![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#8426 closed defect (can't reproduce)
Crash using File→Open dialog on Windows and/or returning from function
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Platform | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19044
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x8001010e
Thread 0x00000cd0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 576 in _handle_results
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\biWindows fatal exception: code 0x8001010e
nWindows fatal exception: code 0x\lib\8001010e
tWindows fatal exception: code 0x8001010e
hreading.py", line 973 in _bootstrap_inner
File Windows fatal exception: code 0x8001010e"C:
\ProgWindows fatal exception: code 0x8001010eram
FWindows fatal exception: code 0xile8001010e
s\Windows fatal exception: code 0xChim8001010e
erWindows fatal exception: code 0xaX 8001010e
1.Windows fatal exception: code 0x8001010e3\b
iWindows fatal exception: code 0xn\lib\8001010e
thWindows fatal exception: code 0xre8001010e
ading.py", line 930 in _bootstrap
Thread 0x00002508 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 528 in _handle_tasks
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"Windows fatal exception: code 0x, line 9738001010e
in _boWindows fatal exception: code 0xot8001010e
stWindows fatal exception: code 0xrap8001010e
_iWindows fatal exception: code 0xnne8001010e
r
Windows fatal exception: File code 0x"8001010eC:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x0000091c (most recent call first):
File "C
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x:\Program8001010e
Windows fatal exception: code 0xFil8001010e
es\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 884 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 499 in _wait_for_updates
File "C:\Program Files\ChiWindows fatal exception: code 0x8001010e
merWindows fatal exception: code 0xaX8001010e
1Windows fatal exception: .code 0x8001010e3\
bWindows fatal exception: code 0x8001010ein\
libWindows fatal exception: code 0x8001010e\m
uWindows fatal exception: lcode 0xt8001010ei
prWindows fatal exception: ocode 0xc8001010ee
ssWindows fatal exception: icode 0xn8001010eg
\pWindows fatal exception: ocode 0xo8001010el
.pWindows fatal exception: ycode 0x"8001010e, line
519 in Windows fatal exception: _code 0xh8001010ea
ndle_workers
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00003024 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program FilWindows fatal exception: code 0xes8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
\CWindows fatal exception: code 0xhim8001010e
erWindows fatal exception: code 0xaX8001010e
1Windows fatal exception: code 0x.3\8001010e
biWindows fatal exception: ncode 0x\8001010el
ibWindows fatal exception: \code 0xt8001010eh
reWindows fatal exception: acode 0xd8001010ei
ng.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00001954 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x0000462c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000045b8 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000033b0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00004b88 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00004344 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00003418 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000032e4 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 17 in _file_open
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 45 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\__init__.py", line 37 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 1284 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py", line 381 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\tool.py", line 165 in callback
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00000cd0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 576 in _handle_results
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00002508 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 528 in _handle_tasks
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x0000091c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 884 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 499 in _wait_for_updates
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pooWindows fatal exception: code 0xl.8001010ep
y", line 519 in Windows fatal exception: _code 0xha8001010end
le_Windows fatal exception: wocode 0xr8001010ek
erWindows fatal exception: scode 0x
8001010e File
"Windows fatal exception: Ccode 0x:\8001010eP
roWindows fatal exception: grcode 0x8001010eam
FWindows fatal exception: ilcode 0xe8001010es
\CWindows fatal exception: hicode 0xm8001010eer
aXWindows fatal exception: 1code 0x.8001010e3\
biWindows fatal exception: n\code 0xl8001010ei
b\Windows fatal exception: tcode 0xh8001010e
reading.pyWindows fatal exception: code 0x", line 9108001010e
in run
Windows fatal exception: code 0x File 8001010e"
C:\PrograWindows fatal exception: code 0x8001010em Fi
leWindows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
s\CWindows fatal exception: code 0xhi8001010e
merWindows fatal exception: code 0xa8001010eX
1Windows fatal exception: .code 0x38001010e\
biWindows fatal exception: ncode 0x\8001010el
iWindows fatal exception: bcode 0x\8001010et
hreading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00003024 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00001954 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x0000462c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000045b8 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000033b0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00004b88 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00004344 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00003418 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000032e4 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 17 in _file_open
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 45 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\__init__.py", line 37 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 1284 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py", line 381 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\tool.py", line 165 in callback
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00000cd0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 576 in _handle_results
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00002508 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 528 in _handle_tasks
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x0000091c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 884 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 499 in _wait_for_updates
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 519 in _handle_workers
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00003024 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00001954 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x0000462c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000045b8 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000033b0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00004b88 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00004344 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00003418 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000032e4 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 17 in _file_open
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 45 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\__init__.py", line 37 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 1284 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py", line 381 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\tool.py", line 165 in callback
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00000cd0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 576 in _handle_results
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00002508 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 528 in _handle_tasks
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program FiWindows fatal exception: code 0x8001010ele
s\CWindows fatal exception: hicode 0xm8001010eer
aXWindows fatal exception: 1code 0x.8001010e3
\bWindows fatal exception: incode 0x\8001010eli
b\Windows fatal exception: thcode 0x8001010ere
adWindows fatal exception: icode 0xn8001010eg
.Windows fatal exception: code 0x8001010e
pWindows fatal exception: ycode 0x", line 8001010e930 in
_bWindows fatal exception: ocode 0xo8001010et
sWindows fatal exception: tcode 0xr8001010ea
pWindows fatal exception:
code 0xThread 0x8001010e0000091c
(most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 884 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 499 in _wait_for_updates
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 519 in _handle_workers
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00003024 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00001954 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x0000462c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000045b8 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000033b0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00004b88 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00004344 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00003418 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000032e4 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 17 in _file_open
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 45 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\__init__.py", line 37 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 1284 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py", line 381 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\tool.py", line 165 in callback
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packaWindows fatal exception: code 0xges8001010e
\chimeWindows fatal exception: code 0xr8001010ea
xWindows fatal exception: code 0x\8001010e
uiWindows fatal exception: code 0x\8001010e
guWindows fatal exception: code 0xi8001010e.
pyWindows fatal exception: code 0x"8001010e, line
301Windows fatal exception: code 0x in 8001010ee
vWindows fatal exception: ecode 0x8001010en
t_Windows fatal exception: code 0xl8001010eo
oWindows fatal exception: code 0xp8001010e
File "Windows fatal exception: code 0xC8001010e
:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00000cd0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 576 in _handle_results
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00002508 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 528 in _handle_tasks
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x0000091c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 884 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 499 in _wait_for_updates
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 519 in _handle_workers
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00003024 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00001954 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x0000462c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000045b8 (most recent call first):
File "C:\ProWindows fatal exception: code 0x8001010egr
am FWindows fatal exception: icode 0xl8001010ee
s\Windows fatal exception: Ccode 0xh8001010ei
meWindows fatal exception: rcode 0xa8001010eX
Windows fatal exception: code 0x8001010e1.
3\bWindows fatal exception: icode 0xn8001010e\
liWindows fatal exception: bcode 0x\8001010em
ulWindows fatal exception: tcode 0xi8001010e
prWindows fatal exception: ocode 0xc8001010ee
ssWindows fatal exception: icode 0xn8001010eg
\pWindows fatal exception: ocode 0xo8001010el
.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000033b0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00004b88 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00004344 (most recent call first):
File "C:\Program Files\ChimeraX 1.3Windows fatal exception: code 0x\b8001010e
in\liWindows fatal exception: code 0xb\8001010e
multWindows fatal exception: code 0xip8001010e
roWindows fatal exception: code 0xces8001010e
singWindows fatal exception: code 0x\p8001010e
ooWindows fatal exception: code 0xl.8001010e
pWindows fatal exception: y", line code 0x8001010e114 in
wWindows fatal exception: code 0xork8001010e
eWindows fatal exception: r
code 0x8001010e File "
C:Windows fatal exception: \code 0xPr8001010e
ogWindows fatal exception: racode 0x8001010em F
iles\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00003418 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000032e4 (most recent call first):
File "C:\Program Files\ChimeraX 1Windows fatal exception: code 0x8001010e.3
\binWindows fatal exception: code 0x\l8001010e
ibWindows fatal exception: code 0x\s8001010e
itWindows fatal exception: code 0xe-8001010e
pacWindows fatal exception: kcode 0xa8001010eg
es\Windows fatal exception: ccode 0xh8001010ei
meWindows fatal exception: rcode 0xa8001010ex
\oWindows fatal exception: pcode 0xe8001010en
_cWindows fatal exception: ocode 0xm8001010em
anWindows fatal exception: dcode 0x\8001010ed
iaWindows fatal exception: lcode 0xo8001010eg
.py", line 135 in show_open_file_dialog
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 17 in _file_open
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 45 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\__init__.py", line 37 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 1284 in run_provideWindows fatal exception: code 0x8001010er
File "C:\Windows fatal exception: Prcode 0x8001010eog
rWindows fatal exception: amcode 0x 8001010eF
iWindows fatal exception: code 0xl8001010ee
s\Windows fatal exception: Ccode 0xhi8001010e
meWindows fatal exception: code 0xr8001010ea
X Windows fatal exception: code 0x18001010e.
