 0.99991970 -0.01233620 -0.00289962 2.01037916 0.01231916 0.99990715 -0.00582431 -0.62951411 0.00297120 0.00578812 0.99997883 -0.74339140 Axis 0.41653941 -0.21058730 0.88439126 Axis point 46.90450042 152.10806215 0.00000000 Rotation angle (degrees) 0.79868134 Shift along axis 0.31252097 > fitmap sel inMap #9 Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map apo_HNH_cent_sharp.mrc (#9) using 751 atoms average map value = 0.04894, steps = 72 shifted from previous position = 1.03 rotated from previous position = 3.1 degrees atoms outside contour = 222, contour level = 0.0019908 Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to apo_HNH_cent_sharp.mrc (#9) coordinates: Matrix rotation and translation 0.99892404 0.03249695 -0.03308647 -0.57194403 -0.03277317 0.99943206 -0.00784060 4.44583961 0.03281289 0.00891651 0.99942174 -4.34188516 Axis 0.17778779 -0.69917177 -0.69249573 Axis point 136.25073516 0.00000000 -20.62446803 Rotation angle (degrees) 2.70116337 Shift along axis -0.20335325 > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type I-F_HNH/Manuscript/apo_HNH_center_refined- > coot-0.pdb"" Chain information for apo_HNH_center_refined-coot-0.pdb #14 --- Chain | Description 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 > style stick Changed 140210 atom styles > hide #!8 models > hide #14 > show #14/A cartoons Computing secondary structure > hide #14/a:1-231 cartoons > hide #!10 models > select up 1257 atoms, 1283 bonds, 157 residues, 1 model selected > select up 2728 atoms, 2786 bonds, 340 residues, 1 model selected > select down 1257 atoms, 1283 bonds, 157 residues, 1 model selected > select down 751 atoms, 92 residues, 1 model selected > show #14/A cartoons > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > volume zone #9 nearAtoms #14/a range 2.5 newMap true Opened apo_HNH_cent_sharp.mrc zone as #21, grid size 420,420,420, pixel 0.725, shown at step 1, values float32 > transparency #21 90 > surface dust #21 > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type > I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_inwards_refined.pdb"" Chain information for apo_HNH_inwards_refined.pdb #22 --- Chain | Description A | No description available B | No description available C | No description available D E | No description available F G | No description available H | No description available I | No description available J | No description available > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type > I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_in_sharp.mrc"" Opened apo_HNH_in_sharp.mrc as #23, grid size 420,420,420, pixel 0.725, shown at level 0.00173, step 2, values float32 > hide #!23 models > hide #!21 models > hide #!14 models > hide #22 > show #22/a cartoons Computing secondary structure > volume zone #23 nearAtoms #22/a range 2.5 newMap true Opened apo_HNH_in_sharp.mrc zone as #24, grid size 420,420,420, pixel 0.725, shown at step 1, values float32 > transparency #24 90 > hide #!24 models > hide #!22 models > show #!21 models > show #!14 models > hide #!14 models > hide #!21 models > show #!22 models > show #!24 models > hide #!24 models > hide #!22 models > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type > I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_outwards_refined.pdb"" Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive- UniversityofCopenhagen/Type I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_outwards_refined.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 ILE a 6 ALA a 9 1 4 Start residue of secondary structure not found: HELIX 2 2 GLU a 16 SER a 30 1 15 Start residue of secondary structure not found: HELIX 3 3 ALA a 41 THR a 44 1 4 Start residue of secondary structure not found: HELIX 4 4 ALA a 84 TYR a 86 5 3 Start residue of secondary structure not found: HELIX 5 5 ARG a 88 VAL a 93 1 6 155 messages similar to the above omitted Chain information for apo_HNH_outwards_refined.pdb #25 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F G | No description available H | No description available I | No description available J | No description available > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type > I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_out_sharp.mrc"" Opened apo_HNH_out_sharp.mrc as #26, grid size 420,420,420, pixel 0.725, shown at level 0.00214, step 