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#7684 closed defect (can't reproduce)

Crash using File→Open on Windows and/or in return statement

Reported by:	chimerax-bug-report@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	Platform	Version:
Keywords:		Cc:	Tom Goddard
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.22000
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 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
Windows fatal exception: code 0x8001010e

  File Windows fatal exception: code 0x8001010e

"Windows fatal exception: code 0x8001010e

DWindows fatal exception: code 0x8001010e

:Windows fatal exception: code 0x8001010e

\Windows fatal exception: chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in code 0x8001010e

rWindows fatal exception: code 0x8001010e

un
Windows fatal exception: code 0x8001010e

  File Windows fatal exception: code 0x8001010e

"D:\chimerax\ChimeraX 1.3\bin\lib\threading.py"Windows fatal exception: code 0x, line 8001010e973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line Windows fatal exception: code 0x8001010e



Windows fatal exception: code 0xWindows fatal exception: code 0x8001010e

930 in 8001010e

_Windows fatal exception: code 0x8001010e

bWindows fatal exception: code 0x8001010e

ootstrap
Windows fatal exception: code 0x8001010e


Windows fatal exception: Thread 0x00003040 (most recent call first):
code 0x8001010e

  File Windows fatal exception: code 0x8001010e

"D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in Windows fatal exception: code 0x8001010e

code 0xWindows fatal exception: code 0x8001010e


Windows fatal exception: code 0x8001010e

8001010eWindows fatal exception: code 0x8001010e

  File Windows fatal exception: code 0x8001010e



Windows fatal exception: code 0xWindows fatal exception: code 0x8001010e

"D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File 8001010e"D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py"Windows fatal exception: code 0x8001010e

, line Windows fatal exception: code 0x8001010e



867Windows fatal exception: code 0x8001010e

 in Windows fatal exception: code 0x8001010e

init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py"code 0x8001010e

, line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimeraWindows fatal exception: code 0x8001010e

xWindows fatal exception: code 0x8001010e

\Windows fatal exception: code 0x8001010e

CWindows fatal exception: code 0x8001010e

hWindows fatal exception: code 0x8001010e

iWindows fatal exception: code 0x8001010e

mWindows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: Windows fatal exception: code 0x8001010e

eWindows fatal exception: code 0x8001010e

Windows fatal exception: Windows fatal exception: code 0x8001010e

code 0x8001010e

rWindows fatal exception: code 0x8001010e

aWindows fatal exception: code 0x8001010e

XWindows fatal exception: code 0x8001010e

 Windows fatal exception: code 0x8001010e

1Windows fatal exception: code 0x8001010e

.Windows fatal exception: code 0x8001010e

3Windows fatal exception: code 0x8001010e

\Windows fatal exception: code 0x8001010e

bWindows fatal exception: code 0x8001010e

iWindows fatal exception: code 0x8001010e

n\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
code 0x  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
8001010eWindows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX Windows fatal exception: code 0x8001010e

1Windows fatal exception: code 0x8001010e

.Windows fatal exception: code 0x8001010e

3Windows fatal exception: code 0x8001010e

\Windows fatal exception: code 0x8001010e

bWindows fatal exception: code 0x8001010e

iWindows fatal exception: code 0x8001010e

nWindows fatal exception: code 0x8001010e

\Windows fatal exception: code 0x8001010e

lWindows fatal exception: code 0x8001010e

iWindows fatal exception: code 0x8001010e

b\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\Windows fatal exception: code 0x8001010e

threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py"

code 0xWindows fatal exception: code 0x8001010e

8001010e

Windows fatal exception: Windows fatal exception: code 0x8001010e

code 0xWindows fatal exception: code 0x8001010e

8001010eWindows fatal exception: code 0x8001010e



, line Windows fatal exception: Windows fatal exception: code 0x867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
code 0x8001010e

Windows fatal exception: Windows fatal exception: code 0x8001010e

code 0xWindows fatal exception: code 0x8001010e

8001010eWindows fatal exception: code 0x8001010e



Windows fatal exception: code 0xWindows fatal exception: code 0x8001010e

8001010eWindows fatal exception: code 0x8001010e



Windows fatal exception: code 0x8001010e

8001010eWindows fatal exception: code 0x8001010e



Windows fatal exception: Windows fatal exception: code 0x8001010e

  File Windows fatal exception: code 0x8001010e

code 0xWindows fatal exception: code 0x8001010e

"Windows fatal exception: code 0x8001010e

8001010e

Windows fatal exception: Windows fatal exception: code 0x8001010e

DWindows fatal exception: code 0x8001010e

code 0x8001010e

:\chimerax\ChimeraX 1.3\bin\lib\runpy.py"Windows fatal exception: code 0x8001010e

, line Windows fatal exception: code 0x8001010e

197 in _run_module_as_main
Windows fatal exception: Windows fatal exception: Windows fatal exception: code 0x8001010e

code 0xThread 0x00006034 (most recent call first):
  File "D:\Windows fatal exception: code 0x8001010e

cWindows fatal exception: code 0x8001010e

hWindows fatal exception: code 0x8001010e

iWindows fatal exception: code 0x8001010e

mWindows fatal exception: code 0x8001010e

eWindows fatal exception: code 0x8001010e

rWindows fatal exception: code 0x8001010e

aWindows fatal exception: code 0x8001010e

xWindows fatal exception: code 0x8001010e

\Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

8001010e

CWindows fatal exception: code 0x8001010e

code 0xWindows fatal exception: code 0x8001010e

hWindows fatal exception: imeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
8001010eWindows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main


Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Thread 0xWindows fatal exception: code 0x8001010e

Windows fatal exception: Windows fatal exception: code 0x8001010e

Windows fatal exception: Windows fatal exception: code 0x8001010e

code 0xWindows fatal exception: code 0x8001010e

00006034Windows fatal exception: code 0x8001010e

code 0xWindows fatal exception: code 0x8001010e

code 0xWindows fatal exception: code 0x8001010e

8001010eWindows fatal exception: code 0x8001010e

 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 8001010e

8001010eWindows fatal exception: code 0x8001010e




Windows fatal exception: Windows fatal exception: code 0x8001010e

  File "D:\chWindows fatal exception: code 0x8001010e

imerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

code 0x8001010e

8001010eWindows fatal exception: code 0x8001010e



Windows fatal exception: code 0xWindows fatal exception: code 0x8001010e

8001010eWindows fatal exception: code 0x8001010e





Windows fatal exception: code 0xWindows fatal exception: code 0xWindows fatal exception: code 0x8001010e

8001010e

8001010eWindows fatal exception: code 0x8001010e



Thread 0xWindows fatal exception: code 0x8001010e

Windows fatal exception: Windows fatal exception: code 0x8001010e

00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
code 0x8001010e

  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in Windows fatal exception: code 0x8001010e

init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Thread 0xWindows fatal exception: code 0x8001010e

Windows fatal exception: Windows fatal exception: code 0x8001010e

00006034Windows fatal exception: code 0x8001010e

code 0x8001010e

 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\Windows fatal exception: code 0x8001010e

Windows fatal exception: Windows fatal exception: code 0x8001010e

code 0xWindows fatal exception: Chimeracode 0x8001010e8001010e

XWindows fatal exception: code 0x8001010e



Windows fatal exception: code 0xWindows fatal exception: code 0x8001010e

 Windows fatal exception: code 0x8001010e

1Windows fatal exception: 8001010ecode 0x.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
8001010e  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command



Windows fatal exception: code 0xWindows fatal exception: code 0x8001010e

\Windows fatal exception: code 0x8001010e

8001010e

dWindows fatal exception: code 0x8001010e

iWindows fatal exception: code 0x8001010e

alog.py"Windows fatal exception: code 0x8001010e

, line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraXWindows fatal exception: code 0x8001010e

 1.3\bin\lib\site-packages\chimWindows fatal exception: code 0x8001010e

eWindows fatal exception: code 0x8001010e

rWindows fatal exception: code 0x8001010e

ax\open_commWindows fatal exception: code 0x8001010e

and\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py"Windows fatal exception: , line 867 in init
  File "D:\chimerax\Chimercode 0x8001010e

aWindows fatal exception: code 0x8001010e

X 1.3\bin\lib\sitWindows fatal exception: e-packages\code 0x8001010e

Windows fatal exception: code 0x8001010e

ChimeraWindows fatal exception: code 0x8001010e

XWindows fatal exception: code 0x8001010e

_main.py"Windows fatal exception: code 0x, line 1018 in 8001010e


  File "D:\chimerax\ChimeraX Windows fatal exception: 1.3\bin\lib\runpy.py", line 87 in _rucode 0x8001010e

n_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316Windows fatal exception: code 0x in wait
  File 8001010e

"Windows fatal exception: code 0x8001010e

D:\chimerax\ChimeWindows fatal exception: code 0x8001010eraX

 Windows fatal exception: code 0x1.38001010e

\Windows fatal exception: code 0x8001010e

bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.pWindows fatal exception: code 0x8001010e

yWindows fatal exception: code 0x8001010e

", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py"Windows fatal exception: code 0x8001010e

, line Windows fatal exception: code 0x8001010e

973 in _bootstrap_inner
Windows fatal exception: code 0x8001010e

  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
Windows fatal exception: code 0x  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
8001010e

  File Windows fatal exception: code 0x8001010e

"Windows fatal exception: code 0x8001010e

D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py"Windows fatal exception: , line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-pWindows fatal exception: code 0x8001010e

Windows fatal exception: Windows fatal exception: code 0x8001010e

Windows fatal exception: Windows fatal exception: code 0x8001010e

code 0x8001010e

code 0x8001010e

Windows fatal exception: Windows fatal exception: code 0x8001010e

aWindows fatal exception: code 0x8001010e

Windows fatal exception: Windows fatal exception: code 0x8001010e

code 0xWindows fatal exception: code 0x8001010e

code 0xWindows fatal exception: code 0x8001010e

cWindows fatal exception: code 0x8001010e

code 0xWindows fatal exception: code 0x8001010e

8001010eWindows fatal exception: code 0x8001010e

8001010eWindows fatal exception: code 0x8001010e

kWindows fatal exception: code 0x8001010e

8001010e

aWindows fatal exception: code 0x8001010e

gWindows fatal exception: code 0x8001010e

eWindows fatal exception: code 0x8001010e

sWindows fatal exception: code 0x8001010e

\Windows fatal exception: code 0x8001010e

CWindows fatal exception: code 0x8001010e

hWindows fatal exception: code 0x8001010e

imeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main


Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in 

ruWindows fatal exception: code 0x8001010e

nWindows fatal exception: code 0x8001010e


Windows fatal exception: code 0x8001010e

  File Windows fatal exception: code 0x8001010e

"Windows fatal exception: code 0x8001010e

DWindows fatal exception: code 0x8001010e

:Windows fatal exception: code 0x8001010e

\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
Windows fatal exception: code 0x8001010e

  File Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

"D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: Windows fatal exception: code 0x8001010e

pWindows fatal exception: code 0x8001010e

code 0xWindows fatal exception: code 0x8001010e

aWindows fatal exception: code 0x8001010e

8001010eWindows fatal exception: code 0x8001010e

cWindows fatal exception: code 0x8001010e



Windows fatal exception: code 0x8001010e

Windows fatal exception: Windows fatal exception: code 0xWindows fatal exception: code 0x8001010e

8001010eWindows fatal exception: code 0x8001010e



Windows fatal exception: code 0x8001010e

code 0xWindows fatal exception: code 0x8001010e

8001010eWindows fatal exception: code 0x8001010e



Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010eWindows fatal exception: kages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
code 0xWindows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main


Thread 0x00006034 (most recent call first):
  File "D:\chimerax\Ch8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: Windows fatal exception: code 0x8001010e

iWindows fatal exception: code 0x8001010e

code 0x8001010e

mWindows fatal exception: Windows fatal exception: code 0x8001010e

code 0xWindows fatal exception: code 0x8001010e

eWindows fatal exception: code 0x8001010e

8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

raX 1.3\bin\lWindows fatal exception: code 0x8001010e

ib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00006034 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "D:\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003040 (most recent call first):
  File "D:\chimerax\ChimeraX 1.3\bin\lib\ctypes\__init__.py", line 510 in cast
Windows fatal exception: access violation

===== Log before crash start =====
restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

Opened postprocess.mrc as #8, grid size 240,240,240, pixel 1.32, shown at
level 0.0348, step 1, values float32  
Opened postprocess.mrc as #10, grid size 240,240,240, pixel 1.32, shown at
level 0.033, step 1, values float32  
Opened hku31.mrc as #6, grid size 240,240,240, pixel 1.32, shown at level
0.0301, step 1, values float32  
Opened job055_postprocess.mrc as #11, grid size 240,240,240, pixel 1.32, shown
at level 0.0255, step 1, values float32  
Opened postprocess.mrc as #12, grid size 240,240,240, pixel 1.32, shown at
level 0.0272, step 1, values float32  

restore_snapshot for "Redust" returned None  

restore_snapshot for "ZoneColor" returned None  

opened ChimeraX session  


===== 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 "D:\\\Structure analysis\\\figure\\\all side view color.cxs"

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

Opened postprocess.mrc as #8, grid size 240,240,240, pixel 1.32, shown at
level 0.0348, step 1, values float32  
Opened postprocess.mrc as #10, grid size 240,240,240, pixel 1.32, shown at
level 0.033, step 1, values float32  
Opened hku31.mrc as #6, grid size 240,240,240, pixel 1.32, shown at level
0.0301, step 1, values float32  
Opened job055_postprocess.mrc as #11, grid size 240,240,240, pixel 1.32, shown
at level 0.0255, step 1, values float32  
Opened postprocess.mrc as #12, grid size 240,240,240, pixel 1.32, shown at
level 0.0272, step 1, values float32  

restore_snapshot for "Redust" returned None  

restore_snapshot for "ZoneColor" returned None  

Log from Fri Sep 23 17:05:41 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "D:\\\Structure analysis\\\figure\\\all side view color.cxs"

Opened postprocess.mrc as #8, grid size 240,240,240, pixel 1.32, shown at
level 0.0348, step 1, values float32  
Opened postprocess.mrc as #10, grid size 240,240,240, pixel 1.32, shown at
level 0.033, step 1, values float32  
Opened postprocess zflip.mrc as #4, grid size 320,320,320, pixel 1.32, shown
at level 0.0225, step 1, values float32  
Opened hku31.mrc as #6, grid size 240,240,240, pixel 1.32, shown at level
0.0301, step 1, values float32  
Opened job055_postprocess.mrc as #11, grid size 240,240,240, pixel 1.32, shown
at level 0.0255, step 1, values float32  
Opened postprocess.mrc as #12, grid size 240,240,240, pixel 1.32, shown at
level 0.0272, step 1, values float32  
Log from Tue Sep 13 14:47:44 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "D:\\\Structure analysis\\\figure\\\all side view color.cxs"

Opened postprocess.mrc as #8, grid size 240,240,240, pixel 1.32, shown at
level 0.0348, step 1, values float32  
Opened postprocess.mrc as #10, grid size 240,240,240, pixel 1.32, shown at
level 0.033, step 1, values float32  
Opened postprocess zflip.mrc as #4, grid size 320,320,320, pixel 1.32, shown
at level 0.0249, step 1, values float32  
Opened hku31.mrc as #6, grid size 240,240,240, pixel 1.32, shown at level
0.0301, step 1, values float32  
Opened job055_postprocess.mrc as #11, grid size 240,240,240, pixel 1.32, shown
at level 0.0255, step 1, values float32  
Opened postprocess.mrc as #12, grid size 240,240,240, pixel 1.32, shown at
level 0.0272, step 1, values float32  
Log from Tue Sep 13 12:17:42 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "D:\\\Structure analysis\\\figure\\\all side view color.cxs"