3Windows fatal exception: code 0x\8001010e
bWindows fatal exception: incode 0x8001010e
\liWindows fatal exception: code 0xb\s8001010e
iteWindows fatal exception: -code 0xp8001010ea
ckages\chimerax\core\toolshed\info.py", line 381 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\tool.py", line 165 in callback
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00000cd0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 576 in _handle_results
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00002508 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 528 in _handle_tasks
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x0000091c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 884 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 499 in _wait_for_updates
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 519 in _handle_workers
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00003024 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00001954 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x0000462c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000045b8 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000033b0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00004b88 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00004344 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00003418 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000032e4 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 17 in _file_open
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 45 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\__init__.py", line 37 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 1284 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py", line 381 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\tool.py", line 165 in callback
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00000cd0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 576 in _handle_results
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00002508 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 528 in _handle_tasks
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x0000091c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 884 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 499 in _wait_for_updates
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 519 in _handle_workers
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00003024 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00001954 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x0000462c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000045b8 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000033b0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00004b88 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00004344 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00003418 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000032e4 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 17 in _file_open
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 45 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\__init__.py", line 37 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 1284 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py", line 381 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\tool.py", line 165 in callback
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00000cd0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 576 in _handle_results
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00002508 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 528 in _handle_tasks
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x0000091c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 884 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 499 in _wait_for_updates
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 519 in _handle_workers
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00003024 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00001954 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x0000462c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000045b8 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000033b0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00004b88 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00004344 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00003418 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000032e4 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 17 in _file_open
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 45 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\__init__.py", line 37 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 1284 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py", line 381 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\tool.py", line 165 in callback
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00000cd0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 576 in _handle_results
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00002508 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 528 in _handle_tasks
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x0000091c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 884 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 499 in _wait_for_updates
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 519 in _handle_workers
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00003024 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00001954 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x0000462c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000045b8 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000033b0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00004b88 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00004344 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00003418 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000032e4 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 17 in _file_open
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 45 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\__init__.py", line 37 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 1284 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py", line 381 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\tool.py", line 165 in callback
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00000cd0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 576 in _handle_results
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00002508 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 528 in _handle_tasks
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x0000091c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 884 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 499 in _wait_for_updates
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 519 in _handle_workers
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00003024 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00001954 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x0000462c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000045b8 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000033b0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00004b88 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00004344 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00003418 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000032e4 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 17 in _file_open
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 45 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\__init__.py", line 37 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 1284 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py", line 381 in run_provider
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\tool.py", line 165 in callback
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00000cd0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 576 in _handle_results
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00002508 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 528 in _handle_tasks
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x0000091c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 884 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 499 in _wait_for_updates
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 519 in _handle_workers
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00003024 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00001954 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x0000462c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000045b8 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000033b0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00004b88 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00004344 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00003418 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000032e4 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\atomic\structure.py", line 1689 in _array
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\atomic\structure.py", line 1668 in _update_graphics_if_needed
Windows fatal exception: access violation
===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:\\\Users\\\petedani\\\Downloads\\\emd_27242.map\\\emd_27242.map
Opened emd_27242.map as #1, grid size 224,224,224, pixel 0.91, shown at level
0.0975, step 1, values float32