2, values float32 > hide #!26 models > style stick Changed 185894 atom styles > hide #25 > show #25/a cartoons Computing secondary structure > volume zone #26 nearAtoms #25/a range 2.5 newMap true Opened apo_HNH_out_sharp.mrc zone as #27, grid size 420,420,420, pixel 0.725, shown at step 1, values float32 > transparency #27 90 > show #!24 models > show #!21 models > hide #!21 models > hide #!24 models > hide #!27 models > show #!22 models > show #!14 models > hide #!14 models > show #!14 models > hide #!14 models > show #!14 models > hide #!14 models > show #!14 models > hide #!14 models > show #!14 models > morph #14,22,25 Computed 101 frame morph #28 > coordset #28 1,101 > close #28 > morph #22,14,25 Computed 101 frame morph #28 > coordset #28 1,101 > close #28 > show #!27 models > volume zone #26 nearAtoms #25/a range 1 newMap true Opened apo_HNH_out_sharp.mrc zone as #28, grid size 420,420,420, pixel 0.725, shown at step 1, values float32 > hide #!27 models > close #28 > volume zone #26 nearAtoms #25/a range 1.5 newMap true Opened apo_HNH_out_sharp.mrc zone as #28, grid size 420,420,420, pixel 0.725, shown at step 1, values float32 > close #28 > volume zone #26 nearAtoms #25/a range 2 newMap true Opened apo_HNH_out_sharp.mrc zone as #28, grid size 420,420,420, pixel 0.725, shown at step 1, values float32 > show #!27 models > hide #!27 models > show #!27 models > hide #!27 models > hide #!28 models > show #!27 models > close #28 > show #!1 models > hide #!1 models > show #!5 models > hide #!5 models > show #!6 models > hide #!6 models > select ~sel & ##selected 22280 atoms, 22901 bonds, 1 pseudobond, 2652 residues, 2 models selected > show #!7 models > hide #!7 models > show #!12 models > hide #!12 models > show #!15 models > hide #!15 models > show #!16 models > show #!17 models > show #!15 models > show #!18 models > show #!19 models > show #!20 models > show #!21 models > hide #!21 models > show #!21 models > hide #!21 models > show #!22 models > hide #!22 models > close #1-3,6,7,12,15-20 > hide #!27 models > show #!4 models > hide #!4 models > show #!4 models > hide #4 > show #4/a cartoons > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > select clear > show #!8 models > hide #!8 models > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type > I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_inwards_refined.pdb"" Chain information for postcleavage_HNH_inwards_refined.pdb #1 --- Chain | Description 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 L | No description available > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type > I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/post_HNH_in_sharp.mrc"" Opened post_HNH_in_sharp.mrc as #2, grid size 420,420,420, pixel 0.725, shown at level 0.0257, step 2, values float32 > hide #!1 models > hide #!2 models > hide #!4 models > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type > I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_outwards.pdb"" Chain information for postcleavage_HNH_outwards.pdb #3 --- Chain | Description A | No description available B | No description available C | No description available D 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 > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type > I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/post_HNH_out_sharp.mrc"" Opened post_HNH_out_sharp.mrc as #6, grid size 420,420,420, pixel 0.725, shown at level 0.00342, step 2, values float32 > hide #!3 models > hide #!6 models > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type > I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_inwards_refined.pdb"" Chain information for halfcleaved_HNH_inwards_refined.pdb #7 --- Chain | Description 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 L | No description available > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type > I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_in_sharp.mrc"" Opened halfcleaved_HNH_in_sharp.mrc as #12, grid size 420,420,420, pixel 0.725, shown at level 0.00277, step 2, values float32 > hide #!7 models > hide #!12 models > show #!7 models > hide #!7 models > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type > I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_outwards_refined.pdb"" Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive- UniversityofCopenhagen/Type I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_outwards_refined.