Opened postprocess.mrc as #8, grid size 240,240,240, pixel 1.32, shown at
level 0.0348, step 1, values float32  
Opened postprocess.mrc as #10, grid size 240,240,240, pixel 1.32, shown at
level 0.033, step 1, values float32  
Opened postprocess zflip.mrc as #4, grid size 320,320,320, pixel 1.32, shown
at level 0.0192, step 2, values float32  
Log from Mon Sep 12 21:09:04 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 "D:\\\Structure
> analysis\\\20211213_HKU\\\job053\\\HKU31_job053_chainABC_nam_real_space_refined_001_real_space_refined_019_gly_real_space_refined_023_6_new_real_space_refined_014-2_LA.pdb"

Chain information for
HKU31_job053_chainABC_nam_real_space_refined_001_real_space_refined_019_gly_real_space_refined_023_6_new_real_space_refined_014-2_LA.pdb
#1  
---  
Chain | Description  
A B C | No description available  
  

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\15428\Desktop\movie1.mp4

D:\chimerax\ChimeraX 1.3\bin\ffmpeg.exe -r 25 -i
C:\Users\15428\AppData\Local\Temp\chimovie_fjDH-%05d.ppm -vf
crop=floor(in_w/2)*2:floor(in_h/2)*2:0:0 -y -vcodec libx264 -f mp4 -pix_fmt
yuv420p -crf 20 C:\Users\15428\Desktop\movie1.mp4  
stdout:  
  
stderr:  
ffmpeg version 3.2.4 Copyright (c) 2000-2017 the FFmpeg developers  
built with gcc 6.3.0 (GCC)  
configuration: --enable-gpl --enable-version3 --enable-d3d11va --enable-dxva2
--enable-libmfx --enable-nvenc --enable-avisynth --enable-bzlib --enable-
fontconfig --enable-frei0r --enable-gnutls --enable-iconv --enable-libass
--enable-libbluray --enable-libbs2b --enable-libcaca --enable-libfreetype
--enable-libgme --enable-libgsm --enable-libilbc --enable-libmodplug --enable-
libmp3lame --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-
libopenh264 --enable-libopenjpeg --enable-libopus --enable-librtmp --enable-
libsnappy --enable-libsoxr --enable-libspeex --enable-libtheora --enable-
libtwolame --enable-libvidstab --enable-libvo-amrwbenc --enable-libvorbis
--enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx264
--enable-libx265 --enable-libxavs --enable-libxvid --enable-libzimg --enable-
lzma --enable-zlib  
libavutil 55. 34.101 / 55. 34.101  
libavcodec 57. 64.101 / 57. 64.101  
libavformat 57. 56.101 / 57. 56.101  
libavdevice 57. 1.100 / 57. 1.100  
libavfilter 6. 65.100 / 6. 65.100  
libswscale 4. 2.100 / 4. 2.100  
libswresample 2. 3.100 / 2. 3.100  
libpostproc 54. 1.100 / 54. 1.100  
Input #0, image2, from
'C:\Users\15428\AppData\Local\Temp\chimovie_fjDH-%05d.ppm':  
Duration: 00:00:07.20, start: 0.000000, bitrate: N/A  
Stream #0:0: Video: ppm, rgb24, 1378x1108, 25 tbr, 25 tbn, 25 tbc  
[libx264 @ 0000000002a25760] using cpu capabilities: MMX2 SSE2Fast SSSE3
SSE4.2 AVX FMA3 AVX2 LZCNT BMI2  
[libx264 @ 0000000002a25760] profile High, level 4.0  
[libx264 @ 0000000002a25760] 264 - core 148 r2762 90a61ec - H.264/MPEG-4 AVC
codec - Copyleft 2003-2017 - http://www.videolan.org/x264.html - options:
cabac=1 ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1
psy_rd=1.00:0.00 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0
deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=24 lookahead_threads=4
sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0
constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1
weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40
intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=20.0 qcomp=0.60 qpmin=0
qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00  
Output #0, mp4, to 'C:\Users\15428\Desktop\movie1.mp4':  
Metadata:  
encoder : Lavf57.56.101  
Stream #0:0: Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p,
1378x1108, q=-1--1, 25 fps, 12800 tbn, 25 tbc  
Metadata:  
encoder : Lavc57.64.101 libx264  
Side data:  
cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: -1  
Stream mapping:  
Stream #0:0 -> #0:0 (ppm (native) -> h264 (libx264))  
Press [q] to stop, [?] for help  
frame= 45 fps=0.0 q=0.0 size= 0kB time=00:00:00.00 bitrate=N/A speed= 0x
frame= 76 fps= 75 q=25.0 size= 965kB time=00:00:00.20 bitrate=39496.1kbits/s
speed=0.198x frame= 110 fps= 73 q=25.0 size= 4633kB time=00:00:01.56
bitrate=24326.1kbits/s speed=1.03x frame= 146 fps= 72 q=25.0 size= 8592kB
time=00:00:03.00 bitrate=23461.5kbits/s speed=1.48x frame= 164 fps= 56 q=-1.0
Lsize= 18830kB time=00:00:06.44 bitrate=23952.6kbits/s speed=2.21x  
video:18827kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB
muxing overhead: 0.015094%  
[libx264 @ 0000000002a25760] frame I:1 Avg QP:12.86 size:158916  
[libx264 @ 0000000002a25760] frame P:41 Avg QP:25.03 size:143970  
[libx264 @ 0000000002a25760] frame B:122 Avg QP:28.55 size:108335  
[libx264 @ 0000000002a25760] consecutive B-frames: 0.6% 0.0% 1.8% 97.6%  
[libx264 @ 0000000002a25760] mb I I16..4: 64.3% 0.6% 35.1%  
[libx264 @ 0000000002a25760] mb P I16..4: 1.8% 2.0% 22.9% P16..4: 2.9% 3.8%
5.8% 0.0% 0.0% skip:60.8%  
[libx264 @ 0000000002a25760] mb B I16..4: 0.2% 0.2% 7.9% B16..8: 4.6% 7.9%
14.8% direct: 1.0% skip:63.3% L0:39.9% L1:36.0% BI:24.1%  
[libx264 @ 0000000002a25760] 8x8 transform intra:4.7% inter:3.1%  
[libx264 @ 0000000002a25760] coded y,uvDC,uvAC intra: 83.6% 89.7% 87.2% inter:
17.1% 10.0% 6.7%  
[libx264 @ 0000000002a25760] i16 v,h,dc,p: 84% 8% 8% 0%  
[libx264 @ 0000000002a25760] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 10% 6% 67% 3% 2%
3% 3% 3% 3%  
[libx264 @ 0000000002a25760] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 16% 12% 16% 9% 9%
10% 9% 10% 10%  
[libx264 @ 0000000002a25760] i8c dc,h,v,p: 61% 13% 16% 10%  
[libx264 @ 0000000002a25760] Weighted P-Frames: Y:14.6% UV:7.3%  
[libx264 @ 0000000002a25760] ref P L0: 51.7% 12.6% 20.4% 13.9% 1.5%  
[libx264 @ 0000000002a25760] ref B L0: 86.0% 11.0% 3.1%  
[libx264 @ 0000000002a25760] ref B L1: 94.9% 5.1%  
[libx264 @ 0000000002a25760] kb/s:23510.38  
Exiting normally, received signal 15.  
  
An error occurred during encoding. See Reply Log for details.  
  
Error during MPEG encoding:  
\-----------------------------  
Exit value: 255  
Error message:  
stdout:  
  
stderr:  
ffmpeg version 3.2.4 Copyright (c) 2000-2017 the FFmpeg developers  
built with gcc 6.3.0 (GCC)  
configuration: --enable-gpl --enable-version3 --enable-d3d11va --enable-dxva2
--enable-libmfx --enable-nvenc --enable-avisynth --enable-bzlib --enable-
fontconfig --enable-frei0r --enable-gnutls --enable-iconv --enable-libass
--enable-libbluray --enable-libbs2b --enable-libcaca --enable-libfreetype
--enable-libgme --enable-libgsm --enable-libilbc --enable-libmodplug --enable-
libmp3lame --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-
libopenh264 --enable-libopenjpeg --enable-libopus --enable-librtmp --enable-
libsnappy --enable-libsoxr --enable-libspeex --enable-libtheora --enable-
libtwolame --enable-libvidstab --enable-libvo-amrwbenc --enable-libvorbis
--enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx264
--enable-libx265 --enable-libxavs --enable-libxvid --enable-libzimg --enable-
lzma --enable-zlib  
libavutil 55. 34.101 / 55. 34.101  
libavcodec 57. 64.101 / 57. 64.101  
libavformat 57. 56.101 / 57. 56.101  
libavdevice 57. 1.100 / 57. 1.100  
libavfilter 6. 65.100 / 6. 65.100  
libswscale 4. 2.100 / 4. 2.100  
libswresample 2. 3.100 / 2. 3.100  
libpostproc 54. 1.100 / 54. 1.100  
Input #0, image2, from
'C:\Users\15428\AppData\Local\Temp\chimovie_fjDH-%05d.ppm':  
Duration: 00:00:07.20, start: 0.000000, bitrate: N/A  
Stream #0:0: Video: ppm, rgb24, 1378x1108, 25 tbr, 25 tbn, 25 tbc  
[libx264 @ 0000000002a25760] using cpu capabilities: MMX2 SSE2Fast SSSE3
SSE4.2 AVX FMA3 AVX2 LZCNT BMI2  
[libx264 @ 0000000002a25760] profile High, level 4.0  
[libx264 @ 0000000002a25760] 264 - core 148 r2762 90a61ec - H.264/MPEG-4 AVC
codec - Copyleft 2003-2017 - http://www.videolan.org/x264.html - options:
cabac=1 ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1
psy_rd=1.00:0.00 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0
deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=24 lookahead_threads=4
sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0
constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1
weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40
intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=20.0 qcomp=0.60 qpmin=0
qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00  
Output #0, mp4, to 'C:\Users\15428\Desktop\movie1.mp4':  
Metadata:  
encoder : Lavf57.56.101  
Stream #0:0: Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p,
1378x1108, q=-1--1, 25 fps, 12800 tbn, 25 tbc  
Metadata:  
encoder : Lavc57.64.101 libx264  
Side data:  
cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: -1  
Stream mapping:  
Stream #0:0 -> #0:0 (ppm (native) -> h264 (libx264))  
Press [q] to stop, [?] for help  
frame= 45 fps=0.0 q=0.0 size= 0kB time=00:00:00.00 bitrate=N/A speed= 0x
frame= 76 fps= 75 q=25.0 size= 965kB time=00:00:00.20 bitrate=39496.1kbits/s
speed=0.198x frame= 110 fps= 73 q=25.0 size= 4633kB time=00:00:01.56
bitrate=24326.1kbits/s speed=1.03x frame= 146 fps= 72 q=25.0 size= 8592kB
time=00:00:03.00 bitrate=23461.5kbits/s speed=1.48x frame= 164 fps= 56 q=-1.0
Lsize= 18830kB time=00:00:06.44 bitrate=23952.6kbits/s speed=2.21x  
video:18827kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB
muxing overhead: 0.015094%  
[libx264 @ 0000000002a25760] frame I:1 Avg QP:12.86 size:158916  
[libx264 @ 0000000002a25760] frame P:41 Avg QP:25.03 size:143970  
[libx264 @ 0000000002a25760] frame B:122 Avg QP:28.55 size:108335  
[libx264 @ 0000000002a25760] consecutive B-frames: 0.6% 0.0% 1.8% 97.6%  
[libx264 @ 0000000002a25760] mb I I16..4: 64.3% 0.6% 35.1%  
[libx264 @ 0000000002a25760] mb P I16..4: 1.8% 2.0% 22.9% P16..4: 2.9% 3.8%
5.8% 0.0% 0.0% skip:60.8%  
[libx264 @ 0000000002a25760] mb B I16..4: 0.2% 0.2% 7.9% B16..8: 4.6% 7.9%
14.8% direct: 1.0% skip:63.3% L0:39.9% L1:36.0% BI:24.1%  
[libx264 @ 0000000002a25760] 8x8 transform intra:4.7% inter:3.1%  
[libx264 @ 0000000002a25760] coded y,uvDC,uvAC intra: 83.6% 89.7% 87.2% inter:
17.1% 10.0% 6.7%  
[libx264 @ 0000000002a25760] i16 v,h,dc,p: 84% 8% 8% 0%  
[libx264 @ 0000000002a25760] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 10% 6% 67% 3% 2%
3% 3% 3% 3%  
[libx264 @ 0000000002a25760] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 16% 12% 16% 9% 9%
10% 9% 10% 10%  
[libx264 @ 0000000002a25760] i8c dc,h,v,p: 61% 13% 16% 10%  
[libx264 @ 0000000002a25760] Weighted P-Frames: Y:14.6% UV:7.3%  
[libx264 @ 0000000002a25760] ref P L0: 51.7% 12.6% 20.4% 13.9% 1.5%  
[libx264 @ 0000000002a25760] ref B L0: 86.0% 11.0% 3.1%  
[libx264 @ 0000000002a25760] ref B L1: 94.9% 5.1%  
[libx264 @ 0000000002a25760] kb/s:23510.38  
Exiting normally, received signal 15.  
  
\-----------------------------  
  

> nucleotides tube/slab shape ellipsoid

[Repeated 1 time(s)]

> view

[Repeated 2 time(s)]

> ui tool show "Side View"

[Repeated 3 time(s)]

> view

[Repeated 5 time(s)]

> view orient

[Repeated 1 time(s)]

> volume projectionMode 2d-xyz

No volumes specified  

> ui mousemode right "crop volume"

> ui mousemode right "move planes"

> volume showOutlineBox true

No volumes specified  

> volume region all imageMode "full region"

No volumes specified  

Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.  

> view orient

> select ::name="BMA"::name="EIC"::name="FOL"::name="MAN"::name="NAG"

1604 atoms, 1644 bonds, 103 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> hide target a

> ui tool show "Color Actions"

> set bgColor white

> select #1:16-340

7392 atoms, 7593 bonds, 9 pseudobonds, 912 residues, 2 models selected  

> select /B

8741 atoms, 8948 bonds, 9 pseudobonds, 1118 residues, 2 models selected  

> color (#!1 & sel) dark gray

> select /C

8742 atoms, 8949 bonds, 9 pseudobonds, 1118 residues, 2 models selected  

> color (#!1 & sel) dark gray

> select #1:16-340.A

Expected an objects specifier or a keyword  

> select clear

> select #1:16-340.A

Expected an objects specifier or a keyword  

> select #1:16-340

7392 atoms, 7593 bonds, 9 pseudobonds, 912 residues, 2 models selected  

> select #1:16-340.A

Expected an objects specifier or a keyword  

> select #1:16-340.A

Expected an objects specifier or a keyword  

> select #1:16-340.A

Expected an objects specifier or a keyword  

> select clear

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> select /A:22

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /A:22-174

1157 atoms, 1188 bonds, 1 pseudobond, 148 residues, 2 models selected  

> select /A:261-340

652 atoms, 671 bonds, 1 pseudobond, 77 residues, 2 models selected  

> select /A:22-340

2464 atoms, 2531 bonds, 3 pseudobonds, 304 residues, 2 models selected  

> color (#!1 & sel) medium blue

> select /A:370-371

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select /A:370-574

1591 atoms, 1628 bonds, 205 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel deep sky blue

> select /A:357-358

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select /A:357-365

79 atoms, 82 bonds, 9 residues, 1 model selected  

> select /A:357

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select /A:357-370

118 atoms, 121 bonds, 14 residues, 1 model selected  

> select /A:357

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select /A:357-369

109 atoms, 112 bonds, 13 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel turquoise

> select /A:583-584

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select /A:583-736

1009 atoms, 1034 bonds, 2 pseudobonds, 135 residues, 2 models selected  

> select /A:583

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:583-643

468 atoms, 481 bonds, 61 residues, 1 model selected  

> select /A:644

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /A:583-644

474 atoms, 487 bonds, 62 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel turquoise