> volume #1 level 0.2483
> volume #1 level 0.1267
> lighting soft
> surface dust #1 size 9.1
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\petedani\\\OneDrive - Boehringer
> Ingelheim\\\Documents\\\presentations\\\2023_Novalix\\\figures\\\CRBN_open-
> vs-closed.cxs"
Opened composite_cryosparc_P23_J433_J445_map_zflip.mrc as #1, grid size
360,360,360, pixel 0.745, shown at level 8, step 1, values float32
Opened composite_cryosparc_P23_J734_J766_volume_map.mrc as #7, grid size
360,360,360, pixel 0.745, shown at level 8, step 1, values float32
Log from Thu Feb 2 16:17:34 2023UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\petedani\\\OneDrive - Boehringer
> Ingelheim\\\Documents\\\presentations\\\2022_CRBN-
> cluster\\\overview_HPK1volume_CRBNopen-volume.cxs"
Opened composite_cryosparc_P23_J433_J445_map_zflip.mrc as #1, grid size
360,360,360, pixel 0.745, shown at level 8, step 1, values float32
Opened composite_cryosparc_P23_J734_J766_volume_map.mrc as #7, grid size
360,360,360, pixel 0.745, shown at level 8, step 1, values float32
Log from Wed Oct 12 11:53:20 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\petedani\\\OneDrive - Boehringer
> Ingelheim\\\Documents\\\presentations\\\2022_CRBN-
> cluster\\\overview_HPK1volume_CRBNopen-volume.cxs"
Opened composite_cryosparc_P23_J433_J445_map_zflip.mrc as #1, grid size
360,360,360, pixel 0.745, shown at level 6, step 1, values float32
Opened composite_cryosparc_P23_J734_J766_volume_map.mrc as #7, grid size
360,360,360, pixel 0.745, shown at level 6, step 1, values float32
Log from Tue Oct 11 17:29:23 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\petedani\\\OneDrive - Boehringer
> Ingelheim\\\Documents\\\presentations\\\2022_CRBN-
> cluster\\\overview_bCAT_HPK1.cxs"
Opened composite_cryosparc_P23_J433_J445_map_zflip.mrc as #1, grid size
360,360,360, pixel 0.745, shown at level 6, step 1, values float32
Opened composite_J523_J527_volume_map.mrc as #2, grid size 350,350,350, pixel
0.86, shown at level 3, step 1, values float32
Log from Tue Oct 11 10:21:47 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\petedani\\\OneDrive - Boehringer
> Ingelheim\\\Documents\\\presentations\\\2022_CRBN-
> cluster\\\overview_bCAT.cxs"
Opened composite_cryosparc_P23_J433_J445_map_zflip.mrc as #1, grid size
360,360,360, pixel 0.745, shown at level 6, step 1, values float32
Log from Tue Oct 11 09:53:29 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\petedani\\\OneDrive - Boehringer
> Ingelheim\\\Documents\\\presentations\\\2022_CRBN-cluster\\\overview.cxs"
Opened composite_cryosparc_P23_J433_J445_map_zflip.mrc as #1, grid size
360,360,360, pixel 0.745, shown at level 6, step 1, values float32
Log from Mon Sep 5 13:07:24 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\petedani\\\OneDrive - Boehringer
> Ingelheim\\\Documents\\\projects\\\HPK1\\\20220722_grid381_BI03051346_KriosIMP\\\figures\\\overview1.cxs"
Opened composite_cryosparc_P23_J433_J445_map_zflip.mrc as #1, grid size
360,360,360, pixel 0.745, shown at level 6, step 1, values float32
Log from Tue Aug 30 10:43:06 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\petedani\\\OneDrive - Boehringer
> Ingelheim\\\Documents\\\projects\\\HPK1\\\20220722_grid381_BI03051346_KriosIMP\\\figures\\\overview1.cxs"
Opened composite_cryosparc_P23_J433_J445_map_zflip.mrc as #1, grid size
360,360,360, pixel 0.745, shown at level 6, step 1, values float32
Log from Tue Aug 30 09:34:18 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\petedani\\\OneDrive - Boehringer
> Ingelheim\\\Documents\\\projects\\\HPK1\\\20220722_grid381_BI03051346_KriosIMP\\\figures\\\overview1.cxs"
Opened composite_cryosparc_P23_J433_J445_map_zflip.mrc as #1, grid size
360,360,360, pixel 0.745, shown at level 6, step 1, values float32
Log from Tue Aug 30 09:30:44 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\petedani\\\OneDrive - Boehringer
> Ingelheim\\\Documents\\\projects\\\HPK1\\\20220722_grid381_BI03051346_KriosIMP\\\figures\\\overview1.cxs"
Opened composite_cryosparc_P23_J433_J445_map_zflip.mrc as #1, grid size
360,360,360, pixel 0.745, shown at level 6, step 1, values float32
Log from Fri Aug 26 09:39:07 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\petedani\\\OneDrive - Boehringer
> Ingelheim\\\Documents\\\projects\\\HPK1\\\20220722_grid381_BI03051346_KriosIMP\\\figures\\\overview1.cxs"
Opened composite_cryosparc_P23_J433_J445_map_zflip.mrc as #1, grid size
360,360,360, pixel 0.745, shown at level 6, step 1, values float32
Log from Fri Aug 26 09:15:30 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\petedani\\\OneDrive - Boehringer
> Ingelheim\\\Documents\\\projects\\\HPK1\\\20220722_grid381_BI03051346_KriosIMP\\\figures\\\overview1.cxs"
Opened composite_cryosparc_P23_J433_J445_map_zflip.mrc as #1, grid size
360,360,360, pixel 0.745, shown at level 6, step 1, values float32
Log from Fri Aug 26 09:01:55 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:\\\Users\\\petedani\\\OneDrive - Boehringer
> Ingelheim\\\Documents\\\projects\\\HPK1\\\20220722_grid381_BI03051346_KriosIMP\\\maps\\\composite_cryosparc_P23_J433_J445_map_zflip.mrc"
Opened composite_cryosparc_P23_J433_J445_map_zflip.mrc as #1, grid size
360,360,360, pixel 0.745, shown at level 2.3, step 2, values float32
> volume #1 step 1
> volume #1 level 5.978
> open "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/HPK1/20220722_grid381_BI03051346_KriosIMP/coot/CRBN-
> DDB1delta-BI03051346-HPK1_fitJ445-coot-10.pdb"
Chain information for CRBN-DDB1delta-BI03051346-HPK1_fitJ445-coot-10.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
> color #1 #b2b2b264 models
> color bychain
> ui mousemode right select
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
56 atoms, 64 bonds, 1 residue, 1 model selected
> select #1
2 models selected
> select #1
2 models selected
> select #1
2 models selected
> select down
2 models selected
> ui mousemode right rotate
> ui mousemode right select
> select #1
2 models selected
> select clear
> select #1
2 models selected
> select /B:451@C18
1 atom, 1 residue, 1 model selected
> ui mousemode right select
> select up
56 atoms, 64 bonds, 1 residue, 1 model selected
> color sel byhetero
[Repeated 1 time(s)]
> ui tool show "Color Actions"
> color sel red
> color sel purple
> color sel deep pink
> color sel dark magenta
> color sel dark orchid
> color sel dark red
> color sel dark magenta
> select clear
[Repeated 1 time(s)]
> volume #1 level 6
> select clear
> cd "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/HPK1/20220722_grid381_BI03051346_KriosIMP/figures"
Current working directory is: C:\Users\petedani\OneDrive - Boehringer
Ingelheim\Documents\projects\HPK1\20220722_grid381_BI03051346_KriosIMP\figures
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/HPK1/20220722_grid381_BI03051346_KriosIMP/figures/overview1.cxs"
> save overview1.png image .png width 600 height 1200 transparentBackground
> true
Expected a keyword
> save overview1.png width 600 height 1200 transparentBackground true
> save overview1.png width 800 height 1200 transparentBackground true
> select clear
> save overview1.png width 800 height 1200 transparentBackground true
[Repeated 2 time(s)]
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/HPK1/20220722_grid381_BI03051346_KriosIMP/figures/overview1.cxs"
——— End of log from Fri Aug 26 09:01:55 2022 ———
opened ChimeraX session
> save overview1.png width 800 height 1200 transparentBackground true
> ui mousemode right select
> select /B:451@C17
1 atom, 1 residue, 1 model selected
> select up
56 atoms, 64 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel cyan
> color sel deep sky blue
> color sel dark blue
> color sel medium blue
> color sel magenta
> color sel deep pink
> color sel purple
[Repeated 1 time(s)]
> select clear
> select #1
2 models selected
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
56 atoms, 64 bonds, 1 residue, 1 model selected
> color sel indigo
> select clear
> save overview1.png width 800 height 1200 transparentBackground true
> select /B:451@C17
1 atom, 1 residue, 1 model selected
> select up
56 atoms, 64 bonds, 1 residue, 1 model selected
> color sel dark cyan
> color sel blue
> color sel byhetero
> color sel goldenrod
> color sel byhetero
> select clear
> save overview1.png width 800 height 1200 transparentBackground true
> select /B:451@C17
1 atom, 1 residue, 1 model selected
> select up
56 atoms, 64 bonds, 1 residue, 1 model selected
> color sel tomato
> color sel crimson
> color sel orange red
> color sel crimson
> color sel byhetero
> color sel blue
> color sel byhetero
> select clear
> save overview1.png width 800 height 1200 transparentBackground true
> select /B:451@C17
1 atom, 1 residue, 1 model selected
> select up
56 atoms, 64 bonds, 1 residue, 1 model selected
> color sel medium violet red
[Repeated 1 time(s)]
> color sel cyan
> color sel deep sky blue
> color sel midnight blue
> color sel blue
> color sel byhetero
> select clear
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/HPK1/20220722_grid381_BI03051346_KriosIMP/figures/overview1.cxs"
QWindowsWindow::setGeometry: Unable to set geometry 746x1+2965+211 (frame:
762x40+2957+180) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 746x2+2965+211 (frame: 762x41+2957+180)
margins: 8, 31, 8, 8 minimum size: 71x1 maximum size: 524287x524287 MINMAXINFO
maxSize=0,0 maxpos=0,0 mintrack=158,41 maxtrack=1048590,1048613)
> save overview1.positions
Must specify models when saving positions file overview1.positions.
