id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5546 Crash saving session including maps joewang@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.18363 ChimeraX Version: 1.3.dev202110050748 (2021-10-05 07:48:25 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Windows fatal exception: code 0x8001010e Thread 0x00002370 (most recent call first): File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1348 in SaveRegsToMRC File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1418 in WriteSelRegionsMRCFile File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 1016 in File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 87 in _run_code File Windows fatal exception: ""code 0xC8001010e: \ProWindows fatal exception: gcode 0xr8001010ea m Windows fatal exception: Fcode 0xi8001010el es\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 197 in _run_module_as_main Windows fatal exception: code 0x8001010e Thread 0x00002370 (most recent call first): File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1348 in SaveRegsToMRC File ""C:\Program Files\ChimeraX 1.3.Windows fatal exception: dcode 0xe8001010ev 20Windows fatal exception: 2code 0x18001010e1 0050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1418 in WriteSelRegionsMRCFile File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 1016 in File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 197 in _run_module_as_main Windows fatal exception: code 0x8001010e Thread 0x00002370 (most recent call first): File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1348 in SaveRegsToMRC File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1418 in WriteSelRegionsMRCFile File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 1016 in File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 197 in _run_module_as_main Windows fatal exception: code 0x8001010e Thread 0x00002370 (most recent call first): File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1348 in SaveRegsToMRC File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1418 in WriteSelRegionsMRCFile File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 1016 in File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 197 in _run_module_as_main Windows fatal exception: code 0x8001010e Thread 0x00002370 (most recent call first): File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1348 in SaveRegsToMRC File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1418 in WriteSelRegionsMRCFile File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 1016 in File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 197 in _run_module_as_main Windows fatal exception: code 0x8001010e Thread 0x00002370 (most recent call first): File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1348 in SaveRegsToMRC File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimeraWindows fatal exception: xcode 0x\8001010es eggeWindows fatal exception: rcode 0x\8001010es egWindows fatal exception: mcode 0xe8001010en t_dialog.py"", line 1418 in WriteSelRegionsMRCFile File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""C:\Program Files\ChimeraX 1.3.Windows fatal exception: dcode 0xe8001010ev2 02110Windows fatal exception: 0code 0x58001010e0 748\bin\lib\site-packages\ChimeraX_main.py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 1016 in Windows fatal exception: File code 0x""8001010eC :\PWindows fatal exception: rcode 0xo8001010eg raWindows fatal exception: mcode 0x 8001010eF iles\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 197 in _run_module_as_mainWindows fatal exception: code 0x8001010e Thread 0xWindows fatal exception: 00002370code 0x (most recent call first): 8001010e File ""CWindows fatal exception: :code 0x\8001010eP rogram Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1348 in SaveRegsToMRC File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-Windows fatal exception: pcode 0xa8001010ec kagWindows fatal exception: ecode 0xs8001010e\ chimerax\segger\segment_dialog.py"", line 1418 in WriteSelRegionsMRCFile File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 1016 in File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 197 in _run_module_as_main Windows fatal exception: code 0x8001010e Thread 0x00002370 (most recent call first): File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1348 in SaveRegsToMRC File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1418 in WriteSelRegionsMRCFile File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 1016 in File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 197 in _run_module_as_main Windows fatal exception: code 0x8001010e Thread 0x00002370 (most recent call first): File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1348 in SaveRegsToMRC File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1418 in WriteSelRegionsMRCFile File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 1016 in File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 197 in _run_modulWindows fatal exception: ecode 0x_8001010ea s_mainWindows fatal exception: code 0x8001010e Thread 0xWindows fatal exception: 00002370code 0x (most recent call first): 8001010e File ""CWindows fatal exception: :code 0x\8001010eP rogram Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1348 in SaveRegsToMRC File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segmentWindows fatal exception: _code 0xd8001010ei alogWindows fatal exception: .code 0xp8001010ey "", line 1418 in WriteSelRegionsMRCFile File ""C:\Program Files\ChimeraX 1.3.dev202110050Windows fatal exception: 7code 0x48001010e8 \biWindows fatal exception: ncode 0x\8001010el ibWindows fatal exception: \code 0xs8001010ei te-packages\chimerax\ui\gui.py"", line 301 in evenWindows fatal exception: tcode 0x_8001010el ooWindows fatal exception: pcode 0x 8001010e File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3.dev202110050748\Windows fatal exception: bcode 0xi8001010en \lWindows fatal exception: icode 0xb8001010e\ siWindows fatal exception: tcode 0xe8001010e- packages\ChimeraX_main.py"", line 1016 in File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 197 in _run_module_as_main Windows fatal exception: code 0x8001010e Thread 0x00002370 (most recent call first): File ""C:\Program Files\ChimeraX 1Windows fatal exception: .code 0x38001010e. devWindows fatal exception: 2code 0x08001010e2 110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1348 in SaveRegsToMRC File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1418 in WriteSelRegionsMRCFile File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\cWindows fatal exception: hcode 0xi8001010e merWindows fatal exception: acode 0xx8001010e\ uWindows fatal exception: icode 0x\8001010eg uWindows fatal exception: icode 0x.8001010ep Windows fatal exception: ycode 0x""8001010e, line 301 in evWindows fatal exception: ecode 0xn8001010et _loop File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_maiWindows fatal exception: ncode 0x.8001010ep y"", line Windows fatal exception: 1016code 0x in 8001010eWindows fatal exception: code 0x File 8001010e"" C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 197 in _run_module_as_main Windows fatal exception: code 0x8001010e Thread 0x00002370 (most recent call first): File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1348 in SaveRegsToMRC File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1418 in WriteSelRegionsMRCFile File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 1016 in File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 197 in _run_module_as_main Windows fatal exception: code 0x8001010e Thread 0x00002370 (most recent call first): File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1348 in SaveRegsToMRC File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1418 in WriteSelRegionsMRCFile File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 1016 in File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 197 in _run_module_as_main Windows fatal exception: code 0x8001010e Thread 0x00002370 (most recent call first): File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1348 in SaveRegsToMRC File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1418 in WriteSelRegionsMRCFile File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 1016 in File ""C:\Program Files\ChimeraX 1.3.dev202Windows fatal exception: 1code 0x18001010e0 0507Windows fatal exception: 4code 0x88001010e\ biWindows fatal exception: ncode 0x\8001010el ib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 197 in _run_module_as_main Windows fatal exception: code 0x8001010e Thread 0x00002370 (most recent call first): File ""C:\Program Files\ChimeraX 1.Windows fatal exception: 3code 0x.8001010ed ev2Windows fatal exception: 0code 0x28001010e1 10050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1348 in SaveRegsToMRC File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialoWindows fatal exception: gcode 0x.8001010ep y"", line Windows fatal exception: 1418code 0x in 8001010eW riWindows fatal exception: tcode 0xe8001010eS elRegionsMRCFile File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""C:\Program Files\ChimerWindows fatal exception: acode 0xX8001010e 1.3Windows fatal exception: .code 0xd8001010ee v202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3.dev2Windows fatal exception: 0code 0x28001010e1 100Windows fatal exception: 5code 0x08001010e7 48Windows fatal exception: \code 0xb8001010ei n\lib\site-packages\ChimeraX_main.py"", line 1016 in File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 87 in _run_code File ""C:\ProgrWindows fatal exception: acode 0xm8001010e FilWindows fatal exception: ecode 0xs8001010e\ ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 197 in _run_module_as_main Windows fatal exception: code 0x8001010e Thread 0x00002370 (most recent call first): File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1348 in SaveRegsToMRC File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chWindows fatal exception: icode 0xm8001010ee raxWindows fatal exception: \code 0xs8001010ee ggWindows fatal exception: ecode 0xr8001010e\ segment_dialog.py"", line 1418 in WriteSelRegionsMRCFile File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""C:\Program Files\ChimeraX 1.3.dev2021100Windows fatal exception: 5code 0x08001010e7 48\Windows fatal exception: bcode 0xi8001010en \lib\site-packages\ChimeraX_main.py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 1016 in File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 197 in _run_module_as_main Windows fatal exception: code 0x8001010e Thread 0x00002370 (most recent call first): File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\seggWindows fatal exception: ecode 0xr8001010e\ segWindows fatal exception: mcode 0xe8001010en t_dialog.py"", line 1348 in SaveRegsToMRC File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1418 in WriteSelRegionsMRCFile File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-Windows fatal exception: pcode 0xa8001010ec kagWindows fatal exception: ecode 0xs8001010e\ ChWindows fatal exception: icode 0xm8001010ee raX_main.py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 1016 in File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 87 in _rWindows fatal exception: ucode 0xn8001010e_ codWindows fatal exception: ecode 0x 8001010e File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 197 in _run_module_as_main Windows fatal exception: code 0x8001010e Thread 0x00002370 (most recent call first): File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1348 in SaveRegsToMRC File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1418 in WriteSelRegionsMRCFile File ""C:\Program FileWindows fatal exception: scode 0x\8001010eC himWindows fatal exception: ecode 0xr8001010ea X Windows fatal exception: 1code 0x.8001010e3 .dev202110050748\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""C:\Program Files\ChimerWindows fatal exception: acode 0xX8001010e 1.3.dWindows fatal exception: ecode 0xv8001010e2 02110050748\bin\lib\site-packagesWindows fatal exception: \code 0xC8001010eh imeWindows fatal exception: rcode 0xa8001010eX _maWindows fatal exception: icode 0xn8001010e. py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packagWindows fatal exception: ecode 0xs8001010e\ ChimWindows fatal exception: ecode 0xr8001010ea X_main.py"", line 1016 in File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpyWindows fatal exception: .code 0xp8001010ey "", line 197 in Windows fatal exception: _code 0xr8001010eu n_moWindows fatal exception: dcode 0xu8001010el e_as_main Windows fatal exception: code 0x8001010e Thread 0x00002370 (most recent call first): File ""C:\Program Files\ChimerWindows fatal exception: acode 0xX8001010e 1.3.Windows fatal exception: dcode 0xe8001010ev 202110050748\bin\lib\site-packages\chimerax\segger\segmWindows fatal exception: ecode 0xn8001010et _diWindows fatal exception: acode 0xl8001010eo g.Windows fatal exception: pcode 0xy8001010e"" , line 1348 in SaveRegsToMRC File ""C:\Program Files\ChimeraX 1Windows fatal exception: .code 0x38001010e. devWindows fatal exception: 2code 0x08001010e2 110050748\bin\lib\site-packages\cWindows fatal exception: code 0x8001010e hiWindows fatal exception: mcode 0xe8001010er ax\Windows fatal exception: scode 0xe8001010e gger\segment_dialog.py"", line 1418 in WriteSelRegionsMRCFiWindows fatal exception: lcode 0xe8001010e File ""Windows fatal exception: Ccode 0x:8001010e\ Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 1016 in File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 197 in _run_module_as_main Windows fatal exception: code 0x8001010e Thread 0x00002370 (most recent call first): File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1348 in SaveRegsToMRC File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1418 in WriteSelRegionsMRCFile File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 1016 in File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 197 in _run_module_as_main Windows fatal exception: code 0x8001010e Thread 0x00002370 (most recent call first): File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1348 in SaveRegsToMRC File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1418 in WriteSelRegionsMRCFile