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 ASN a 4 ILE a 10 1 7 Start residue of secondary structure not found: HELIX 2 2 GLU a 16 ILE a 31 1 16 Start residue of secondary structure not found: HELIX 3 3 ALA a 41 PHE a 43 5 3 Start residue of secondary structure not found: HELIX 4 4 ALA a 84 TYR a 86 5 3 Start residue of secondary structure not found: HELIX 5 5 ARG a 88 ALA a 94 1 7 169 messages similar to the above omitted Chain information for halfcleaved_HNH_outwards_refined.pdb #15 --- Chain | Description 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 L | No description available > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type > I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_out_sharp.mrc"" Opened halfcleaved_HNH_out_sharp.mrc as #16, grid size 420,420,420, pixel 0.725, shown at level 0.0029, step 2, values float32 > hide #!16 models > hide #!15 models > style stick Changed 234593 atom styles > show #!1 models > hide #!1 models > volume zone #2 nearAtoms #1/a range 2.5 newMap true Opened post_HNH_in_sharp.mrc zone as #17, grid size 420,420,420, pixel 0.725, shown at step 1, values float32 > show #!1 models > hide #1 > show #1 cartoons Computing secondary structure > select vol Expected an objects specifier or a keyword > transparency 90 > hide #1 cartoons > show #1/a cartoons > hide #!1 models > hide #!17 models > show #!3 models > show #!6 models > hide #!6 models > hide #3 > show #3/a cartoons Computing secondary structure > show #!6 models > hide #!6 models > volume zone #6 nearAtoms #3/a range 2.5 newMap true Opened post_HNH_out_sharp.mrc zone as #18, grid size 420,420,420, pixel 0.725, shown at step 1, values float32 > hide #!18 models > hide #!3 models > show #!4 models > show #!5 models > hide #!5 models > volume zone #5 nearAtoms #4/a range 2.5 newMap true Opened post_HNH_cent_sharp.mrc zone as #19, grid size 420,420,420, pixel 0.725, shown at step 1, values float32 > hide #!19 models > hide #!4 models > volume zone #13 nearAtoms #32/a range 2.5 newMap true Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #20, grid size 420,420,420, pixel 0.725, shown at step 1, values float32 > show #!32 models > hide #32 cartoons > show #32/a cartoons > transparency 90 > hide #!20 models > hide #!32 models > show #!7 models > volume zone #12 nearAtoms #7/a range 2.5 newMap true Opened halfcleaved_HNH_in_sharp.mrc zone as #28, grid size 420,420,420, pixel 0.725, shown at step 1, values float32 > hide #7 > show #7/a cartoons Computing secondary structure > transparency 90 > hide #!28 models > hide #!7 models > hide #15 > show #15/a cartoons Computing secondary structure > volume zone #16 nearAtoms #15/a range 2.5 newMap true Opened halfcleaved_HNH_out_sharp.mrc zone as #29, grid size 420,420,420, pixel 0.725, shown at step 1, values float32 > hide #!29 models > show #!27 models > hide #!27 models > show #!21 models > hide #!21 models > show #!14 models > hide #!14 models > show #!14 models > show #!21 models > hide #!21 models > hide #!14 models > cd ""/Users/zxc755/Library/CloudStorage/OneDrive-UniversityofCopenhagen/Type > I-F_HNH/Manuscript/figures/structure/cas8_movement"" Current working directory is: /Users/zxc755/Library/CloudStorage/OneDrive- UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/structure/cas8_movement > save cas8_movement.cxs includeMaps true ——— End of log from Sat May 17 13:40:51 2025 ——— opened ChimeraX session > rename #1 postcleavage_HNH_inwards.pdb > rename #4 postcleavage_HNH_center.pdb > show #!2 models > hide #!2 models > show #!1 models > show #!3 models > hide #!3 models > show #!3 models > show #!4 models > show #!5 models > hide #!5 models > show #!6 models > hide #!6 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > rename #7 halfcleaved_HNH_inwards.pdb > rename #32 halfcleaved_HNH_center_main_model.pdb > show #!32 models > hide #!32 models > show #!32 models > hide #!32 models > show #!29 models > show #!28 models > hide #!28 models > hide #!29 models > show #!29 models > hide #!29 models > hide #!4 models > hide #!3 models > hide #!1 models > show #!5 models > hide #!5 models > rename #8 apo_HNH_center.pdb > show #!10 models > show #!8 models > hide #!8 models > hide #!10 models > show #!10 models > hide #!10 models > show #!1 models > show #!12 models > hide #!12 models > show #!17 models > rename #22 apo_HNH_inwards.pdb > show #!22 models > hide #!22 models > show #!23 models > hide #!23 models > show #!28 models > hide #!28 models > show #!28 models > hide #!28 models > show #!28 models > hide #!28 models > show #!28 models > rename #15 halfcleaved_HNH_outwards.pdb > rename #14 apo_HNH_center.pdb > show #!14 models > show #!8 models > hide #!8 models > show #!15 models > hide #!15 models > show #!15 models > hide #!15 models > hide #!14 models > show #!14 models > hide #!14 models > show #!14 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > hide #!14 models > hide #!17 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!7 models > hide #!7 models > show #!7 models > rename #20 ""halfcleaved_HNH_center.mrc zone"" > show #!13 models > hide #!13 models > rename #13 halfcleaved_HNH_center_sharp.mrc > show #!13 models > hide #!13 models > show #!12 models > hide #!12 models > show #!17 models > hide #!17 models > show #!17 models > show #!22 models > show #!24 models > show #!3 models > show #!18 models > show #!4 models > show #!19 models > show #!15 models > show #!29 models > show #!32 models > show #!20 models > show #!27 models > show #!25 models > show #!14 models > show #!21 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > close #8,10 > hide #!29 models > show #!29 models > hide #!29 models > show #!29 models > transparency 90 > hide #!32 models > hide #!29 models > hide #!28 models > hide #!27 models > hide #!25 models > hide #!24 models > hide #!22 models > hide #!21 models > hide #!20 models > hide #!19 models > hide #!18 models > hide #!17 models > hide #!15 models > hide #!14 models > hide #!7 models > hide #!4 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!1 models > show #!3 models > show #!18 models > hide #!18 models > hide #!3 models > show #!1 models > show #!17 models > hide #!17 models > hide #!1 models > show #!4 models > show #!19 models > hide #!19 models > hide #!4 models > show #!7 models > show #!28 models > hide #!7 models > hide #!28 models > show #!15 models > show #!29 models > hide #!15 models > hide #!29 models > show #!32 models > show #!20 models > hide #32 > hide #!32 models > hide #!20 models > show #!22 models > show #!24 models > hide #!22 models > hide #!24 models > show #!25 models > show #!27 models > hide #!25 models > hide #!27 models > show #!21 models > show #!14 models > hide #!21 models > hide #!14 models > cd ""/Users/zxc755/Library/CloudStorage/OneDrive-UniversityofCopenhagen/Type > I-F_HNH/Manuscript/figures/structure/cas8_movement"" Current working directory is: /Users/zxc755/Library/CloudStorage/OneDrive- UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/structure/cas8_movement > save cas8_movment.cxs includeMaps true ——— End of log from Wed May 28 12:25:00 2025 ——— opened ChimeraX session > show #!14 models > log metadata #3 No models had metadata > log chains #3 Chain information for postcleavage_HNH_outwards.pdb #3 --- Chain | Description A | No description available B | No description available C | No description available D 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 > show #!1 models > show #!3 models > show #!4 models > show #!7 models > show #!15 models > show #!32 models > show #!22 models > show #!25 models > matchmaker #22/A to #14/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker apo_HNH_center.pdb, chain A (#14) with apo_HNH_inwards.pdb, chain A (#22), sequence alignment score = 1518.4 RMSD between 77 pruned atom pairs is 1.474 angstroms; (across all 340 pairs: 10.274) > matchmaker #25/A to #14/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker apo_HNH_center.pdb, chain A (#14) with apo_HNH_outwards_refined.pdb, chain A (#25), sequence alignment score = 1501.9 RMSD between 82 pruned atom pairs is 1.427 angstroms; (across all 336 pairs: 9.925) > matchmaker #7/A to #14/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker apo_HNH_center.pdb, chain A (#14) with halfcleaved_HNH_inwards.pdb, chain A (#7), sequence alignment score = 1519 RMSD between 63 pruned atom pairs is 1.325 angstroms; (across all 340 pairs: 10.974) > matchmaker #32/A to #14/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker apo_HNH_center.pdb, chain A (#14) with halfcleaved_HNH_center_main_model.pdb, chain A (#32), sequence alignment score = 1526.2 RMSD between 181 pruned atom pairs is 1.066 angstroms; (across all 340 pairs: 4.116) > matchmaker #15/A to #14/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker apo_HNH_center.pdb, chain A (#14) with halfcleaved_HNH_outwards.pdb, chain A (#15), sequence alignment score = 1484.2 RMSD between 67 pruned atom pairs is 1.302 angstroms; (across all 340 pairs: 10.332) > matchmaker #1/A to #14/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker apo_HNH_center.pdb, chain A (#14) with postcleavage_HNH_inwards.pdb, chain A (#1), sequence alignment score = 1501.2 RMSD between 65 pruned atom pairs is 1.199 angstroms; (across all 338 pairs: 10.667) > matchmaker #3/A to #14/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker apo_HNH_center.pdb, chain A (#14) with postcleavage_HNH_outwards.pdb, chain A (#3), sequence alignment score = 1520.2 RMSD between 70 pruned atom pairs is 1.370 angstroms; (across all 340 pairs: 10.928) > matchmaker #4/A to #14/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker apo_HNH_center.pdb, chain A (#14) with postcleavage_HNH_center.pdb, chain A (#4), sequence alignment score = 1511.2 RMSD between 184 pruned atom pairs is 1.025 angstroms; (across all 340 pairs: 3.799) > dssp > graphics silhouettes true > graphics silhouettes width 1 > lighting multiShadow 600 > save /Users/gmontoya/Downloads/cas8_movment2.cxs ——— End of log from Wed May 28 15:04:16 2025 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M2 Max OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,6 Model Number: Z176001C0DK/A Chip: Apple M2 Max Total Number of Cores: 12 (8 performance and 4 efficiency) Memory: 64 GB System Firmware Version: 11881.41.5 OS Loader Version: 11881.41.5 Software: System Software Overview: System Version: macOS 15.1.1 (24B91) Kernel Version: Darwin 24.1.0 Time since boot: 27 days, 1 hour, 36 minutes Graphics/Displays: Apple M2 Max: Chipset Model: Apple M2 Max Type: GPU Bus: Built-In Total Number of Cores: 38 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 autocommand: 2.2.2 babel: 2.16.0 backports.tarfile: 1.2.0 beautifulsoup4: 4.12.3 biopython: 1.83 blockdiag: 3.0.0 blosc2: 2.7.1 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.7 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-Clipper: 0.23.0 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.7 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10.dev202412070146 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMalign: 0.1.3 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ISOLDE: 1.8.dev0 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.5 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.7 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-ProfileGrids: 1.0 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.15 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.42.2 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 coverage: 7.6.9 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 DiffFit: 0.6.2 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 finufft: 2.3.1 fonttools: 4.55.2 fsspec: 2024.10.0 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h5py: 3.12.1 html2text: 2024.2.26 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 importlib_metadata: 8.0.0 importlib_resources: 6.4.0 inflect: 7.3.1 iniconfig: 2.0.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jaraco.context: 5.3.0 jaraco.functools: 4.0.1 jaraco.text: 3.12.1 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 more-itertools: 10.3.0 mpmath: 1.3.0 mrcfile: 1.5.0 msgpack: 1.0.8 narwhals: 1.35.0 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 numpy: 1.26.4 openvr: 1.26.701 ordered-set: 4.1.0 packaging: 23.2 packaging: 24.1 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 platformdirs: 4.2.2 plotly: 6.0.1 pluggy: 1.5.0 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pyKVFinder: 0.7.3 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 pytest: 8.3.4 pytest-cov: 6.0.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 sympy: 1.13.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 toml: 0.10.2 tomli: 2.0.1 torch: 2.2.1 tornado: 6.4.2 traitlets: 5.14.3 typeguard: 4.3.0 typing_extensions: 4.12.2 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 zipp: 3.19.2 }}} " defect assigned normal Window Toolkit all ChimeraX