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Opened 4 years ago
Closed 4 years ago
#5673 closed defect (can't reproduce)
Crash saving session
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | pett | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: Windows-10-10.0.19042
ChimeraX Version: 1.3.dev202109020559 (2021-09-02 05:59:02 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x8001010e
Thread 0x00004df0Windows fatal exception: code 0x (most recent call first):
File 8001010e"
C:\PrWindows fatal exception: ocode 0xg8001010er
aWindows fatal exception: mcode 0x 8001010eF
iWindows fatal exception: lcode 0xe8001010es
\Windows fatal exception: Ccode 0xh8001010ei
mWindows fatal exception: ecode 0xr8001010ea
XWindows fatal exception: code 0x18001010e.
3Windows fatal exception: .code 0xd8001010ee
vWindows fatal exception: 2code 0x08001010e2
1Windows fatal exception: 0code 0x98001010e0
2Windows fatal exception: 0code 0x58001010e
59\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 882 in init
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 1031 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00004df0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 882 in init
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 1031 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00004df0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 882 in init
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 1031 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00004df0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 882 in init
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 1031 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00004df0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 882 in init
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\Windows fatal exception: Ccode 0xh8001010ei
merWindows fatal exception: acode 0xX8001010e_
maWindows fatal exception: icode 0xn8001010e.
pyWindows fatal exception: "code 0x, line 8001010e1031
in 8001010e
File "Windows fatal exception: Ccode 0x:8001010e\
PrWindows fatal exception: ocode 0xg8001010er
amWindows fatal exception: code 0xF8001010ei
leWindows fatal exception: scode 0x\8001010eC
hiWindows fatal exception: mcode 0xe8001010er
aX 1.3.dev202109020559\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00004df0 (most recent call first):
File "C:\Program Files\CWindows fatal exception: hcode 0xi8001010em
eraWindows fatal exception: Xcode 0x 8001010e1
.3Windows fatal exception: .code 0xd8001010ee
v2Windows fatal exception: 0code 0x28001010e1
09Windows fatal exception: 0code 0x28001010e0
55Windows fatal exception: 9code 0x\8001010eb
inWindows fatal exception: \code 0xl8001010ei
b\Windows fatal exception: scode 0xi8001010et
e-Windows fatal exception: pcode 0xa8001010ec
kaWindows fatal exception: gcode 0xe8001010es
\cWindows fatal exception: hcode 0xi8001010em
erax\open_command\dialog.py", line 135 in show_open_file_dialog
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 882 in init
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 1031 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00004df0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 882 in init
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 1031 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00004df0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 882 in init
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 1031 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00004df0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 882 in init
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 1031 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00004df0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 882 in init
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 1031 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program FiWindows fatal exception: lecode 0xs8001010e\
ChimerWindows fatal exception: acode 0xX8001010e
1.3.Windows fatal exception: dcode 0xev8001010e2
021090Windows fatal exception: 2code 0x08001010e55
9\biWindows fatal exception: ncode 0x\8001010el
ib\rWindows fatal exception: ucode 0xn8001010ep
y.pyWindows fatal exception: "code 0x, line 8001010e197
in _ruWindows fatal exception: ncode 0x_8001010em
oduWindows fatal exception: lcode 0xe8001010e_a
s_maWindows fatal exception: icode 0xn8001010e
[deleted a lot of chatter from open-dialog thread "errors"]
Windows fatal exception: Windows fatal exception: 1code 0x.8001010e3
.dcode 0xeWindows fatal exception: 8001010ecode 0x
v8001010e2
02Windows fatal exception: 1code 0x08001010e9
02Windows fatal exception: 0code 0x58001010e5
9\Windows fatal exception: bcode 0xi8001010en
\lWindows fatal exception: icode 0xb8001010e\
runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00004df0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 882 in init
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 1031 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00004df0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 882 in init