File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 1016 in File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 197 in _run_module_as_main Windows fatal exception: code 0x8001010e Thread 0x00001774 (most recent call first): File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\threading.py"", line 316 in wait File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\threading.py"", line 574 in wait File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\threading.py"", line 1284 in run File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00002370 (most recent call first): File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1348 in SaveRegsToMRC File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1418 in WriteSelRegionsMRCFile File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 1016 in File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 197 in _run_module_as_main Windows fatal exception: code 0x8001010e Thread 0x00001774 (most recent call first): File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\threading.py"", line 316 in wait File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\threading.py"", line 574 in wait File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\threading.py"", line 1284 in run File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\threading.py"", line 930 in _bootstrap Thread 0xWindows fatal exception: 00002370code 0x (most recent call first): 8001010e File ""C:\Windows fatal exception: Pcode 0xr8001010eo grWindows fatal exception: acode 0xm8001010e Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\seWindows fatal exception: gcode 0xm8001010ee nt_Windows fatal exception: dcode 0xi8001010ea loWindows fatal exception: gcode 0x.8001010ep y"", line 1348 in SaveRegsToMRC File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1418 in WriteSelRegionsMRCFile File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_lWindows fatal exception: ocode 0xo8001010ep File ""Windows fatal exception: Ccode 0x:8001010e\ Program Files\ChimeraX 1.3.dev202110050748\bin\lib\siteWindows fatal exception: -code 0xp8001010ea ckaWindows fatal exception: gcode 0xe8001010es \ChimeraX_main.py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 1016 in File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 197 in _run_module_as_main Windows fatal exception: code 0x8001010e Thread 0x00001774 (most recent call first): File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\threading.py"", line 316 in wait File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\threading.py"", line 574 in wait File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\threading.py"", line 1284 in run File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00002370 (most recent call first): File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1348 in SaveRegsToMRC File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\segger\segment_dialog.py"", line 1418 in WriteSelRegionsMRCFile File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\ChimeraX_main.py"", line 1016 in File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\runpy.py"", line 197 in _run_module_as_main Windows fatal exception: code 0x8001010e Thread 0x00001774 (most recent call first): File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\threading.py"", line 316 in wait File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\threading.py"", line 574 in wait File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\threading.py"", line 1284 in run File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00002370 (most recent call first): File ""C:\Program Files\ChimeraX 1.3.dev202110050748\bin\lib\site-packages\chimerax\atomic\molc.py"", line 196 in get_prop Windows fatal exception: access violation Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e ===== Log before crash start ===== UCSF ChimeraX version: 1.3.dev202110050748 (2021-10-05) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > D:\\\Projects\\\WHV\\\2020_0913\\\2x_034_5.9A-6.7Apo_3dc_34520p\\\run_class001.mrc Opened run_class001.mrc as #1, grid size 200,200,200, pixel 1.68, shown at level 0.00914, step 1, values float32 > volume #1 level 0.00707 > volume #1 level 0.007924 > close #1 > open D:/Projects/WHV/2020_0913/2x_034_5.9A-6.7Apo_3dc_34520p/postprocess.mrc Opened postprocess.mrc as #1, grid size 200,200,200, pixel 1.68, shown at level 0.0232, step 1, values float32 > view orient > view > volume #1 level 0.01763 > ui tool show ""Hide Dust"" > surface dust #1 size 10.08 > open > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_PostProcess_6.6A_job051/postprocess.mrc Opened postprocess.mrc as #2, grid size 200,200,200, pixel 1.68, shown at level 0.0218, step 1, values float32 > hide #!1 models > view > view orient > volume #2 level 0.01765 > surface dust #2 size 10.08 > surface dust #2 size 5 > volume #2 level 0.01418 > lighting soft > surface undust #2 > volume #2 level 0.0173 > volume #2 level 0.02148 > volume #2 level 0.02182 > open > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/run_class001.mrc Opened run_class001.mrc as #3, grid size 200,200,200, pixel 1.68, shown at level 0.00978, step 1, values float32 > volume #3 level 0.007635 > open > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/4x_0415_oct.mrc Opened 4x_0415_oct.mrc as #4, grid size 100,100,100, pixel 3.36, shown at level 0.0339, step 1, values float32 > hide #!3 models > volume #4 level 0.02377 > volume #4 level 0.02853 > close #4 > volume #3 level 0.008508 > close #3 > open > D:/Projects/HBV/Analysis/Focus_Classification/3DC_ABCD/C70_Masked_ABCD.mrc Opened C70_Masked_ABCD.mrc as #3, grid size 640,640,640, pixel 0.84, shown at level 5e-05, step 4, values float32 > hide #!3 models > open D:/Projects/HBV/HBc_WT/mask_60-100.mrc Opened mask_60-100.mrc as #4, grid size 320,320,320, pixel 1, shown at level 1, step 2, values float32 > volume #4 level 0.02617 > select #4 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #4,1,0,0,195.75,0,1,0,183.38,0,0,1,145.42 > view matrix models #4,1,0,0,192.21,0,1,0,177.8,0,0,1,142.91 > view matrix models #4,1,0,0,191.82,0,1,0,177.67,0,0,1,142.61 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.60072,-0.45549,-0.65701,189.86,-0.68468,0.13114,-0.71694,174.53,0.41273,0.88053,-0.23309,143.55 > view orient > view matrix models > #4,0.6918,0.26372,-0.67221,191.37,-0.71046,0.082176,-0.69892,174.42,-0.12908,0.96109,0.24421,143.64 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.6918,0.26372,-0.67221,147.3,-0.71046,0.082176,-0.69892,180.93,-0.12908,0.96109,0.24421,143.64 > view matrix models > #4,0.6918,0.26372,-0.67221,147.59,-0.71046,0.082176,-0.69892,216.25,-0.12908,0.96109,0.24421,183.61 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.54305,-0.34105,-0.76732,146.14,-0.50277,0.59984,-0.62243,217.57,0.67255,0.72379,0.15427,183.85 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.54305,-0.34105,-0.76732,155.04,-0.50277,0.59984,-0.62243,186.35,0.67255,0.72379,0.15427,201.86 > close #3 > ui tool show ""Map Coordinates"" > color #4 #ffb2b29b models > view matrix models > #4,0.54305,-0.34105,-0.76732,157.69,-0.50277,0.59984,-0.62243,185.25,0.67255,0.72379,0.15427,202.54 > view matrix models > #4,0.54305,-0.34105,-0.76732,149.49,-0.50277,0.59984,-0.62243,189.28,0.67255,0.72379,0.15427,200.38 > view matrix models > #4,0.54305,-0.34105,-0.76732,147.34,-0.50277,0.59984,-0.62243,211.22,0.67255,0.72379,0.15427,220.42 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.81027,-0.37561,-0.44987,147.59,-0.52205,-0.11375,-0.8453,210.39,0.26633,0.91977,-0.28825,220.19 > view matrix models > #4,0.57064,-0.46389,-0.67762,147.27,-0.4708,0.49127,-0.7328,211.08,0.67284,0.73719,0.061937,220.39 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.57064,-0.46389,-0.67762,149.55,-0.4708,0.49127,-0.7328,193.7,0.67284,0.73719,0.061937,223.41 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.59366,-0.50262,-0.62845,149.55,-0.48597,0.39855,-0.77781,193.58,0.64141,0.76716,-0.007652,223.39 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.59366,-0.50262,-0.62845,148.46,-0.48597,0.39855,-0.77781,189.4,0.64141,0.76716,-0.007652,225.53 > open > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/run_class001.mrc Opened run_class001.mrc as #3, grid size 200,200,200, pixel 1.68, shown at level 0.00978, step 1, values float32 > volume #3 level 0.008977 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.65089,-0.36708,-0.66453,148.64,-0.55588,0.36571,-0.74649,189.33,0.51705,0.85528,0.033987,225.59 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.65089,-0.36708,-0.66453,141.44,-0.55588,0.36571,-0.74649,198.23,0.51705,0.85528,0.033987,241.53 > view matrix models > #4,0.65089,-0.36708,-0.66453,140.51,-0.55588,0.36571,-0.74649,194.94,0.51705,0.85528,0.033987,242.77 > ui tool show ""Side View"" > open D:/Projects/HBV/HBc_WT/mask_80-140.mrc Opened mask_80-140.mrc as #5, grid size 320,320,320, pixel 1, shown at level 1, step 2, values float32 > volume #5 level 0 > view > volume #5 level 0.5187 > select #5 2 models selected > ~select #4 2 models selected > view matrix models #5,1,0,0,179.26,0,1,0,191.94,0,0,1,175.54 > view matrix models #5,1,0,0,177.96,0,1,0,189.9,0,0,1,174.15 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.85114,0.42385,0.30971,178.97,-0.25543,-0.18105,0.94973,188.23,0.45861,-0.88745,-0.045834,171.79 > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > view matrix models > #5,0.85114,0.42385,0.30971,166.92,-0.25543,-0.18105,0.94973,203.29,0.45861,-0.88745,-0.045834,200.64 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.86082,0.37272,0.34651,166.86,-0.21876,-0.34377,0.91322,202.97,0.45949,-0.86192,-0.21439,200.52 > view matrix models > #5,0.78451,0.35877,0.5058,166.9,-0.40103,-0.32861,0.8551,202.84,0.473,-0.87367,-0.11392,200.58 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.78451,0.35877,0.5058,150.03,-0.40103,-0.32861,0.8551,217.82,0.473,-0.87367,-0.11392,224.18 > hide #!3 models > show #!3 models > hide #!3 models > view matrix models > #5,0.78451,0.35877,0.5058,149.39,-0.40103,-0.32861,0.8551,220.55,0.473,-0.87367,-0.11392,231.02 > close #5 > open D:/Projects/HBV/HBc_WT/Class005_2L_DNA/mask_60-180.mrc Opened mask_60-180.mrc as #5, grid size 320,320,320, pixel 1, shown at level 1, step 2, values float32 > volume #5 level 0.8676 > select #5 2 models selected > view matrix models #5,1,0,0,213.65,0,1,0,40.986,0,0,1,48.903 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.91625,-0.35462,0.18639,213.05,0.36788,0.56058,-0.7419,39.733,0.15861,0.74833,0.64408,50.203 > view matrix models > #5,0.94062,-0.26022,0.218,213.29,0.32209,0.48126,-0.81526,39.455,0.10723,0.83706,0.5365,50.221 > view matrix models > #5,0.87663,-0.3738,0.30298,213.08,0.45191,0.42338,-0.78519,39.499,0.16523,0.82524,0.54007,50.259 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.87663,-0.3738,0.30298,152.71,0.45191,0.42338,-0.78519,200.04,0.16523,0.82524,0.54007,215.33 > select #3 2 models selected > view > ~select #3 Nothing selected > show #!3 models > hide #!4 models > color #5 #99bfe59b models > view orient > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > ~select #5 Nothing selected > select #5 2 models selected > view matrix models > #5,0.87663,-0.3738,0.30298,150.97,0.45191,0.42338,-0.78519,179.47,0.16523,0.82524,0.54007,217.87 > view matrix models > #5,0.87663,-0.3738,0.30298,147.18,0.45191,0.42338,-0.78519,185.65,0.16523,0.82524,0.54007,227.02 > ui mousemode right ""move picked models"" > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.8404,-0.36965,0.39635,147.22,0.49954,0.24462,-0.83104,185.44,0.21023,0.89639,0.39023,227.04 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.8404,-0.36965,0.39635,149.58,0.49954,0.24462,-0.83104,192.02,0.21023,0.89639,0.39023,224.44 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.8882,-0.30346,0.34498,149.65,0.44976,0.42086,-0.78777,192.22,0.093868,0.85486,0.51029,224.39 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.8882,-0.30346,0.34498,146.86,0.44976,0.42086,-0.78777,186.07,0.093868,0.85486,0.51029,226.59 > ui tool show ""Side View"" QWindowsWindow::setGeometry: Unable to set geometry 575x96-356+333 (frame: 591x135-364+302) on QWidgetWindow/""QDockWidgetClassWindow"" on ""\\\\.