> save overview1.positions #1 #2
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/HPK1/20220722_grid381_BI03051346_KriosIMP/figures/overview1.cxs"
——— End of log from Fri Aug 26 09:15:30 2022 ———
opened ChimeraX session
> surface dust #1 size 5
> lighting multiShadow 64
> save overview1.png width 800 height 1200 transparentBackground true
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/HPK1/20220722_grid381_BI03051346_KriosIMP/figures/overview1.cxs"
——— End of log from Fri Aug 26 09:39:07 2022 ———
opened ChimeraX session
> open "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/HPK1/20220722_grid381_BI03051346_KriosIMP/coot/CRBN-
> DDB1delta-BI03051346-HPK1_fitJ445-s2_coot-12.pdb"
Chain information for CRBN-DDB1delta-BI03051346-HPK1_fitJ445-s2_coot-12.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #!2 models
> color #!3 bychain
> ui mousemode right select
> select #1
2 models selected
> select #1
2 models selected
> select clear
> select #1
2 models selected
> select #1
2 models selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
56 atoms, 64 bonds, 1 residue, 1 model selected
> color sel blue
> color sel byhetero
> close #2
> select #3
11607 atoms, 11848 bonds, 7 pseudobonds, 1468 residues, 3 models selected
> ~select #3
Nothing selected
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/HPK1/20220722_grid381_BI03051346_KriosIMP/figures/overview1.cxs"
——— End of log from Tue Aug 30 09:30:44 2022 ———
opened ChimeraX session
> hide #!1 models
> ui mousemode right select
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /B:378@CB
1 atom, 1 residue, 1 model selected
> select up
10 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /B:501@ZN
1 atom, 1 residue, 1 model selected
> color sel yellow
> select clear
> show #!1 models
> save overview1.png width 800 height 1200 transparentBackground true
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/HPK1/20220722_grid381_BI03051346_KriosIMP/figures/overview1.cxs"
——— End of log from Tue Aug 30 09:34:18 2022 ———
opened ChimeraX session
> ui mousemode right select
> select /C:104
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
61 atoms, 61 bonds, 7 residues, 1 model selected
> select up
2064 atoms, 2108 bonds, 259 residues, 1 model selected
> hide sel atoms
> select clear
> save overview1.png width 800 height 1200 transparentBackground true
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/HPK1/20220722_grid381_BI03051346_KriosIMP/figures/overview1.cxs"
——— End of log from Tue Aug 30 10:43:06 2022 ———
opened ChimeraX session
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/HPK1/20220722_grid381_BI03051346_KriosIMP/figures/overview1.cxs"
> includeMaps true
——— End of log from Mon Sep 5 13:07:24 2022 ———
opened ChimeraX session
> cd "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-cluster"
Current working directory is: C:\Users\petedani\OneDrive - Boehringer
Ingelheim\Documents\presentations\2022_CRBN-cluster
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-cluster/overview.cxs"
——— End of log from Tue Oct 11 09:53:29 2022 ———
opened ChimeraX session
> open "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/bCAT/20220921_reprocessing_eBIC-
> data/maps/composite_J523_J527_volume_map.mrc"
Opened composite_J523_J527_volume_map.mrc as #2, grid size 350,350,350, pixel
0.86, shown at level 2.3, step 2, values float32
> volume #2 step 1
> volume #2 level 3.008
> volume #2 level 4
> surface dust #1 size 7.45
> surface dust #2 size 8.6
> ui mousemode right select
> select #2
2 models selected
Drag select of 2 composite_J523_J527_volume_map.mrc
> ui mousemode right "move picked models"
> view matrix models #2,1,0,0,23.005,0,1,0,76.629,0,0,1,-47.458
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.86473,0.27742,0.41867,-62.197,0.24568,-0.96071,0.12915,277.93,0.43805,-0.0088244,-0.89891,200.02
> view matrix models
> #2,0.9927,-0.027216,0.1175,8.4213,-0.066368,-0.93671,0.34375,285.85,0.10071,-0.34904,-0.93168,300.34
> view matrix models
> #2,0.93151,0.2571,-0.25727,41.382,0.31113,-0.92962,0.19751,252.92,-0.18838,-0.26403,-0.94594,334.31
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.93151,0.2571,-0.25727,-0.12954,0.31113,-0.92962,0.19751,210.81,-0.18838,-0.26403,-0.94594,351.24
> ui mousemode right select
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.92435,0.083445,-0.3723,42.718,0.14214,-0.98086,0.13307,253.19,-0.35408,-0.17592,-0.91852,359.68
> view matrix models
> #2,0.87795,0.47861,0.011547,-65.501,0.42652,-0.79289,0.43522,136.68,0.21746,-0.37717,-0.90025,298.52
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.87795,0.47861,0.011547,-66.977,0.42652,-0.79289,0.43522,126.73,0.21746,-0.37717,-0.90025,292.15
> ui tool show "Fit in Map"
Fit map composite_J523_J527_volume_map.mrc in map
composite_cryosparc_P23_J433_J445_map_zflip.mrc using 284588 points
correlation = 0.703, correlation about mean = 0.5157, overlap = 1.419e+07
steps = 364, shift = 9.41, angle = 19.3 degrees
Position of composite_J523_J527_volume_map.mrc (#2) relative to
composite_cryosparc_P23_J433_J445_map_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.96730181 0.21167358 -0.13971935 -24.38960912
0.24835283 -0.90227271 0.35245543 174.76786298
-0.05145944 -0.37563046 -0.92533976 336.24844663
Axis -0.99149347 -0.12019065 0.04994910
Axis point 0.00000000 121.02254247 150.51427057
Rotation angle (degrees) 158.45904113
Shift along axis 19.97198036
Fit map composite_J523_J527_volume_map.mrc in map
composite_cryosparc_P23_J433_J445_map_zflip.mrc using 284588 points
correlation = 0.703, correlation about mean = 0.5157, overlap = 1.419e+07
steps = 136, shift = 0.0155, angle = 0.0048 degrees
Position of composite_J523_J527_volume_map.mrc (#2) relative to
composite_cryosparc_P23_J433_J445_map_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.96730465 0.21162287 -0.13977650 -24.36674064
0.24832915 -0.90226535 0.35249095 174.76223447
-0.05152034 -0.37567671 -0.92531760 336.27430569
Axis -0.99149414 -0.12017214 0.04998032
Axis point 0.00000000 121.02440577 150.52602037
Rotation angle (degrees) 158.45651659
Shift along axis 19.96502729
> ui mousemode right select
> select clear
> open "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/bCAT/20220921_reprocessing_eBIC-
> data/coot/composite_bCATtrunc-CRBN-DDB1delta-coot-0.pdb"
Chain information for composite_bCATtrunc-CRBN-DDB1delta-coot-0.pdb #4
---
Chain | Description
A | No description available
B | No description available
H | No description available
> ui tool show Matchmaker
> matchmaker #4/A to #3/A & sel pairing ss
No 'to' chains specified
> matchmaker #4/A & sel to #3/A & sel pairing ss
No 'to' chains specified
> matchmaker #!4 & sel to #3/A & sel pairing bs
No 'to' chains specified
> matchmaker #!4 to #3/A pairing bs
Parameters
---
Chain pairing | bs
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 CRBN-DDB1delta-BI03051346-HPK1_fitJ445-s2_coot-12.pdb, chain A (#3)
with composite_bCATtrunc-CRBN-DDB1delta-coot-0.pdb, chain A (#4), sequence
alignment score = 3596.2
RMSD between 800 pruned atom pairs is 0.826 angstroms; (across all 826 pairs:
0.965)
Fit molecule composite_bCATtrunc-CRBN-DDB1delta-coot-0.pdb (#4) to map
composite_J523_J527_volume_map.mrc (#2) using 11493 atoms
average map value = 9.081, steps = 112
shifted from previous position = 0.373
rotated from previous position = 0.682 degrees
atoms outside contour = 2497, contour level = 4
Position of composite_bCATtrunc-CRBN-DDB1delta-coot-0.pdb (#4) relative to
composite_J523_J527_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.99999152 -0.00226012 0.00344352 -0.12315944
0.00225330 0.99999550 0.00198277 -0.58773949
-0.00344798 -0.00197499 0.99999211 0.84507479
Axis -0.43304652 0.75404733 0.49384546
Axis point 241.08048433 0.00000000 32.90286241
Rotation angle (degrees) 0.26182374
Shift along axis 0.02748673
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-cluster/overview_bCAT_HPK1.cxs"
> select clear
> volume #2 color #b2b2b264
> hide #!1 models
> hide #!3 models
> ui mousemode right select
> select #4/B:262
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
133 atoms, 134 bonds, 15 residues, 1 model selected
> select up
3076 atoms, 3148 bonds, 382 residues, 1 model selected
> ui tool show "Color Actions"
> color sel salmon
> show #!3 models
> select clear
> hide #!3 models
> select #2
2 models selected
> select clear
> select #4/A:184
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
68 atoms, 69 bonds, 8 residues, 1 model selected
> select up
6468 atoms, 6585 bonds, 826 residues, 1 model selected
> color sel slate blue
> show #!3 models
> select clear
> hide #!3 models
Drag select of 2 composite_J523_J527_volume_map.mrc , 53 residues
> select clear
[Repeated 2 time(s)]
> select #4/H:148
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 4 residues, 1 model selected
> select up
1949 atoms, 1975 bonds, 255 residues, 1 model selected
> color sel rebecca purple