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 1031 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00004df0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 882 in init
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 1031 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00004df0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 882 in init
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 1031 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00004df0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 882 in init
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 1031 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00004df0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 882 in init
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 1031 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00004df0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 882 in init
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 1031 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00004df0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 882 in init
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 1031 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00004df0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 882 in init
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\ChimeraX_main.py", line 1031 in
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00004df0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3.dev202109020559\bin\lib\site-packages\chimerax\atomic\molc.py", line 196 in get_prop
Windows fatal exception: access violation
===== Log before crash start =====
UCSF ChimeraX version: 1.3.dev202109020559 (2021-09-02)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:\\\Nature\\\Supplementary_video_2\\\morph_separate_wings.cxs
Log from Tue Nov 23 16:30:10 2021UCSF ChimeraX version: 1.3.dev202109020559
(2021-09-02)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> E:/Nature/3D_variability/cryosparc_P11_J946_component_000/wing_component1_A.pdb
> E:/Nature/3D_variability/cryosparc_P11_J946_component_000/wing_component1_B.pdb
Chain information for wing_component1_A.pdb #1
---
Chain | Description
C | No description available
S | No description available
U | No description available
W | No description available
Chain information for wing_component1_B.pdb #2
---
Chain | Description
C | No description available
S | No description available
U | No description available
W | No description available
> open
> E:/Nature/3D_variability/cryosparc_P11_J946_component_001/cryosparc_P11_J946_component_001/wing_component2_A.pdb
> E:/Nature/3D_variability/cryosparc_P11_J946_component_001/cryosparc_P11_J946_component_001/wing_component2_B.pdb
Chain information for wing_component2_A.pdb #3
---
Chain | Description
C | No description available
S | No description available
U | No description available
W | No description available
Chain information for wing_component2_B.pdb #4
---
Chain | Description
C | No description available
S | No description available
U | No description available
W | No description available
> set bgColor white
> open E:/Nature/Figure4/core.pdb
Chain information for core.pdb #5
---
Chain | Description
A I | No description available
B | No description available
C K | No description available
D E F L M N | No description available
G O | No description available
H P | No description available
J | No description available
> hide atoms
> show cartoons
> open E:\Nature\color_sea_last.cxc format cmd
> color #1,9,14,5/A,I #4682B4 target csa
> color #1,9,14,5/B,G,O,J #8B008B target csa
> color #1,9,14/C,K #9ACD32 target csa
> color #2,3,4,8,10,5/C #9ACD32 target csa
> color #1,14,9,5/E,M,N,F,L,D #ADD8E6 target csa
> color #1,14,9,5/H,P #D8BFD8 target csa
> color #1,2,3,4,14,8,10,5/S,T #00008B target csa
> color #1,2,3,4,14,8,10,5/U,V #FFA500 target csa
> color #1,2,3,4,14,8,10,5/W,X #1f7f564a154d target csa
executed color_sea_last.cxc
> hide #!1 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> close #1-4
> open
> E:/Nature/3D_variability/cryosparc_P11_J946_component_000/component_1_merged.pdb
Chain information for component_1_merged.pdb #1
---
Chain | Description
A C | No description available
B S | No description available
D U | No description available
E W | No description available
> hide atoms
> show cartoons
> open
> E:/Nature/3D_variability/cryosparc_P11_J946_component_001/cryosparc_P11_J946_component_001/component_2_merged.pdb
Chain information for component_2_merged.pdb #2
---
Chain | Description
A C | No description available
B S | No description available
D U | No description available
E W | No description available
> hide atoms
> show cartoons
> hide #!5 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> close #1-2
> open
> E:/Nature/3D_variability/cryosparc_P11_J946_component_001/cryosparc_P11_J946_component_001/component_2_merged.pdb
Chain information for component_2_merged.pdb #1
---
Chain | Description
A C | No description available
B S | No description available
D U | No description available
E W | No description available
> open