> select /A:733

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:733-1198

3453 atoms, 3522 bonds, 3 pseudobonds, 446 residues, 2 models selected  

> color (#!1 & sel) red

> select
> /A:60-67,75-77,109-113,120-122,129-131,139-142,145-147,153-156,159-166,171-180,198-200,221-223,227-232,240-247,250-255,267-272,280-282,286-288,302-306,308-315,325-327,348-350,354-356,389-393,396-398,408-415,429-436,466-473,490-496,529-533,536-544,554-563,571-573,604-607,618-620,626-630,636-640,644-652,657-662,722-724,737-739,757-764,769-774,781-783,912-914,1104-1110,1113-1119,1125-1131,1135-1137,1143-1146,1149-1153,1159-1163,1177-1180,1187-1189

2294 atoms, 2309 bonds, 280 residues, 1 model selected  

> select /A:345-346

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select /A:345-365

172 atoms, 178 bonds, 21 residues, 1 model selected  

> select /A:356

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:345-356

93 atoms, 95 bonds, 12 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel chartreuse

> select /A:645-735

524 atoms, 534 bonds, 2 pseudobonds, 72 residues, 2 models selected  

> select /A:645-797

1026 atoms, 1047 bonds, 2 pseudobonds, 134 residues, 2 models selected  

> select /A:751

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:645-751

652 atoms, 665 bonds, 2 pseudobonds, 88 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel chartreuse

> ui tool show "Show Sequence Viewer"

> sequence chain /B

Alignment identifier is 1/B  

> select
> /B:60-67,75-78,109-112,139-142,145-147,153-156,160-166,171-177,198-200,228-232,241-247,250-255,267-272,280-283,286-288,301-306,308-316,322-327,348-350,389-393,396-398,408-415,429-436,466-473,490-496,529-533,536-544,554-563,571-573,591-593,602-607,637-640,647-652,657-662,722-724,737-739,757-764,769-775,781-783,912-914,1104-1110,1113-1119,1125-1131,1135-1137,1144-1146,1149-1153,1159-1163,1177-1179,1187-1189

2123 atoms, 2133 bonds, 260 residues, 1 model selected  

> select /B:868-869

11 atoms, 10 bonds, 2 residues, 1 model selected  

> select /B:868-890

159 atoms, 160 bonds, 1 pseudobond, 20 residues, 2 models selected  

> select /B:884

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /B:868-884

106 atoms, 105 bonds, 1 pseudobond, 14 residues, 2 models selected  

> color (#!1 & sel) orange

> select /B:885-886

20 atoms, 20 bonds, 2 residues, 1 model selected  

> select /B:885-910

128 atoms, 130 bonds, 1 pseudobond, 16 residues, 2 models selected  

> select /B:910

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select /B:885-910

128 atoms, 130 bonds, 1 pseudobond, 16 residues, 2 models selected  

> select /B:908-909

19 atoms, 19 bonds, 2 residues, 1 model selected  

> select /B:885-909

123 atoms, 125 bonds, 1 pseudobond, 15 residues, 2 models selected  

> color (#!1 & sel) yellow

> open "D:/Structure analysis/20211213_HKU/job053/job055_postprocess.mrc"

Opened job055_postprocess.mrc as #2, grid size 240,240,240, pixel 1.32, shown
at level 0.0156, step 1, values float32  

> volume #2 level 0.02976

> color zone #2 near sel & #1 distance 7.92

[Repeated 1 time(s)]

> select clear

> color zone #2 near #1 distance 7.92

> surface dust #2 size 13.2

> volume #2 level 0.02555

> lighting soft

> volume #2 level 0.02315

> volume #2 level 0.02405

> lighting simple

> lighting soft

> lighting simple

> hide #!2 models

> show #!2 models

> volume #2 level 0.02706

> volume #2 level 0.02615

> surface dust #2 size 13.2

> lighting full

> lighting soft

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> lighting full

> lighting soft

> hide #!2 models

> show #!2 models

> hide #!1 models

> save "D:/Structure analysis/figure/hku31/hku31 with color.cxs"

> open "D:/Structure analysis/20211213_HKU/Model
> building/HKU31_job135_gly_new_1.pdb"

Chain information for HKU31_job135_gly_new_1.pdb #3  
---  
Chain | Description  
A | No description available  
B C | No description available  
  

> select ::name="BMA"::name="FOL"::name="NAG"

1179 atoms, 1206 bonds, 81 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> hide #2-3 target a

> ui tool show "Fit in Map"

> open "D:/Structure analysis/20211213_HKU/hku31.mrc"

Opened hku31.mrc as #4, grid size 240,240,240, pixel 1.32, shown at level
0.0198, step 1, values float32  

> volume #4 level 0.0282

> volume #4 level 0.03268

> volume #4 level 0.03436

> show #!1 models

> hide #!1 models

> hide #!2 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> select #3/B

8859 atoms, 9067 bonds, 9 pseudobonds, 1131 residues, 2 models selected  

> color (#!3 & sel) dark gray

> select #1/C

8742 atoms, 8949 bonds, 9 pseudobonds, 1118 residues, 2 models selected  

> color #3 dark gray

> select #3/C

8859 atoms, 9067 bonds, 9 pseudobonds, 1131 residues, 2 models selected  

> select #1/A

8741 atoms, 8948 bonds, 9 pseudobonds, 1118 residues, 2 models selected  

> select #1/A

8741 atoms, 8948 bonds, 9 pseudobonds, 1118 residues, 2 models selected  

> show #!1 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> select #3/A

8863 atoms, 9071 bonds, 9 pseudobonds, 1132 residues, 2 models selected  

> color (#!3 & sel) medium blue

> ui tool show "Show Sequence Viewer"

> sequence chain #3/A

Alignment identifier is 3/A  

> select #3/A:22-23

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select #3/A:22

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #3/A:370

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:370-574

1591 atoms, 1628 bonds, 205 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel deep sky blue

> select #3/A:733

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:733-1198

3484 atoms, 3554 bonds, 3 pseudobonds, 449 residues, 2 models selected  

> color (#!3 & sel) red

> select #3/A:22-24

21 atoms, 20 bonds, 3 residues, 1 model selected  

> select #3/A:22-365

2668 atoms, 2743 bonds, 3 pseudobonds, 329 residues, 2 models selected  

> select #3/A:340

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #3/A:22-340

2464 atoms, 2531 bonds, 3 pseudobonds, 304 residues, 2 models selected  

> color (#!3 & sel) medium blue

> select #3/A:357-358

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select #3/A:357-369

109 atoms, 112 bonds, 13 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel turquoise

> select #3/A:583-647

484 atoms, 497 bonds, 1 pseudobond, 63 residues, 2 models selected  

> select #3/A:583-644

463 atoms, 475 bonds, 1 pseudobond, 60 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel turquoise

> select #3/A:345-346

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #3/A:345-357

98 atoms, 100 bonds, 13 residues, 1 model selected  

> select #3/A:356

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:345-356

93 atoms, 95 bonds, 12 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel chartreuse

> select #3/A:645-646

14 atoms, 14 bonds, 2 residues, 1 model selected  

> select #3/A:645-788

1063 atoms, 1083 bonds, 1 pseudobond, 139 residues, 2 models selected  

> select #3/A:751

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/A:645-751

760 atoms, 774 bonds, 1 pseudobond, 102 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel chartreuse

> select #3/A:575

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:575

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:576

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:575-576

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select #3/A:575-576

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select #3/A:575-576

18 atoms, 17 bonds, 2 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #3/B

Alignment identifier is 3/B  

> select #3/B:868-869

11 atoms, 10 bonds, 2 residues, 1 model selected  

> select #3/B:868-884

126 atoms, 127 bonds, 17 residues, 1 model selected  

> color sel orange

> select #3/B:885

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #3/B:885-903

110 atoms, 110 bonds, 1 pseudobond, 13 residues, 2 models selected  

> select #3/B:885-886

20 atoms, 20 bonds, 2 residues, 1 model selected  

> select #3/B:885-909

157 atoms, 159 bonds, 1 pseudobond, 19 residues, 2 models selected  

> color (#!3 & sel) yellow

> show #!4 models

> color zone #4 near sel & #3 distance 7.92

> select clear

> color zone #4 near #3 distance 7.92

> surface dust #4 size 13.2

> hide #!3 models

> volume #2 level 0.02469

> volume #2 level 0.02703

> volume #2 level 0.03025

> volume #2 level 0.03142

> volume #2 level 0.03288

> volume #2 level 0.03142

> hide #!2 models

> volume #2 level 0.02937

> hide #!2 models

[Repeated 1 time(s)]

> volume #4 level 0.03894

> show #!2 models

> hide #!4 models

> show #!4 models

> hide #!2 models

> volume #4 level 0.03837

> volume #4 level 0.03665

> show #!2 models

> hide #!2 models

> save "D:/Structure analysis/figure/hku31/HKU31 WITHOUT color.bmp" width 661
> height 546 supersample 3

> show #!2 models

> hide #!4 models

> volume #2 level 0.02762

> show #!4 models

> hide #!2 models

> hide #!4 models

> show #!2 models

> show #!1 models

> hide #!2 models

> select #1/A:575

9 atoms, 8 bonds, 1 residue, 1 model selected  

> color sel medium blue

> select #1/A:582

8 atoms, 7 bonds, 1 residue, 1 model selected  

> color sel medium blue

> select #1/A:581

7 atoms, 6 bonds, 1 residue, 1 model selected  

> color sel medium blue

> show #!2 models

> color zone #2 near sel & #1 distance 7.92

> select clear

> color zone #2 near #1 distance 7.92

> hide #!1 models

> show #!4 models

> hide #!4 models

> save "D:/Structure analysis/figure/hku31/HKU31 WITH color.bmp" width 661
> height 546 supersample 3

> show #!4 models

> hide #!4 models

> hide #!2 models

> show #!2 models

> show #!4 models

> open "D:/Structure
> analysis/20220413_japan/model/japan_real_space_refined_056_1_gly_LA_new_1.pdb"

Chain information for japan_real_space_refined_056_1_gly_LA_new_1.pdb #5  
---  
Chain | Description  
A B C | No description available  
  

> hide #!2 models

> hide #!5 models

> show #!5 models

> hide #!4 models

> select ::name="BMA"::name="EIC"::name="NAG"

1036 atoms, 1056 bonds, 74 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> hide #5 target a

> open "D:/Structure
> analysis/20220413_japan/job040_postprocess/postprocess.mrc"

Opened postprocess.mrc as #6, grid size 240,240,240, pixel 1.32, shown at
level 0.0172, step 1, values float32  

> volume #2 level 0.03113

> volume #2 level 0.02528

> hide #!5 models

> hide #!2 models

> show #!2 models

> hide #!6 models

> show #!6 models

> hide #!2 models

> volume #6 level 0.03981

> show #!5 models

> volume #6 level 0.03743

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!6 models

> select #5/B

8932 atoms, 9165 bonds, 5 pseudobonds, 1147 residues, 2 models selected  

> color (#!5 & sel) dark gray

> select #5/C

8932 atoms, 9165 bonds, 5 pseudobonds, 1147 residues, 2 models selected  

> color (#!5 & sel) dark gray

> select #5/B

8932 atoms, 9165 bonds, 5 pseudobonds, 1147 residues, 2 models selected  

> color (#!5 & sel) medium blue

> select #5/A

8999 atoms, 9232 bonds, 5 pseudobonds, 1147 residues, 2 models selected  

> color (#!5 & sel) dark gray

> ui tool show "Show Sequence Viewer"

> sequence chain #5/B

Alignment identifier is 5/B  

> select #5/B:18-19

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select #5/B:18-292

2092 atoms, 2152 bonds, 1 pseudobond, 265 residues, 2 models selected  

> select #5/B:356

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #5/B:18-356

2631 atoms, 2707 bonds, 1 pseudobond, 329 residues, 2 models selected  

> select #5/B:386

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #5/B:386-582

1527 atoms, 1575 bonds, 197 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel deep sky blue

> select #5/B:747

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #5/B:747-1218

3538 atoms, 3614 bonds, 2 pseudobonds, 458 residues, 2 models selected  

> color (#!5 & sel) red

> select #5/B:373-374

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select #5/B:373-385

107 atoms, 111 bonds, 13 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel turquoise

> select #5/B:587-588

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #5/B:587-737

975 atoms, 997 bonds, 1 pseudobond, 130 residues, 2 models selected  

> select #5/B:587-588

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #5/B:587-651

515 atoms, 528 bonds, 65 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel turquoise

> select #5/B:361

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #5/B:361-368

57 atoms, 57 bonds, 8 residues, 1 model selected  

> select #5/B:372-373

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select #5/B:361-373

94 atoms, 95 bonds, 13 residues, 1 model selected  

> select #5/B:372

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #5/B:364-372

68 atoms, 69 bonds, 9 residues, 1 model selected  

> select #5/B:361-362

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select #5/B:361-372

89 atoms, 90 bonds, 12 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel chartreuse

> select #5/B:652

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #5/B:652-711

279 atoms, 284 bonds, 1 pseudobond, 39 residues, 2 models selected  

> select #5/B:764

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #5/B:652-764

599 atoms, 610 bonds, 2 pseudobonds, 83 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel turquoise

> select #5/A

8999 atoms, 9232 bonds, 5 pseudobonds, 1147 residues, 2 models selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #5/A

Alignment identifier is 5/A  

> select #5/A:18

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #5/A:18-306

2248 atoms, 2311 bonds, 1 pseudobond, 279 residues, 2 models selected  

> select #5/A:880

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #5/A:880-896

126 atoms, 127 bonds, 17 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #5/C

Alignment identifier is 5/C  

> select #5/C:880-881

11 atoms, 10 bonds, 2 residues, 1 model selected  

> select #5/C:880-896

126 atoms, 127 bonds, 17 residues, 1 model selected  

> color sel orange

> select #5/C:897

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #5/C:897-922

161 atoms, 163 bonds, 1 pseudobond, 20 residues, 2 models selected  

> select #5/C:897

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #5/C:897-921

156 atoms, 158 bonds, 1 pseudobond, 19 residues, 2 models selected  

> color (#!5 & sel) yellow

> select clear

> show #!6 models

> color zone #6 near #5 distance 7.92

> surface dust #6 size 13.2

> volume #6 level 0.03446

> volume #6 level 0.0297

> hide #!5 models

> save "D:/Structure analysis/figure/Japan/Japan color.bmp" width 661 height
> 546 supersample 3

> show #!5 models

> hide #!6 models

> ui tool show "Show Sequence Viewer"

> sequence chain #5/B

Alignment identifier is 5/B  

> select #5/B:361-362

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select #5/B:361-372

89 atoms, 90 bonds, 12 residues, 1 model selected  

> select #5/B:652-653

14 atoms, 14 bonds, 2 residues, 1 model selected  

> select #5/B:652-869

1426 atoms, 1453 bonds, 2 pseudobonds, 188 residues, 2 models selected  

> select #5/B:652

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #5/B:652-813

994 atoms, 1013 bonds, 2 pseudobonds, 132 residues, 2 models selected  

> select #5/B:652

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #5/B:652-795

849 atoms, 865 bonds, 2 pseudobonds, 114 residues, 2 models selected  

> select #5/B:764

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #5/B:652-764

599 atoms, 610 bonds, 2 pseudobonds, 83 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel chartreuse

> show #!6 models

> select clear

> color zone #6 near #5 distance 7.92

> hide #!5 models

> save "D:/Structure analysis/figure/Japan/Japan color.bmp" width 661 height
> 546 supersample 3

> save "D:/Structure analysis/figure/all side view color.cxs"

> open "D:/Structure analysis/20220330_eri/model build/Eri-
> job033-withgly_real_space_refined_083_gly_LA.pdb"

Chain information for Eri-job033-withgly_real_space_refined_083_gly_LA.pdb #7  
---  
Chain | Description  
A B C | No description available  
  

> open "D:/Structure analysis/20220330_eri/job033_postprocess/postprocess.mrc"

Opened postprocess.mrc as #8, grid size 240,240,240, pixel 1.32, shown at
level 0.0207, step 1, values float32  

> volume #8 level 0.03008

> hide #!6 models

> volume #8 level 0.0365

> hide #!8 models

> select ::name="BMA"::name="EIC"::name="FOL"::name="MAN"::name="NAG"