> select clear
> show #!1 models
> hide #!1 models
> color zone #2 near #4 distance 5.16
> select clear
> lighting soft
> select clear
> show #!1 models
> hide #!2 models
> show #!3 models
> hide #!4 models
> volume #1 color #b2b2b2
> hide #!1 models
> select clear
[Repeated 2 time(s)]
> select #3/B:451@N23
1 atom, 1 residue, 1 model selected
> ui mousemode right select
> select clear
[Repeated 2 time(s)]
> select #3/B:451@C28
1 atom, 1 residue, 1 model selected
> select up
56 atoms, 64 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel blue
> select clear
> select #3/B:501@ZN
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> show #!1 models
> color zone #1 near #3 distance 4.47
> select clear
> show #!2 models
> hide #!1 models
> hide #!3 models
> volume #2 color #b2b2b2
> volume #2 level 5
> show #!4 models
> color zone #2 near #4 distance 5.16
> volume #2 level 4.5
> select clear
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-cluster/overview_bCAT_HPK1.cxs"
> volume #2 color #b2b2b264
> volume #2 color #b2b2b250
> volume #1 color #b2b2b250
> show #!3 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> volume #2 level 4
> volume #2 level 3
> select clear
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-cluster/overview_bCAT_HPK1.cxs"
[Repeated 1 time(s)]
——— End of log from Tue Oct 11 10:21:47 2022 ———
opened ChimeraX session
> hide #!4 models
> show #!4 models
> hide #!2 models
> show #!2 models
> lighting simple
> lighting soft
> volume #!2 style surface
[Repeated 1 time(s)]
> volume #!2 style mesh
> volume #!2 style surface
> show #!1 models
> hide #!2 models
> show #!2 models
> color #2 #7c72b250 models
> color #2 #b2b2b250 models
> hide #!1 models
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-cluster/overview_bCAT_HPK1.cxs"
> show #!3 models
> hide #!4 models
> hide #!2 models
> ui mousemode right select
> select #3/C:225
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
75 atoms, 76 bonds, 9 residues, 1 model selected
> select up
2064 atoms, 2108 bonds, 259 residues, 1 model selected
> ui tool show "Color Actions"
> color sel forest green
> color sel light sea green
> color sel forest green
> select clear
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-cluster/overview_bCAT_HPK1.cxs"
> hide #!3 models
> open "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/BRAF-CRBN/20220920_grid440_Krios-
> IMP/maps/composite_P29_J482_J497_map.mrc"
Opened composite_P29_J482_J497_map.mrc as #5, grid size 480,480,480, pixel
0.745, shown at level 2.55, step 2, values float32
Drag select of 5 composite_P29_J482_J497_map.mrc
> select clear
> volume #5 step 1
> volume #5 level 6
> select clear
> show #!1 models
> show #!2 models
> select #5
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #5,1,0,0,-54.814,0,1,0,72.703,0,0,1,-30.834
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.23616,0.97141,0.024409,41.293,-0.20298,-0.073881,0.97639,130.54,0.95028,0.22563,0.21463,-137.87
> view matrix models
> #5,-0.83141,0.54387,-0.11389,284.43,-0.2289,-0.14846,0.96206,153.22,0.50633,0.82593,0.24792,-155.22
> view matrix models
> #5,-0.80347,-0.24566,-0.5423,509.17,-0.3625,-0.5207,0.77296,290.26,-0.47226,0.81763,0.32932,54.392
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.80347,-0.24566,-0.5423,495.13,-0.3625,-0.5207,0.77296,198.53,-0.47226,0.81763,0.32932,30.509
> view matrix models
> #5,-0.80347,-0.24566,-0.5423,447.14,-0.3625,-0.5207,0.77296,151.57,-0.47226,0.81763,0.32932,7.5324
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.60963,-0.701,-0.37007,454.61,-0.50513,-0.016242,0.86289,72.24,-0.6109,0.71297,-0.3442,189.73
> view matrix models
> #5,-0.92887,-0.366,0.056947,381.92,0.053329,0.019996,0.99838,-88.637,-0.36654,0.9304,0.00094426,26.036
> view matrix models
> #5,-0.83574,-0.48903,-0.24976,443.26,-0.24943,-0.067117,0.96606,3.2233,-0.4892,0.86968,-0.065889,78.458
> view matrix models
> #5,-0.81469,-0.50616,-0.28299,448.11,-0.2853,-0.075005,0.9555,14.959,-0.50486,0.85917,-0.0833,87.392
> ui mousemode right select
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.81469,-0.50616,-0.28299,439.51,-0.2853,-0.075005,0.9555,17.247,-0.50486,0.85917,-0.0833,78.302
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.97938,-0.096816,-0.17733,379.99,-0.18593,0.088514,0.97857,-40.596,-0.079045,0.99136,-0.10469,-39.714
> ui mousemode right select
> select clear
> ui tool show "Fit in Map"
Fit map composite_P29_J482_J497_map.mrc in map
composite_cryosparc_P23_J433_J445_map_zflip.mrc using 319259 points
correlation = 0.8338, correlation about mean = 0.6838, overlap = 3.109e+07
steps = 532, shift = 36.1, angle = 13.6 degrees
Position of composite_P29_J482_J497_map.mrc (#5) relative to
composite_cryosparc_P23_J433_J445_map_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.97426897 0.08825764 -0.20739012 331.77511000
-0.18261063 0.23024596 0.95584531 -54.76477731
0.13211139 0.96912200 -0.20820468 -25.85519404
Axis 0.03055487 -0.78132636 -0.62337430
Axis point 163.60764671 0.00000000 32.11333872
Rotation angle (degrees) 167.45186546
Shift along axis 69.04397418
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> surface dust #5 size 7.45
> cd "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-cluster"
Current working directory is: C:\Users\petedani\OneDrive - Boehringer
Ingelheim\Documents\presentations\2022_CRBN-cluster
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-
> cluster/overview_BRAF_bCAT_HPK1.cxs"
> open "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/BRAF-CRBN/20220920_grid440_Krios-IMP/coot/BRAF-
> CRBN-DDB1delta_fitJ497-coot-1.pdb"
Chain information for BRAF-CRBN-DDB1delta_fitJ497-coot-1.pdb #6
---
Chain | Description
A | No description available
B | No description available
C | No description available
> ui tool show Matchmaker
> matchmaker #!6 to #3/B pairing bs
Parameters
---
Chain pairing | bs
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 CRBN-DDB1delta-BI03051346-HPK1_fitJ445-s2_coot-12.pdb, chain B (#3)
with BRAF-CRBN-DDB1delta_fitJ497-coot-1.pdb, chain B (#6), sequence alignment
score = 1722.1
RMSD between 356 pruned atom pairs is 0.897 angstroms; (across all 381 pairs:
1.211)
> volume #5 color #b2b2b250
> lighting soft
> select #6/A:90
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
80 atoms, 80 bonds, 10 residues, 1 model selected
> select up
6448 atoms, 6565 bonds, 826 residues, 1 model selected
Fit molecule BRAF-CRBN-DDB1delta_fitJ497-coot-1.pdb (#6) to map
composite_P29_J482_J497_map.mrc (#5) using 11647 atoms
average map value = 14.89, steps = 92
shifted from previous position = 0.284
rotated from previous position = 1.75 degrees
atoms outside contour = 1620, contour level = 6
Position of BRAF-CRBN-DDB1delta_fitJ497-coot-1.pdb (#6) relative to
composite_P29_J482_J497_map.mrc (#5) coordinates:
Matrix rotation and translation
0.99999994 0.00018012 -0.00008854 -0.01189073
-0.00018013 0.99999995 0.00003814 0.02093733
0.00008851 -0.00003815 0.99999994 -0.00459851
Axis -0.18672402 -0.43333603 -0.88167682
Axis point 109.50097967 68.92638099 0.00000000
Rotation angle (degrees) 0.01170538
Shift along axis -0.00279821
> ui tool show "Color Actions"
> color sel slate blue
> show #!3 models
> select clear
> hide #!3 models
> show #!3 models
> hide #!3 models
> select #6/B:262
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
141 atoms, 142 bonds, 16 residues, 1 model selected
> select up
3039 atoms, 3111 bonds, 382 residues, 1 model selected
> color sel salmon
> select clear
> select #6/C:492
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
110 atoms, 111 bonds, 14 residues, 1 model selected
> select up
2160 atoms, 2209 bonds, 270 residues, 1 model selected
> color sel teal
> select clear
> show #!3 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> show #!4 models
> hide #!4 models
> show #!3 models
> cd "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-cluster"
Current working directory is: C:\Users\petedani\OneDrive - Boehringer
Ingelheim\Documents\presentations\2022_CRBN-cluster
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-
> cluster/overview_BRAF_bCAT_HPK1.cxs"
> show #!2 models
> show #!4 models
> hide #!3 models
> hide #!1 models
Drag select of 2 composite_J523_J527_volume_map.mrc , 2 residues
Drag select of 2 composite_J523_J527_volume_map.mrc
> select clear
> show #!1 models
> show #!3 models
> hide #!2 models
> hide #!4 models
Drag select of 1 composite_cryosparc_P23_J433_J445_map_zflip.mrc , 3 residues
> select clear
> show #!4 models
> show #!2 models
> hide #!3 models
> hide #!1 models
> show #!3 models
> show #!1 models
> hide #!2 models
> hide #!4 models
> cd "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-cluster"
Current working directory is: C:\Users\petedani\OneDrive - Boehringer
Ingelheim\Documents\presentations\2022_CRBN-cluster
> save HPK1-CRBN_overview.png width 600 height 600 transparentBackground true