> E:/Nature/3D_variability/cryosparc_P11_J946_component_000/component_1_merged.pdb
Chain information for component_1_merged.pdb #2
---
Chain | Description
A C | No description available
B S | No description available
D U | No description available
E W | No description available
> hide #!1-2 atoms
> show #!1-2 cartoons
> mmaker #1/D to #2/D
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 component_1_merged.pdb, chain D (#2) with component_2_merged.pdb,
chain D (#1), sequence alignment score = 2945.5
RMSD between 564 pruned atom pairs is 0.001 angstroms; (across all 564 pairs:
0.001)
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> mmaker #1/E to #2/E
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 component_1_merged.pdb, chain E (#2) with component_2_merged.pdb,
chain E (#1), sequence alignment score = 5107.1
RMSD between 981 pruned atom pairs is 0.001 angstroms; (across all 981 pairs:
0.001)
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> close #1-2
> open
> E:/Nature/3D_variability/cryosparc_P11_J946_component_000/component_1_merged.pdb
Chain information for component_1_merged.pdb #1
---
Chain | Description
A C | No description available
B S | No description available
D U | No description available
E W | No description available
> hide #!1 atoms
> show #!1 cartoons
> open
> E:/Nature/3D_variability/cryosparc_P11_J946_component_001/cryosparc_P11_J946_component_001/component_2_merged.pdb
Chain information for component_2_merged.pdb #2
---
Chain | Description
A C | No description available
B S | No description available
D U | No description available
E W | No description available
> hide #!1-2 atoms
> show #!1-2 cartoons
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> mmaker #2/U to #1/U
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 component_1_merged.pdb, chain U (#1) with component_2_merged.pdb,
chain U (#2), sequence alignment score = 2945.5
RMSD between 564 pruned atom pairs is 0.001 angstroms; (across all 564 pairs:
0.001)
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> close #1-2
> open
> E:/Nature/3D_variability/cryosparc_P11_J946_component_001/cryosparc_P11_J946_component_001/component_2_merged.pdb
Chain information for component_2_merged.pdb #1
---
Chain | Description
A C | No description available
B S | No description available
D U | No description available
E W | No description available
> open
> E:/Nature/3D_variability/cryosparc_P11_J946_component_000/component_1_merged.pdb
Chain information for component_1_merged.pdb #2
---
Chain | Description
A C | No description available
B S | No description available
D U | No description available
E W | No description available
> hide #!1-2 atoms
> show #!1-2 cartoons
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> show #!5 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> morph #1,2 frames 40
Computed 41 frame morph #3
> coordset #3 1,41
> show #!1 models
> close #1-3
> open
> E:/Nature/3D_variability/cryosparc_P11_J946_component_000/wing_component1_A.pdb
Chain information for wing_component1_A.pdb #1
---
Chain | Description
C | No description available
S | No description available
U | No description available
W | No description available
> open
> E:/Nature/3D_variability/cryosparc_P11_J946_component_001/cryosparc_P11_J946_component_001/wing_component2_A.pdb
Chain information for wing_component2_A.pdb #2
---
Chain | Description
C | No description available
S | No description available
U | No description available
W | No description available
> close #2
> open
> E:/Nature/3D_variability/cryosparc_P11_J946_component_001/cryosparc_P11_J946_component_001/wing_component2_B.pdb
Chain information for wing_component2_B.pdb #2
---
Chain | Description
C | No description available
S | No description available
U | No description available
W | No description available
> morph #1,2 frames 40
Computed 41 frame morph #3
> coordset #3 1,41
> open
> E:/Nature/3D_variability/cryosparc_P11_J946_component_001/cryosparc_P11_J946_component_001/wing_component2_A.pdb
Chain information for wing_component2_A.pdb #4
---
Chain | Description
C | No description available
S | No description available
U | No description available
W | No description available
> open
> E:/Nature/3D_variability/cryosparc_P11_J946_component_000/wing_component1_B.pdb
Chain information for wing_component1_B.pdb #6
---
Chain | Description
C | No description available
S | No description available
U | No description available
W | No description available
> hide #!4 models
> show #!4 models
> hide #!4 models
> morph #6,4 frames 40
Computed 41 frame morph #7
> coordset #7 1,41
> save E:/Nature/Supplementary_video_2/morph_separate_wings.cxs
> select #5
58995 atoms, 60321 bonds, 56 pseudobonds, 7371 residues, 2 models selected
> hide sel cartoons
> show sel surfaces
> select clear
> coordset #3,7 loop 2 bounce true
> save E:/Nature/Supplementary_video_2/morph_separate_wings.cxs
> open E:\Nature\color_sea_last.cxc format cmd
> color #1,9,14,5/A,I #4682B4 target csa
> color #1,9,14,5/B,G,O,J #8B008B target csa
> color #1,9,14/C,K #9ACD32 target csa
> color #2,3,4,8,10,5/C #9ACD32 target csa