1362 atoms, 1404 bonds, 96 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> hide #7 target a

> select #7/B

8846 atoms, 9061 bonds, 6 pseudobonds, 1132 residues, 2 models selected  

> color (#!7 & sel) dark gray

> select #7/C

8846 atoms, 9060 bonds, 6 pseudobonds, 1132 residues, 2 models selected  

> color (#!7 & sel) dark gray

> select #1/A#3/A#5/A#7/A

35449 atoms, 36312 bonds, 29 pseudobonds, 4529 residues, 8 models selected  

> select clear

> select #7/A

8846 atoms, 9061 bonds, 6 pseudobonds, 1132 residues, 2 models selected  

> color (#!7 & sel) medium blue

> ui tool show "Show Sequence Viewer"

> sequence chain #7/A

Alignment identifier is 7/A  

> select #7/A:367-373

53 atoms, 52 bonds, 7 residues, 1 model selected  

> select #7/A:367-571

1594 atoms, 1635 bonds, 205 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel deep sky blue

> select #7/A:730

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #7/A:730-1197

3527 atoms, 3601 bonds, 2 pseudobonds, 454 residues, 2 models selected  

> color (#!7 & sel) red

> select #7/A:354

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #7/A:354-365

101 atoms, 103 bonds, 12 residues, 1 model selected  

> select #7/A:366

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #7/A:354-366

109 atoms, 111 bonds, 13 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel turquoise

> select #7/A:343

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #7/A:343-352

77 atoms, 79 bonds, 10 residues, 1 model selected  

> select #7/A:342-343

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #7/A:342-353

93 atoms, 95 bonds, 12 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel chartreuse

> select #7/A:584

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #7/A:584-641

437 atoms, 449 bonds, 58 residues, 1 model selected  

> ui tool show "Color Actions"

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

> color sel turquoise

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

> select #7/A:642-643

14 atoms, 14 bonds, 2 residues, 1 model selected  

> select #7/A:642-708

445 atoms, 451 bonds, 1 pseudobond, 59 residues, 2 models selected  

> select #7/A:748

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #7/A:642-748

709 atoms, 722 bonds, 2 pseudobonds, 94 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel chartreuse

> show #!3 models

> show #!5 models

> hide #!3 models

> hide #!5 models

> ui tool show "Show Sequence Viewer"

> sequence chain #7/B

Alignment identifier is 7/B  

> select #7/B:865

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #7/B:865-881

127 atoms, 128 bonds, 17 residues, 1 model selected  

> color sel orange

> select #7/B:882

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #7/B:882-899

103 atoms, 103 bonds, 1 pseudobond, 12 residues, 2 models selected  

> select #7/B:906

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #7/B:882-906

158 atoms, 160 bonds, 1 pseudobond, 19 residues, 2 models selected  

> color (#!7 & sel) yellow

> select clear

> show #!8 models

> color zone #8 near #7 distance 7.92

> surface dust #8 size 13.2

> volume #8 level 0.03417

> volume #8 level 0.03592

> volume #8 level 0.03475

> hide #!7 models

> save "D:/Structure analysis/figure/Eri/Eri color.bmp" width 661 height 546
> supersample 3

> open "D:/Structure analysis/20220410_neo/model
> build/Neo_real_space_refined_057_gly_LA_new.pdb"

Chain information for Neo_real_space_refined_057_gly_LA_new.pdb #9  
---  
Chain | Description  
A B C | No description available  
  

> hide #!8 models

> open "D:/Structure analysis/20220410_neo/job031_postprocess/postprocess.mrc"

Opened postprocess.mrc as #10, grid size 240,240,240, pixel 1.32, shown at
level 0.0194, step 1, values float32  

> volume #10 level 0.02664

> volume #10 level 0.03586

> ui tool show "Volume Viewer"

> close #2

> close #4

> close #6

> hide #!10 models

> select ::name="EIC"::name="NAG"

942 atoms, 954 bonds, 66 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> hide #9 target a

> show #!1 models

> hide #!1 models

> select #9/B

8986 atoms, 9215 bonds, 5 pseudobonds, 1154 residues, 2 models selected  

> color (#!9 & sel) dark gray

> show #!10 models

> hide #!10 models

> select #9/C

8986 atoms, 9214 bonds, 5 pseudobonds, 1154 residues, 2 models selected  

> color (#!9 & sel) dark gray

> select #9/A

8986 atoms, 9215 bonds, 5 pseudobonds, 1154 residues, 2 models selected  

> color (#!9 & sel) medium blue

> ui tool show "Show Sequence Viewer"

> sequence chain #9/A

Alignment identifier is 9/A  

> select #9/A:384-516

1067 atoms, 1096 bonds, 133 residues, 1 model selected  

> select #9/A:384-516

1067 atoms, 1096 bonds, 133 residues, 1 model selected  

> select #9/A:384

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #9/A:384-584

1588 atoms, 1634 bonds, 201 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel deep sky blue

> select #9/A:738

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #9/A:738-1215

3590 atoms, 3663 bonds, 1 pseudobond, 471 residues, 2 models selected  

> color (#!9 & sel) red

> select #9/A:371-372

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select #9/A:371-379

70 atoms, 72 bonds, 9 residues, 1 model selected  

> select #9/A:371-372

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select #9/A:371-388

144 atoms, 150 bonds, 18 residues, 1 model selected  

> select #9/A:384

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #9/A:369-384

129 atoms, 135 bonds, 16 residues, 1 model selected  

> select #9/A:371-372

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select #9/A:371-383

104 atoms, 108 bonds, 13 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel turquoise

> select #9/A:370

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #9/A:358-370

103 atoms, 105 bonds, 13 residues, 1 model selected  

> select #9/A:359-360

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #9/A:359-370

95 atoms, 97 bonds, 12 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel chartreuse

> select #9/A:593

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #9/A:593-596

33 atoms, 33 bonds, 4 residues, 1 model selected  

> select #9/A:596

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select #9/A:596-654

439 atoms, 451 bonds, 1 pseudobond, 56 residues, 2 models selected  

> select #9/A:593-594

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #9/A:593-654

462 atoms, 474 bonds, 1 pseudobond, 59 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel turquoise

> select #9/A:655-656

14 atoms, 14 bonds, 2 residues, 1 model selected  

> select #9/A:655-757

777 atoms, 791 bonds, 103 residues, 1 model selected  

> select #9/A:763

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #9/A:655-763

823 atoms, 838 bonds, 109 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel chartreuse

> ui tool show "Show Sequence Viewer"

> sequence chain #9/B

Alignment identifier is 9/B  

> select #9/B:879-880

11 atoms, 10 bonds, 2 residues, 1 model selected  

> select #9/B:879-895

124 atoms, 125 bonds, 17 residues, 1 model selected  

> color sel orange

> select #9/B:896-897

20 atoms, 20 bonds, 2 residues, 1 model selected  

> select #9/B:896-911

120 atoms, 122 bonds, 16 residues, 1 model selected  

> select #9/B:920-921

12 atoms, 11 bonds, 2 residues, 1 model selected  

> select #9/B:896-920

194 atoms, 198 bonds, 25 residues, 1 model selected  

> color sel yellow

> select clear

> show #!10 models

> color zone #10 near #9 distance 7.92

> surface dust #10 size 13.2

> volume #10 level 0.03199

> volume #10 level 0.033

> volume #10 level 0.034

> volume #10 level 0.033

> hide #!9 models

> save "D:/Structure analysis/figure/NEO/Neo color.bmp" width 661 height 573
> supersample 3

> open "D:/Structure analysis/20220409_GD_6P/model build/GD-
> fit_chainABC_namdinator_real_space_refined_011_1_real_space_refined_018_gly_3_real_space_refined_034_1_new_LA.pdb"

Chain information for GD-
fit_chainABC_namdinator_real_space_refined_011_1_real_space_refined_018_gly_3_real_space_refined_034_1_new_LA.pdb
#2  
---  
Chain | Description  
A B C | No description available  
  

> ui tool show Matchmaker

[Repeated 1 time(s)]

> matchmaker #!2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
HKU31_job053_chainABC_nam_real_space_refined_001_real_space_refined_019_gly_real_space_refined_023_6_new_real_space_refined_014-2_LA.pdb,
chain C (#1) with GD-
fit_chainABC_namdinator_real_space_refined_011_1_real_space_refined_018_gly_3_real_space_refined_034_1_new_LA.pdb,
chain C (#2), sequence alignment score = 3156.8  
RMSD between 808 pruned atom pairs is 1.165 angstroms; (across all 1009 pairs:
2.497)  
  

> hide #!10 models

> open "D:/Structure
> analysis/20220409_GD_6P/job132_postprocess_spike(final)/postprocess
> zflip.mrc"

Opened postprocess zflip.mrc as #4, grid size 320,320,320, pixel 1.32, shown
at level 0.0135, step 2, values float32  

> volume #4 level 0.01787

> volume #4 level 0.02194

> volume #4 level 0.01923

> ui tool show "Fit in Map"

Fit map postprocess zflip.mrc in map postprocess.mrc using 11217 points  
correlation = 0.1172, correlation about mean = -0.01059, overlap = 0.6566  
steps = 336, shift = 7.07, angle = 7.85 degrees  
  
Position of postprocess zflip.mrc (#4) relative to postprocess.mrc (#10)
coordinates:  
Matrix rotation and translation  
0.99144423 -0.13032688 -0.00729684 24.12750515  
0.13051585 0.99063061 0.04020714 -31.64791859  
0.00198840 -0.04081549 0.99916472 8.43532800  
Axis -0.29646653 -0.03397522 0.95443872  
Axis point 254.38311828 172.91953945 0.00000000  
Rotation angle (degrees) 7.85387938  
Shift along axis 1.97325091  
  
Fit map postprocess zflip.mrc in map postprocess.mrc using 11217 points  
correlation = 0.1173, correlation about mean = -0.01064, overlap = 0.6567  
steps = 48, shift = 0.0167, angle = 0.0129 degrees  
  
Position of postprocess zflip.mrc (#4) relative to postprocess.mrc (#10)
coordinates:  
Matrix rotation and translation  
0.99144461 -0.13031463 -0.00746176 24.17096774  
0.13051067 0.99062506 0.04036043 -31.67329701  
0.00213225 -0.04098897 0.99915732 8.45427895  
Axis -0.29756304 -0.03509337 0.95405697  
Axis point 254.60221903 173.29910727 0.00000000  
Rotation angle (degrees) 7.85651369  
Shift along axis 1.98499998  
  
Fit map postprocess zflip.mrc in map postprocess.mrc using 11217 points  
correlation = 0.1173, correlation about mean = -0.01058, overlap = 0.6567  
steps = 48, shift = 0.0178, angle = 0.00992 degrees  
  
Position of postprocess zflip.mrc (#4) relative to postprocess.mrc (#10)
coordinates:  
Matrix rotation and translation  
0.99145228 -0.13026130 -0.00737346 24.14419920  
0.13045404 0.99062684 0.04049956 -31.69907882  
0.00202882 -0.04111528 0.99915235 8.48873326  
Axis -0.29856940 -0.03439609 0.95376791  
Axis point 254.91037784 173.15836888 0.00000000  
Rotation angle (degrees) 7.85557550  
Shift along axis 1.97788667  
  
Fit map postprocess zflip.mrc in map postprocess.mrc using 11217 points  
correlation = 0.1172, correlation about mean = -0.01052, overlap = 0.6565  
steps = 48, shift = 0.0104, angle = 0.00235 degrees  
  
Position of postprocess zflip.mrc (#4) relative to postprocess.mrc (#10)
coordinates:  
Matrix rotation and translation  
0.99145031 -0.13027784 -0.00734667 24.13643116  
0.13046942 0.99062588 0.04047330 -31.69542882  
0.00200503 -0.04108578 0.99915361 8.47888473  
Axis -0.29835223 -0.03420955 0.95384257  
Axis point 254.85105232 173.05690531 0.00000000  
Rotation angle (degrees) 7.85592469  
Shift along axis 1.97064947  
  
Fit map postprocess zflip.mrc in map postprocess.mrc using 11217 points  
correlation = 0.1173, correlation about mean = -0.01064, overlap = 0.6568  
steps = 44, shift = 0.0191, angle = 0.00173 degrees  
  
Position of postprocess zflip.mrc (#4) relative to postprocess.mrc (#10)
coordinates:  
Matrix rotation and translation  
0.99144967 -0.13028118 -0.00737373 24.15072599  
0.13047384 0.99062583 0.04046048 -31.68983270  
0.00203336 -0.04107661 0.99915393 8.48787105  
Axis -0.29826877 -0.03441184 0.95386140  
Axis point 254.80290583 173.19192501 0.00000000  
Rotation angle (degrees) 7.85600369  
Shift along axis 1.98335076  
  

> select #4

2 models selected  

> hide #!2 models

> show #!2 models

> ~select #4

Nothing selected  

> hide #!2 models

> show #!2 models

> select #4

2 models selected  

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> ~select #4

Nothing selected  

> ui tool show "Map Coordinates"

> ui tool show "Show Volume Menu"

> save "D:/Structure analysis/figure/all side view color.cxs"

——— End of log from Mon Sep 12 21:09:04 2022 ———

opened ChimeraX session  

> show #!1 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> show #!2 models

> show #!5 models

> hide #!5 models

> hide #!2 models

> show #!1 models

> show #!2 models

> ui tool show Matchmaker

> matchmaker #!2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
HKU31_job053_chainABC_nam_real_space_refined_001_real_space_refined_019_gly_real_space_refined_023_6_new_real_space_refined_014-2_LA.pdb,
chain C (#1) with GD-
fit_chainABC_namdinator_real_space_refined_011_1_real_space_refined_018_gly_3_real_space_refined_034_1_new_LA.pdb,
chain C (#2), sequence alignment score = 3156.8  
RMSD between 808 pruned atom pairs is 1.165 angstroms; (across all 1009 pairs:
2.497)  
  

> hide #!1 models

> show #!4 models

> volume #4 step 1

> volume #4 level 0.0249

> ui mousemode right "rotate selected models"

> select #4

2 models selected  

> view matrix models
> #4,0.58844,0.023072,-0.80822,238.4,0.35046,0.89353,0.28067,-105.04,0.72864,-0.4484,0.5177,48.449

> view matrix models
> #4,0.41541,-0.12998,-0.9003,326.04,0.12526,0.98848,-0.084911,-4.2591,0.90097,-0.077498,0.4269,-48.695

> view matrix models
> #4,0.41295,-0.13004,-0.90142,326.78,0.12625,0.98837,-0.084745,-4.4705,0.90196,-0.078806,0.42457,-48.13

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.41295,-0.13004,-0.90142,309.91,0.12625,0.98837,-0.084745,-3.2194,0.90196,-0.078806,0.42457,-95.52

> view matrix models
> #4,0.41295,-0.13004,-0.90142,309.98,0.12625,0.98837,-0.084745,-3.4218,0.90196,-0.078806,0.42457,-97.273

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.37706,-0.13053,-0.91694,320.61,0.1406,0.98661,-0.082633,-6.4022,0.91545,-0.097765,0.39037,-88.831

> ~select #4

Nothing selected  

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> hide #!2 models

> show #!10 models

> ui tool show "Fit in Map"

Fit map postprocess zflip.mrc in map postprocess.mrc using 55012 points  
correlation = 0.7066, correlation about mean = 0.3231, overlap = 95.46  
steps = 664, shift = 61.8, angle = 12.5 degrees  
  
Position of postprocess zflip.mrc (#4) relative to postprocess.mrc (#10)
coordinates:  
Matrix rotation and translation  
0.26703994 -0.20262453 -0.94214276 340.60246307  
0.00312930 0.97782267 -0.20941116 -5.77737870  
0.96368038 0.05297289 0.26175178 -100.84871982  
Axis 0.13561499 -0.98503769 0.10634527  
Axis point 239.10195638 0.00000000 169.58022238  
Rotation angle (degrees) 75.32669864  
Shift along axis 41.15695072  
  