\DISPLAY2"". Resulting geometry: 458x75-357+326 (frame: 474x114-365+295) margins: 8, 31, 8, 8 minimum size: 156x70 maximum size: 524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=172,109 maxtrack=524303,524326) > select #5 3 models selected > ~select #5 Nothing selected > select #5 3 models selected > ui mousemode right ""translate selected models"" > view matrix models > #5,0.8882,-0.30346,0.34498,149.65,0.44976,0.42086,-0.78777,185.64,0.093868,0.85486,0.51029,227.57 > ~select #5 Nothing selected > volume mask #5 surfaces #3 Opened mask_60-180.mrc masked as #6, grid size 320,238,320, pixel 0.6, shown at step 1, values float32 > close #6 > volume mask #3 surfaces #5 Opened run_class001.mrc masked as #6, grid size 62,68,79, pixel 1.68, shown at step 1, values float32 > volume #6 level 0.007367 > ui tool show ""Map Coordinates"" > close #6 > show #!3 models > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > view orient > show #!5 models > select #5 3 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.89779,-0.21771,0.38284,149.8,0.43722,0.33611,-0.83419,185.48,0.052931,0.91631,0.39695,227.55 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.89779,-0.21771,0.38284,142.52,0.43722,0.33611,-0.83419,187.64,0.052931,0.91631,0.39695,223.86 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.89199,-0.24295,0.38123,142.48,0.44658,0.34267,-0.82652,187.66,0.070165,0.9075,0.41415,223.87 > volume #3 level 0.009581 > ~select #5 Nothing selected > hide #!5 models > volume #3 level 0.00891 > show #!5 models > volume #3 level 0.007837 > volume mask #3 surfaces #5 Opened run_class001.mrc masked as #6, grid size 64,70,85, pixel 1.68, shown at step 1, values float32 QWindowsWindow::setGeometry: Unable to set geometry 1920x1055+0+29 (frame: 1938x1102-9-9) on QWidgetWindow/""MainWindowClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 1920x1001+0+29 (frame: 1938x1048-9-9) margins: 9, 38, 9, 9 minimum size: 470x1055 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=488,1102 maxtrack=0,0) > hide #!5 models > volume #6 level 0.006965 > volume #6 level 0.009044 > volume #6 level 0.008105 > volume #6 level 0.00247 > close #6 > show #!3 models > ui mousemode right ""rotate selected models"" > select #5 3 models selected > view matrix models > #5,0.89669,-0.29168,0.33297,142.38,0.42028,0.32484,-0.84726,187.6,0.13897,0.89967,0.41387,223.9 > view matrix models > #5,0.91795,-0.29375,0.26661,142.35,0.36226,0.34682,-0.86515,187.58,0.16167,0.89074,0.42478,223.91 > ~select #5 Nothing selected > volume mask #3 surfaces #5 Opened run_class001.mrc masked as #6, grid size 72,74,92, pixel 1.68, shown at step 1, values float32 QWindowsWindow::setGeometry: Unable to set geometry 1920x1055+0+29 (frame: 1938x1102-9-9) on QWidgetWindow/""MainWindowClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 1920x1001+0+29 (frame: 1938x1048-9-9) margins: 9, 38, 9, 9 minimum size: 470x1055 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=488,1102 maxtrack=0,0) > volume #6 level 0.007904 > volume #6 level 0.004147 > volume #6 level 0.006898 > volume #6 level 0.002873 > close #6 > volume mask #3 surfaces #5 Opened run_class001.mrc masked as #6, grid size 76,80,98, pixel 1.68, shown at step 1, values float32 QWindowsWindow::setGeometry: Unable to set geometry 1920x1055+0+29 (frame: 1938x1102-9-9) on QWidgetWindow/""MainWindowClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 1920x1001+0+29 (frame: 1938x1048-9-9) margins: 9, 38, 9, 9 minimum size: 470x1055 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=488,1102 maxtrack=0,0) > volume #6 level 0.0073 > volume #6 level 0.006093 > volume #6 level 0.004483 > volume #6 level 0.004348 > show #!3 models > show #!5 models > ui mousemode right ""translate selected models"" > select #5 3 models selected > view matrix models > #5,0.91795,-0.29375,0.26661,139.61,0.36226,0.34682,-0.86515,189.64,0.16167,0.89074,0.42478,229.49 > close #6 > ~select #5 Nothing selected > volume mask #3 surfaces #5 Opened run_class001.mrc masked as #6, grid size 77,80,98, pixel 1.68, shown at step 1, values float32 QWindowsWindow::setGeometry: Unable to set geometry 1920x1055+0+29 (frame: 1938x1102-9-9) on QWidgetWindow/""MainWindowClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 1920x1001+0+29 (frame: 1938x1048-9-9) margins: 9, 38, 9, 9 minimum size: 470x1055 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=488,1102 maxtrack=0,0) > hide #!5 models > volume #6 level 0.007971 > volume #6 level 0.009178 > volume #6 level 0.007367 > volume #6 level 0.00891 > volume #6 level 0.007837 > show #!5 models > select #5 3 models selected > ui mousemode right ""translate selected models"" > view matrix models > #5,0.91795,-0.29375,0.26661,137.88,0.36226,0.34682,-0.86515,191.43,0.16167,0.89074,0.42478,234.08 > ~select #5 Nothing selected > close #6 > volume mask #3 surfaces #5 Opened run_class001.mrc masked as #6, grid size 77,80,98, pixel 1.68, shown at step 1, values float32 QWindowsWindow::setGeometry: Unable to set geometry 1920x1055+0+29 (frame: 1938x1102-9-9) on QWidgetWindow/""MainWindowClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 1920x1001+0+29 (frame: 1938x1048-9-9) margins: 9, 38, 9, 9 minimum size: 470x1055 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=488,1102 maxtrack=0,0) > volume #6 level 0.004751 > volume #6 level 0.008508 > volume #6 level 0.007166 > close #6 > volume resample #5 ogGrid #3 Expected a keyword > volume resample #5 onGrid #3 Opened mask_60-180.mrc resampled as #6, grid size 200,200,200, pixel 1.68, shown at step 1, values float32 QWindowsWindow::setGeometry: Unable to set geometry 1920x1055+0+29 (frame: 1938x1102-9-9) on QWidgetWindow/""MainWindowClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 1920x1001+0+29 (frame: 1938x1048-9-9) margins: 9, 38, 9, 9 minimum size: 470x1055 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=488,1102 maxtrack=0,0) > save > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/Mask_1Spike.mrc > models #6 > hide #!6 models > show #!6 models > close #5 > close #4 > show #!1 models > hide #!1 models > open > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/WHV_0913_job048_6.1A_DeepEM.mrc Opened WHV_0913_job048_6.1A_DeepEM.mrc as #4, grid size 200,200,200, pixel 1.68, shown at level 0.133, step 1, values float32 > hide #!4 models > show #!4 models > hide #!6 models > volume #4 level 0.07975 > volume #4 level 0.01814 > volume #4 level 0.09583 > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!1 models > hide #!4 models > open > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/AlphaFold/rank_1_model_3_ptm_seed_0_unrelaxed.pdb Chain information for rank_1_model_3_ptm_seed_0_unrelaxed.pdb #5 --- Chain | Description A | No description available > open > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/AlphaFold/rank_2_model_4_ptm_seed_0_unrelaxed.pdb Chain information for rank_2_model_4_ptm_seed_0_unrelaxed.pdb #7 --- Chain | Description A | No description available > open > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/AlphaFold/rank_3_model_5_ptm_seed_0_unrelaxed.pdb Chain information for rank_3_model_5_ptm_seed_0_unrelaxed.pdb #8 --- Chain | Description A | No description available > open > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/AlphaFold/rank_4_model_1_ptm_seed_0_unrelaxed.pdb Chain information for rank_4_model_1_ptm_seed_0_unrelaxed.pdb #9 --- Chain | Description A | No description available > open > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/AlphaFold/rank_5_model_2_ptm_seed_0_unrelaxed.pdb Chain information for rank_5_model_2_ptm_seed_0_unrelaxed.pdb #10 --- Chain | Description A | No description available > hide #!1 models > preset ""overall look"" publication Preset expands to these ChimeraX commands: set bg white graphics silhouettes t > view > hide #10 models > hide #9 models > hide #8 models > hide #7 models > hide #5 models > show #5 models > select #5 1808 atoms, 1881 bonds, 222 residues, 1 model selected > view matrix models #5,1,0,0,-5.6579,0,1,0,3.983,0,0,1,2.3951 > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.61581,-0.78727,0.031334,-8.1594,-0.70516,0.53297,-0.46765,-0.91207,0.35147,-0.31008,-0.88336,-11.889 > select clear > show #7 models > hide #7 models > ui tool show Matchmaker > matchmaker #7 to #5 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 rank_1_model_3_ptm_seed_0_unrelaxed.pdb, chain A (#5) with rank_2_model_4_ptm_seed_0_unrelaxed.pdb, chain A (#7), sequence alignment score = 1179.4 RMSD between 57 pruned atom pairs is 0.913 angstroms; (across all 222 pairs: 15.130) > matchmaker #8 to #5 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 rank_1_model_3_ptm_seed_0_unrelaxed.pdb, chain A (#5) with rank_3_model_5_ptm_seed_0_unrelaxed.pdb, chain A (#8), sequence alignment score = 1214.2 RMSD between 97 pruned atom pairs is 0.773 angstroms; (across all 222 pairs: 8.587) > matchmaker #9 to #5 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 rank_1_model_3_ptm_seed_0_unrelaxed.pdb, chain A (#5) with rank_4_model_1_ptm_seed_0_unrelaxed.pdb, chain A (#9), sequence alignment score = 1193.2 RMSD between 85 pruned atom pairs is 1.062 angstroms; (across all 222 pairs: 17.265) > matchmaker #10 to #5 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 rank_1_model_3_ptm_seed_0_unrelaxed.pdb, chain A (#5) with rank_5_model_2_ptm_seed_0_unrelaxed.pdb, chain A (#10), sequence alignment score = 1200.4 RMSD between 34 pruned atom pairs is 0.536 angstroms; (across all 222 pairs: 27.054) > show #7 models > show #8 models > show #9 models > show #10 models > hide #10 models > hide #9 models > hide #8 models > hide #7 models > show #7 models > show #8 models > hide #7 models > show #7 models > hide #5 models > hide #8 models > show #9 models > hide #9 models > show #10 models > select clear > hide #10 models > hide #7 models > show #7 models > show #5 models > hide #7 models > show #7 models > select #7/A:98 14 atoms, 15 bonds, 1 residue, 1 model selected > select up 264 atoms, 271 bonds, 29 residues, 1 model selected > select add #5/A:97 272 atoms, 278 bonds, 30 residues, 2 models selected > select up 528 atoms, 542 bonds, 58 residues, 2 models selected > matchmaker #5 & sel to #7 & sel 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 rank_2_model_4_ptm_seed_0_unrelaxed.pdb, chain A (#7) with rank_1_model_3_ptm_seed_0_unrelaxed.pdb, chain A (#5), sequence alignment score = 158.6 RMSD between 29 pruned atom pairs is 0.283 angstroms; (across all 29 pairs: 0.283) > hide #7 models > show #8 models > select add #8/A:85 536 atoms, 549 bonds, 59 residues, 3 models selected > select up 792 atoms, 813 bonds, 87 residues, 3 models selected > matchmaker #8 & sel to #7 & sel 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 rank_2_model_4_ptm_seed_0_unrelaxed.pdb, chain A (#7) with rank_3_model_5_ptm_seed_0_unrelaxed.pdb, chain A (#8), sequence alignment score = 158.6 RMSD between 29 pruned atom pairs is 0.340 angstroms; (across all 29 pairs: 0.340) > hide #5 models > show #7 models > hide #8 models > show #9 models > select add #9/A:73 800 atoms, 820 bonds, 88 residues, 4 models selected > select up 1067 atoms, 1096 bonds, 117 residues, 4 models selected > matchmaker #9 & sel to #7 & sel 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 rank_2_model_4_ptm_seed_0_unrelaxed.pdb, chain A (#7) with rank_4_model_1_ptm_seed_0_unrelaxed.pdb, chain A (#9), sequence alignment score = 158.6 RMSD between 29 pruned atom pairs is 0.443 angstroms; (across all 29 pairs: 0.443) > show #10 models > hide #9 models > select add #10/A:91 1078 atoms, 1107 bonds, 118 residues, 5 models selected > select up 1354 atoms, 1391 bonds, 149 residues, 5 models selected > matchmaker #10 & sel to #7 & sel 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 rank_2_model_4_ptm_seed_0_unrelaxed.pdb, chain A (#7) with rank_5_model_2_ptm_seed_0_unrelaxed.pdb, chain A (#10), sequence alignment score = 158.6 RMSD between 29 pruned atom pairs is 0.303 angstroms; (across all 29 pairs: 0.303) > show #9 models > show #8 models > show #5 models > select clear > hide #10 models > hide #9 models > hide #8 models > hide #7 models > hide #5 models > show #5 models > hide #5 models > show #7 models > ui tool show ""Scale Bar"" > scalebar > scalebar 10 > scalebar 100 > scalebar xpos 0.15 > scalebar xpos 0.2 > save > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/AlphaFold_model2_10nm.png > width 1340 height 839 supersample 3 > hide #7 models > show #5 models > show #7 models > hide #7 models > show #7 models > hide #7 models > save > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/AlphaFold_model1_10nm.png > width 1340 height 839 supersample 3 > hide #5 models > show #8 models > save > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/AlphaFold_model3_10nm.png > width 1340 height 839 supersample 3 > lighting full > graphics silhouettes false > graphics silhouettes true > save > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/AlphaFold_model3_10nm.png > width 1340 height 839 supersample 3 > hide #8 models > show #7 models > save > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/AlphaFold_model2_10nm.png > width 1340 height 839 supersample 3 > hide #7 models > show #5 models > save > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/AlphaFold_model1_10nm.png > width 1340 height 839 supersample 3 > show #9 models > hide #5 models > save > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/AlphaFold_model4_10nm.png > width 1340 height 839 supersample 3 > hide #9 models > show #10 models > save > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/AlphaFold_model5_10nm.png > width 1340 height 839 supersample 3 > hide #10 models > hide #!11 models > view orient > volume flip #4 Opened WHV_0913_job048_6.1A_DeepEM.mrc z flip as #12, grid size 200,200,200, pixel 1.68, shown at step 1, values float32 > lighting soft No map chosen to save > save > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/WHV_0913_job048_6.1A_DeepEM- > CH.mrc models #12 > save > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/AlphaFoldAnalysis/5_model_Comparison.cxs > view orient > close #3 > volume #6 color #b2ffb29b > ui mousemode right ""rotate selected models"" > select #6 3 models selected > view matrix models > #6,0.99567,0.036497,0.085527,-26.291,-0.037586,0.99923,0.011158,2.7104,-0.085054,-0.014325,0.99627,15.285 > ~select #6 Nothing selected > close #4 > volume mask #12 surfaces #6 Opened WHV_0913_job048_6.1A_DeepEM-CH.mrc masked as #3, grid size 70,81,98, pixel 1.68, shown at step 1, values float32 > volume #12 level 0.1574 > volume #3 level 0.1527 > volume #3 level 0.08807 > volume #3 level 0.01054 > volume #3 level 0.005369 > hide #!6 models > show #!6 models > select #6 3 models selected > view matrix models > #6,0.99567,0.042348,0.082694,-26.753,-0.045563,0.99826,0.037388,-2.112,-0.080967,-0.040994,0.99587,19.922 > close #3 > volume mask #12 surfaces #6 Opened WHV_0913_job048_6.1A_DeepEM-CH.mrc masked as #3, grid size 70,83,98, pixel 1.68, shown at step 1, values float32 > ~select #6 Nothing selected > volume #12 level 0.1012 > volume #3 level 0.02304 > volume #3 level 0.01529 > volume #3 level 0.02046 > volume #3 level 0.02304 > volume #3 level 0.02563 > volume #3 level 0.0308 > volume #3 level 0.04372 > volume #3 level 0.0463 > volume #3 level 0.04889 > volume #3 level 0.05664 > volume #3 level 0.06181 > volume #3 level 0.0644 > volume #3 level 0.06956 > volume #3 level 0.07473 > volume #3 level 0.07732 > volume #3 level 0.0799 > volume #3 level 0.07732 > volume #3 level 0.07473 > volume #3 level 0.07215 > volume #3 level 0.06956 > volume #3 level 0.05923 > volume #3 level 0.1135 > camera ortho > ui mousemode right ""translate selected models"" > select #6 3 models selected > view matrix models > #6,0.99567,0.042348,0.082694,-28.27,-0.045563,0.99826,0.037388,0.5582,-0.080967,-0.040994,0.99587,18.388 > view matrix models > #6,0.99567,0.042348,0.082694,-28.894,-0.045563,0.99826,0.037388,0.71738,-0.080967,-0.040994,0.99587,18.175 > close #3 > volume mask #12 surfaces #6 Opened WHV_0913_job048_6.1A_DeepEM-CH.mrc masked as #3, grid size 70,82,98, pixel 1.68, shown at step 1, values float32 > volume #3 level 