> color #1,14,9,5/E,M,N,F,L,D #ADD8E6 target csa
> color #1,14,9,5/H,P #D8BFD8 target csa
> color #1,2,3,4,14,8,10,5/S,T #00008B target csa
> color #1,2,3,4,14,8,10,5/U,V #FFA500 target csa
> color #1,2,3,4,14,8,10,5/W,X #1f7f564a154d target csa
executed color_sea_last.cxc
> hide #!3 models
> show #!3 models
> open E:\Nature\color_sea_last.cxc format cmd
> color #1,9,14,5/A,I #4682B4 target csa
> color #1,9,14,5/B,G,O,J #8B008B target csa
> color #1,9,14/C,K #9ACD32 target csa
> color #2,3,4,8,10,5,7/C #9ACD32 target csa
> color #1,14,9,5/E,M,N,F,L,D #ADD8E6 target csa
> color #1,14,9,5/H,P #D8BFD8 target csa
> color #1,2,3,4,14,8,10,5,7/S,T #00008B target csa
> color #1,2,3,4,14,8,10,5,7/U,V #FFA500 target csa
> color #1,2,3,4,14,8,10,5,7/W,X #1f7f564a154d target csa
executed color_sea_last.cxc
> save E:/Nature/Supplementary_video_2/morph_separate_wings.cxs
——— End of log from Tue Nov 23 16:30:10 2021 ———
opened ChimeraX session
> coordset #3,7 loop 1 bounce true
> select #3,7/S.84
Expected an objects specifier or a keyword
> select #3,7/S:84
22 atoms, 20 bonds, 2 residues, 2 models selected
> show sel atoms
> style sel sphere
Changed 22 atom styles
> color sel red
> select clear
> coordset #3,7 loop 1 bounce true
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> coordset #3,7 loop 1 bounce true
> open E:\Nature\color_sea_last.cxc format cmd
> color #1,9,14,5/A,I #4682B4 target csa
> color #1,9,14,5/B,G,O,J #8B008B target csa
> color #1,9,14/C,K #9ACD32 target csa
> color #2,3,4,8,10,5,7/C,N #9ACD32 target csa
> color #1,14,9,5/E,M,N,F,L,D #ADD8E6 target csa
> color #1,14,9,5/H,P #D8BFD8 target csa
> color #1,2,3,4,14,8,10,5,7/S,T #00008B target csa
> color #1,2,3,4,14,8,10,5,7/U,V #FFA500 target csa
> color #1,2,3,4,14,8,10,5,7/W,X #1f7f564a154d target csa
executed color_sea_last.cxc
> open E:\Nature\color_sea_last.cxc format cmd
> color #1,9,14,5/A,I #4682B4 target csa
> color #1,9,14,5/B,G,O,J #8B008B target csa
> color #1,9,14,5/C,K #9ACD32 target csa
> color #2,3,4,8,10,5,7/C #9ACD32 target csa
> color #1,14,9,5/E,M,N,F,L,D #ADD8E6 target csa
> color #1,14,9,5/H,P #D8BFD8 target csa
> color #1,2,3,4,14,8,10,5,7/S,T #00008B target csa
> color #1,2,3,4,14,8,10,5,7/U,V #FFA500 target csa
> color #1,2,3,4,14,8,10,5,7/W,X #1f7f564a154d target csa
executed color_sea_last.cxc
> select #3,7/S:84
22 atoms, 20 bonds, 2 residues, 2 models selected
> color sel red
> select clear
> coordset slider #3,7
> select clear
> hide #!3 models
> hide #!7 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!4 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!4 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!4 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!4 models
> hide #!1 models
> show #!3 models
> show #!7 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!1 models
> hide #!1 models
> select #1
20099 atoms, 20590 bonds, 8 pseudobonds, 2457 residues, 2 models selected
> color #3,5-7 light sea green
> undo
> show #!1 models
> color (#!1 & sel) light sea green
> hide #!1 models
> show #!1 models
> hide #!1 models
> select clear
> hide #!6 models
> select #3,7/S:84
22 atoms, 20 bonds, 2 residues, 2 models selected
> coordset #3,7 loop 1 bounce true
> select clear
> save E:/Nature/Supplementary_video_2/morph_separate_wings.cxs
> open E:/eLife/Figure5/6jwp.pdb E:/eLife/Figure5/6jwp_B.pdb
Summary of feedback from opening E:/eLife/Figure5/6jwp.pdb
---
warnings | Cannot find LINK/SSBOND residue SER (20 )
Cannot find LINK/SSBOND residue THR (41 )
Cannot find LINK/SSBOND residue GNP (401 )
Cannot find LINK/SSBOND residue GNP (401 )
Cannot find LINK/SSBOND residue GNP (401 )
1 messages similar to the above omitted
Summary of feedback from opening E:/eLife/Figure5/6jwp_B.pdb
---
warnings | Cannot find LINK/SSBOND residue SER (20 )
Cannot find LINK/SSBOND residue THR (41 )
Cannot find LINK/SSBOND residue GNP (401 )
Cannot find LINK/SSBOND residue GNP (401 )
Cannot find LINK/SSBOND residue GNP (401 )
1 messages similar to the above omitted
6jwp.pdb title:
Crystal structure of egoc [more info...]
Chain information for 6jwp.pdb #8
---
Chain | Description | UniProt
A | GTP-binding protein GTR1 | GTR1_YEAST
B | GTP-binding protein GTR2 | GTR2_YEAST
C | protein MEH1 | MEH1_YEAST
D | EGO2 | YC075_YEAST
E | protein SLM4 | SLM4_YEAST
Non-standard residues in 6jwp.pdb #8
---
GNP — phosphoaminophosphonic acid-guanylate ester
MG — magnesium ion
6jwp_B.pdb title:
Crystal structure of egoc [more info...]
Chain information for 6jwp_B.pdb #9
---
Chain | Description | UniProt
A | GTP-binding protein GTR1 | GTR1_YEAST
B | GTP-binding protein GTR2 | GTR2_YEAST
C | protein MEH1 | MEH1_YEAST
D | EGO2 | YC075_YEAST
E | protein SLM4 | SLM4_YEAST
Non-standard residues in 6jwp_B.pdb #9
---
GNP — phosphoaminophosphonic acid-guanylate ester
MG — magnesium ion
> color grey #8,9
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #8,9 grey
> select #8
7009 atoms, 7116 bonds, 18 pseudobonds, 886 residues, 3 models selected
> select #8,9
14018 atoms, 14232 bonds, 36 pseudobonds, 1772 residues, 6 models selected
> hide sel atoms
> show sel surfaces
> color #8,9 grey