> save HPK1-CRBN_overview.png width 800 height 400 transparentBackground true
> save HPK1-CRBN_overview.png width 400 height 800 transparentBackground true
[Repeated 3 time(s)]
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-
> cluster/overview_BRAF_bCAT_HPK1.cxs"
> show #!2 models
> show #!4 models
> hide #!3 models
> hide #!1 models
> save bCat-CRBN_overview.png width 400 height 800 transparentBackground true
> volume #2 level 4
> save bCat-CRBN_overview.png width 400 height 800 transparentBackground true
> volume #2 level 5
> save bCAT-CRBN_overview.png width 400 height 800 transparentBackground true
[Repeated 1 time(s)]
> volume #2 level 4.5
> volume #2 level 4
> save bCAT-CRBN_overview.png width 400 height 800 transparentBackground true
> show #!5 models
> show #!6 models
> hide #!4 models
> hide #!2 models
> save BRAF-CRBN_overview.png width 400 height 800 transparentBackground true
[Repeated 1 time(s)]
> hide #!5 models
> hide #!6 models
> show #!4 models
> show #!2 models
> save bCAT-CRBN_overview.png width 400 height 800 transparentBackground true
[Repeated 1 time(s)]
> hide #!2 models
> hide #!4 models
> show #!5 models
> show #!6 models
> save BRAF-CRBN_overview.png width 400 height 800 transparentBackground true
> hide #!5 models
> hide #!6 models
> show #!3 models
> show #!1 models
> save HPK1-CRBN_overview.png width 400 height 800 transparentBackground true
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-
> cluster/overview_BRAF_bCAT_HPK1.cxs"
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-cluster/overview_HPK1volume.cxs"
> color zone #1 near #3 distance 4.47
> hide #!3 models
> save HPK1-CRBN_volume.png width 400 height 800 transparentBackground true
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-cluster/overview_HPK1volume.cxs"
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-
> cluster/overview_HPK1volume_CRBNopen-volume.cxs"
> open "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/HPK1/20220722_grid381_BI03051346_KriosIMP/maps/CRBNopen/composite_cryosparc_P23_J734_J766_volume_map.mrc"
Opened composite_cryosparc_P23_J734_J766_volume_map.mrc as #7, grid size
360,360,360, pixel 0.745, shown at level 2.02, step 2, values float32
> volume #7 step 1
> volume #7 level 5.278
Drag select of 1 composite_cryosparc_P23_J433_J445_map_zflip.mrc , 7
composite_cryosparc_P23_J734_J766_volume_map.mrc
> select clear
> close #2
> close #5
> close #4,6
> volume #7 level 6
> select #7
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.94172,0.28308,-0.18174,260.47,0.04441,0.64015,0.76697,-65.632,0.33345,0.7142,-0.61541,84.086
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.94172,0.28308,-0.18174,246.98,0.04441,0.64015,0.76697,-9.9756,0.33345,0.7142,-0.61541,33.045
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.30997,-0.90137,-0.3024,333.6,0.22326,-0.37819,0.89841,82.713,-0.92416,0.21097,0.31846,146.16
> view matrix models
> #7,-0.43473,-0.054215,-0.89893,321.43,0.84152,0.33101,-0.42693,86.772,0.3207,-0.94207,-0.098277,183.93
> view matrix models
> #7,-0.096,-0.039772,-0.99459,285.31,0.61772,0.78113,-0.09086,10.876,0.78052,-0.62309,-0.050421,69.927
> view matrix models
> #7,0.14541,-0.4943,-0.85704,292.91,0.93985,-0.2016,0.27573,45.693,-0.30908,-0.84559,0.43525,184.71
> view matrix models
> #7,-0.85749,0.078165,-0.50853,308.38,0.34448,0.82137,-0.45463,94.893,0.38215,-0.56502,-0.73124,213.6
> view matrix models
> #7,-0.95849,0.040024,-0.28231,295.96,-0.075222,0.91953,0.38576,22.906,0.27503,0.39098,-0.87835,121.37
> view matrix models
> #7,-0.98451,0.10116,-0.14317,271.93,0.037723,0.91982,0.39052,6.3275,0.1712,0.37907,-0.90939,141.9
> ui mousemode right "move picked models"
> view matrix models
> #7,-0.98451,0.10116,-0.14317,271.68,0.037723,0.91982,0.39052,-41.079,0.1712,0.37907,-0.90939,187.61
> ui tool show "Fit in Map"
Fit map composite_cryosparc_P23_J734_J766_volume_map.mrc in map
composite_cryosparc_P23_J433_J445_map_zflip.mrc using 163830 points
correlation = 0.8988, correlation about mean = 0.6716, overlap = 2.114e+07
steps = 196, shift = 6.78, angle = 22 degrees
Position of composite_cryosparc_P23_J734_J766_volume_map.mrc (#7) relative to
composite_cryosparc_P23_J433_J445_map_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.96251318 0.21368040 0.16705999 213.31725333
0.27094792 0.78579517 0.55597943 -77.88310522
-0.01247302 0.58040208 -0.81423448 165.97118762
Axis 0.12852581 0.94480411 0.30137404
Axis point 116.10879253 0.00000000 90.04464060
Rotation angle (degrees) 174.54806393
Shift along axis 3.85190155
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-
> cluster/overview_HPK1volume_CRBNopen-volume.cxs"
——— End of log from Tue Oct 11 17:29:23 2022 ———
opened ChimeraX session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connectionpool.py", line 699, in urlopen
httplib_response = self._make_request(
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connectionpool.py", line 382, in _make_request
self._validate_conn(conn)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connectionpool.py", line 1010, in _validate_conn
conn.connect()
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connection.py", line 416, in connect
self.sock = ssl_wrap_socket(
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\util\ssl_.py", line 449, in ssl_wrap_socket
ssl_sock = _ssl_wrap_socket_impl(
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\util\ssl_.py", line 493, in _ssl_wrap_socket_impl
return ssl_context.wrap_socket(sock, server_hostname=server_hostname)
File "C:\Program Files\ChimeraX 1.3\bin\lib\ssl.py", line 500, in wrap_socket
return self.sslsocket_class._create(
File "C:\Program Files\ChimeraX 1.3\bin\lib\ssl.py", line 1040, in _create
self.do_handshake()
File "C:\Program Files\ChimeraX 1.3\bin\lib\ssl.py", line 1309, in
do_handshake
self._sslobj.do_handshake()
ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate
verify failed: unable to get local issuer certificate (_ssl.c:1129)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py",
line 676, in customEvent
func(*args, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1502, in on_finish
versions = self.result.get()
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line
771, in get
raise self._value
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line
125, in worker
result = (True, func(*args, **kwds))
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\cxservices\api_client.py", line 148, in __call_api
response_data = self.request(
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\cxservices\api_client.py", line 338, in request
return self.rest_client.GET(url,
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\cxservices\rest.py",
line 233, in GET
return self.request("GET", url,
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\cxservices\rest.py",
line 206, in request
r = self.pool_manager.request(method, url,
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\urllib3\request.py",
line 74, in request
return self.request_encode_url(
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\urllib3\request.py",
line 96, in request_encode_url
return self.urlopen(method, url, **extra_kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\poolmanager.py", line 417, in urlopen
return self.urlopen(method, redirect_location, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\poolmanager.py", line 375, in urlopen
response = conn.urlopen(method, u.request_uri, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connectionpool.py", line 783, in urlopen
return self.urlopen(
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connectionpool.py", line 783, in urlopen
return self.urlopen(
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connectionpool.py", line 755, in urlopen
retries = retries.increment(
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\util\retry.py", line 574, in increment
raise MaxRetryError(_pool, url, error or ResponseError(cause))
urllib3.exceptions.MaxRetryError:
HTTPSConnectionPool(host='webservices.rbvi.ucsf.edu', port=443): Max retries
exceeded with url:
/cxservices/api/v1/chimerax/newer?uuid=cb868ed8-17ef-5986-b333-a192c9b95fc2&OS=windows&OSVersion=10.0.19042&ChimeraXVersion=1.3
(Caused by SSLError(SSLCertVerificationError(1, '[SSL:
CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local
issuer certificate (_ssl.c:1129)')))
urllib3.exceptions.MaxRetryError:
HTTPSConnectionPool(host='webservices.rbvi.ucsf.edu', port=443): Max retries
exceeded with url:
/cxservices/api/v1/chimerax/newer?uuid=cb868ed8-17ef-5986-b333-a192c9b95fc2&OS=windows&OSVersion=10.0.19042&ChimeraXVersion=1.3
(Caused by SSLError(SSLCertVerificationError(1, '[SSL:
CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local
issuer certificate (_ssl.c:1129)')))
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\util\retry.py", line 574, in increment
raise MaxRetryError(_pool, url, error or ResponseError(cause))
See log for complete Python traceback.