0.1167 > volume #3 level 0.1296 > view matrix models > #6,0.99567,0.042348,0.082694,-25.364,-0.045563,0.99826,0.037388,3.5671,-0.080967,-0.040994,0.99587,17.783 > close #3 > volume mask #12 surfaces #6 Opened WHV_0913_job048_6.1A_DeepEM-CH.mrc masked as #3, grid size 70,83,98, pixel 1.68, shown at step 1, values float32 > ~select #6 Nothing selected > volume #12 level 0.08779 > volume #3 level 0.06507 > volume #3 level 0.1012 > volume #3 level 0.03928 > volume #3 level 0.1038 > view > select #6 2 models selected > view matrix models > #6,0.99567,0.042348,0.082694,-23.082,-0.045563,0.99826,0.037388,4.6632,-0.080967,-0.040994,0.99587,17.827 > ~select #6 Nothing selected > hide #!6 models > close #3 > volume mask #12 surfaces #6 Opened WHV_0913_job048_6.1A_DeepEM-CH.mrc masked as #3, grid size 70,83,98, pixel 1.68, shown at step 1, values float32 > volume #3 level 0.1317 > volume #3 level 0.1033 > volume #3 level 0.02318 > select #6 2 models selected > view matrix models > #6,0.99567,0.042348,0.082694,-21.981,-0.045563,0.99826,0.037388,6.9013,-0.080967,-0.040994,0.99587,17.106 > close #3 > volume mask #12 surfaces #6 Opened WHV_0913_job048_6.1A_DeepEM-CH.mrc masked as #3, grid size 70,83,98, pixel 1.68, shown at step 1, values float32 > ~select #6 Nothing selected > volume #12 level 0.06368 > volume #3 level 0.09038 > view > show #5 models > save > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/DeepEM/1_Spike.mrc > models #3 > save > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/DeepEM/All_data_in_Here.cxs > includeMaps true > close #1-2 > close #6 > show #!12 models > hide #!12 models > close #12 > volume #3 color #b2b2b2 > volume #3 color #b2b2b29b > volume #3 color #b2b2b2c8 > volume #3 color #b2b2b296 > set bgColor black > lighting soft > lighting simple > set bgColor white > select #5 1808 atoms, 1881 bonds, 222 residues, 1 model selected > view matrix models > #5,0.43417,-0.77441,0.46021,46.155,-0.59333,-0.63024,-0.50077,83.324,0.67784,-0.055636,-0.7331,54.714 > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.97797,-0.10309,0.18151,47.904,-0.17865,0.86309,-0.47239,89.917,-0.10796,-0.49441,-0.8625,52.272 > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.97797,-0.10309,0.18151,68.607,-0.17865,0.86309,-0.47239,61.189,-0.10796,-0.49441,-0.8625,72.845 > view matrix models > #5,-0.97797,-0.10309,0.18151,67.827,-0.17865,0.86309,-0.47239,62.37,-0.10796,-0.49441,-0.8625,78.364 > ui tool show ""Fit in Map"" Fit molecule rank_1_model_3_ptm_seed_0_unrelaxed.pdb (#5) to map 1_Spike.mrc (#3) using 1808 atoms average map value = 0.08383, steps = 468 shifted from previous position = 8.28 rotated from previous position = 20.1 degrees atoms outside contour = 1295, contour level = 0.090375 Position of rank_1_model_3_ptm_seed_0_unrelaxed.pdb (#5) relative to 1_Spike.mrc (#3) coordinates: Matrix rotation and translation -0.99891010 0.02873312 0.03678316 71.92260147 0.01979510 0.97447142 -0.22363719 59.40363872 -0.04226994 -0.22266533 -0.97397813 84.72968812 Axis 0.01221512 0.99359482 -0.11233932 Axis point 36.50126023 0.00000000 45.00900784 Rotation angle (degrees) 177.72009464 Shift along axis 50.38321539 Fit molecule rank_1_model_3_ptm_seed_0_unrelaxed.pdb (#5) to map 1_Spike.mrc (#3) using 1808 atoms average map value = 0.08386, steps = 408 shifted from previous position = 0.0143 rotated from previous position = 0.0159 degrees atoms outside contour = 1292, contour level = 0.090375 Position of rank_1_model_3_ptm_seed_0_unrelaxed.pdb (#5) relative to 1_Spike.mrc (#3) coordinates: Matrix rotation and translation -0.99891650 0.02883098 0.03653185 71.93333862 0.01994349 0.97445182 -0.22370939 59.41091670 -0.04204829 -0.22273843 -0.97397101 84.73264445 Axis 0.01227711 0.99358992 -0.11237592 Axis point 36.49937548 0.00000000 45.01620156 Rotation angle (degrees) 177.73373059 Shift along axis 50.39131244 > select clear > volume #3 level 0.165 > select #5/A:186 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 143 atoms, 152 bonds, 15 residues, 1 model selected > select up 1808 atoms, 1881 bonds, 222 residues, 1 model selected > select down 143 atoms, 152 bonds, 15 residues, 1 model selected > select down 5 atoms, 4 bonds, 1 residue, 1 model selected > select clear > select #5/A:201 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #5/A:211 16 atoms, 14 bonds, 2 residues, 1 model selected > select up 154 atoms, 160 bonds, 18 residues, 1 model selected > select up 1808 atoms, 1881 bonds, 222 residues, 1 model selected > select down 154 atoms, 160 bonds, 18 residues, 1 model selected > select clear Drag select of 5 residues Drag select of 17 residues > select up 338 atoms, 358 bonds, 38 residues, 1 model selected > show #7 models > matchmaker #7 to #5 & sel 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 rank_1_model_3_ptm_seed_0_unrelaxed.pdb, chain A (#5) with rank_2_model_4_ptm_seed_0_unrelaxed.pdb, chain A (#7), sequence alignment score = 219.1 RMSD between 38 pruned atom pairs is 0.513 angstroms; (across all 38 pairs: 0.513) > matchmaker #8 to #5 & sel 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 rank_1_model_3_ptm_seed_0_unrelaxed.pdb, chain A (#5) with rank_3_model_5_ptm_seed_0_unrelaxed.pdb, chain A (#8), sequence alignment score = 219.1 RMSD between 38 pruned atom pairs is 0.804 angstroms; (across all 38 pairs: 0.804) > matchmaker #9 to #5 & sel 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 rank_1_model_3_ptm_seed_0_unrelaxed.pdb, chain A (#5) with rank_4_model_1_ptm_seed_0_unrelaxed.pdb, chain A (#9), sequence alignment score = 208.3 RMSD between 24 pruned atom pairs is 0.493 angstroms; (across all 38 pairs: 4.484) > matchmaker #10 to #5 & sel 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 rank_1_model_3_ptm_seed_0_unrelaxed.pdb, chain A (#5) with rank_5_model_2_ptm_seed_0_unrelaxed.pdb, chain A (#10), sequence alignment score = 215.5 RMSD between 20 pruned atom pairs is 1.177 angstroms; (across all 38 pairs: 3.026) > show #8 models > hide #8 models > hide #7 models > show #!3 models > select clear > rename #3 id 1 > rename #5 id 2 > rename #7 id 3 > rename #8 id 4 > rename #9 id 5 > rename #10 id 6 > show #3 models > hide #2 models Fit molecule rank_1_model_3_ptm_seed_0_unrelaxed.pdb (#2) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.08384, steps = 748 shifted from previous position = 0.021 rotated from previous position = 0.0196 degrees atoms outside contour = 1468, contour level = 0.16499 Position of rank_1_model_3_ptm_seed_0_unrelaxed.pdb (#2) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation -0.99890750 0.02877183 0.03682364 71.91400405 0.01982805 0.97449300 -0.22354022 59.41815434 -0.04231604 -0.22256586 -0.97399886 84.73528968 Axis 0.01223310 0.99360025 -0.11228936 Axis point 36.49737180 0.00000000 45.01043977 Rotation angle (degrees) 177.71760856 Shift along axis 50.40275280 Fit molecule rank_1_model_3_ptm_seed_0_unrelaxed.pdb (#2) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.08386, steps = 848 shifted from previous position = 0.0208 rotated from previous position = 0.0355 degrees atoms outside contour = 1471, contour level = 0.16499 Position of rank_1_model_3_ptm_seed_0_unrelaxed.pdb (#2) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation -0.99891110 0.02870192 0.03678038 71.93070753 0.01974366 0.97435799 -0.22413540 59.41099724 -0.04227037 -0.22316516 -0.97386371 84.72367233 Axis 0.01219467 0.99356627 -0.11259377 Axis point 36.50594349 0.00000000 45.01400669 Rotation angle (degrees) 177.72009692 Shift along axis 50.36657611 Fit molecule rank_2_model_4_ptm_seed_0_unrelaxed.pdb (#3) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.1077, steps = 108 shifted from previous position = 6.52 rotated from previous position = 14.5 degrees atoms outside contour = 1402, contour level = 0.16499 Position of rank_2_model_4_ptm_seed_0_unrelaxed.pdb (#3) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation 0.16692019 0.66492686 0.72801780 64.25308734 0.55664524 -0.67300009 0.48704923 63.72657059 0.81380816 0.32394930 -0.48246567 84.40229706 Axis -0.76306216 -0.40136974 -0.50659497 Axis point -0.00000000 15.84073159 20.28881706 Rotation angle (degrees) 173.86496995 Shift along axis -117.36479637 Fit molecule rank_2_model_4_ptm_seed_0_unrelaxed.pdb (#3) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.1077, steps = 76 shifted from previous position = 0.0271 rotated from previous position = 0.0291 degrees atoms outside contour = 1401, contour level = 0.16499 Position of rank_2_model_4_ptm_seed_0_unrelaxed.pdb (#3) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation 0.16656878 0.66501103 0.72802141 64.22915208 0.55639646 -0.67294917 0.48740372 63.71229485 0.81405026 0.32388229 -0.48210211 84.39785151 Axis -0.76294236 -0.40138502 -0.50676328 Axis point 0.00000000 15.83862917 20.28270662 Rotation angle (degrees) 173.84808434 Shift along axis -117.34603358 Fit molecule rank_2_model_4_ptm_seed_0_unrelaxed.pdb (#3) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.1077, steps = 104 shifted from previous position = 0.0292 rotated from previous position = 0.0259 degrees atoms outside contour = 1402, contour level = 0.16499 Position of rank_2_model_4_ptm_seed_0_unrelaxed.pdb (#3) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation 0.16674928 0.66489599 0.72808516 64.25186277 0.55668174 -0.67296069 0.48706196 63.73035231 0.81381823 0.32409449 -0.48235116 84.40478836 Axis -0.76300717 -0.40139881 -0.50665477 Axis point 0.00000000 15.83966233 20.28686717 Rotation angle (degrees) 173.86952799 Shift along axis -117.37000800 > hide #3 models > show #4 models Fit molecule rank_2_model_4_ptm_seed_0_unrelaxed.pdb (#3) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.1077, steps = 48 shifted from previous position = 0.0235 rotated from previous position = 0.0181 degrees atoms outside contour = 1401, contour level = 0.16499 Position of rank_2_model_4_ptm_seed_0_unrelaxed.pdb (#3) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation 0.16691260 0.66505237 0.72790489 64.22982793 0.55659458 -0.67293425 0.48719808 63.72352147 0.81384437 0.32382842 -0.48248575 84.39990670 Axis -0.76305705 -0.40140087 -0.50657802 Axis point -0.00000000 15.84571149 20.29488901 Rotation angle (degrees) 173.85474327 Shift along axis -117.34483686 Fit molecule rank_3_model_5_ptm_seed_0_unrelaxed.pdb (#4) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.08876, steps = 460 shifted from previous position = 11.2 rotated from previous position = 16.2 degrees atoms outside contour = 1481, contour level = 0.16499 Position of rank_3_model_5_ptm_seed_0_unrelaxed.pdb (#4) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation -0.79392390 0.58086582 0.17966560 72.82365923 0.59929068 0.69770103 0.39250982 52.00863593 0.10264267 0.41929485 -0.90202900 84.98477018 Axis 0.32038395 0.92129497 0.22038534 Axis point 28.10811384 0.00000000 35.77254698 Rotation angle (degrees) 177.60425525 Shift along axis 89.97622365 Fit molecule rank_3_model_5_ptm_seed_0_unrelaxed.pdb (#4) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.08878, steps = 240 shifted from previous position = 0.0271 rotated from previous position = 0.0343 degrees atoms outside contour = 1481, contour level = 0.16499 Position of rank_3_model_5_ptm_seed_0_unrelaxed.pdb (#4) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation -0.79363285 0.58129882 0.17955105 72.82068408 0.59960534 0.69733663 0.39267679 51.98707878 0.10305503 0.41930097 -0.90197913 84.96698099 Axis 0.32061930 0.92119653 0.22045459 Axis point 28.09760843 0.00000000 35.76717211 Rotation angle (degrees) 177.62039941 Shift along axis 89.96939397 > hide #4 models > show #3 models Drag select of 2 residues > select clear > select #3:165 11 atoms, 10 bonds, 1 residue, 1 model selected > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain #3/A Alignment identifier is 3/A QWindowsWindow::setGeometry: Unable to set geometry 575x215-445+593 (frame: 591x254-453+562) on QWidgetWindow/""QDockWidgetClassWindow"" on ""\\\\.\DISPLAY2"". Resulting geometry: 458x171-446+586 (frame: 474x210-454+555) margins: 8, 31, 8, 8 minimum size: 87x50 maximum size: 524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=103,89 maxtrack=524303,524326) > select #3/A:142 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:142 8 atoms, 7 bonds, 1 residue, 1 model selected > volume #1 level 0.06053 > volume #1 level 0.1003 > volume #1 level 0.1401 > volume #1 level 0.08043 > show #4 models > hide #3 models > hide #4 models > show #5 models Fit molecule rank_4_model_1_ptm_seed_0_unrelaxed.pdb (#5) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.08484, steps = 120 shifted from previous position = 7.34 rotated from previous position = 22.7 degrees atoms outside contour = 1286, contour level = 0.080427 Position of rank_4_model_1_ptm_seed_0_unrelaxed.pdb (#5) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation 0.05037843 0.02178740 -0.99849253 66.25587986 -0.40585933 -0.91304218 -0.04040027 49.39178141 -0.91254601 0.40728281 -0.03715501 87.12447420 Axis 0.71623456 -0.13750322 -0.68417901 Axis point 0.00000000 22.75789695 80.44241239 Rotation angle (degrees) 161.78850701 Shift along axis -18.94551446 Fit molecule rank_4_model_1_ptm_seed_0_unrelaxed.pdb (#5) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.08419, steps = 176 shifted from previous position = 3.24 rotated from previous position = 6.85 degrees atoms outside contour = 1271, contour level = 0.080427 Position of rank_4_model_1_ptm_seed_0_unrelaxed.pdb (#5) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation 0.08702727 0.06822680 -0.99386687 63.91267027 -0.49426294 -0.86324375 -0.10253960 50.07313907 -0.86494532 0.50015530 -0.04140377 85.00992281 Axis 0.72229208 -0.15450441 -0.67410870 Axis point 0.00000000 20.93554576 79.46443333 Rotation angle (degrees) 155.34143432 Shift along axis -18.87883406 Fit molecule rank_4_model_1_ptm_seed_0_unrelaxed.pdb (#5) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.08423, steps = 48 shifted from previous position = 0.0339 rotated from previous position = 0.0165 degrees atoms outside contour = 1268, contour level = 0.080427 Position of rank_4_model_1_ptm_seed_0_unrelaxed.pdb (#5) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation 0.08720530 0.06839672 -0.99383959 63.88679188 -0.49436960 -0.86315388 -0.10278172 50.08823711 -0.86486642 0.50028719 -0.04145833 85.02532400 Axis 0.72233814 -0.15448025 -0.67406488 Axis point 0.00000000 20.93276418 79.46193964 Rotation angle (degrees) 155.32678912 Shift along axis -18.90236205 Fit molecule rank_4_model_1_ptm_seed_0_unrelaxed.pdb (#5) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.08424, steps = 48 shifted from previous position = 0.00785 rotated from previous position = 0.0208 degrees atoms outside contour = 1271, contour level = 0.080427 Position of rank_4_model_1_ptm_seed_0_unrelaxed.pdb (#5) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation 0.08714520 0.06856440 -0.99383330 63.89029221 -0.49408665 -0.86330374 -0.10288364 50.09354353 -0.86503416 0.50000558 -0.04135602 85.02990986 Axis 0.72232568 -0.15431513 -0.67411605 Axis point 0.00000000 20.93107358 79.46787648 Rotation angle (degrees) 155.33417755 Shift along axis -18.90062048 Fit molecule rank_4_model_1_ptm_seed_0_unrelaxed.pdb (#5) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.08419, steps = 60 shifted from previous position = 0.033 rotated from previous position = 0.0232 degrees atoms outside contour = 1270, contour level = 0.080427 Position of rank_4_model_1_ptm_seed_0_unrelaxed.pdb (#5) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation 0.08696536 0.06822262 -0.99387258 63.91370129 -0.49401926 -0.86338874 -0.10249322 50.07557434 -0.86509075 0.49990555 -0.04138163 85.01572671 Axis 0.72228565 -0.15441145 -0.67413689 Axis point 0.00000000 20.93790564 79.46619921 Rotation angle (degrees) 155.35412346 Shift along axis -18.88053059 > hide #5 models > show #6 models Fit molecule rank_5_model_2_ptm_seed_0_unrelaxed.pdb (#6) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.07106, steps = 176 shifted from previous position = 14.5 rotated from previous position = 21.2 degrees atoms outside contour = 1369, contour level = 0.080427 Position of rank_5_model_2_ptm_seed_0_unrelaxed.pdb (#6) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation 0.30735478 0.04338102 0.95060566 60.06531713 0.32385805 -0.94409640 -0.06162750 36.68575082 0.89478992 0.32680280 -0.30422184 79.58470679 Axis 0.80528839 0.11571643 0.58148113 Axis point 0.00000000 12.34930738 20.02468554 Rotation angle (degrees) 166.04412021 Shift along axis 98.89205254 Fit molecule rank_5_model_2_ptm_seed_0_unrelaxed.pdb (#6) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.07107, steps = 44 shifted from previous position = 0.0353 rotated from previous position = 0.0197 degrees atoms outside contour = 1368, contour level = 0.080427 Position of rank_5_model_2_ptm_seed_0_unrelaxed.pdb (#6) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation 0.30758553 0.04313455 0.95054224 60.05952385 0.32374488 -0.94411624 -0.06191751 36.68408310 0.89475158 0.32677812 -0.30436109 79.61946354 Axis 0.80535713 0.11559535 0.58141001 Axis point 0.00000000 12.35011994 20.05037695 Rotation angle (degrees) 166.03561018 Shift along axis 98.90142866 Fit molecule rank_5_model_2_ptm_seed_0_unrelaxed.pdb (#6) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.07106, steps = 44 shifted from previous position = 0.00273 rotated from previous position = 0.0168 degrees atoms outside contour = 1367, contour level = 0.080427 Position of rank_5_model_2_ptm_seed_0_unrelaxed.pdb (#6) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation 0.30776927 0.04323068 0.95047840 60.06123438 0.32392933 -0.94405074 -0.06195148 36.68398795 0.89462163 0.32695459 -0.30455349 79.62157631 Axis 0.80541188 0.11567755 0.58131782 Axis point 0.00000000 12.34568618 20.05589353 Rotation angle (degrees) 166.02886548 Shift along axis 98.90298691 > hide #6 models > show #3 models > save > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/DeepEM/All_AlphaFold_Fit_1Spike.cxs > includeMaps true > save > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/DeepEM/AlphaFold_model2_Fit_1Spike.pdb > models #3 relModel #1 > close #4-6 > close #2 > volume #1 level 0.01328 > hide #3 models > select #3 1808 atoms, 1881 bonds, 222 residues, 1 model selected > ui tool show ""Segment Map"" > close #11 Segmenting 1_Spike.mrc, density threshold 0.013276 Showing 14 region surfaces 646 watershed regions, grouped to 14 regions Showing 1_Spike.seg - 14 regions, 14 surfaces > ~select #3 Nothing selected > select #3 1808 atoms, 1881 bonds, 222 residues, 1 model selected > ~select #3 Nothing selected > hide #!2 models > show #3 models > volume #1 level 0.1053 Fit molecule rank_2_model_4_ptm_seed_0_unrelaxed.pdb (#3) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.1077, steps = 60 shifted from previous position = 0.0147 rotated from previous position = 0.0448 degrees atoms outside contour = 1241, contour level = 0.1053 Position of rank_2_model_4_ptm_seed_0_unrelaxed.pdb (#3) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation 0.16616695 0.66501324 0.72811121 64.22780849 0.55672889 -0.67270821 0.48735676 63.73447982 0.81390508 0.32437796 -0.48201396 84.40891666 Axis -0.76281529 -0.40155455 -0.50682025 Axis point 0.00000000 15.83726685 20.28470607 Rotation angle (degrees) 173.86755211 Shift along axis -117.36697361 Fit molecule rank_2_model_4_ptm_seed_0_unrelaxed.pdb (#3) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.1077, steps = 48 shifted from previous position = 0.0365 rotated from previous position = 0.045 degrees atoms outside contour = 1243, contour level = 0.1053 Position of rank_2_model_4_ptm_seed_0_unrelaxed.pdb (#3) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation 0.16691043 0.66506030 0.72789814 64.23503748 0.55657811 -0.67293491 0.48721598 63.70878050 0.81385607 0.32381074 -0.48247787 84.38440752 Axis -0.76305599 -0.40139913 -0.50658099 Axis point 0.00000000 15.83683083 20.28549999 Rotation angle (degrees) 173.85339173 Shift along axis -117.33511551 Fit molecule rank_2_model_4_ptm_seed_0_unrelaxed.pdb (#3) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.1077, steps = 40 shifted from previous position = 0.0352 rotated from previous position = 0.0155 degrees atoms outside contour = 1241, contour level = 0.1053 Position of rank_2_model_4_ptm_seed_0_unrelaxed.pdb (#3) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation 0.16683618 0.66487671 0.72808286 64.24319702 0.55656184 -0.67304447 0.48708322 63.73212765 0.81388243 0.32396004 -0.48233317 84.40962113 Axis -0.76303428 -0.40134094 -0.50665979 Axis point 0.00000000 15.84688169 20.29181727 Rotation angle (degrees) 173.86386686 Shift along axis -117.36503436 > open > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/DeepEM/AlphaFold_model2_Fit_1Spike.pdb Chain information for AlphaFold_model2_Fit_1Spike.pdb #4 --- Chain | Description A | No description available > select #4 1808 atoms, 1881 bonds, 222 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #4,1,0,0,-10.886,0,1,0,29.735,0,0,1,-17.374 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.82128,-0.57049,-0.0062091,142.77,0.32028,-0.47003,0.82249,30.03,-0.47214,0.67351,0.56874,8.1702 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.82128,-0.57049,-0.0062091,131.42,0.32028,-0.47003,0.82249,6.6419,-0.47214,0.67351,0.56874,18.506 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.69496,-0.51705,-0.49969,160.3,0.12265,-0.76998,0.62616,53.629,-0.70851,0.37387,0.59852,49.518 > view matrix models > #4,-0.68588,-0.28156,-0.67104,159.55,-0.064662,-0.89489,0.44157,88.453,-0.72483,0.34626,0.59558,52.484 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.68588,-0.28156,-0.67104,173.4,-0.064662,-0.89489,0.44157,81.754,-0.72483,0.34626,0.59558,51.61 > view matrix models > #4,-0.68588,-0.28156,-0.67104,175.81,-0.064662,-0.89489,0.44157,85.677,-0.72483,0.34626,0.59558,51.046 Fit molecule AlphaFold_model2_Fit_1Spike.pdb (#4) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.1147, steps = 156 shifted from previous position = 3.35 rotated from previous position = 16.7 degrees atoms outside contour = 1197, contour level = 0.1053 Position of AlphaFold_model2_Fit_1Spike.pdb (#4) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation -0.79458038 -0.08289587 -0.60147344 164.25964220 -0.26523645 -0.84372038 0.46667500 92.45959518 -0.54616083 0.53034348 0.64841665 27.23948533 Axis 0.31691455 -0.27532261 -0.90761370 Axis point 89.46454638 37.55838027 0.00000000 Rotation angle (degrees) 174.23488446 Shift along axis 1.87712270 Fit molecule AlphaFold_model2_Fit_1Spike.pdb (#4) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.1148, steps = 104 shifted from previous position = 0.031 rotated from previous position = 0.0543 degrees atoms outside contour = 1198, contour level = 0.1053 Position of AlphaFold_model2_Fit_1Spike.pdb (#4) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation -0.79410722 -0.08244713 -0.60215962 164.26536116 -0.26591482 -0.84376567 0.46620684 92.53416658 -0.54651902 0.53034138 0.64811649 27.25932864 Axis 0.31724316 -0.27522764 -0.90752770 Axis point 89.49506844 37.56472502 0.00000000 Rotation angle (degrees) 174.19857492 Shift along axis 1.90550589 > select clear > show #!2 models > hide #3 models > hide #4 models > show #3 models > show #4 models QWindowsWindow::setGeometry: Unable to set geometry 575x167-407+736 (frame: 591x206-415+705) on QWidgetWindow/""QDockWidgetClassWindow"" on ""\\\\.\DISPLAY2"". Resulting geometry: 481x144-408+729 (frame: 497x183-416+698) margins: 8, 31, 8, 8 minimum size: 481x144 maximum size: 524287x144 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=497,183 maxtrack=524303,183) Deleted 1 regions > hide #!1 models Ungrouped to 4 regions Ungrouped to 9 regions Ungrouped to 4 regions Ungrouped to 10 regions > select clear > save > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/DeepEM/1_Spike.seg > models #2 Deleted 1 regions Deleted 2 regions Deleted 1 regions Ungrouped to 5 regions Deleted 1 regions Ungrouped to 9 regions Deleted 1 regions Drag select of 811, 120 of 136 triangles Deleted 1 regions Ungrouped to 4 regions Grouped 2 regions Grouped 4 regions > select clear Ungrouped to 2 regions Ungrouped to 3 regions Ungrouped to 2 regions > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models Grouped 2 regions Ungrouped to 3 regions > hide #!2 models > show #!1 models > volume #1 level 0.252 > show #!2 models > hide #!1 models Ungrouped to 5 regions Ungrouped to 10 regions Grouped 4 regions Grouped 6 regions Grouped 4 regions Grouped 2 regions > show #!1 models > volume #1 level 0.2297 > volume #1 level 0.161 > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models Grouped 3 regions Grouped 2 regions > hide #!2 models > show #!2 models > select clear > hide #!1 models Ungrouped to 7 regions Grouped 2 regions Ungrouped to 3 regions Grouped 2 regions Ungrouped to 2 regions > select clear Ungrouped to 5 regions > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models Region has 5 adjacent regions Grouped 2 regions > select clear Grouped 2 regions > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models Grouped 2 regions > hide #!1 models Region has 5 adjacent regions Grouped 3 regions Grouped 2 regions Ungrouped to 2 regions Ungrouped to 11 regions > hide #!2 models > show #!1 models > show #!2 models Grouped 2 regions > select clear Grouped 3 regions Grouped 6 regions > hide #!1 models Grouped 3 regions > select clear Grouped 3 regions Ungrouped to 2 regions Grouped 2 regions > select clear Saving 1 regions to mrc file... Opened 1_Spike-Sub1.mrc as #5, grid size 41,52,46, pixel 1.68, shown at step 1, values float32 Wrote 1_Spike-Sub1.mrc ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.3.dev202110050748 (2021-10-05) © 2016-2021 Regents of the University of California. All rights reserved. > open > C:\\\Users\\\cwang6\\\Desktop\\\HBV\\\WHV\\\DeepEM\\\0913_2x_Refine3D_6.1A_job048\\\DeepEM\\\All_AlphaFold_Fit_1Spike.cxs Opened 1_Spike.mrc as #1, grid size 70,83,98, pixel 1.68, shown at level 0.0804, step 1, values float32 Log from Fri Nov 5 00:49:02 2021UCSF ChimeraX version: 1.3.dev202110050748 (2021-10-05) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > D:\\\Projects\\\WHV\\\2020_0913\\\2x_034_5.9A-6.7Apo_3dc_34520p\\\run_class001.mrc Opened run_class001.mrc as #1, grid size 200,200,200, pixel 1.68, shown at level 0.00914, step 1, values float32 > volume #1 level 0.00707 > volume #1 level 0.007924 > close #1 > open D:/Projects/WHV/2020_0913/2x_034_5.9A-6.7Apo_3dc_34520p/postprocess.mrc Opened postprocess.mrc as #1, grid size 200,200,200, pixel 1.68, shown at level 0.0232, step 1, values float32 > view orient > view > volume #1 level 0.01763 > ui tool show ""Hide Dust"" > surface dust #1 size 10.08 > open > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_PostProcess_6.6A_job051/postprocess.mrc Opened postprocess.mrc as #2, grid size 200,200,200, pixel 1.68, shown at level 0.0218, step 1, values float32 > hide #!1 models > view > view orient > volume #2 level 0.01765 > surface dust #2 size 10.08 > surface dust #2 size 5 > volume #2 level 0.01418 > lighting soft > surface undust #2 > volume #2 level 0.0173 > volume #2 level 0.02148 > volume #2 level 0.02182 > open > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/run_class001.mrc Opened run_class001.mrc as #3, grid size 200,200,200, pixel 1.68, shown at level 0.00978, step 1, values float32 > volume #3 level 0.007635 > open > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/4x_0415_oct.mrc Opened 4x_0415_oct.mrc as #4, grid size 100,100,100, pixel 3.36, shown at level 0.0339, step 1, values float32 > hide #!3 models > volume #4 level 0.02377 > volume #4 level 0.02853 > close #4 > volume #3 level 0.008508 > close #3 > open > D:/Projects/HBV/Analysis/Focus_Classification/3DC_ABCD/C70_Masked_ABCD.mrc Opened C70_Masked_ABCD.mrc as #3, grid size 640,640,640, pixel 0.84, shown at level 5e-05, step 4, values float32 > hide #!3 models > open D:/Projects/HBV/HBc_WT/mask_60-100.mrc Opened mask_60-100.mrc as #4, grid size 320,320,320, pixel 1, shown at level 1, step 2, values float32 > volume #4 level 0.02617 > select #4 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #4,1,0,0,195.75,0,1,0,183.38,0,0,1,145.42 > view matrix models #4,1,0,0,192.21,0,1,0,177.8,0,0,1,142.91 > view matrix models #4,1,0,0,191.82,0,1,0,177.67,0,0,1,142.61 