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Opened 4 years ago
Closed 4 years ago
#5546 closed defect (can't reproduce)
Crash saving session including maps
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | Greg Couch | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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
Change History (2)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash saving session including maps |
comment:2 by , 4 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
Looks like it crashed getting the attribute of an atomic structure, possibly a deleted structure.
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
Unfortunately on Windows we get almost no information about where it crashed in the code. I don't see any more clues in this bug report about where it crashed, so there is not enough information to debug it. Sorry it crashed while you were trying to save your work -- that is very frustrating when work is lost.
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Reported by Joseph Wang