Fit map postprocess zflip.mrc in map postprocess.mrc using 55012 points  
correlation = 0.7066, correlation about mean = 0.323, overlap = 95.46  
steps = 24, shift = 0.000723, angle = 0.00256 degrees  
  
Position of postprocess zflip.mrc (#4) relative to postprocess.mrc (#10)
coordinates:  
Matrix rotation and translation  
0.26704143 -0.20266813 -0.94213295 340.60934880  
0.00314266 0.97781369 -0.20945288 -5.76967961  
0.96367993 0.05297180 0.26175368 -100.84950840  
Axis 0.13563588 -0.98503165 0.10637463  
Axis point 239.10721479 0.00000000 169.58504826  
Rotation angle (degrees) 75.32686366  
Shift along axis 41.15433654  
  
Fit map postprocess zflip.mrc in map postprocess.mrc using 55012 points  
correlation = 0.7066, correlation about mean = 0.323, overlap = 95.46  
steps = 24, shift = 0.000244, angle = 0.000184 degrees  
  
Position of postprocess zflip.mrc (#4) relative to postprocess.mrc (#10)
coordinates:  
Matrix rotation and translation  
0.26704165 -0.20267126 -0.94213222 340.60982383  
0.00314357 0.97781305 -0.20945588 -5.76911881  
0.96367986 0.05297179 0.26175392 -100.84978631  
Axis 0.13563743 -0.98503121 0.10637671  
Axis point 239.10773482 0.00000000 169.58529766  
Rotation angle (degrees) 75.32686927  
Shift along axis 41.15413299  
  
Fit map postprocess zflip.mrc in map postprocess.mrc using 55012 points  
correlation = 0.7066, correlation about mean = 0.323, overlap = 95.46  
steps = 24, shift = 0.000102, angle = 0.00032 degrees  
  
Position of postprocess zflip.mrc (#4) relative to postprocess.mrc (#10)
coordinates:  
Matrix rotation and translation  
0.26704140 -0.20267672 -0.94213111 340.61078227  
0.00314498 0.97781191 -0.20946116 -5.76807888  
0.96367993 0.05297181 0.26175368 -100.84985358  
Axis 0.13564014 -0.98503045 0.10638025  
Axis point 239.10838625 0.00000000 169.58587330  
Rotation angle (degrees) 75.32691765  
Shift along axis 41.15379407  
  

> show #!8 models

> hide #!10 models

Fit map postprocess zflip.mrc in map postprocess.mrc using 55012 points  
correlation = 0.8252, correlation about mean = 0.4889, overlap = 109  
steps = 60, shift = 0.798, angle = 1.3 degrees  
  
Position of postprocess zflip.mrc (#4) relative to postprocess.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.26703006 -0.22471761 -0.93712163 344.24014440  
0.00960916 0.97300494 -0.23058416 -1.74697389  
0.96364029 0.05256796 0.26198092 -101.60060287  
Axis 0.14625852 -0.98181370 0.12103842  
Axis point 242.02738277 0.00000000 171.82964771  
Rotation angle (degrees) 75.46283407  
Shift along axis 39.76568124  
  
Fit map postprocess zflip.mrc in map postprocess.mrc using 55012 points  
correlation = 0.8252, correlation about mean = 0.4888, overlap = 109  
steps = 24, shift = 0.00703, angle = 0.00195 degrees  
  
Position of postprocess zflip.mrc (#4) relative to postprocess.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.26702862 -0.22475026 -0.93711421 344.24631141  
0.00962334 0.97299770 -0.23061413 -1.74203757  
0.96364055 0.05256240 0.26198108 -101.60652536  
Axis 0.14627096 -0.98180888 0.12106248  
Axis point 242.03514940 0.00000000 171.83105475  
Rotation angle (degrees) 75.46308637  
Shift along axis 39.76285002  
  

> hide #!8 models

> show #!2 models

> ui tool show "Fit in Map"

Fit molecule GD-
fit_chainABC_namdinator_real_space_refined_011_1_real_space_refined_018_gly_3_real_space_refined_034_1_new_LA.pdb
(#2) to map postprocess zflip.mrc (#4) using 25934 atoms  
average map value = 0.03724, steps = 60  
shifted from previous position = 1.26  
rotated from previous position = 2.28 degrees  
atoms outside contour = 8161, contour level = 0.024903  
  
Position of GD-
fit_chainABC_namdinator_real_space_refined_011_1_real_space_refined_018_gly_3_real_space_refined_034_1_new_LA.pdb
(#2) relative to postprocess zflip.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99998653 0.00511743 -0.00086739 -0.80867842  
-0.00511306 0.99997462 0.00496189 0.16385272  
0.00089276 -0.00495739 0.99998731 0.86062161  
Axis -0.69085236 -0.12258959 -0.71252706  
Axis point 29.42183990 168.17624606 0.00000000  
Rotation angle (degrees) 0.41133107  
Shift along axis -0.07462543  
  

> hide #!4 models

> show #!1 models

> hide #!2 models

> show #!2 models

> show #!3 models

> hide #!3 models

> hide #!1 models

> select ::name="BMA"::name="EIC"::name="MAN"::name="NAG"

1189 atoms, 1221 bonds, 80 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> hide #2 target a

> select #2/B

8249 atoms, 8452 bonds, 7 pseudobonds, 1067 residues, 2 models selected  

> color (#!2 & sel) dark gray

> select #2/C

8248 atoms, 8451 bonds, 7 pseudobonds, 1067 residues, 2 models selected  

> color (#!2 & sel) dark gray

> select #2/A

8248 atoms, 8451 bonds, 7 pseudobonds, 1067 residues, 2 models selected  

> color (#!2 & sel) medium blue

> show #!1 models

> hide #!1 models

> hide #!2 models

> show #!4 models

> show #!10 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> hide #!10 models

> show #!1 models

> show #!3 models

> open "D:/Structure analysis/20211213_HKU/hku31.mrc"

Opened hku31.mrc as #6, grid size 240,240,240, pixel 1.32, shown at level
0.0198, step 1, values float32  

> volume #6 level 0.02944

> volume #6 level 0.03219

> volume #6 level 0.03082

> volume #6 level 0.03013

> hide #!1 models

> open "D:/Structure analysis/20211213_HKU/job053/job055_postprocess.mrc"

Opened job055_postprocess.mrc as #11, grid size 240,240,240, pixel 1.32, shown
at level 0.0156, step 1, values float32  

> volume #11 level 0.0188

> volume #11 level 0.02056

> volume #11 level 0.02091

> volume #11 level 0.02197

> volume #11 level 0.02232

> volume #11 level 0.02302

> hide #!6 models

> show #!1 models

> hide #!3 models

> show #!6 models

> hide #!1 models

> hide #!11 models

> show #!3 models

> color zone #6 near #3 distance 7.92

> surface dust #6 size 13.2

> hide #!3 models

> save "D:/Structure analysis/figure/hku31/HKU31 WITHOUT color.bmp" width 757
> height 573 supersample 3

> show #!3 models

> hide #!3 models

> hide #!6 models

> show #!1 models

> show #!11 models

> color zone #11 near #1 distance 7.92

> surface dust #11 size 13.2

> volume #11 level 0.02162

> volume #11 level 0.02373

> volume #11 level 0.02583

> volume #11 level 0.02654

> color #11 #0061b2 models transparency 0

> color #11 white models transparency 0

[Repeated 1 time(s)]

> color #11 #050708 models transparency 0

> color zone #11 near #1 distance 7.92

> volume #11 level 0.02443

> volume #11 level 0.025

> volume #11 level 0.0248

> color #1,11 dark gray

> color zone #11 near #1 distance 7.92

[Repeated 1 time(s)]

> hide #!1 models

> show #!1 models

> hide #!11 models

> show #!11 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> show #!3 models

> hide #!3 models

> hide #!11 models

> select #1/A

8741 atoms, 8948 bonds, 9 pseudobonds, 1118 residues, 2 models selected  

> color (#!1 & sel) medium blue

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> select #1/A:733

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:733-1198

3453 atoms, 3522 bonds, 3 pseudobonds, 446 residues, 2 models selected  

> color (#!1 & sel) red

> select #1/A:370-371

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select #1/A:370-574

1591 atoms, 1628 bonds, 205 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel deep sky blue

> select #1/A:357

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/A:357-369

109 atoms, 112 bonds, 13 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel turquoise

> select #1/A:345-346

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #1/A:345-356

93 atoms, 95 bonds, 12 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel chartreuse

> select #1/A:583-584

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #1/A:583-644

474 atoms, 487 bonds, 62 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel turquoise

> select #1/A:645-646

14 atoms, 14 bonds, 2 residues, 1 model selected  

> select #1/A:645-739

552 atoms, 563 bonds, 2 pseudobonds, 76 residues, 2 models selected  

> select #1/A:751

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/A:645-751

652 atoms, 665 bonds, 2 pseudobonds, 88 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel chartreuse

> ui tool show "Show Sequence Viewer"

> sequence chain #1/B

Alignment identifier is 1/B  

> select #1/B:868

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #1/B:868-884

106 atoms, 105 bonds, 1 pseudobond, 14 residues, 2 models selected  

> color (#!1 & sel) orange

> select #1/B:885-886

20 atoms, 20 bonds, 2 residues, 1 model selected  

> select #1/B:885-909

123 atoms, 125 bonds, 1 pseudobond, 15 residues, 2 models selected  

> color (#!1 & sel) yellow

> select clear

> show #!11 models

> color zone #11 near #1 distance 7.92

> surface dust #11 size 13.2

> volume #11 level 0.0255

> save "D:/Structure analysis/figure/hku31/HKU31 WITH color.bmp" width 757
> height 573 supersample 3

> hide #!11 models

> hide #!1 models

> show #!7 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!7 models

> show #!7 models

> hide #!8 models

> show #!8 models

> hide #!7 models

> save "D:/Structure analysis/figure/Eri/Eri color.bmp" width 757 height 573
> supersample 3

> hide #!8 models

> show #!9 models

> show #!10 models

> hide #!9 models

> color #10 dark gray

> show #!9 models

> color zone #10 near #9 distance 7.92

> save "D:/Structure analysis/figure/NEO/Neo color.bmp" width 757 height 573
> supersample 3

> hide #!10 models

> hide #!9 models

> show #!7 models

> show #!8 models

> hide #!7 models

> color #8 dark gray

> show #!7 models

> color zone #8 near #7 distance 7.92

> hide #!7 models

> save "D:/Structure analysis/figure/Eri/Eri color.bmp" width 757 height 573
> supersample 3

> show #!5 models

> hide #!8 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> ui tool show Matchmaker

> matchmaker #!5 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
HKU31_job053_chainABC_nam_real_space_refined_001_real_space_refined_019_gly_real_space_refined_023_6_new_real_space_refined_014-2_LA.pdb,
chain A (#1) with japan_real_space_refined_056_1_gly_LA_new_1.pdb, chain A
(#5), sequence alignment score = 3517.3  
RMSD between 894 pruned atom pairs is 1.206 angstroms; (across all 1101 pairs:
2.290)  
  

> open "D:/Structure
> analysis/20220413_japan/job040_postprocess/postprocess.mrc"

Opened postprocess.mrc as #12, grid size 240,240,240, pixel 1.32, shown at
level 0.0172, step 1, values float32  

> hide #!1 models

> hide #!5 models

> volume #12 level 0.02685

> color #12 dark gray

> show #!11 models

> hide #!11 models

> show #!11 models

> ui tool show "Fit in Map"

Fit map postprocess.mrc in map job055_postprocess.mrc using 75509 points  
correlation = 0.8308, correlation about mean = 0.4606, overlap = 129.4  
steps = 80, shift = 3.31, angle = 0.39 degrees  
  
Position of postprocess.mrc (#12) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99997682 -0.00680853 0.00000549 1.08137209  
0.00680853 0.99997682 -0.00007965 -1.04530791  
-0.00000495 0.00007968 1.00000000 3.29666750  
Axis 0.01169994 0.00076715 0.99993126  
Axis point 154.42162837 152.61542010 0.00000000  
Rotation angle (degrees) 0.39012965  
Shift along axis 3.30829096  
  

> hide #!11 models

> show #!5 models

> ui tool show "Fit in Map"

Fit molecule japan_real_space_refined_056_1_gly_LA_new_1.pdb (#5) to map
postprocess.mrc (#12) using 26863 atoms  
average map value = 0.06293, steps = 52  
shifted from previous position = 0.624  
rotated from previous position = 0.4 degrees  
atoms outside contour = 3141, contour level = 0.026853  
  
Position of japan_real_space_refined_056_1_gly_LA_new_1.pdb (#5) relative to
postprocess.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.50007787 -0.86598043 0.00014435 374.78012784  
0.86598044 -0.50007788 0.00000663 100.43811056  
0.00006645 0.00012832 0.99999999 -0.03372808  
Axis 0.00007026 0.00004498 1.00000000  
Axis point 158.39909058 158.39752605 0.00000000  
Rotation angle (degrees) 120.00515256  
Shift along axis -0.00287699  
  

> color zone #12 near #5 distance 7.92

> hide #!5 models

> show #!5 models

> hide #!12 models

> show #!12 models

> hide #!5 models

> show #!5 models

> hide #!12 models

> select #5/B

8932 atoms, 9165 bonds, 5 pseudobonds, 1147 residues, 2 models selected  

> color (#!5 & sel) dark gray

> select #5/C

8932 atoms, 9165 bonds, 5 pseudobonds, 1147 residues, 2 models selected  

> color (#!5 & sel) dark gray

> select #5/A

8999 atoms, 9232 bonds, 5 pseudobonds, 1147 residues, 2 models selected  

> color (#!5 & sel) medium blue

> ui tool show "Show Sequence Viewer"

> sequence chain #5/A

Alignment identifier is 5/A  

> select #5/A:747

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #5/A:747-1218

3538 atoms, 3614 bonds, 2 pseudobonds, 458 residues, 2 models selected  

> color (#!5 & sel) red

> select #5/A:386

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #5/A:386-557

1340 atoms, 1384 bonds, 172 residues, 1 model selected  

> select #5/A:386

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #5/A:386-582

1527 atoms, 1575 bonds, 197 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel deep sky blue

> select #5/A:587

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #5/A:587-651

515 atoms, 528 bonds, 65 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel turquoise

> select #5/A:652-653

14 atoms, 14 bonds, 2 residues, 1 model selected  

> select #5/A:652-784

758 atoms, 773 bonds, 2 pseudobonds, 103 residues, 2 models selected  

> select #5/A:652

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #5/A:652-764

599 atoms, 610 bonds, 2 pseudobonds, 83 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel chartreuse

> select #5/A:373

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #5/A:373-381

75 atoms, 77 bonds, 9 residues, 1 model selected  

> select #5/A:373

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #5/A:373-385

107 atoms, 111 bonds, 13 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel turquoise

> select #5/A:372

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #5/A:363-372

74 atoms, 75 bonds, 10 residues, 1 model selected  

> select #5/A:361

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #5/A:361-372

89 atoms, 90 bonds, 12 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel chartreuse

> show #!12 models

> select clear

> color zone #12 near #5 distance 7.92

> surface dust #12 size 13.2

> hide #!5 models

> show #!5 models

> hide #!12 models

> ui tool show "Show Sequence Viewer"

> sequence chain #5/B

Alignment identifier is 5/B  

> select #5/B:880

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #5/B:880-896

126 atoms, 127 bonds, 17 residues, 1 model selected  

> color sel orange

> select #5/B:897

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #5/B:897-918

129 atoms, 130 bonds, 1 pseudobond, 16 residues, 2 models selected  

> select #5/B:897

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #5/B:897-921

156 atoms, 158 bonds, 1 pseudobond, 19 residues, 2 models selected  

> color (#!5 & sel) yellow

> select clear

> show #!12 models

> color zone #12 near #5 distance 7.92

> hide #!5 models

> volume #12 level 0.0272

> save "D:/Structure analysis/figure/Japan/Japan color.bmp" width 766 height
> 573 supersample 3