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.60072,-0.45549,-0.65701,189.86,-0.68468,0.13114,-0.71694,174.53,0.41273,0.88053,-0.23309,143.55 > view orient > view matrix models > #4,0.6918,0.26372,-0.67221,191.37,-0.71046,0.082176,-0.69892,174.42,-0.12908,0.96109,0.24421,143.64 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.6918,0.26372,-0.67221,147.3,-0.71046,0.082176,-0.69892,180.93,-0.12908,0.96109,0.24421,143.64 > view matrix models > #4,0.6918,0.26372,-0.67221,147.59,-0.71046,0.082176,-0.69892,216.25,-0.12908,0.96109,0.24421,183.61 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.54305,-0.34105,-0.76732,146.14,-0.50277,0.59984,-0.62243,217.57,0.67255,0.72379,0.15427,183.85 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.54305,-0.34105,-0.76732,155.04,-0.50277,0.59984,-0.62243,186.35,0.67255,0.72379,0.15427,201.86 > close #3 > ui tool show ""Map Coordinates"" > color #4 #ffb2b29b models > view matrix models > #4,0.54305,-0.34105,-0.76732,157.69,-0.50277,0.59984,-0.62243,185.25,0.67255,0.72379,0.15427,202.54 > view matrix models > #4,0.54305,-0.34105,-0.76732,149.49,-0.50277,0.59984,-0.62243,189.28,0.67255,0.72379,0.15427,200.38 > view matrix models > #4,0.54305,-0.34105,-0.76732,147.34,-0.50277,0.59984,-0.62243,211.22,0.67255,0.72379,0.15427,220.42 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.81027,-0.37561,-0.44987,147.59,-0.52205,-0.11375,-0.8453,210.39,0.26633,0.91977,-0.28825,220.19 > view matrix models > #4,0.57064,-0.46389,-0.67762,147.27,-0.4708,0.49127,-0.7328,211.08,0.67284,0.73719,0.061937,220.39 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.57064,-0.46389,-0.67762,149.55,-0.4708,0.49127,-0.7328,193.7,0.67284,0.73719,0.061937,223.41 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.59366,-0.50262,-0.62845,149.55,-0.48597,0.39855,-0.77781,193.58,0.64141,0.76716,-0.007652,223.39 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.59366,-0.50262,-0.62845,148.46,-0.48597,0.39855,-0.77781,189.4,0.64141,0.76716,-0.007652,225.53 > open > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/run_class001.mrc Opened run_class001.mrc as #3, grid size 200,200,200, pixel 1.68, shown at level 0.00978, step 1, values float32 > volume #3 level 0.008977 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.65089,-0.36708,-0.66453,148.64,-0.55588,0.36571,-0.74649,189.33,0.51705,0.85528,0.033987,225.59 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.65089,-0.36708,-0.66453,141.44,-0.55588,0.36571,-0.74649,198.23,0.51705,0.85528,0.033987,241.53 > view matrix models > #4,0.65089,-0.36708,-0.66453,140.51,-0.55588,0.36571,-0.74649,194.94,0.51705,0.85528,0.033987,242.77 > ui tool show ""Side View"" > open D:/Projects/HBV/HBc_WT/mask_80-140.mrc Opened mask_80-140.mrc as #5, grid size 320,320,320, pixel 1, shown at level 1, step 2, values float32 > volume #5 level 0 > view > volume #5 level 0.5187 > select #5 2 models selected > ~select #4 2 models selected > view matrix models #5,1,0,0,179.26,0,1,0,191.94,0,0,1,175.54 > view matrix models #5,1,0,0,177.96,0,1,0,189.9,0,0,1,174.15 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.85114,0.42385,0.30971,178.97,-0.25543,-0.18105,0.94973,188.23,0.45861,-0.88745,-0.045834,171.79 > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > view matrix models > #5,0.85114,0.42385,0.30971,166.92,-0.25543,-0.18105,0.94973,203.29,0.45861,-0.88745,-0.045834,200.64 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.86082,0.37272,0.34651,166.86,-0.21876,-0.34377,0.91322,202.97,0.45949,-0.86192,-0.21439,200.52 > view matrix models > #5,0.78451,0.35877,0.5058,166.9,-0.40103,-0.32861,0.8551,202.84,0.473,-0.87367,-0.11392,200.58 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.78451,0.35877,0.5058,150.03,-0.40103,-0.32861,0.8551,217.82,0.473,-0.87367,-0.11392,224.18 > hide #!3 models > show #!3 models > hide #!3 models > view matrix models > #5,0.78451,0.35877,0.5058,149.39,-0.40103,-0.32861,0.8551,220.55,0.473,-0.87367,-0.11392,231.02 > close #5 > open D:/Projects/HBV/HBc_WT/Class005_2L_DNA/mask_60-180.mrc Opened mask_60-180.mrc as #5, grid size 320,320,320, pixel 1, shown at level 1, step 2, values float32 > volume #5 level 0.8676 > select #5 2 models selected > view matrix models #5,1,0,0,213.65,0,1,0,40.986,0,0,1,48.903 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.91625,-0.35462,0.18639,213.05,0.36788,0.56058,-0.7419,39.733,0.15861,0.74833,0.64408,50.203 > view matrix models > #5,0.94062,-0.26022,0.218,213.29,0.32209,0.48126,-0.81526,39.455,0.10723,0.83706,0.5365,50.221 > view matrix models > #5,0.87663,-0.3738,0.30298,213.08,0.45191,0.42338,-0.78519,39.499,0.16523,0.82524,0.54007,50.259 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.87663,-0.3738,0.30298,152.71,0.45191,0.42338,-0.78519,200.04,0.16523,0.82524,0.54007,215.33 > select #3 2 models selected > view > ~select #3 Nothing selected > show #!3 models > hide #!4 models > color #5 #99bfe59b models > view orient > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" [Repeated 1 time(s)] > ~select #5 Nothing selected > select #5 2 models selected > view matrix models > #5,0.87663,-0.3738,0.30298,150.97,0.45191,0.42338,-0.78519,179.47,0.16523,0.82524,0.54007,217.87 > view matrix models > #5,0.87663,-0.3738,0.30298,147.18,0.45191,0.42338,-0.78519,185.65,0.16523,0.82524,0.54007,227.02 > ui mousemode right ""move picked models"" > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.8404,-0.36965,0.39635,147.22,0.49954,0.24462,-0.83104,185.44,0.21023,0.89639,0.39023,227.04 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.8404,-0.36965,0.39635,149.58,0.49954,0.24462,-0.83104,192.02,0.21023,0.89639,0.39023,224.44 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.8882,-0.30346,0.34498,149.65,0.44976,0.42086,-0.78777,192.22,0.093868,0.85486,0.51029,224.39 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.8882,-0.30346,0.34498,146.86,0.44976,0.42086,-0.78777,186.07,0.093868,0.85486,0.51029,226.59 > ui tool show ""Side View"" [Repeated 4 time(s)] QWindowsWindow::setGeometry: Unable to set geometry 575x96-356+333 (frame: 591x135-364+302) on QWidgetWindow/""QDockWidgetClassWindow"" on ""\\\\.\DISPLAY2"". Resulting geometry: 458x75-357+326 (frame: 474x114-365+295) margins: 8, 31, 8, 8 minimum size: 156x70 maximum size: 524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=172,109 maxtrack=524303,524326) > select #5 3 models selected > ~select #5 Nothing selected > select #5 3 models selected > ui mousemode right ""translate selected models"" > view matrix models > #5,0.8882,-0.30346,0.34498,149.65,0.44976,0.42086,-0.78777,185.64,0.093868,0.85486,0.51029,227.57 > ~select #5 Nothing selected > volume mask #5 surfaces #3 Opened mask_60-180.mrc masked as #6, grid size 320,238,320, pixel 0.6, shown at step 1, values float32 > close #6 > volume mask #3 surfaces #5 Opened run_class001.mrc masked as #6, grid size 62,68,79, pixel 1.68, shown at step 1, values float32 > volume #6 level 0.007367 > ui tool show ""Map Coordinates"" > close #6 > show #!3 models > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > view orient > show #!5 models > select #5 3 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.89779,-0.21771,0.38284,149.8,0.43722,0.33611,-0.83419,185.48,0.052931,0.91631,0.39695,227.55 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.89779,-0.21771,0.38284,142.52,0.43722,0.33611,-0.83419,187.64,0.052931,0.91631,0.39695,223.86 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.89199,-0.24295,0.38123,142.48,0.44658,0.34267,-0.82652,187.66,0.070165,0.9075,0.41415,223.87 > volume #3 level 0.009581 > ~select #5 Nothing selected > hide #!5 models > volume #3 level 0.00891 > show #!5 models > volume #3 level 0.007837 > volume mask #3 surfaces #5 Opened run_class001.mrc masked as #6, grid size 64,70,85, pixel 1.68, shown at step 1, values float32 QWindowsWindow::setGeometry: Unable to set geometry 1920x1055+0+29 (frame: 1938x1102-9-9) on QWidgetWindow/""MainWindowClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 1920x1001+0+29 (frame: 1938x1048-9-9) margins: 9, 38, 9, 9 minimum size: 470x1055 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=488,1102 maxtrack=0,0) > hide #!5 models > volume #6 level 0.006965 > volume #6 level 0.009044 > volume #6 level 0.008105 > volume #6 level 0.00247 > close #6 > show #!3 models > ui mousemode right ""rotate selected models"" [Repeated 1 time(s)] > select #5 3 models selected > view matrix models > #5,0.89669,-0.29168,0.33297,142.38,0.42028,0.32484,-0.84726,187.6,0.13897,0.89967,0.41387,223.9 > view matrix models > #5,0.91795,-0.29375,0.26661,142.35,0.36226,0.34682,-0.86515,187.58,0.16167,0.89074,0.42478,223.91 > ~select #5 Nothing selected > volume mask #3 surfaces #5 Opened run_class001.mrc masked as #6, grid size 72,74,92, pixel 1.68, shown at step 1, values float32 QWindowsWindow::setGeometry: Unable to set geometry 1920x1055+0+29 (frame: 1938x1102-9-9) on QWidgetWindow/""MainWindowClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 1920x1001+0+29 (frame: 1938x1048-9-9) margins: 9, 38, 9, 9 minimum size: 470x1055 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=488,1102 maxtrack=0,0) > volume #6 level 0.007904 > volume #6 level 0.004147 > volume #6 level 0.006898 > volume #6 level 0.002873 > close #6 > volume mask #3 surfaces #5 Opened run_class001.mrc masked as #6, grid size 76,80,98, pixel 1.68, shown at step 1, values float32 QWindowsWindow::setGeometry: Unable to set geometry 1920x1055+0+29 (frame: 1938x1102-9-9) on QWidgetWindow/""MainWindowClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 1920x1001+0+29 (frame: 1938x1048-9-9) margins: 9, 38, 9, 9 minimum size: 470x1055 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=488,1102 maxtrack=0,0) > volume #6 level 0.0073 > volume #6 level 0.006093 > volume #6 level 0.004483 > volume #6 level 0.004348 > show #!3 models > show #!5 models > ui mousemode right ""translate selected models"" > select #5 3 models selected > view matrix models > #5,0.91795,-0.29375,0.26661,139.61,0.36226,0.34682,-0.86515,189.64,0.16167,0.89074,0.42478,229.49 > close #6 > ~select #5 Nothing selected > volume mask #3 surfaces #5 Opened run_class001.mrc masked as #6, grid size 77,80,98, pixel 1.68, shown at step 1, values float32 QWindowsWindow::setGeometry: Unable to set geometry 1920x1055+0+29 (frame: 1938x1102-9-9) on QWidgetWindow/""MainWindowClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 1920x1001+0+29 (frame: 1938x1048-9-9) margins: 9, 38, 9, 9 minimum size: 470x1055 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=488,1102 maxtrack=0,0) > hide #!5 models > volume #6 level 0.007971 > volume #6 level 0.009178 > volume #6 level 0.007367 > volume #6 level 0.00891 > volume #6 level 0.007837 > show #!5 models > select #5 3 models selected > ui mousemode right ""translate selected models"" > view matrix models > #5,0.91795,-0.29375,0.26661,137.88,0.36226,0.34682,-0.86515,191.43,0.16167,0.89074,0.42478,234.08 > ~select #5 Nothing selected > close #6 > volume mask #3 surfaces #5 Opened run_class001.mrc masked as #6, grid size 77,80,98, pixel 1.68, shown at step 1, values float32 QWindowsWindow::setGeometry: Unable to set geometry 1920x1055+0+29 (frame: 1938x1102-9-9) on QWidgetWindow/""MainWindowClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 1920x1001+0+29 (frame: 1938x1048-9-9) margins: 9, 38, 9, 9 minimum size: 470x1055 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=488,1102 maxtrack=0,0) > volume #6 level 0.004751 > volume #6 level 0.008508 > volume #6 level 0.007166 > close #6 > volume resample #5 ogGrid #3 Expected a keyword > volume resample #5 onGrid #3 Opened mask_60-180.mrc resampled as #6, grid size 200,200,200, pixel 1.68, shown at step 1, values float32 QWindowsWindow::setGeometry: Unable to set geometry 1920x1055+0+29 (frame: 1938x1102-9-9) on QWidgetWindow/""MainWindowClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 1920x1001+0+29 (frame: 1938x1048-9-9) margins: 9, 38, 9, 9 minimum size: 470x1055 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=488,1102 maxtrack=0,0) > save > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/Mask_1Spike.mrc > models #6 > hide #!6 models > show #!6 models > close #5 > close #4 > show #!1 models > hide #!1 models > open > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/WHV_0913_job048_6.1A_DeepEM.mrc Opened WHV_0913_job048_6.1A_DeepEM.mrc as #4, grid size 200,200,200, pixel 1.68, shown at level 0.133, step 1, values float32 > hide #!4 models > show #!4 models > hide #!6 models > volume #4 level 0.07975 > volume #4 level 0.01814 > volume #4 level 0.09583 > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!1 models > hide #!4 models > open > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/AlphaFold/rank_1_model_3_ptm_seed_0_unrelaxed.pdb Chain information for rank_1_model_3_ptm_seed_0_unrelaxed.pdb #5 --- Chain | Description A | No description available > open > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/AlphaFold/rank_2_model_4_ptm_seed_0_unrelaxed.pdb Chain information for rank_2_model_4_ptm_seed_0_unrelaxed.pdb #7 --- Chain | Description A | No description available > open > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/AlphaFold/rank_3_model_5_ptm_seed_0_unrelaxed.pdb Chain information for rank_3_model_5_ptm_seed_0_unrelaxed.pdb #8 --- Chain | Description A | No description available > open > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/AlphaFold/rank_4_model_1_ptm_seed_0_unrelaxed.pdb Chain information for rank_4_model_1_ptm_seed_0_unrelaxed.pdb #9 --- Chain | Description A | No description available > open > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/AlphaFold/rank_5_model_2_ptm_seed_0_unrelaxed.pdb Chain information for rank_5_model_2_ptm_seed_0_unrelaxed.pdb #10 --- Chain | Description A | No description available > hide #!1 models > preset ""overall look"" publication Preset expands to these ChimeraX commands: set bg white graphics silhouettes t > view > hide #10 models > hide #9 models > hide #8 models > hide #7 models > hide #5 models > show #5 models > select #5 1808 atoms, 1881 bonds, 222 residues, 1 model selected > view matrix models #5,1,0,0,-5.6579,0,1,0,3.983,0,0,1,2.3951 > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.61581,-0.78727,0.031334,-8.1594,-0.70516,0.53297,-0.46765,-0.91207,0.35147,-0.31008,-0.88336,-11.889 > select clear > show #7 models > hide #7 models > ui tool show Matchmaker > matchmaker #7 to #5 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 rank_1_model_3_ptm_seed_0_unrelaxed.pdb, chain A (#5) with rank_2_model_4_ptm_seed_0_unrelaxed.pdb, chain A (#7), sequence alignment score = 1179.4 RMSD between 57 pruned atom pairs is 0.913 angstroms; (across all 222 pairs: 15.130) > matchmaker #8 to #5 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 rank_1_model_3_ptm_seed_0_unrelaxed.pdb, chain A (#5) with rank_3_model_5_ptm_seed_0_unrelaxed.pdb, chain A (#8), sequence alignment score = 1214.2 RMSD between 97 pruned atom pairs is 0.773 angstroms; (across all 222 pairs: 8.587) > matchmaker #9 to #5 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 rank_1_model_3_ptm_seed_0_unrelaxed.pdb, chain A (#5) with rank_4_model_1_ptm_seed_0_unrelaxed.pdb, chain A (#9), sequence alignment score = 1193.2 RMSD between 85 pruned atom pairs is 1.062 angstroms; (across all 222 pairs: 17.265) > matchmaker #10 to #5 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 rank_1_model_3_ptm_seed_0_unrelaxed.pdb, chain A (#5) with rank_5_model_2_ptm_seed_0_unrelaxed.pdb, chain A (#10), sequence alignment score = 1200.4 RMSD between 34 pruned atom pairs is 0.536 angstroms; (across all 222 pairs: 27.054) > show #7 models > show #8 models > show #9 models > show #10 models > hide #10 models > hide #9 models > hide #8 models > hide #7 models > show #7 models > show #8 models > hide #7 models > show #7 models > hide #5 models > hide #8 models > show #9 models > hide #9 models > show #10 models > select clear > hide #10 models > hide #7 models > show #7 models > show #5 models > hide #7 models > show #7 models > select #7/A:98 14 atoms, 15 bonds, 1 residue, 1 model selected > select up 264 atoms, 271 bonds, 29 residues, 1 model selected > select add #5/A:97 272 atoms, 278 bonds, 30 residues, 2 models selected > select up 528 atoms, 542 bonds, 58 residues, 2 models selected > matchmaker #5 & sel to #7 & sel 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 rank_2_model_4_ptm_seed_0_unrelaxed.pdb, chain A (#7) with rank_1_model_3_ptm_seed_0_unrelaxed.pdb, chain A (#5), sequence alignment score = 158.6 RMSD between 29 pruned atom pairs is 0.283 angstroms; (across all 29 pairs: 0.283) > hide #7 models > show #8 models > select add #8/A:85 536 atoms, 549 bonds, 59 residues, 3 models selected > select up 792 atoms, 813 bonds, 87 residues, 3 models selected > matchmaker #8 & sel to #7 & sel 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 rank_2_model_4_ptm_seed_0_unrelaxed.pdb, chain A (#7) with rank_3_model_5_ptm_seed_0_unrelaxed.pdb, chain A (#8), sequence alignment score = 158.6 RMSD between 29 pruned atom pairs is 0.340 angstroms; (across all 29 pairs: 0.340) > hide #5 models > show #7 models > hide #8 models > show #9 models > select add #9/A:73 800 atoms, 820 bonds, 88 residues, 4 models selected > select up 1067 atoms, 1096 bonds, 117 residues, 4 models selected > matchmaker #9 & sel to #7 & sel 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 rank_2_model_4_ptm_seed_0_unrelaxed.pdb, chain A (#7) with rank_4_model_1_ptm_seed_0_unrelaxed.pdb, chain A (#9), sequence alignment score = 158.6 RMSD between 29 pruned atom pairs is 0.443 angstroms; (across all 29 pairs: 0.443) > show #10 models > hide #9 models > select add #10/A:91 1078 atoms, 1107 bonds, 118 residues, 5 models selected > select up 1354 atoms, 1391 bonds, 149 residues, 5 models selected > matchmaker #10 & sel to #7 & sel 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 rank_2_model_4_ptm_seed_0_unrelaxed.pdb, chain A (#7) with rank_5_model_2_ptm_seed_0_unrelaxed.pdb, chain A (#10), sequence alignment score = 158.6 RMSD between 29 pruned atom pairs is 0.303 angstroms; (across all 29 pairs: 0.303) > show #9 models > show #8 models > show #5 models > select clear > hide #10 models > hide #9 models > hide #8 models > hide #7 models > hide #5 models > show #5 models > hide #5 models > show #7 models > ui tool show ""Scale Bar"" > scalebar > scalebar 10 > scalebar 100 > scalebar xpos 0.15 > scalebar xpos 0.2 > save > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/AlphaFold_model2_10nm.png > width 1340 height 839 supersample 3 > hide #7 models > show #5 models > show #7 models > hide #7 models > show #7 models > hide #7 models > save > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/AlphaFold_model1_10nm.png > width 1340 height 839 supersample 3 > hide #5 models > show #8 models > save > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/AlphaFold_model3_10nm.png > width 1340 height 839 supersample 3 > lighting full > graphics silhouettes false > graphics silhouettes true > save > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/AlphaFold_model3_10nm.png > width 1340 height 839 supersample 3 > hide #8 models > show #7 models > save > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/AlphaFold_model2_10nm.png > width 1340 height 839 supersample 3 > hide #7 models > show #5 models > save > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/AlphaFold_model1_10nm.png > width 1340 height 839 supersample 3 > show #9 models > hide #5 models > save > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/AlphaFold_model4_10nm.png > width 1340 height 839 supersample 3 > hide #9 models > show #10 models > save > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/AlphaFold_model5_10nm.png > width 1340 height 839 supersample 3 > hide #10 models > hide #!11 models > view orient > volume flip #4 Opened WHV_0913_job048_6.1A_DeepEM.mrc z flip as #12, grid size 200,200,200, pixel 1.68, shown at step 1, values float32 > lighting soft No map chosen to save > save > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/WHV_0913_job048_6.1A_DeepEM- > CH.mrc models #12 > save > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/AlphaFoldAnalysis/5_model_Comparison.cxs > view orient > close #3 > volume #6 color #b2ffb29b > ui mousemode right ""rotate selected models"" > select #6 3 models selected > view matrix models > #6,0.99567,0.036497,0.085527,-26.291,-0.037586,0.99923,0.011158,2.7104,-0.085054,-0.014325,0.99627,15.285 > ~select #6 Nothing selected > close #4 > volume mask #12 surfaces #6 Opened WHV_0913_job048_6.1A_DeepEM-CH.mrc masked as #3, grid size 70,81,98, pixel 1.68, shown at step 1, values float32 > volume #12 level 0.1574 > volume #3 level 0.1527 > volume #3 level 0.08807 > volume #3 level 0.01054 > volume #3 level 0.005369 > hide #!6 models > show #!6 models > select #6 3 models selected > view matrix models > #6,0.99567,0.042348,0.082694,-26.753,-0.045563,0.99826,0.037388,-2.112,-0.080967,-0.040994,0.99587,19.922 > close #3 > volume mask #12 surfaces #6 Opened WHV_0913_job048_6.1A_DeepEM-CH.mrc masked as #3, grid size 70,83,98, pixel 1.68, shown at step 1, values float32 > ~select #6 Nothing selected > volume #12 level 0.1012 > volume #3 level 0.02304 > volume #3 level 0.01529 > volume #3 level 0.02046 > volume #3 level 0.02304 > volume #3 level 0.02563 > volume #3 level 0.0308 > volume #3 level 0.04372 > volume #3 level 0.0463 > volume #3 level 0.04889 > volume #3 level 0.05664 > volume #3 level 0.06181 > volume #3 level 0.0644 > volume #3 level 0.06956 > volume #3 level 0.07473 > volume #3 level 0.07732 > volume #3 level 0.0799 > volume #3 level 0.07732 > volume #3 level 0.07473 > volume #3 level 0.07215 > volume #3 level 0.06956 > volume #3 level 0.05923 > volume #3 level 0.1135 > camera ortho > ui mousemode right ""translate selected models"" > select #6 3 models selected > view matrix models > #6,0.99567,0.042348,0.082694,-28.27,-0.045563,0.99826,0.037388,0.5582,-0.080967,-0.040994,0.99587,18.388 > view matrix models > #6,0.99567,0.042348,0.082694,-28.894,-0.045563,0.99826,0.037388,0.71738,-0.080967,-0.040994,0.99587,18.175 > close #3 > volume mask #12 surfaces #6 Opened WHV_0913_job048_6.1A_DeepEM-CH.mrc masked as #3, grid size 70,82,98, pixel 1.68, shown at step 1, values float32 > volume #3 level 0.1167 > volume #3 level 0.1296 > view matrix models > #6,0.99567,0.042348,0.082694,-25.364,-0.045563,0.99826,0.037388,3.5671,-0.080967,-0.040994,0.99587,17.783 > close #3 > volume mask #12 surfaces #6 Opened WHV_0913_job048_6.1A_DeepEM-CH.mrc masked as #3, grid size 70,83,98, pixel 1.68, shown at step 1, values float32 > ~select #6 Nothing selected > volume #12 level 0.08779 > volume #3 level 0.06507 > volume #3 level 0.1012 > volume #3 level 0.03928 > volume #3 level 0.1038 > view > select #6 2 models selected > view matrix models > #6,0.99567,0.042348,0.082694,-23.082,-0.045563,0.99826,0.037388,4.6632,-0.080967,-0.040994,0.99587,17.827 > ~select #6 Nothing selected > hide #!6 models > close #3 > volume mask #12 surfaces #6 Opened WHV_0913_job048_6.1A_DeepEM-CH.mrc masked as #3, grid size 70,83,98, pixel 1.68, shown at step 1, values float32 > volume #3 level 0.1317 > volume #3 level 0.1033 > volume #3 level 0.02318 > select #6 2 models selected > view matrix models > #6,0.99567,0.042348,0.082694,-21.981,-0.045563,0.99826,0.037388,6.9013,-0.080967,-0.040994,0.99587,17.106 > close #3 > volume mask #12 surfaces #6 Opened WHV_0913_job048_6.1A_DeepEM-CH.mrc masked as #3, grid size 70,83,98, pixel 1.68, shown at step 1, values float32 > ~select #6 Nothing selected > volume #12 level 0.06368 > volume #3 level 0.09038 > view > show #5 models > save > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/DeepEM/1_Spike.mrc > models #3 > save > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/DeepEM/All_data_in_Here.cxs > includeMaps true > close #1-2 > close #6 > show #!12 models > hide #!12 models > close #12 > volume #3 color #b2b2b2 > volume #3 color #b2b2b29b > volume #3 color #b2b2b2c8 > volume #3 color #b2b2b296 > set bgColor black > lighting soft > lighting simple > set bgColor white > select #5 1808 atoms, 1881 bonds, 222 residues, 1 model selected > view matrix models > #5,0.43417,-0.77441,0.46021,46.155,-0.59333,-0.63024,-0.50077,83.324,0.67784,-0.055636,-0.7331,54.714 > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.97797,-0.10309,0.18151,47.904,-0.17865,0.86309,-0.47239,89.917,-0.10796,-0.49441,-0.8625,52.272 > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.97797,-0.10309,0.18151,68.607,-0.17865,0.86309,-0.47239,61.189,-0.10796,-0.49441,-0.8625,72.845 > view matrix models > #5,-0.97797,-0.10309,0.18151,67.827,-0.17865,0.86309,-0.47239,62.37,-0.10796,-0.49441,-0.8625,78.364 > ui tool show ""Fit in Map"" Fit molecule rank_1_model_3_ptm_seed_0_unrelaxed.pdb (#5) to map 1_Spike.mrc (#3) using 1808 atoms average map value = 0.08383, steps = 468 shifted from previous position = 8.28 rotated from previous position = 20.1 degrees atoms outside contour = 1295, contour level = 0.090375 Position of rank_1_model_3_ptm_seed_0_unrelaxed.pdb (#5) relative to 1_Spike.mrc (#3) coordinates: Matrix rotation and translation -0.99891010 0.02873312 0.03678316 71.92260147 0.01979510 0.97447142 -0.22363719 59.40363872 -0.04226994 -0.22266533 -0.97397813 84.72968812 Axis 0.01221512 0.99359482 -0.11233932 Axis point 36.50126023 0.00000000 45.00900784 Rotation angle (degrees) 177.72009464 Shift along axis 50.38321539 Fit molecule rank_1_model_3_ptm_seed_0_unrelaxed.pdb (#5) to map 1_Spike.mrc (#3) using 1808 atoms average map value = 0.08386, steps = 408 shifted from previous position = 0.0143 rotated from previous position = 0.0159 degrees atoms outside contour = 1292, contour level = 0.090375 Position of rank_1_model_3_ptm_seed_0_unrelaxed.pdb (#5) relative to 1_Spike.mrc (#3) coordinates: Matrix rotation and translation -0.99891650 0.02883098 0.03653185 71.93333862 0.01994349 0.97445182 -0.22370939 59.41091670 -0.04204829 -0.22273843 -0.97397101 84.73264445 Axis 0.01227711 0.99358992 -0.11237592 Axis point 36.49937548 0.00000000 45.01620156 Rotation angle (degrees) 177.73373059 Shift along axis 50.39131244 > select clear > volume #3 level 0.165 > select #5/A:186 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 143 atoms, 152 bonds, 15 residues, 1 model selected > select up 1808 atoms, 1881 bonds, 222 residues, 1 model selected > select down 143 atoms, 152 bonds, 15 residues, 1 model selected > select down 5 atoms, 4 bonds, 1 residue, 1 model selected > select clear > select #5/A:201 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #5/A:211 16 atoms, 14 bonds, 2 residues, 1 model selected > select up 154 atoms, 160 bonds, 18 residues, 1 model selected > select up 1808 atoms, 1881 bonds, 222 residues, 1 model selected > select down 154 atoms, 160 bonds, 18 residues, 1 model selected > select clear Drag select of 5 residues Drag select of 17 residues > select up 338 atoms, 358 bonds, 38 residues, 1 model selected > show #7 models > matchmaker #7 to #5 & sel 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 rank_1_model_3_ptm_seed_0_unrelaxed.pdb, chain A (#5) with rank_2_model_4_ptm_seed_0_unrelaxed.pdb, chain A (#7), sequence alignment score = 219.1 RMSD between 38 pruned atom pairs is 0.513 angstroms; (across all 38 pairs: 0.513) > matchmaker #8 to #5 & sel 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 rank_1_model_3_ptm_seed_0_unrelaxed.pdb, chain A (#5) with rank_3_model_5_ptm_seed_0_unrelaxed.pdb, chain A (#8), sequence alignment score = 219.1 RMSD between 38 pruned atom pairs is 0.804 angstroms; (across all 38 pairs: 0.804) > matchmaker #9 to #5 & sel 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 rank_1_model_3_ptm_seed_0_unrelaxed.pdb, chain A (#5) with rank_4_model_1_ptm_seed_0_unrelaxed.pdb, chain A (#9), sequence alignment score = 208.3 RMSD between 24 pruned atom pairs is 0.493 angstroms; (across all 38 pairs: 4.484) > matchmaker #10 to #5 & sel 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 rank_1_model_3_ptm_seed_0_unrelaxed.pdb, chain A (#5) with rank_5_model_2_ptm_seed_0_unrelaxed.pdb, chain A (#10), sequence alignment score = 215.5 RMSD between 20 pruned atom pairs is 1.177 angstroms; (across all 38 pairs: 3.026) > show #8 models > hide #8 models > hide #7 models > show #!3 models > select clear > rename #3 id 1 > rename #5 id 2 > rename #7 id 3 > rename #8 id 4 > rename #9 id 5 > rename #10 id 6 > show #3 models > hide #2 models Fit molecule rank_1_model_3_ptm_seed_0_unrelaxed.pdb (#2) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.08384, steps = 748 shifted from previous position = 0.021 rotated from previous position = 0.0196 degrees atoms outside contour = 1468, contour level = 0.16499 Position of rank_1_model_3_ptm_seed_0_unrelaxed.pdb (#2) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation -0.99890750 0.02877183 0.03682364 71.91400405 0.01982805 0.97449300 -0.22354022 59.41815434 -0.04231604 -0.22256586 -0.97399886 84.73528968 Axis 0.01223310 0.99360025 -0.11228936 Axis point 36.49737180 0.00000000 45.01043977 Rotation angle (degrees) 177.71760856 Shift along axis 50.40275280 Fit molecule rank_1_model_3_ptm_seed_0_unrelaxed.pdb (#2) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.08386, steps = 848 shifted from previous position = 0.0208 rotated from previous position = 0.0355 degrees atoms outside contour = 1471, contour level = 0.16499 Position of rank_1_model_3_ptm_seed_0_unrelaxed.pdb (#2) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation -0.99891110 0.02870192 0.03678038 71.93070753 0.01974366 0.97435799 -0.22413540 59.41099724 -0.04227037 -0.22316516 -0.97386371 84.72367233 Axis 0.01219467 0.99356627 -0.11259377 Axis point 36.50594349 0.00000000 45.01400669 Rotation angle (degrees) 177.72009692 Shift along axis 50.36657611 Fit molecule rank_2_model_4_ptm_seed_0_unrelaxed.pdb (#3) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.1077, steps = 108 shifted from previous position = 6.52 rotated from previous position = 14.5 degrees atoms outside contour = 1402, contour level = 0.16499 Position of rank_2_model_4_ptm_seed_0_unrelaxed.pdb (#3) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation 0.16692019 0.66492686 0.72801780 64.25308734 0.55664524 -0.67300009 0.48704923 63.72657059 0.81380816 0.32394930 -0.48246567 84.40229706 Axis -0.76306216 -0.40136974 -0.50659497 Axis point -0.00000000 15.84073159 20.28881706 Rotation angle (degrees) 173.86496995 Shift along axis -117.36479637 Fit molecule rank_2_model_4_ptm_seed_0_unrelaxed.pdb (#3) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.1077, steps = 76 shifted from previous position = 0.0271 rotated from previous position = 0.0291 degrees atoms outside contour = 1401, contour level = 0.16499 Position of rank_2_model_4_ptm_seed_0_unrelaxed.pdb (#3) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation 0.16656878 0.66501103 0.72802141 64.22915208 0.55639646 -0.67294917 0.48740372 63.71229485 0.81405026 0.32388229 -0.48210211 84.39785151 Axis -0.76294236 -0.40138502 -0.50676328 Axis point 0.00000000 15.83862917 20.28270662 Rotation angle (degrees) 173.84808434 Shift along axis -117.34603358 Fit molecule rank_2_model_4_ptm_seed_0_unrelaxed.pdb (#3) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.1077, steps = 104 shifted from previous position = 0.0292 rotated from previous position = 0.0259 degrees atoms outside contour = 1402, contour level = 0.16499 Position of rank_2_model_4_ptm_seed_0_unrelaxed.pdb (#3) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation 0.16674928 0.66489599 0.72808516 64.25186277 0.55668174 -0.67296069 0.48706196 63.73035231 0.81381823 0.32409449 -0.48235116 84.40478836 Axis -0.76300717 -0.40139881 -0.50665477 Axis point 0.00000000 15.83966233 20.28686717 Rotation angle (degrees) 173.86952799 Shift along axis -117.37000800 > hide #3 models > show #4 models Fit molecule rank_2_model_4_ptm_seed_0_unrelaxed.pdb (#3) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.1077, steps = 48 shifted from previous position = 0.0235 rotated from previous position = 0.0181 degrees atoms outside contour = 1401, contour level = 0.16499 Position of rank_2_model_4_ptm_seed_0_unrelaxed.pdb (#3) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation 0.16691260 0.66505237 0.72790489 64.22982793 0.55659458 -0.67293425 0.48719808 63.72352147 0.81384437 0.32382842 -0.48248575 84.39990670 Axis -0.76305705 -0.40140087 -0.50657802 Axis point -0.00000000 15.84571149 20.29488901 Rotation angle (degrees) 173.85474327 Shift along axis -117.34483686 Fit molecule rank_3_model_5_ptm_seed_0_unrelaxed.pdb (#4) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.08876, steps = 460 shifted from previous position = 11.2 rotated from previous position = 16.2 degrees atoms outside contour = 1481, contour level = 0.16499 Position of rank_3_model_5_ptm_seed_0_unrelaxed.pdb (#4) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation -0.79392390 0.58086582 0.17966560 72.82365923 0.59929068 0.69770103 0.39250982 52.00863593 0.10264267 0.41929485 -0.90202900 84.98477018 Axis 0.32038395 0.92129497 0.22038534 Axis point 28.10811384 0.00000000 35.77254698 Rotation angle (degrees) 177.60425525 Shift along axis 89.97622365 Fit molecule rank_3_model_5_ptm_seed_0_unrelaxed.pdb (#4) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.08878, steps = 240 shifted from previous position = 0.0271 rotated from previous position = 0.0343 degrees atoms outside contour = 1481, contour level = 0.16499 Position of rank_3_model_5_ptm_seed_0_unrelaxed.pdb (#4) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation -0.79363285 0.58129882 0.17955105 72.82068408 0.59960534 0.69733663 0.39267679 51.98707878 0.10305503 0.41930097 -0.90197913 84.96698099 Axis 0.32061930 0.92119653 0.22045459 Axis point 28.09760843 0.00000000 35.76717211 Rotation angle (degrees) 177.62039941 Shift along axis 89.96939397 > hide #4 models > show #3 models Drag select of 2 residues > select clear > select #3:165 11 atoms, 10 bonds, 1 residue, 1 model selected > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain #3/A Alignment identifier is 3/A QWindowsWindow::setGeometry: Unable to set geometry 575x215-445+593 (frame: 591x254-453+562) on QWidgetWindow/""QDockWidgetClassWindow"" on ""\\\\.\DISPLAY2"". Resulting geometry: 458x171-446+586 (frame: 474x210-454+555) margins: 8, 31, 8, 8 minimum size: 87x50 maximum size: 524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=103,89 maxtrack=524303,524326) > select #3/A:142 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:142 8 atoms, 7 bonds, 1 residue, 1 model selected > volume #1 level 0.06053 > volume #1 level 0.1003 > volume #1 level 0.1401 > volume #1 level 0.08043 > show #4 models > hide #3 models > hide #4 models > show #5 models Fit molecule rank_4_model_1_ptm_seed_0_unrelaxed.pdb (#5) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.08484, steps = 120 shifted from previous position = 7.34 rotated from previous position = 22.7 degrees atoms outside contour = 1286, contour level = 0.080427 Position of rank_4_model_1_ptm_seed_0_unrelaxed.pdb (#5) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation 0.05037843 0.02178740 -0.99849253 66.25587986 -0.40585933 -0.91304218 -0.04040027 49.39178141 -0.91254601 0.40728281 -0.03715501 87.12447420 Axis 0.71623456 -0.13750322 -0.68417901 Axis point 0.00000000 22.75789695 80.44241239 Rotation angle (degrees) 161.78850701 Shift along axis -18.94551446 Fit molecule rank_4_model_1_ptm_seed_0_unrelaxed.pdb (#5) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.08419, steps = 176 shifted from previous position = 3.24 rotated from previous position = 6.85 degrees atoms outside contour = 1271, contour level = 0.080427 Position of rank_4_model_1_ptm_seed_0_unrelaxed.pdb (#5) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation 0.08702727 0.06822680 -0.99386687 63.91267027 -0.49426294 -0.86324375 -0.10253960 50.07313907 -0.86494532 0.50015530 -0.04140377 85.00992281 Axis 0.72229208 -0.15450441 -0.67410870 Axis point 0.00000000 20.93554576 79.46443333 Rotation angle (degrees) 155.34143432 Shift along axis -18.87883406 Fit molecule rank_4_model_1_ptm_seed_0_unrelaxed.pdb (#5) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.08423, steps = 48 shifted from previous position = 0.0339 rotated from previous position = 0.0165 degrees atoms outside contour = 1268, contour level = 0.080427 Position of rank_4_model_1_ptm_seed_0_unrelaxed.pdb (#5) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation 0.08720530 0.06839672 -0.99383959 63.88679188 -0.49436960 -0.86315388 -0.10278172 50.08823711 -0.86486642 0.50028719 -0.04145833 85.02532400 Axis 0.72233814 -0.15448025 -0.67406488 Axis point 0.00000000 20.93276418 79.46193964 Rotation angle (degrees) 155.32678912 Shift along axis -18.90236205 Fit molecule rank_4_model_1_ptm_seed_0_unrelaxed.pdb (#5) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.08424, steps = 48 shifted from previous position = 0.00785 rotated from previous position = 0.0208 degrees atoms outside contour = 1271, contour level = 0.080427 Position of rank_4_model_1_ptm_seed_0_unrelaxed.pdb (#5) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation 0.08714520 0.06856440 -0.99383330 63.89029221 -0.49408665 -0.86330374 -0.10288364 50.09354353 -0.86503416 0.50000558 -0.04135602 85.02990986 Axis 0.72232568 -0.15431513 -0.67411605 Axis point 0.00000000 20.93107358 79.46787648 Rotation angle (degrees) 155.33417755 Shift along axis -18.90062048 Fit molecule rank_4_model_1_ptm_seed_0_unrelaxed.pdb (#5) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.08419, steps = 60 shifted from previous position = 0.033 rotated from previous position = 0.0232 degrees atoms outside contour = 1270, contour level = 0.080427 Position of rank_4_model_1_ptm_seed_0_unrelaxed.pdb (#5) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation 0.08696536 0.06822262 -0.99387258 63.91370129 -0.49401926 -0.86338874 -0.10249322 50.07557434 -0.86509075 0.49990555 -0.04138163 85.01572671 Axis 0.72228565 -0.15441145 -0.67413689 Axis point 0.00000000 20.93790564 79.46619921 Rotation angle (degrees) 155.35412346 Shift along axis -18.88053059 > hide #5 models > show #6 models Fit molecule rank_5_model_2_ptm_seed_0_unrelaxed.pdb (#6) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.07106, steps = 176 shifted from previous position = 14.5 rotated from previous position = 21.2 degrees atoms outside contour = 1369, contour level = 0.080427 Position of rank_5_model_2_ptm_seed_0_unrelaxed.pdb (#6) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation 0.30735478 0.04338102 0.95060566 60.06531713 0.32385805 -0.94409640 -0.06162750 36.68575082 0.89478992 0.32680280 -0.30422184 79.58470679 Axis 0.80528839 0.11571643 0.58148113 Axis point 0.00000000 12.34930738 20.02468554 Rotation angle (degrees) 166.04412021 Shift along axis 98.89205254 Fit molecule rank_5_model_2_ptm_seed_0_unrelaxed.pdb (#6) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.07107, steps = 44 shifted from previous position = 0.0353 rotated from previous position = 0.0197 degrees atoms outside contour = 1368, contour level = 0.080427 Position of rank_5_model_2_ptm_seed_0_unrelaxed.pdb (#6) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation 0.30758553 0.04313455 0.95054224 60.05952385 0.32374488 -0.94411624 -0.06191751 36.68408310 0.89475158 0.32677812 -0.30436109 79.61946354 Axis 0.80535713 0.11559535 0.58141001 Axis point 0.00000000 12.35011994 20.05037695 Rotation angle (degrees) 166.03561018 Shift along axis 98.90142866 Fit molecule rank_5_model_2_ptm_seed_0_unrelaxed.pdb (#6) to map 1_Spike.mrc (#1) using 1808 atoms average map value = 0.07106, steps = 44 shifted from previous position = 0.00273 rotated from previous position = 0.0168 degrees atoms outside contour = 1367, contour level = 0.080427 Position of rank_5_model_2_ptm_seed_0_unrelaxed.pdb (#6) relative to 1_Spike.mrc (#1) coordinates: Matrix rotation and translation 0.30776927 0.04323068 0.95047840 60.06123438 0.32392933 -0.94405074 -0.06195148 36.68398795 0.89462163 0.32695459 -0.30455349 79.62157631 Axis 0.80541188 0.11567755 0.58131782 Axis point 0.00000000 12.34568618 20.05589353 Rotation angle (degrees) 166.02886548 Shift along axis 98.90298691 > hide #6 models > show #3 models > save > C:/Users/cwang6/Desktop/HBV/WHV/DeepEM/0913_2x_Refine3D_6.1A_job048/DeepEM/All_AlphaFold_Fit_1Spike.cxs > includeMaps true ——— End of log from Fri Nov 5 00:49:02 2021 ——— opened ChimeraX session OpenGL version: 3.3.0 NVIDIA 471.68 OpenGL renderer: Quadro T2000/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Dell Inc. Model: Precision 5540 OS: Microsoft Windows 10 Enterprise (Build 18363) Memory: 34,040,614,912 MaxProcessMemory: 137,438,953,344 CPU: 16 Intel(R) Core(TM) i9-9880H CPU @ 2.30GHz OSLanguage: en-US Locale: ('en_US', 'cp1252') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.5.30 cftime: 1.5.1 charset-normalizer: 2.0.6 ChimeraX-AddCharge: 1.1.4 ChimeraX-AddH: 2.1.10 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.30.1 ChimeraX-AtomicLibrary: 4.1.4 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3.dev202110050748 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.1 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.1 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2 ChimeraX-ModelPanel: 1.2 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.3 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-Phenix: 0.3 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.4 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.3 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 comtypes: 1.1.10 cxservices: 1.1 cycler: 0.10.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.4.0 html2text: 2020.1.16 idna: 3.2 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.2.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.8.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 MolecularDynamicsViewer: 1.2 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.7.3 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.2 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.20 psutil: 5.8.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pywin32: 228 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.2 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 Send2Trash: 1.8.0 SEQCROW: 1.3 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.1.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.0 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 WMI: 1.5.1 }}} " defect closed normal Sessions can't reproduce Greg Couch all ChimeraX