> cd "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-cluster"
Current working directory is: C:\Users\petedani\OneDrive - Boehringer
Ingelheim\Documents\presentations\2022_CRBN-cluster
> open "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/HPK1/20220722_grid381_BI03051346_KriosIMP/coot/CRBNopen/DDB1delta-
> CRBNopen_fitJ734-coot-0.pdb"
Chain information for DDB1delta-CRBNopen_fitJ734-coot-0.pdb #2
---
Chain | Description
A | No description available
B | No description available
> ui mousemode right select
> select #2/B:107
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
106 atoms, 106 bonds, 13 residues, 1 model selected
> select up
2828 atoms, 2889 bonds, 349 residues, 1 model selected
> select up
9230 atoms, 9407 bonds, 1173 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,57.793,0,1,0,33.58,0,0,1,-4.3748
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.03709,-0.97464,0.2207,293.37,0.18637,0.22372,0.95667,-22.123,-0.98178,0.0056481,0.18994,246.29
> view matrix models
> #2,-0.078404,-0.98717,0.13908,322.72,0.10436,0.13061,0.98593,-2.1645,-0.99144,0.091814,0.092777,249.65
> view matrix models
> #2,0.91052,0.24838,-0.33055,83.235,-0.32164,0.92786,-0.18875,114.92,0.25983,0.27818,0.92472,-67.782
> view matrix models
> #2,0.37592,0.92257,-0.086821,36.093,0.7505,-0.35808,-0.55546,183.82,-0.54354,0.14365,-0.827,306.23
> view matrix models
> #2,0.18121,0.88885,-0.42085,114.38,0.96598,-0.080591,0.24572,5.7064,0.1845,-0.45106,-0.87322,288.06
> view matrix models
> #2,0.059989,0.98836,-0.13982,79.576,0.99725,-0.065434,-0.03467,37.995,-0.043415,-0.13736,-0.98957,294.91
> view matrix models
> #2,-0.18891,0.92589,-0.32716,149.11,0.95964,0.10338,-0.26154,52.297,-0.20834,-0.36337,-0.90805,337.05
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.18891,0.92589,-0.32716,120.67,0.95964,0.10338,-0.26154,33.429,-0.20834,-0.36337,-0.90805,333.3
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.57181,0.81729,-0.071244,154.11,0.82039,0.56986,-0.047197,-38.272,0.0020251,-0.085435,-0.99634,278.75
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.57181,0.81729,-0.071244,112.34,0.82039,0.56986,-0.047197,-69.022,0.0020251,-0.085435,-0.99634,276.38
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.71373,0.69844,-0.052616,145.69,0.68435,0.71139,0.15997,-97.09,0.14916,0.07817,-0.98572,232.31
> view matrix models
> #2,-0.80353,0.59003,0.078831,154.67,0.59525,0.79552,0.11323,-89.132,0.0040971,0.13791,-0.99044,245.65
> view matrix models
> #2,-0.93428,0.34778,0.078581,205.41,0.3534,0.87406,0.33335,-95.602,0.047246,0.33921,-0.93952,205.78
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.93428,0.34778,0.078581,213.09,0.3534,0.87406,0.33335,-85.814,0.047246,0.33921,-0.93952,201.94
> ui tool show "Fit in Map"
QWindowsWindow::setGeometry: Unable to set geometry 1880x218+478+380 (frame:
1902x274+467+335) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 2822x330+481+394 (frame:
2844x386+470+349) margins: 11, 45, 11, 11 minimum size: 706x83 maximum size:
524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=1434,222
maxtrack=1048596,1048630)
QWindowsWindow::setGeometry: Unable to set geometry 1411x165+538+376 (frame:
1433x221+527+331) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1412x166+538+376 (frame:
1434x222+527+331) margins: 11, 45, 11, 11 minimum size: 706x83 maximum size:
524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=1434,222
maxtrack=1048596,1048630)
Fit molecule DDB1delta-CRBNopen_fitJ734-coot-0.pdb (#2) to map
composite_cryosparc_P23_J734_J766_volume_map.mrc (#7) using 9230 atoms
average map value = 10.15, steps = 200
shifted from previous position = 18.5
rotated from previous position = 16.7 degrees
atoms outside contour = 2999, contour level = 6
Position of DDB1delta-CRBNopen_fitJ734-coot-0.pdb (#2) relative to
composite_cryosparc_P23_J734_J766_volume_map.mrc (#7) coordinates:
Matrix rotation and translation
0.99999959 0.00027508 -0.00082667 0.06004787
-0.00027477 0.99999986 0.00037734 -0.01525099
0.00082678 -0.00037713 0.99999956 -0.13518563
Axis -0.39733949 -0.87078539 -0.28957578
Axis point 153.54647911 0.00000000 86.29828955
Rotation angle (degrees) 0.05439678
Shift along axis 0.02856743
> select #2
9230 atoms, 9407 bonds, 2 pseudobonds, 1173 residues, 2 models selected
> hide #!1 models
> surface dust #7 size 7.45
> hide #!7 models
> ui mousemode right select
> select #2/A:792
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
90 atoms, 90 bonds, 11 residues, 1 model selected
> select up
6402 atoms, 6518 bonds, 824 residues, 1 model selected
> ui tool show "Color Actions"
> color sel slate blue
> select clear
[Repeated 1 time(s)]
> select #2/B:223
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
117 atoms, 122 bonds, 11 residues, 1 model selected
> select up
2828 atoms, 2889 bonds, 349 residues, 1 model selected
> color sel salmon
> color sel gold
> color sel green yellow
> color sel dark red
> show #!3 models
> color sel dark cyan
> color sel magenta
> color sel violet
> color sel plum
> color sel violet
> color sel dim gray
> color sel dark slate gray
> select clear
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!7 models
> color zone #7 near #2 distance 4.47
> volume #7 level 8
> volume #7 level 10
> volume #7 level 9
> volume #7 level 8
> volume #1 level 8
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> hide #!7 models
> select clear
> select #2/B:263
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
133 atoms, 134 bonds, 15 residues, 1 model selected
> select up
2828 atoms, 2889 bonds, 349 residues, 1 model selected
> color sel plum
> show #!7 models
> select clear
> color zone #7 near #2 distance 4.47
> show #!1 models
> hide #!2 models
> show #!3 models
> hide #!7 models
> hide #!1 models
> select #3/C:221
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
75 atoms, 76 bonds, 9 residues, 1 model selected
> select up
2064 atoms, 2108 bonds, 259 residues, 1 model selected
> color sel dark gray
> color sel silver
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
56 atoms, 64 bonds, 1 residue, 1 model selected
> color sel dim gray
> select clear
> show #!1 models
> color zone #1 near #3 distance 4.47
> select clear
> hide #!1 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
56 atoms, 64 bonds, 1 residue, 1 model selected
> color sel medium violet red
> select clear
> show #!1 models
> color zone #1 near #3 distance 4.47
> show #!7 models
> hide #!1 models
> show #!1 models
> hide #!7 models
> show #!7 models
> hide #!3 models
> hide #!1 models
> show #!2 models
> hide #!7 models
> select clear
[Repeated 2 time(s)]
> select #2/B:287
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
86 atoms, 88 bonds, 11 residues, 1 model selected
> select up
2828 atoms, 2889 bonds, 349 residues, 1 model selected
> color sel dim gray
> color sel dark slate gray
> color sel dim gray
> select clear
> show #!7 models
> hide #!7 models
> volume #7 color black
> ui tool show "Color Actions"
> color dim gray
> select clear
> show #!7 models
> undo
[Repeated 1 time(s)]
> select #2/A:750
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
23 atoms, 22 bonds, 4 residues, 1 model selected
> select up
6402 atoms, 6518 bonds, 824 residues, 1 model selected
> color sel slate blue
> show #!7 models
> color zone #7 near sel & #2 distance 4.47
> select clear
> hide #!7 models
> hide #!2 models
> show #!3 models
> show #!1 models
> hide #!1 models
> select #3/A:280
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
71 atoms, 71 bonds, 8 residues, 1 model selected
> select up
6448 atoms, 6565 bonds, 826 residues, 1 model selected
> color sel slate blue