> hide #!12 models

> show #!1 models

> show #!9 models

> hide #!9 models

> show #!3 models

> hide #!3 models

> show #!5 models

> hide #!5 models

> show #!3 models

> hide #!3 models

> show #!7 models

> ui tool show Matchmaker

> matchmaker #!7 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
HKU31_job053_chainABC_nam_real_space_refined_001_real_space_refined_019_gly_real_space_refined_023_6_new_real_space_refined_014-2_LA.pdb,
chain B (#1) with Eri-job033-withgly_real_space_refined_083_gly_LA.pdb, chain
B (#7), sequence alignment score = 4666.2  
RMSD between 1052 pruned atom pairs is 0.782 angstroms; (across all 1110
pairs: 1.387)  
  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!8 models

> toolshed show

> ui tool show "Fit in Map"

Fit map postprocess.mrc in map job055_postprocess.mrc using 62033 points  
correlation = 0.9305, correlation about mean = 0.6227, overlap = 147.5  
steps = 64, shift = 1.1, angle = 2.19 degrees  
  
Position of postprocess.mrc (#8) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99926639 0.03829716 0.00012980 -5.98000513  
-0.03829714 0.99926638 -0.00015896 6.21328342  
-0.00013579 0.00015387 0.99999998 1.09938374  
Axis 0.00408427 0.00346753 -0.99998565  
Axis point 159.29128922 159.08128659 0.00000000  
Rotation angle (degrees) 2.19483331  
Shift along axis -1.10224718  
  

> ui tool show "Fit in Map"

Fit molecule Eri-job033-withgly_real_space_refined_083_gly_LA.pdb (#7) to map
postprocess.mrc (#8) using 26538 atoms  
average map value = 0.05925, steps = 48  
shifted from previous position = 0.169  
rotated from previous position = 0.167 degrees  
atoms outside contour = 6293, contour level = 0.034751  
  
Position of Eri-job033-withgly_real_space_refined_083_gly_LA.pdb (#7) relative
to postprocess.mrc (#8) coordinates:  
Matrix rotation and translation  
0.99999998 0.00002164 -0.00018621 0.03123356  
-0.00002161 0.99999998 0.00019234 -0.01513561  
0.00018621 -0.00019234 0.99999996 -0.00555979  
Axis -0.71612620 -0.69331079 -0.08051969  
Axis point 0.00000000 -33.71217436 119.87379888  
Rotation angle (degrees) 0.01538863  
Shift along axis -0.01142582  
  

> hide #!7 models

> save "D:/Structure analysis/figure/Eri/Eri color.bmp" width 811 height 573
> supersample 3

> hide #!8 models

> show #!1 models

> show #!9 models

> ui tool show "Fit in Map"

> ui tool show Matchmaker

> matchmaker #!9 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
HKU31_job053_chainABC_nam_real_space_refined_001_real_space_refined_019_gly_real_space_refined_023_6_new_real_space_refined_014-2_LA.pdb,
chain B (#1) with Neo_real_space_refined_057_gly_LA_new.pdb, chain A (#9),
sequence alignment score = 3795.4  
RMSD between 750 pruned atom pairs is 1.097 angstroms; (across all 1081 pairs:
2.807)  
  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!9 models

> show #!9 models

> ui tool show Matchmaker

> matchmaker #!9 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
HKU31_job053_chainABC_nam_real_space_refined_001_real_space_refined_019_gly_real_space_refined_023_6_new_real_space_refined_014-2_LA.pdb,
chain B (#1) with Neo_real_space_refined_057_gly_LA_new.pdb, chain A (#9),
sequence alignment score = 3795.4  
RMSD between 750 pruned atom pairs is 1.097 angstroms; (across all 1081 pairs:
2.807)  
  

> select #1/A#2/A#3/A#5/A#7/A#9/A

52683 atoms, 53978 bonds, 41 pseudobonds, 6750 residues, 12 models selected  

> ui tool show Matchmaker

> select clear

> show #!10 models

> hide #!1 models

> hide #!9 models

> show #!11 models

> ui tool show "Fit in Map"

Fit map postprocess.mrc in map job055_postprocess.mrc using 71607 points  
correlation = 0.8583, correlation about mean = 0.4809, overlap = 149.6  
steps = 52, shift = 0.307, angle = 0.891 degrees  
  
Position of postprocess.mrc (#10) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99987902 0.01555458 0.00003140 -2.45424093  
-0.01555458 0.99987901 -0.00016539 2.49415884  
-0.00003396 0.00016488 0.99999999 0.28570413  
Axis 0.01061583 0.00210083 -0.99994144  
Axis point 159.15493694 158.81119767 0.00000000  
Rotation angle (degrees) 0.89129988  
Shift along axis -0.30650139  
  

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> save "D:/Structure analysis/figure/NEO/Neo color.bmp" width 740 height 573
> supersample 3

> hide #!10 models

> show #!1 models

> show #!3 models

> ui tool show Matchmaker

> matchmaker #!3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
HKU31_job053_chainABC_nam_real_space_refined_001_real_space_refined_019_gly_real_space_refined_023_6_new_real_space_refined_014-2_LA.pdb,
chain B (#1) with HKU31_job135_gly_new_1.pdb, chain A (#3), sequence alignment
score = 5263.9  
RMSD between 752 pruned atom pairs is 1.221 angstroms; (across all 1110 pairs:
2.402)  
  

> hide #!1 models

> hide #!3 models

> show #!11 models

> show #!6 models

> ui tool show "Fit in Map"

Fit map hku31.mrc in map job055_postprocess.mrc using 71593 points  
correlation = 0.862, correlation about mean = 0.4783, overlap = 134.3  
steps = 140, shift = 0.29, angle = 0.398 degrees  
  
Position of hku31.mrc (#6) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99997603 -0.00691943 -0.00023209 1.13979403  
0.00691954 0.99997595 0.00047798 -1.19510723  
0.00022878 -0.00047958 0.99999986 -0.24872229  
Axis -0.06898981 -0.03320421 0.99706463  
Axis point 174.65227246 161.25772716 0.00000000  
Rotation angle (degrees) 0.39762783  
Shift along axis -0.28694378  
  

> hide #!11 models

> show #!3 models

> hide #!3 models

> save "D:/Structure analysis/figure/hku31/HKU31 WITHOUT color.bmp" width 731
> height 573 supersample 3

> save "D:/Structure analysis/figure/all side view color.cxs"

——— End of log from Tue Sep 13 12:17:42 2022 ———

opened ChimeraX session  

> show #!4 models

> hide #!6 models

> show #!11 models

> ui tool show "Fit in Map"

Fit map postprocess zflip.mrc in map job055_postprocess.mrc using 55012 points  
correlation = 0.8805, correlation about mean = 0.4737, overlap = 76.52  
steps = 68, shift = 1.18, angle = 2.23 degrees  
  
Position of postprocess zflip.mrc (#4) relative to job055_postprocess.mrc
(#11) coordinates:  
Matrix rotation and translation  
0.26726143 -0.18675949 -0.94535296 337.86567994  
-0.00067465 0.98100268 -0.19399301 -8.86033432  
0.96362382 0.05248463 0.26205819 -100.42092330  
Axis 0.12745786 -0.98716499 0.09622770  
Axis point 237.05471062 0.00000000 167.97386240  
Rotation angle (degrees) 75.21686577  
Shift along axis 42.14697401  
  
Fit map postprocess zflip.mrc in map job055_postprocess.mrc using 55012 points  
correlation = 0.8805, correlation about mean = 0.4737, overlap = 76.52  
steps = 24, shift = 0.0015, angle = 0.00202 degrees  
  
Position of postprocess zflip.mrc (#4) relative to job055_postprocess.mrc
(#11) coordinates:  
Matrix rotation and translation  
0.26724535 -0.18674223 -0.94536092 337.86737438  
-0.00065549 0.98100744 -0.19396898 -8.87040674  
0.96362830 0.05245698 0.26204727 -100.41227831  
Axis 0.12743075 -0.98716843 0.09622839  
Axis point 237.04842398 0.00000000 167.97604737  
Rotation angle (degrees) 75.21752462  
Shift along axis 42.14876670  
  
Fit map postprocess zflip.mrc in map job055_postprocess.mrc using 55012 points  
correlation = 0.8805, correlation about mean = 0.4738, overlap = 76.52  
steps = 24, shift = 0.00351, angle = 0.00122 degrees  
  
Position of postprocess zflip.mrc (#4) relative to job055_postprocess.mrc
(#11) coordinates:  
Matrix rotation and translation  
0.26723731 -0.18673203 -0.94536520 337.87085785  
-0.00064258 0.98101033 -0.19395443 -8.87841287  
0.96363053 0.05243934 0.26204257 -100.40736909  
Axis 0.12741393 -0.98717047 0.09622966  
Axis point 237.04622074 0.00000000 167.97900520  
Rotation angle (degrees) 75.21781633  
Shift along axis 42.15179519  
  

> hide #!11 models

> show #!2 models

> ui tool show "Fit in Map"

Fit molecule GD-
fit_chainABC_namdinator_real_space_refined_011_1_real_space_refined_018_gly_3_real_space_refined_034_1_new_LA.pdb
(#2) to map postprocess zflip.mrc (#4) using 24745 atoms  
average map value = 0.03801, steps = 56  
shifted from previous position = 1.21  
rotated from previous position = 2.22 degrees  
atoms outside contour = 7349, contour level = 0.024903  
  
Position of GD-
fit_chainABC_namdinator_real_space_refined_011_1_real_space_refined_018_gly_3_real_space_refined_034_1_new_LA.pdb
(#2) relative to postprocess zflip.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99998698 0.00498766 -0.00107440 -0.70916053  
-0.00498244 0.99997607 0.00479969 0.16735461  
0.00109832 -0.00479427 0.99998790 0.79225116  
Axis -0.68499014 -0.15512788 -0.71184538  
Axis point 29.59404760 156.56453756 0.00000000  
Rotation angle (degrees) 0.40124536  
Shift along axis -0.10415372  
  

> show #!11 models

> hide #!11 models

> hide #!4 models

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A

Alignment identifier is 2/A  

> select #2/A:751-752

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select #2/A:751-1140

2735 atoms, 2788 bonds, 4 pseudobonds, 354 residues, 2 models selected  

> color (#!2 & sel) red

> select #2/A:385

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #2/A:385-591

1586 atoms, 1628 bonds, 207 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel deep sky blue

> select #2/A:599

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #2/A:599-660

485 atoms, 497 bonds, 62 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel turquoise

> select #2/A:661

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #2/A:661-807

915 atoms, 930 bonds, 3 pseudobonds, 121 residues, 2 models selected  

> select #2/A:764

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select #2/A:661-764

665 atoms, 676 bonds, 2 pseudobonds, 90 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel chartreuse

> select #2/A:372

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #2/A:372-391

162 atoms, 165 bonds, 20 residues, 1 model selected  

> select #2/A:384

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #2/A:373-384

98 atoms, 100 bonds, 12 residues, 1 model selected  

> select #2/A:372

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #2/A:372-384

105 atoms, 107 bonds, 13 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel turquoise

> select #2/A:371

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #2/A:360-371

85 atoms, 86 bonds, 12 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel chartreuse

> ui tool show "Show Sequence Viewer"

> sequence chain #2/B

Alignment identifier is 2/B  

> select #2/B:884

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #2/B:884-900

128 atoms, 130 bonds, 17 residues, 1 model selected  

> color sel orange

> select #2/B:901-902

20 atoms, 20 bonds, 2 residues, 1 model selected  

> select #2/B:901-925

168 atoms, 171 bonds, 1 pseudobond, 21 residues, 2 models selected  

> color (#!2 & sel) yellow

> select clear

> show #!4 models

> hide #!2 models

> color #4 dark gray

> show #!2 models

> color zone #4 near #2 distance 7.92

> surface dust #4 size 13.2

> volume #4 level 0.02252

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> save "D:/Structure analysis/figure/GD/GD color.bmp" width 716 height 560
> supersample 3

> save "D:/Structure analysis/figure/all side view color.cxs"

> hide #!4 models

> show #!1 models

> show #!11 models

> hide #!1 models

> save "D:/Structure analysis/figure/hku31/HKU31 WITH color.bmp" width 716
> height 560 supersample 3

[Repeated 1 time(s)]

> hide #!11 models

> show #!6 models

> save "D:/Structure analysis/figure/hku31/HKU31 WITHOUT color.bmp" width 716
> height 560 supersample 3

> save "D:/Structure analysis/figure/all side view color.cxs"

——— End of log from Tue Sep 13 14:47:44 2022 ———

opened ChimeraX session  

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> select #1/A:581

7 atoms, 6 bonds, 1 residue, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A #1/B #1/C

Alignment identifier is 1  

> show #!11 models

> hide #!11 models

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> select #1/A:573

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:573

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:582

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:582-584

24 atoms, 23 bonds, 3 residues, 1 model selected  

> select #1/A:574

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:574-581

24 atoms, 22 bonds, 1 pseudobond, 3 residues, 2 models selected  

> select #1/A:582

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:582

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:573

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:573

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:574

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:574

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:581

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/A:581

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/A:574

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:574-581

24 atoms, 22 bonds, 1 pseudobond, 3 residues, 2 models selected  

> select #1/A:573

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:573

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:574-575

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #1/A:574-575

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #1/A:595

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:591-595

42 atoms, 42 bonds, 5 residues, 1 model selected  

> select #1/A:594

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #1/A:591-594

34 atoms, 34 bonds, 4 residues, 1 model selected  

> select #1/A:571

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/A:571-594

145 atoms, 145 bonds, 1 pseudobond, 19 residues, 2 models selected  

> select #1/A:575

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:575-584

40 atoms, 38 bonds, 1 pseudobond, 5 residues, 2 models selected  

> select #1/A:581

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/A:581-583

23 atoms, 22 bonds, 3 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel turquoise

> select #1/A:575

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:575

9 atoms, 8 bonds, 1 residue, 1 model selected  

> color sel dodger blue

> color sel deep sky blue

> select clear

> select #1/A:575

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:575-581

16 atoms, 14 bonds, 1 pseudobond, 2 residues, 2 models selected  

> select #1/A:575

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:575

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:581

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/A:581

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/A:582

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:582-583

16 atoms, 15 bonds, 2 residues, 1 model selected  

> view orient

> turn x 90

[Repeated 2 time(s)]

> ui tool show "Side View"

[Repeated 2 time(s)]

> turn y 45

> turn y -45

> turn y 30

> turn y -30

> turn y -20

[Repeated 16 time(s)]

> turn y 5

> ui tool show "Side View"

> view

> select clear

> show #!11 models

> color zone #11 near #1 distance 7.92

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!11 models

> show #!4 models

> show #!11 models

> hide #!2 models

> ui tool show "Fit in Map"

Fit map postprocess zflip.mrc in map job055_postprocess.mrc using 64270 points  
correlation = 0.8715, correlation about mean = 0.5063, overlap = 79.66  
steps = 28, shift = 0.0341, angle = 0.00963 degrees  
  
Position of postprocess zflip.mrc (#4) relative to job055_postprocess.mrc
(#11) coordinates:  
Matrix rotation and translation  
0.26723354 -0.18688638 -0.94533577 337.89219241  
-0.00054314 0.98098410 -0.19408735 -8.86413320  
0.96363164 0.05238010 0.26205035 -100.43019670  
Axis 0.12745165 -0.98715283 0.09636061  
Axis point 237.07578375 0.00000000 167.98316766  
Rotation angle (degrees) 75.21847468  
Shift along axis 42.13765722  
  
Fit map postprocess zflip.mrc in map job055_postprocess.mrc using 64270 points  
correlation = 0.8715, correlation about mean = 0.5063, overlap = 79.66  
steps = 24, shift = 0.00289, angle = 0.00109 degrees  
  