> color #8,9/A blue
> color #8,9/B yellow
> select clear
> save E:/Nature/Supplementary_video_2/morph_separate_wings.cxs
> open E:/Nature/Supplementary_video_2/supvid2.cxc
> movie record supersample 3
> coordset #3,7 loop 3 bounce true
> wait 40
> movie encode C:\Users\tafurpet/Desktop/Sup_vid_2.mp4 quality high
Movie saved to C:\Users\tafurpet/Desktop/Sup_vid_2.mp4
executed supvid2.cxc
> open E:\Nature\Supplementary_video_2\supvid2.cxc
> movie record supersample 3
> coordset #3,7 loop 3 bounce true
> wait 130
> movie stop
> movie encode C:\Users\tafurpet/Desktop/Sup_vid_2.mp4 quality high
Movie saved to C:\Users\tafurpet/Desktop/Sup_vid_2.mp4
executed supvid2.cxc
> show #!4 models
> hide #!3 models
> hide #!7 models
> close #8-9
> hide #!4 models
> show #!3 models
> show #!7 models
> open E:/Nature/Supplementary_video_2/EGOC_component2_B.pdb
> E:/Nature/Supplementary_video_2/EGOC_component1_B.pdb
> E:/Nature/Supplementary_video_2/EGOC_component2_A.pdb
> E:/Nature/Supplementary_video_2/EGOC_component1_A.pdb
Summary of feedback from opening
E:/Nature/Supplementary_video_2/EGOC_component2_B.pdb
---
warnings | Cannot find LINK/SSBOND residue SER (20 )
Cannot find LINK/SSBOND residue THR (41 )
Cannot find LINK/SSBOND residue GNP (401 )
Cannot find LINK/SSBOND residue GNP (401 )
Cannot find LINK/SSBOND residue GNP (401 )
1 messages similar to the above omitted
Summary of feedback from opening
E:/Nature/Supplementary_video_2/EGOC_component1_B.pdb
---
warnings | Cannot find LINK/SSBOND residue SER (20 )
Cannot find LINK/SSBOND residue THR (41 )
Cannot find LINK/SSBOND residue GNP (401 )
Cannot find LINK/SSBOND residue GNP (401 )
Cannot find LINK/SSBOND residue GNP (401 )
1 messages similar to the above omitted
Summary of feedback from opening
E:/Nature/Supplementary_video_2/EGOC_component2_A.pdb
---
warnings | Cannot find LINK/SSBOND residue SER (20 )
Cannot find LINK/SSBOND residue THR (41 )
Cannot find LINK/SSBOND residue GNP (401 )
Cannot find LINK/SSBOND residue GNP (401 )
Cannot find LINK/SSBOND residue GNP (401 )
1 messages similar to the above omitted
Summary of feedback from opening
E:/Nature/Supplementary_video_2/EGOC_component1_A.pdb
---
warnings | Cannot find LINK/SSBOND residue SER (20 )
Cannot find LINK/SSBOND residue THR (41 )
Cannot find LINK/SSBOND residue GNP (401 )
Cannot find LINK/SSBOND residue GNP (401 )
Cannot find LINK/SSBOND residue GNP (401 )
1 messages similar to the above omitted
EGOC_component2_B.pdb title:
Crystal structure of egoc [more info...]
Chain information for EGOC_component2_B.pdb #8
---
Chain | Description | UniProt
A | GTP-binding protein GTR1 | GTR1_YEAST
B | GTP-binding protein GTR2 | GTR2_YEAST
C | protein MEH1 | MEH1_YEAST
D | EGO2 | YC075_YEAST
E | protein SLM4 | SLM4_YEAST
Non-standard residues in EGOC_component2_B.pdb #8
---
GNP — phosphoaminophosphonic acid-guanylate ester
MG — magnesium ion
EGOC_component1_B.pdb title:
Crystal structure of egoc [more info...]
Chain information for EGOC_component1_B.pdb #9
---
Chain | Description | UniProt
A | GTP-binding protein GTR1 | GTR1_YEAST
B | GTP-binding protein GTR2 | GTR2_YEAST
C | protein MEH1 | MEH1_YEAST
D | EGO2 | YC075_YEAST
E | protein SLM4 | SLM4_YEAST
Non-standard residues in EGOC_component1_B.pdb #9
---
GNP — phosphoaminophosphonic acid-guanylate ester
MG — magnesium ion
EGOC_component2_A.pdb title:
Crystal structure of egoc [more info...]
Chain information for EGOC_component2_A.pdb #10
---
Chain | Description | UniProt
A | GTP-binding protein GTR1 | GTR1_YEAST
B | GTP-binding protein GTR2 | GTR2_YEAST
C | protein MEH1 | MEH1_YEAST
D | EGO2 | YC075_YEAST
E | protein SLM4 | SLM4_YEAST
Non-standard residues in EGOC_component2_A.pdb #10
---
GNP — phosphoaminophosphonic acid-guanylate ester
MG — magnesium ion
EGOC_component1_A.pdb title:
Crystal structure of egoc [more info...]
Chain information for EGOC_component1_A.pdb #11
---
Chain | Description | UniProt
A | GTP-binding protein GTR1 | GTR1_YEAST
B | GTP-binding protein GTR2 | GTR2_YEAST
C | protein MEH1 | MEH1_YEAST
D | EGO2 | YC075_YEAST
E | protein SLM4 | SLM4_YEAST
Non-standard residues in EGOC_component1_A.pdb #11
---
GNP — phosphoaminophosphonic acid-guanylate ester
MG — magnesium ion
> hide #!8 models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!10 models
> hide #!11 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> hide #!9 models
> close #8-11
> open E:/Nature/Supplementary_video_2/EGOC_component2_A.pdb
> E:/Nature/Supplementary_video_2/EGOC_component2_B.pdb
Summary of feedback from opening
E:/Nature/Supplementary_video_2/EGOC_component2_B.pdb
---
warnings | Cannot find LINK/SSBOND residue SER (20 )
Cannot find LINK/SSBOND residue THR (41 )
Cannot find LINK/SSBOND residue GNP (401 )
Cannot find LINK/SSBOND residue GNP (401 )
Cannot find LINK/SSBOND residue GNP (401 )
1 messages similar to the above omitted
Chain information for EGOC_component2_A.pdb #8
---
Chain | Description
C | No description available
S | No description available
U | No description available
W | No description available
EGOC_component2_B.pdb title:
Crystal structure of egoc [more info...]