> select clear
[Repeated 1 time(s)]
> select #3/B:258
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
133 atoms, 134 bonds, 15 residues, 1 model selected
> select up
3095 atoms, 3175 bonds, 383 residues, 1 model selected
> color sel salmon
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
56 atoms, 64 bonds, 1 residue, 1 model selected
> color sel medium violet red
> select clear
> select #3/C:225
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
75 atoms, 76 bonds, 9 residues, 1 model selected
> select up
2064 atoms, 2108 bonds, 259 residues, 1 model selected
> color sel silver
> show #!1 models
> select clear
> color zone #1 near #3 distance 4.47
> select clear
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!1 models
> show #!1 models
> hide #!7 models
> show #!7 models
> hide #!1 models
> show #!1 models
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-
> cluster/overview_HPK1volume_CRBNopen-volume.cxs"
> cd "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-cluster"
Current working directory is: C:\Users\petedani\OneDrive - Boehringer
Ingelheim\Documents\presentations\2022_CRBN-cluster
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-
> cluster/overview_HPK1volume_CRBNopen-volume.cxs"
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-
> cluster/overview_HPK1volume_CRBNopen-volume.cxs" includeMaps true
> save CRBNclosed_volumeHPK1.png width 400 height 800 transparentBackground
> true
[Repeated 1 time(s)]
> save CRBNclosed_volumeHPK1.png width 400 height 600 transparentBackground
> true
> hide #!7 models
> save CRBNclosed_volumeHPK1.png width 400 height 600 transparentBackground
> true
> show #!7 models
> hide #!1 models
> save CRBNopen_volume.png width 400 height 600 transparentBackground true
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-
> cluster/overview_HPK1volume_CRBNopen-volume.cxs" includeMaps true
[Repeated 1 time(s)]
——— End of log from Wed Oct 12 11:53:20 2022 ———
opened ChimeraX session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connectionpool.py", line 699, in urlopen
httplib_response = self._make_request(
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connectionpool.py", line 382, in _make_request
self._validate_conn(conn)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connectionpool.py", line 1010, in _validate_conn
conn.connect()
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connection.py", line 416, in connect
self.sock = ssl_wrap_socket(
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\util\ssl_.py", line 449, in ssl_wrap_socket
ssl_sock = _ssl_wrap_socket_impl(
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\util\ssl_.py", line 493, in _ssl_wrap_socket_impl
return ssl_context.wrap_socket(sock, server_hostname=server_hostname)
File "C:\Program Files\ChimeraX 1.3\bin\lib\ssl.py", line 500, in wrap_socket
return self.sslsocket_class._create(
File "C:\Program Files\ChimeraX 1.3\bin\lib\ssl.py", line 1040, in _create
self.do_handshake()
File "C:\Program Files\ChimeraX 1.3\bin\lib\ssl.py", line 1309, in
do_handshake
self._sslobj.do_handshake()
ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate
verify failed: unable to get local issuer certificate (_ssl.c:1129)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py",
line 676, in customEvent
func(*args, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1502, in on_finish
versions = self.result.get()
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line
771, in get
raise self._value
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line
125, in worker
result = (True, func(*args, **kwds))
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\cxservices\api_client.py", line 148, in __call_api
response_data = self.request(
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\cxservices\api_client.py", line 338, in request
return self.rest_client.GET(url,
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\cxservices\rest.py",
line 233, in GET
return self.request("GET", url,
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\cxservices\rest.py",
line 206, in request
r = self.pool_manager.request(method, url,
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\urllib3\request.py",
line 74, in request
return self.request_encode_url(
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\urllib3\request.py",
line 96, in request_encode_url
return self.urlopen(method, url, **extra_kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\poolmanager.py", line 417, in urlopen
return self.urlopen(method, redirect_location, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\poolmanager.py", line 375, in urlopen
response = conn.urlopen(method, u.request_uri, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connectionpool.py", line 783, in urlopen
return self.urlopen(
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connectionpool.py", line 783, in urlopen
return self.urlopen(
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connectionpool.py", line 755, in urlopen
retries = retries.increment(
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\util\retry.py", line 574, in increment
raise MaxRetryError(_pool, url, error or ResponseError(cause))
urllib3.exceptions.MaxRetryError:
HTTPSConnectionPool(host='webservices.rbvi.ucsf.edu', port=443): Max retries
exceeded with url:
/cxservices/api/v1/chimerax/newer?uuid=cb868ed8-17ef-5986-b333-a192c9b95fc2&OS=windows&OSVersion=10.0.19044&ChimeraXVersion=1.3
(Caused by SSLError(SSLCertVerificationError(1, '[SSL:
CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local
issuer certificate (_ssl.c:1129)')))
urllib3.exceptions.MaxRetryError:
HTTPSConnectionPool(host='webservices.rbvi.ucsf.edu', port=443): Max retries
exceeded with url:
/cxservices/api/v1/chimerax/newer?uuid=cb868ed8-17ef-5986-b333-a192c9b95fc2&OS=windows&OSVersion=10.0.19044&ChimeraXVersion=1.3
(Caused by SSLError(SSLCertVerificationError(1, '[SSL:
CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local
issuer certificate (_ssl.c:1129)')))
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\util\retry.py", line 574, in increment
raise MaxRetryError(_pool, url, error or ResponseError(cause))
See log for complete Python traceback.
> hide #!7 models
> show #!7 models
> show #!3 models
> hide #!3 models
> show #!2 models
> show #!1 models
> hide #!2 models
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2023_Novalix/figures/CRBN_open-vs-
> closed.cxs"
——— End of log from Thu Feb 2 16:17:34 2023 ———
opened ChimeraX session
OpenGL version: 3.3.0 - Build 30.0.101.1692
OpenGL renderer: Intel(R) UHD Graphics
OpenGL vendor: Intel
Manufacturer: LENOVO
Model: 20S1S1J52S
OS: Microsoft Windows 10 Enterprise (Build 19044)
Memory: 16,885,047,296
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-10310U CPU @ 1.70GHz
OSLanguage: en-US
Locale: ('de_AT', '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: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
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: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
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: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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: 2.4.6
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: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pywin32: 228
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Platform |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash using File→Open dialog on Windows and/or returning from function |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
Note:
See TracTickets
for help on using tickets.
1.3