Position of postprocess zflip.mrc (#4) relative to job055_postprocess.mrc
(#11) coordinates:  
Matrix rotation and translation  
0.26724225 -0.18686999 -0.94533655 337.88777474  
-0.00055132 0.98098692 -0.19407306 -8.86648851  
0.96362922 0.05238570 0.26205812 -100.43523057  
Axis 0.12744749 -0.98715458 0.09634816  
Axis point 237.07706652 0.00000000 167.97957625  
Rotation angle (degrees) 75.21790293  
Shift along axis 42.13879302  
  
Fit map postprocess zflip.mrc in map job055_postprocess.mrc using 64270 points  
correlation = 0.8715, correlation about mean = 0.5062, overlap = 79.66  
steps = 24, shift = 0.00262, angle = 0.000203 degrees  
  
Position of postprocess zflip.mrc (#4) relative to job055_postprocess.mrc
(#11) coordinates:  
Matrix rotation and translation  
0.26724515 -0.18686808 -0.94533611 337.88592519  
-0.00055228 0.98098723 -0.19407150 -8.86679497  
0.96362842 0.05238675 0.26206088 -100.43836242  
Axis 0.12744733 -0.98715474 0.09634675  
Axis point 237.07834189 0.00000000 167.97746431  
Rotation angle (degrees) 75.21772630  
Shift along axis 42.13864815  
  
Fit map postprocess zflip.mrc in map job055_postprocess.mrc using 64270 points  
correlation = 0.8715, correlation about mean = 0.5064, overlap = 79.65  
steps = 28, shift = 0.0392, angle = 0.00176 degrees  
  
Position of postprocess zflip.mrc (#4) relative to job055_postprocess.mrc
(#11) coordinates:  
Matrix rotation and translation  
0.26725373 -0.18689573 -0.94532821 337.89263939  
-0.00053825 0.98098222 -0.19409686 -8.86200499  
0.96362604 0.05238193 0.26207056 -100.39993836  
Axis 0.12745819 -0.98715122 0.09636848  
Axis point 237.05810916 0.00000000 168.00314818  
Rotation angle (degrees) 75.21733334  
Shift along axis 42.13993254  
  

> hide #!4 models

> hide #!11 models

> show #!2 models

> show #!4 models

> hide #!4 models

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A

Alignment identifier is 2/A  

> select #2/A:596

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A:596

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A:596

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A:596-599

28 atoms, 27 bonds, 4 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel turquoise

> select clear

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!4 models

> color zone #4 near #2 distance 7.92

> hide #!2 models

> show #!11 models

> ui tool show "Fit in Map"

Fit map postprocess zflip.mrc in map job055_postprocess.mrc using 64270 points  
correlation = 0.8715, correlation about mean = 0.5063, overlap = 79.66  
steps = 28, shift = 0.0381, angle = 0.00171 degrees  
  
Position of postprocess zflip.mrc (#4) relative to job055_postprocess.mrc
(#11) coordinates:  
Matrix rotation and translation  
0.26724379 -0.18686966 -0.94533618 337.88711935  
-0.00055209 0.98098693 -0.19407301 -8.86659960  
0.96362879 0.05238672 0.26205950 -100.43709091  
Axis 0.12744804 -0.98715456 0.09634762  
Axis point 237.07805175 0.00000000 167.97853547  
Rotation angle (degrees) 75.21781633  
Shift along axis 42.13888051  
  
Fit map postprocess zflip.mrc in map job055_postprocess.mrc using 64270 points  
correlation = 0.8715, correlation about mean = 0.5064, overlap = 79.65  
steps = 28, shift = 0.037, angle = 0.00382 degrees  
  
Position of postprocess zflip.mrc (#4) relative to job055_postprocess.mrc
(#11) coordinates:  
Matrix rotation and translation  
0.26730324 -0.18688848 -0.94531565 337.86546425  
-0.00053498 0.98098333 -0.19409124 -8.86654761  
0.96361232 0.05238695 0.26212004 -100.41029427  
Axis 0.12745961 -0.98715111 0.09636773  
Axis point 237.05473203 0.00000000 167.99152407  
Rotation angle (degrees) 75.21436769  
Shift along axis 42.14051108  
  
Fit map postprocess zflip.mrc in map job055_postprocess.mrc using 64270 points  
correlation = 0.8715, correlation about mean = 0.5063, overlap = 79.66  
steps = 28, shift = 0.0314, angle = 0.00432 degrees  
  
Position of postprocess zflip.mrc (#4) relative to job055_postprocess.mrc
(#11) coordinates:  
Matrix rotation and translation  
0.26724777 -0.18684549 -0.94533983 337.88146421  
-0.00056047 0.98099139 -0.19405043 -8.87018149  
0.96362768 0.05238938 0.26206304 -100.43246278  
Axis 0.12743795 -0.98715749 0.09633095  
Axis point 237.07187029 0.00000000 167.97793576  
Rotation angle (degrees) 75.21746093  
Shift along axis 42.14043374  
  
Fit map postprocess zflip.mrc in map job055_postprocess.mrc using 64270 points  
correlation = 0.8715, correlation about mean = 0.5063, overlap = 79.66  
steps = 24, shift = 0.00447, angle = 0.00131 degrees  
  
Position of postprocess zflip.mrc (#4) relative to job055_postprocess.mrc
(#11) coordinates:  
Matrix rotation and translation  
0.26724296 -0.18686728 -0.94533688 337.88692237  
-0.00055078 0.98098750 -0.19407014 -8.86759424  
0.96362903 0.05238455 0.26205908 -100.43533920  
Axis 0.12744542 -0.98715496 0.09634706  
Axis point 237.07670069 0.00000000 167.97911753  
Rotation angle (degrees) 75.21783626  
Shift along axis 42.13918204  
  

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> hide #!11 models

> show #!3 models

> turn y 30

[Repeated 7 time(s)]

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!3 models

> show #!11 models

> hide #!11 models

> hide #!1 models

> show #!3 models

> show #!6 models

> hide #!6 models

> show #!6 models

> color zone #6 near #3 distance 7.92

> hide #!6 models

> ui tool show "Show Sequence Viewer"

> sequence chain #3/A

Alignment identifier is 3/A  

> select #3/A:575

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:575

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:576

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:576

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:575

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:575-576

18 atoms, 17 bonds, 2 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel deep sky blue

> select clear

> show #!6 models

> color zone #6 near #3 distance 7.92

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!6 models

> show #!6 models

> ui tool show "Color Zone"

> color zone #6 near #3 distance 1.32

> color zone #6 near #3 distance 3.04

> color zone #6 near #3 distance 4.72

> color zone #6 near #3 distance 10.57

> color zone #6 near #3 distance 12.11

> color zone #6 near #3 distance 23.27

> color zone #6 near #3 distance 7.92

[Repeated 5 time(s)]

> ui tool show "Color Zone"

> color zone #6 near #3 distance 1.32

> color zone #6 near #3 distance 1.33

> color zone #6 near #3 distance 9.08

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> save "D:/Structure analysis/figure/hku31/hku31_withoutla_sideview.bmp" width
> 641 height 566 supersample 3

> hide #!6 models

> show #!1 models

> turn y 30

[Repeated 15 time(s)]

> show #!11 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> color zone #11 near #1 distance 7.92

> hide #!1 models

> save "D:/Structure analysis/figure/hku31/hku31 with job055/HKU31 WITH
> color.bmp" width 661 height 566 supersample 3

> hide #!11 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!6 models

> show #!10 models

> ui tool show "Fit in Map"

Fit map hku31.mrc in map job055_postprocess.mrc using 71593 points  
correlation = 0.862, correlation about mean = 0.4783, overlap = 134.3  
steps = 84, shift = 0.00227, angle = 0.00305 degrees  
  
Position of hku31.mrc (#6) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99997587 -0.00694387 -0.00018655 1.13708489  
0.00694396 0.99997577 0.00049051 -1.20263583  
0.00018314 -0.00049179 0.99999986 -0.23822825  
Axis -0.07052974 -0.02654353 0.99715646  
Axis point 174.84346970 160.24321081 0.00000000  
Rotation angle (degrees) 0.39899455  
Shift along axis -0.28582694  
  
Fit map hku31.mrc in map job055_postprocess.mrc using 71593 points  
correlation = 0.862, correlation about mean = 0.4782, overlap = 134.2  
steps = 80, shift = 0.0119, angle = 0.00977 degrees  
  
Position of hku31.mrc (#6) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99997670 -0.00682442 -0.00018397 1.11702635  
0.00682449 0.99997664 0.00036876 -1.15646079  
0.00018145 -0.00037001 0.99999992 -0.26639565  
Axis -0.05402814 -0.02672410 0.99818174  
Axis point 171.16415598 160.75787673 0.00000000  
Rotation angle (degrees) 0.39172798  
Shift along axis -0.29535675  
  
Fit map hku31.mrc in map job055_postprocess.mrc using 71593 points  
correlation = 0.8621, correlation about mean = 0.4783, overlap = 134.3  
steps = 84, shift = 0.00847, angle = 0.00924 degrees  
  
Position of hku31.mrc (#6) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99997566 -0.00697363 -0.00022921 1.14759698  
0.00697373 0.99997560 0.00040999 -1.19230377  
0.00022635 -0.00041158 0.99999989 -0.26063913  
Axis -0.05877166 -0.03258874 0.99773938  
Axis point 172.88485194 161.52625176 0.00000000  
Rotation angle (degrees) 0.40047094  
Shift along axis -0.28864043  
  
Fit map hku31.mrc in map job055_postprocess.mrc using 71593 points  
correlation = 0.8621, correlation about mean = 0.478, overlap = 134.1  
steps = 64, shift = 0.0232, angle = 0.018 degrees  
  
Position of hku31.mrc (#6) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99997778 -0.00666347 -0.00019115 1.09474331  
0.00666356 0.99997770 0.00044496 -1.15027828  
0.00018818 -0.00044622 0.99999988 -0.27212511  
Axis -0.06669388 -0.02838848 0.99736955  
Axis point 174.48791461 160.58794710 0.00000000  
Rotation angle (degrees) 0.38280103  
Shift along axis -0.31176732  
  
Fit map hku31.mrc in map job055_postprocess.mrc using 71593 points  
correlation = 0.862, correlation about mean = 0.4783, overlap = 134.3  
steps = 84, shift = 0.0248, angle = 0.0182 degrees  
  
Position of hku31.mrc (#6) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99997563 -0.00697995 -0.00015956 1.13945234  
0.00698002 0.99997554 0.00045514 -1.20224057  
0.00015637 -0.00045625 0.99999988 -0.24073291  
Axis -0.06513069 -0.02257724 0.99762130  
Axis point 173.72985934 159.95961063 0.00000000  
Rotation angle (degrees) 0.40088074  
Shift along axis -0.28723032  
  
Fit map hku31.mrc in map job055_postprocess.mrc using 71593 points  
correlation = 0.8622, correlation about mean = 0.478, overlap = 134.1  
steps = 124, shift = 0.0263, angle = 0.0174 degrees  
  
Position of hku31.mrc (#6) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99997759 -0.00669169 -0.00017641 1.09515407  
0.00669175 0.99997755 0.00036021 -1.13970237  
0.00017400 -0.00036138 0.99999992 -0.28475061  
Axis -0.05382017 -0.02613520 0.99820857  
Axis point 172.07728439 160.56211726 0.00000000  
Rotation angle (degrees) 0.38409827  
Shift along axis -0.31339553  
  
Fit map hku31.mrc in map job055_postprocess.mrc using 71593 points  
correlation = 0.862, correlation about mean = 0.4783, overlap = 134.3  
steps = 48, shift = 0.0286, angle = 0.0173 degrees  
  
Position of hku31.mrc (#6) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99997575 -0.00696070 -0.00022868 1.14632161  
0.00696081 0.99997566 0.00048631 -1.20192022  
0.00022529 -0.00048789 0.99999986 -0.24421399  
Axis -0.06977037 -0.03251254 0.99703311  
Axis point 174.56182002 161.22605992 0.00000000  
Rotation angle (degrees) 0.40001186  
Shift along axis -0.28439123  
  
Fit map hku31.mrc in map job055_postprocess.mrc using 71593 points  
correlation = 0.862, correlation about mean = 0.4783, overlap = 134.3  
steps = 44, shift = 0.00572, angle = 0.00579 degrees  
  
Position of hku31.mrc (#6) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99997612 -0.00690824 -0.00018696 1.13087823  
0.00690831 0.99997605 0.00041069 -1.18379583  
0.00018412 -0.00041197 0.99999990 -0.25488803  
Axis -0.05941499 -0.02680058 0.99787353  
Axis point 173.03921210 160.60929358 0.00000000  
Rotation angle (degrees) 0.39666164  
Shift along axis -0.28981072  
  
Fit map hku31.mrc in map job055_postprocess.mrc using 71593 points  
correlation = 0.8619, correlation about mean = 0.4783, overlap = 134.4  
steps = 84, shift = 0.00705, angle = 0.00669 degrees  
  
Position of hku31.mrc (#6) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99997618 -0.00690165 -0.00010781 1.11649161  
0.00690170 0.99997606 0.00049624 -1.19651139  
0.00010438 -0.00049697 0.99999987 -0.22175321  
Axis -0.07175992 -0.01533099 0.99730410  
Axis point 174.54202119 158.22746815 0.00000000  
Rotation angle (degrees) 0.39650898  
Shift along axis -0.28293103  
  
Fit map hku31.mrc in map job055_postprocess.mrc using 71593 points  
correlation = 0.862, correlation about mean = 0.4783, overlap = 134.3  
steps = 120, shift = 0.0057, angle = 0.00452 degrees  
  
Position of hku31.mrc (#6) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99997584 -0.00694906 -0.00016295 1.13510052  
0.00694913 0.99997575 0.00046547 -1.19835796  
0.00015971 -0.00046659 0.99999988 -0.24061255  
Axis -0.06689499 -0.02315776 0.99749124  
Axis point 173.96587167 159.96696194 0.00000000  
Rotation angle (degrees) 0.39915833  
Shift along axis -0.28819016  
  
Fit map hku31.mrc in map job055_postprocess.mrc using 71593 points  
correlation = 0.8621, correlation about mean = 0.478, overlap = 134.1  
steps = 104, shift = 0.0245, angle = 0.0174 degrees  
  
Position of hku31.mrc (#6) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99997783 -0.00665462 -0.00021497 1.09463316  
0.00665471 0.99997777 0.00041291 -1.14192325  
0.00021222 -0.00041434 0.99999989 -0.28155894  
Axis -0.06200410 -0.03201920 0.99756216  
Axis point 173.63609224 161.00508767 0.00000000  
Rotation angle (degrees) 0.38221889  
Shift along axis -0.31218082  
  
Fit map hku31.mrc in map job055_postprocess.mrc using 71593 points  
correlation = 0.862, correlation about mean = 0.4783, overlap = 134.3  
steps = 100, shift = 0.0249, angle = 0.0177 degrees  
  
Position of hku31.mrc (#6) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99997575 -0.00696102 -0.00018894 1.14108520  
0.00696110 0.99997567 0.00044035 -1.19662581  
0.00018587 -0.00044165 0.99999989 -0.24826380  
Axis -0.06320317 -0.02685902 0.99763919  
Axis point 173.57334624 160.70867954 0.00000000  
Rotation angle (degrees) 0.39978632  
Shift along axis -0.28765770  
  
Fit map hku31.mrc in map job055_postprocess.mrc using 71593 points  
correlation = 0.8621, correlation about mean = 0.478, overlap = 134.1  
steps = 80, shift = 0.0227, angle = 0.0152 degrees  
  
Position of hku31.mrc (#6) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99997754 -0.00670074 -0.00016395 1.09484645  
0.00670080 0.99997747 0.00039494 -1.14728527  
0.00016130 -0.00039603 0.99999991 -0.27427360  
Axis -0.05890054 -0.02422002 0.99797000  
Axis point 172.87638247 160.08381736 0.00000000  
Rotation angle (degrees) 0.38470955  
Shift along axis -0.31041660  
  