Chain information for EGOC_component2_B.pdb #9
---
Chain | Description | UniProt
A | GTP-binding protein GTR1 | GTR1_YEAST
B | GTP-binding protein GTR2 | GTR2_YEAST
C | protein MEH1 | MEH1_YEAST
D | EGO2 | YC075_YEAST
E | protein SLM4 | SLM4_YEAST
Non-standard residues in EGOC_component2_B.pdb #9
---
GNP — phosphoaminophosphonic acid-guanylate ester
MG — magnesium ion
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> close #8-9
> hide #!3 models
> hide #!7 models
> show #!2 models
> show #!4 models
> open E:/Nature/Supplementary_video_2/EGOC_component2_A.pdb
> E:/Nature/Supplementary_video_2/EGOC_component2_B.pdb
Summary of feedback from opening
E:/Nature/Supplementary_video_2/EGOC_component2_A.pdb
---
warnings | Cannot find LINK/SSBOND residue SER (20 )
Cannot find LINK/SSBOND residue THR (41 )
Cannot find LINK/SSBOND residue GNP (401 )
Cannot find LINK/SSBOND residue GNP (401 )
Cannot find LINK/SSBOND residue GNP (401 )
1 messages similar to the above omitted
Summary of feedback from opening
E:/Nature/Supplementary_video_2/EGOC_component2_B.pdb
---
warnings | Cannot find LINK/SSBOND residue SER (20 )
Cannot find LINK/SSBOND residue THR (41 )
Cannot find LINK/SSBOND residue GNP (401 )
Cannot find LINK/SSBOND residue GNP (401 )
Cannot find LINK/SSBOND residue GNP (401 )
1 messages similar to the above omitted
EGOC_component2_A.pdb title:
Crystal structure of egoc [more info...]
Chain information for EGOC_component2_A.pdb #8
---
Chain | Description | UniProt
A | GTP-binding protein GTR1 | GTR1_YEAST
B | GTP-binding protein GTR2 | GTR2_YEAST
C | protein MEH1 | MEH1_YEAST
D | EGO2 | YC075_YEAST
E | protein SLM4 | SLM4_YEAST
Non-standard residues in EGOC_component2_A.pdb #8
---
GNP — phosphoaminophosphonic acid-guanylate ester
MG — magnesium ion
EGOC_component2_B.pdb title:
Crystal structure of egoc [more info...]
Chain information for EGOC_component2_B.pdb #9
---
Chain | Description | UniProt
A | GTP-binding protein GTR1 | GTR1_YEAST
B | GTP-binding protein GTR2 | GTR2_YEAST
C | protein MEH1 | MEH1_YEAST
D | EGO2 | YC075_YEAST
E | protein SLM4 | SLM4_YEAST
Non-standard residues in EGOC_component2_B.pdb #9
---
GNP — phosphoaminophosphonic acid-guanylate ester
MG — magnesium ion
> hide #!8 models
> hide #!9 models
> hide #!2 models
> show #!6 models
> hide #!4 models
> open E:/Nature/Supplementary_video_2/EGOC_component1_B.pdb
Summary of feedback from opening
E:/Nature/Supplementary_video_2/EGOC_component1_B.pdb
---
warnings | Cannot find LINK/SSBOND residue SER (20 )
Cannot find LINK/SSBOND residue THR (41 )
Cannot find LINK/SSBOND residue GNP (401 )
Cannot find LINK/SSBOND residue GNP (401 )
Cannot find LINK/SSBOND residue GNP (401 )
1 messages similar to the above omitted
EGOC_component1_B.pdb title:
Crystal structure of egoc [more info...]
Chain information for EGOC_component1_B.pdb #10
---
Chain | Description | UniProt
A | GTP-binding protein GTR1 | GTR1_YEAST
B | GTP-binding protein GTR2 | GTR2_YEAST
C | protein MEH1 | MEH1_YEAST
D | EGO2 | YC075_YEAST
E | protein SLM4 | SLM4_YEAST
Non-standard residues in EGOC_component1_B.pdb #10
---
GNP — phosphoaminophosphonic acid-guanylate ester
MG — magnesium ion
> show #!1 models
> open E:/Nature/Supplementary_video_2/EGOC_component1_A.pdb
Summary of feedback from opening
E:/Nature/Supplementary_video_2/EGOC_component1_A.pdb
---
warnings | Cannot find LINK/SSBOND residue SER (20 )
Cannot find LINK/SSBOND residue THR (41 )
Cannot find LINK/SSBOND residue GNP (401 )
Cannot find LINK/SSBOND residue GNP (401 )
Cannot find LINK/SSBOND residue GNP (401 )
1 messages similar to the above omitted
EGOC_component1_A.pdb title:
Crystal structure of egoc [more info...]
