![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 years ago
Last modified 4 years ago
#5673 closed defect
Crash saving session — at Version 1
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| 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 (1)
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 |
Note:
See TracTickets
for help on using tickets.
Crash saving session after morphing (and 2D labels). Crash creating empty array while fetching vector property.