Chain information for EGOC_component1_A.pdb #11
---
Chain | Description | UniProt
A | GTP-binding protein GTR1 | GTR1_YEAST
B | GTP-binding protein GTR2 | GTR2_YEAST
C | protein MEH1 | MEH1_YEAST
D | EGO2 | YC075_YEAST
E | protein SLM4 | SLM4_YEAST
Non-standard residues in EGOC_component1_A.pdb #11
---
GNP — phosphoaminophosphonic acid-guanylate ester
MG — magnesium ion
> select #8,9,10,11
28036 atoms, 28464 bonds, 72 pseudobonds, 3544 residues, 12 models selected
> hide sel & #!10-11 atoms
> show sel & #!10-11 surfaces
> color #8,9,10,11 grey
> color #8,9.10.11/A blue
> color #8,9,10,11/A blue
> color #8,9,10,11/B yellow
> select clear
> hide #!10 models
> hide #!11 models
> hide #!1 models
> hide #!6 models
> show #!4 models
> show #!8 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!10 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> hide #!9 models
> show #!9 models
> select #9
7009 atoms, 7116 bonds, 18 pseudobonds, 886 residues, 3 models selected
> hide sel atoms
> show sel surfaces
> color #8,9,10,11 grey
> color #8,9,10,11/B yellow
> color #8,9,10,11/A blue
> show #!10 models
> show #!8 models
> show #!11 models
> hide #!10 models
> hide #!9 models
> select #8
7009 atoms, 7116 bonds, 18 pseudobonds, 886 residues, 3 models selected
> hide sel atoms
> show sel surfaces
> color #8,9,10,11 grey
> color #8,9,10,11/A blue
> color #8,9,10,11/B yellow
> hide #!8 models
> hide #!11 models
> show #!11 models
> show #!10 models
> show #!9 models
> hide #!10 models
> hide #!11 models
> show #!8 models
> hide #!8 models
> show #!10 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!9 models
> show #!3 models
> show #!9 models
> hide #!11 models
> show #!11 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!11 models
> hide #!9 models
> show #!11 models
> morph #11,9
Computed 51 frame morph #12
> coordset #12 1,51
> select #12
7009 atoms, 7116 bonds, 9 pseudobonds, 886 residues, 2 models selected
> show sel surfaces
> select clear
> show #!8 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!10 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> morph #10,8
Computed 51 frame morph #13
> coordset #13 1,51
> select #12
7009 atoms, 7116 bonds, 9 pseudobonds, 886 residues, 2 models selected
> select #13
7009 atoms, 7116 bonds, 9 pseudobonds, 886 residues, 2 models selected
> select #12,13
14018 atoms, 14232 bonds, 18 pseudobonds, 1772 residues, 4 models selected
> hide sel surfaces
> show sel cartoons
> select clear
> hide #!12 models
> show #!12 models
> hide #!13 models
> show #!13 models
> save E:/Nature/Supplementary_video_2/morph_separate_wings.cxs
> coordset #3,7,12,13 loop 1 bounce true
> hide #!4 models
> show #!7 models
> morph #11,9 frames 41
Computed 42 frame morph #14
> coordset #14 1,42
> close #12-14
> morph #11,9 frames 40
Computed 41 frame morph #12
> coordset #12 1,41
> select #12
7009 atoms, 7116 bonds, 9 pseudobonds, 886 residues, 2 models selected
> show sel cartoons
> select clear
> morph #10,8 frames 40
Computed 41 frame morph #13
> coordset #13 1,41
> select #13
7009 atoms, 7116 bonds, 9 pseudobonds, 886 residues, 2 models selected
> show sel cartoons
> select clear
> hide #!3 models
> show #!3 models
> save E:/Nature/Supplementary_video_2/morph_separate_wings.cxs
> open E:\Nature\Supplementary_video_2\supvid2.cxc
> movie record supersample 3
> coordset #3,7,12,13 loop 3 bounce true
> wait 150
> movie stop
> movie encode C:\Users\tafurpet/Desktop/Sup_vid_2.mp4 quality high
Movie saved to C:\Users\tafurpet/Desktop/Sup_vid_2.mp4
executed supvid2.cxc
> open E:\Nature\Supplementary_video_2\supvid2.cxc
> movie record supersample 3
> coordset #3,7,12,13 loop 3 bounce true
> wait 200
> wait
wait requires a frame count argument unless motion is in progress
> movie stop
> movie encode C:\Users\tafurpet/Desktop/Sup_vid_2.mp4 quality high
Movie saved to C:\Users\tafurpet/Desktop/Sup_vid_2.mp4
executed supvid2.cxc
> open E:\Nature\Supplementary_video_2\supvid2.cxc
> movie record supersample 3
> coordset #3,7,12,13 1,41
> wait 200
> coordset #3,7,12,13 41,1
> wait 200
> movie stop
> movie encode C:\Users\tafurpet/Desktop/Sup_vid_2.mp4 quality high
Movie saved to C:\Users\tafurpet/Desktop/Sup_vid_2.mp4
executed supvid2.cxc
> turn y -45
> turn y 45
> turn y -45
> turn y -20
> turn y 20
> turn y -30
> turn y 30
> turn y -30
> turn y 45
> turn y -45
> open E:\Nature\Supplementary_video_2\supvid2.cxc
> movie record supersample 3
> wait 100
> coordset #3,7,12,13 41,1
> wait 200
> coordset #3,7,12,13 1,41
> wait 200
> turn y 45
> wait 100
> coordset #3,7,12,13 41,1
> wait 200
> coordset #3,7,12,13 1,41
> wait 200
> movie stop
> movie encode C:\Users\tafurpet/Desktop/Sup_vid_2.mp4 quality high
Movie saved to C:\Users\tafurpet/Desktop/Sup_vid_2.mp4
executed supvid2.cxc
> turn y -45
> 2dlabels text "Open SEAC" xpos 0.5 ypos 1
> ui mousemode right "move label"
> select #14
2 models selected
> close #14
> 2dlabels text "Open SEAC" color black size 12 xpos 0.5 ypos 1
> hide #!3 models
> hide #!5 models
> hide #!7 models
> hide #!12 models
> hide #!13 models
> close #15
> 2dlabels text "Open SEAC" color black size 12
> ui mousemode right "move label"
> 2dlabels #16.1 xpos 0.169 ypos 0.858
> show #!5 models
> show #!6 models
> hide #!6 models
> show #!7 models
> show #!12 models
> show #!13 models
> show #!3 models
> 2dlabels #16 size 32
> 2dlabels #16 size 24
> 2dlabels #16 size 24 font bold
> 2dlabels #16 size 24
> close #16
> 2dlabels text "Open SEAC" bold true
> ui mousemode right "move label"
> 2dlabels #17.1 xpos 0.114 ypos 0.913
> 2dlabels text core
> hide #!17 models
> show #!17 models
> close #17
> 2dlabels text "Open SEAC" bold true
> 2dlabels #18.1 xpos 0.129 ypos 0.891
> 2dlabels text core
> hide #18.2 models
> show #18.2 models
> ui mousemode right "move label"
> close #18.2
> 2dlabels text Core
> 2dlabels #18.2 xpos 0.757 ypos 0.804
> 2dlabels #18.2 xpos 0.739 ypos 0.799
> 2dlabels text Wing
> 2dlabels #18.3 xpos 0.487 ypos 0.315
> close #18.3
> 2dlabels text Wings
> 2dlabels #18.3 xpos 0.478 ypos 0.341
> 2dlabels text EGOC
> 2dlabels #18.4 xpos 0.545 ypos 0.100
> hide #!18 models
> show #!18 models
> 2dlabels text "Closed SEAC" bold true
> ui mousemode right "move label"
> 2dlabels #18.5 xpos 0.109 ypos 0.891
> hide #18.5 models
> show #18.5 models
> hide #18.1 models
> show #18.1 models
> hide #18.5 models
> save E:/Nature/Supplementary_video_2/morph_separate_wings.cxs
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.3.dev202109020559 (2021-09-02)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 3.3.0 NVIDIA 430.86
OpenGL renderer: Quadro P2000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: System manufacturer
Model: System Product Name
OS: Microsoft Windows 10 Education N (Build 19042)
Memory: 137,098,870,784
MaxProcessMemory: 137,438,953,344
CPU: 20 Intel(R) Core(TM) i9-9820X CPU @ 3.30GHz
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: 1.5.0
chardet: 4.0.0
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: 1.29
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: 2.5.3
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.4.1
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3.dev202109020559
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: 1.1.4
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: 2.5
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.1
ChimeraX-ModelPanel: 1.1
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: 2.6.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
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: 2.4.2
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: 1.12
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: 1.0.1
cycler: 0.10.0
Cython: 0.29.23
decorator: 5.0.9
distlib: 0.3.1
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: 2.10
ihm: 0.20
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: 2.11.3
jupyter-client: 6.1.12
jupyter-core: 4.7.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 1.1.1
matplotlib: 3.4.2
matplotlib-inline: 0.1.2
msgpack: 1.0.2
netCDF4: 1.5.6
networkx: 2.6.2
numexpr: 2.7.3
numpy: 1.21.0
numpydoc: 1.1.0
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.2
pickleshare: 0.7.5
Pillow: 8.2.0
pip: 21.1.1
pkginfo: 1.7.0
prompt-toolkit: 3.0.20
psutil: 5.8.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.9.0
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: 2.8.1
pytz: 2021.1
pywin32: 228
pyzmq: 22.2.1
qtconsole: 5.1.0
QtPy: 1.10.0
RandomWords: 0.3.0
requests: 2.25.1
scipy: 1.6.3
setuptools: 57.0.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.1.0
sortedcontainers: 2.4.0
Sphinx: 4.0.1
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: 1.26.6
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.2
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (2)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash saving session |
comment:2 by , 4 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
This ChimeraX crash we think happens because of a bug in deallocating objects. It crashes in Python garbage collection which deallocates no longer used data structures. It is probably deleting something that was already deleted. This frequently happens when allocating arrays which your crash report shows. Unfortunately we have no way so far to find what object is causing the problem. Sorry this happened during a session save.
If you see it again, please report again. We are hoping for a very simple case where you have done very little in ChimeraX and it crashes so it will narrow down what data is causing the crash.
Note:
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Crash saving session after morphing (and 2D labels). Crash creating empty array while fetching vector property.