Fit map hku31.mrc in map job055_postprocess.mrc using 71593 points  
correlation = 0.862, correlation about mean = 0.4783, overlap = 134.3  
steps = 48, shift = 0.0243, angle = 0.0149 degrees  
  
Position of hku31.mrc (#6) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99997578 -0.00695765 -0.00020125 1.14006425  
0.00695772 0.99997572 0.00038385 -1.18333800  
0.00019858 -0.00038524 0.99999991 -0.25782078  
Axis -0.05516268 -0.02867748 0.99806547  
Axis point 171.81719290 160.98983985 0.00000000  
Rotation angle (degrees) 0.39942185  
Shift along axis -0.28627586  
  

> hide #!6 models

> show #!6 models

> hide #!10 models

> show #!10 models

> hide #!6 models

> show #!6 models

> hide #!10 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!2 models

> show #!4 models

> hide #!2 models

> save "D:/Structure analysis/figure/GD/GD color.bmp" width 658 height 566
> supersample 3

> hide #!4 models

> show #!7 models

> show #!8 models

> show #!11 models

> hide #!11 models

> hide #!8 models

> ui tool show "Show Sequence Viewer"

> sequence chain #7/A

Alignment identifier is 7/A  

> select #7/A:572-573

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select #7/A:572-573

18 atoms, 17 bonds, 2 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel turquoise

> color sel deep sky blue

> select clear

> show #!8 models

> color zone #8 near #7 distance 7.92

> hide #!7 models

> show #!11 models

> ui tool show "Fit in Map"

Fit map postprocess.mrc in map job055_postprocess.mrc using 62033 points  
correlation = 0.9305, correlation about mean = 0.6227, overlap = 147.4  
steps = 36, shift = 0.0149, angle = 0.0139 degrees  
  
Position of postprocess.mrc (#8) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99926360 0.03837001 -0.00002297 -5.95743064  
-0.03837001 0.99926360 0.00001407 6.18780913  
0.00002349 -0.00001317 1.00000000 1.09344728  
Axis -0.00035498 -0.00060536 -0.99999975  
Axis point 158.21123326 158.30919640 0.00000000  
Rotation angle (degrees) 2.19898023  
Shift along axis -1.09507813  
  
Fit map postprocess.mrc in map job055_postprocess.mrc using 62033 points  
correlation = 0.9307, correlation about mean = 0.6223, overlap = 147  
steps = 36, shift = 0.0201, angle = 0.00775 degrees  
  
Position of postprocess.mrc (#8) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99926213 0.03840837 0.00000718 -5.97164822  
-0.03840837 0.99926212 -0.00011215 6.22198625  
-0.00001149 0.00011179 0.99999999 1.06087764  
Axis 0.00291514 0.00024304 -0.99999572  
Axis point 158.95835175 158.44985103 0.00000000  
Rotation angle (degrees) 2.20118830  
Shift along axis -1.07676906  
  
Fit map postprocess.mrc in map job055_postprocess.mrc using 62033 points  
correlation = 0.9306, correlation about mean = 0.6225, overlap = 147.2  
steps = 36, shift = 0.0148, angle = 0.00751 degrees  
  
Position of postprocess.mrc (#8) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99926318 0.03838105 -0.00003473 -5.96234496  
-0.03838105 0.99926318 0.00000901 6.18485202  
0.00003505 -0.00000767 1.00000000 1.07920383  
Axis -0.00021737 -0.00090916 -0.99999956  
Axis point 158.07706494 158.38690144 0.00000000  
Rotation angle (degrees) 2.19961339  
Shift along axis -1.08353034  
  
Fit map postprocess.mrc in map job055_postprocess.mrc using 62033 points  
correlation = 0.9305, correlation about mean = 0.6226, overlap = 147.4  
steps = 24, shift = 0.0113, angle = 0.00333 degrees  
  
Position of postprocess.mrc (#8) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99926341 0.03837501 0.00001203 -5.96727134  
-0.03837501 0.99926341 0.00004286 6.17846832  
-0.00001037 -0.00004329 1.00000000 1.10318261  
Axis -0.00112254 0.00029182 -0.99999933  
Axis point 157.96717485 158.56303660 0.00000000  
Rotation angle (degrees) 2.19926740  
Shift along axis -1.09468039  
  
Fit map postprocess.mrc in map job055_postprocess.mrc using 62033 points  
correlation = 0.9306, correlation about mean = 0.6225, overlap = 147.3  
steps = 40, shift = 0.0232, angle = 0.0108 degrees  
  
Position of postprocess.mrc (#8) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99926326 0.03837876 0.00000840 -5.96915315  
-0.03837875 0.99926325 -0.00014471 6.23236023  
-0.00001394 0.00014428 0.99999999 1.07157374  
Axis 0.00376499 0.00029105 -0.99999287  
Axis point 159.35679472 158.48468206 0.00000000  
Rotation angle (degrees) 2.19949650  
Shift along axis -1.09222600  
  

> show #!6 models

> hide #!6 models

> hide #!11 models

> ui tool show "Color Zone"

> color zone #8 near #1 distance 1.32

> color zone #8 near #7 distance 4.16

> color zone #8 near #7 distance 11.62

> color zone #8 near #7 distance 12.99

> color zone #8 near #7 distance 15.23

> color zone #8 near #7 distance 54.23

> color zone #8 near #7 distance 13.62

> color zone #8 near #7 distance 13.72

> save "D:/Structure analysis/figure/Eri/Eri color.bmp" width 661 height 566
> supersample 3

> hide #!8 models

> show #!1 models

> hide #!1 models

> show #!9 models

> show #!10 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!11 models

> ui tool show "Fit in Map"

Fit map postprocess.mrc in map job055_postprocess.mrc using 71607 points  
correlation = 0.8583, correlation about mean = 0.4809, overlap = 149.6  
steps = 44, shift = 0.00455, angle = 0.00639 degrees  
  
Position of postprocess.mrc (#10) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99987752 0.01565072 0.00003428 -2.47021758  
-0.01565071 0.99987750 -0.00022169 2.51901127  
-0.00003775 0.00022112 0.99999997 0.27288574  
Axis 0.01414513 0.00230111 -0.99989730  
Axis point 159.75320093 158.81139119 0.00000000  
Rotation angle (degrees) 0.89684861  
Shift along axis -0.30200276  
  
Fit map postprocess.mrc in map job055_postprocess.mrc using 71607 points  
correlation = 0.8587, correlation about mean = 0.4804, overlap = 149.2  
steps = 48, shift = 0.0387, angle = 0.0176 degrees  
  
Position of postprocess.mrc (#10) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99988017 0.01547959 -0.00015492 -2.41277483  
-0.01547959 0.99988018 -0.00004999 2.46312007  
0.00015412 0.00005238 0.99999999 0.30788947  
Axis 0.00330631 -0.00998158 -0.99994472  
Axis point 157.68557904 157.01611042 0.00000000  
Rotation angle (degrees) 0.88699964  
Shift along axis -0.34043566  
  
Fit map postprocess.mrc in map job055_postprocess.mrc using 71607 points  
correlation = 0.8587, correlation about mean = 0.4804, overlap = 149.1  
steps = 48, shift = 0.00305, angle = 0.0106 degrees  
  
Position of postprocess.mrc (#10) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99988040 0.01546533 -0.00007137 -2.42348520  
-0.01546534 0.99988038 -0.00021452 2.48821081  
0.00006805 0.00021560 0.99999997 0.29858033  
Axis 0.01390444 -0.00450702 -0.99989317  
Axis point 159.57015003 157.62960512 0.00000000  
Rotation angle (degrees) 0.88622857  
Shift along axis -0.34346005  
  
Fit map postprocess.mrc in map job055_postprocess.mrc using 71607 points  
correlation = 0.8583, correlation about mean = 0.4808, overlap = 149.6  
steps = 44, shift = 0.0341, angle = 0.00414 degrees  
  
Position of postprocess.mrc (#10) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99987937 0.01553185 -0.00009713 -2.42960174  
-0.01553187 0.99987935 -0.00020281 2.49703408  
0.00009397 0.00020430 0.99999997 0.26215197  
Axis 0.01310424 -0.00615133 -0.99989521  
Axis point 159.42319131 157.40423673 0.00000000  
Rotation angle (degrees) 0.89003933  
Shift along axis -0.30932267  
  
Fit map postprocess.mrc in map job055_postprocess.mrc using 71607 points  
correlation = 0.8586, correlation about mean = 0.4805, overlap = 149.2  
steps = 40, shift = 0.0272, angle = 0.00365 degrees  
  
Position of postprocess.mrc (#10) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99988027 0.01547343 -0.00012226 -2.41731797  
-0.01547346 0.99988026 -0.00020034 2.48563549  
0.00011914 0.00020221 0.99999997 0.28560718  
Axis 0.01300609 -0.00779947 -0.99988500  
Axis point 159.25280566 157.17324116 0.00000000  
Rotation angle (degrees) 0.88670052  
Shift along axis -0.33640084  
  
Fit map postprocess.mrc in map job055_postprocess.mrc using 71607 points  
correlation = 0.8587, correlation about mean = 0.4804, overlap = 149.1  
steps = 28, shift = 0.00743, angle = 0.0137 degrees  
  
Position of postprocess.mrc (#10) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99988126 0.01540948 -0.00014214 -2.40378149  
-0.01540947 0.99988127 0.00002993 2.43908121  
0.00014259 -0.00002774 0.99999999 0.32564325  
Axis -0.00187098 -0.00923836 -0.99995558  
Axis point 156.86688549 157.24422093 0.00000000  
Rotation angle (degrees) 0.88297211  
Shift along axis -0.34366447  
  
Fit map postprocess.mrc in map job055_postprocess.mrc using 71607 points  
correlation = 0.8584, correlation about mean = 0.4808, overlap = 149.5  
steps = 40, shift = 0.0279, angle = 0.0123 degrees  
  
Position of postprocess.mrc (#10) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99987973 0.01550879 -0.00009819 -2.42601048  
-0.01550881 0.99987972 -0.00015463 2.48516446  
0.00009578 0.00015614 0.99999998 0.27607183  
Axis 0.01001850 -0.00625342 -0.99993026  
Axis point 158.89357107 157.45623616 0.00000000  
Rotation angle (degrees) 0.88868648  
Shift along axis -0.31589834  
  
Fit map postprocess.mrc in map job055_postprocess.mrc using 71607 points  
correlation = 0.8586, correlation about mean = 0.4805, overlap = 149.2  
steps = 40, shift = 0.0168, angle = 0.0037 degrees  
  
Position of postprocess.mrc (#10) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99988020 0.01547837 -0.00009843 -2.42158416  
-0.01547839 0.99988018 -0.00021155 2.48917539  
0.00009514 0.00021305 0.99999997 0.28396838  
Axis 0.01371415 -0.00625215 -0.99988641  
Axis point 159.46336443 157.38896979 0.00000000  
Rotation angle (degrees) 0.88698228  
Shift along axis -0.33270880  
  

> hide #!10 models

> show #!10 models

> hide #!11 models

> show #!9 models

> hide #!9 models

> hide #!10 models

> show #!9 models

> show #!1 models

> hide #!1 models

> turn y 30

[Repeated 7 time(s)]

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> show #!6 models

> hide #!6 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!9 models

> ui tool show "Fit in Map"

Fit map postprocess.mrc in map job055_postprocess.mrc using 71607 points  
correlation = 0.8587, correlation about mean = 0.4804, overlap = 149.2  
steps = 28, shift = 0.00745, angle = 0.00929 degrees  
  
Position of postprocess.mrc (#10) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99988004 0.01548903 -0.00001611 -2.43696232  
-0.01548903 0.99988004 -0.00007227 2.46794087  
0.00001499 0.00007251 1.00000000 0.32634451  
Axis 0.00467356 -0.00100394 -0.99998857  
Axis point 158.08544132 158.45645840 0.00000000  
Rotation angle (degrees) 0.88750163  
Shift along axis -0.34020774  
  
Fit map postprocess.mrc in map job055_postprocess.mrc using 71607 points  
correlation = 0.8584, correlation about mean = 0.4808, overlap = 149.5  
steps = 40, shift = 0.0261, angle = 0.0082 degrees  
  
Position of postprocess.mrc (#10) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99987956 0.01551893 -0.00013892 -2.42094202  
-0.01551895 0.99987956 -0.00013936 2.48444917  
0.00013674 0.00014150 0.99999998 0.27009841  
Axis 0.00904796 -0.00888049 -0.99991963  
Axis point 158.69286855 157.04776417 0.00000000  
Rotation angle (degrees) 0.88927675  
Shift along axis -0.31404442  
  
Fit map postprocess.mrc in map job055_postprocess.mrc using 71607 points  
correlation = 0.8586, correlation about mean = 0.4805, overlap = 149.2  
steps = 40, shift = 0.0216, angle = 0.00438 degrees  
  
Position of postprocess.mrc (#10) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99988001 0.01549052 -0.00008713 -2.42502057  
-0.01549052 0.99988001 -0.00009088 2.47200410  
0.00008571 0.00009222 0.99999999 0.30761464  
Axis 0.00591008 -0.00557889 -0.99996697  
Axis point 158.23965304 157.64635244 0.00000000  
Rotation angle (degrees) 0.88760626  
Shift along axis -0.33572757  
  
Fit map postprocess.mrc in map job055_postprocess.mrc using 71607 points  
correlation = 0.8587, correlation about mean = 0.4805, overlap = 149.2  
steps = 48, shift = 0.00325, angle = 0.00739 degrees  
  
Position of postprocess.mrc (#10) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99988023 0.01547667 -0.00005262 -2.42887142  
-0.01547667 0.99988023 0.00003254 2.44929639  
0.00005312 -0.00003172 1.00000000 0.33559081  
Axis -0.00207595 -0.00341616 -0.99999201  
Axis point 156.95829987 158.19777179 0.00000000  
Rotation angle (degrees) 0.88679014  
Shift along axis -0.33891309  
  
Fit map postprocess.mrc in map job055_postprocess.mrc using 71607 points  
correlation = 0.8587, correlation about mean = 0.4804, overlap = 149.1  
steps = 48, shift = 0.00255, angle = 0.0132 degrees  
  
Position of postprocess.mrc (#10) relative to job055_postprocess.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.99988070 0.01544619 0.00005694 -2.44188217  
-0.01544618 0.99988069 -0.00016786 2.47700967  
-0.00005953 0.00016696 0.99999998 0.32451607  
Axis 0.01083734 0.00376975 -0.99993417  
Axis point 159.21851623 159.07972106 0.00000000  
Rotation angle (degrees) 0.88509442  
Shift along axis -0.34162050  
  

> hide #!11 models

> show #!9 models

> hide #!10 models

> ui tool show "Show Sequence Viewer"

> sequence chain #9/A

Alignment identifier is 9/A  

> select #9/A:585-586

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #9/A:585-586

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #9/A:587

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #9/A:585-587

28 atoms, 27 bonds, 3 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel deep sky blue

> select #9/A:588-589

15 atoms, 15 bonds, 2 residues, 1 model selected  

> select #9/A:588-594

56 atoms, 57 bonds, 7 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel turquoise

> show #!10 models

> color zone #10 near sel & #9 distance 7.92

[Repeated 1 time(s)]

> select clear

> color zone #10 near #9 distance 7.92

> hide #!9 models

> show #!9 models

> hide #!9 models

> save "D:/Structure analysis/figure/NEO/Neo color.bmp" width 656 height 566
> supersample 3

> show #!5 models

> hide #!10 models

> show #!12 models

> hide #!12 models

> turn y 30

[Repeated 3 time(s)]

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> ui tool show "Show Sequence Viewer"

> sequence chain #5/A

Alignment identifier is 5/A  

> select #5/A:582-583

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #5/A:582-583

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #5/A:584

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #5/A:584-585

12 atoms, 11 bonds, 2 residues, 1 model selected  

> select #5/A:583

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #5/A:583-584

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select #5/A:584-585

12 atoms, 11 bonds, 2 residues, 1 model selected  

> select #5/A:583-585

21 atoms, 20 bonds, 3 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #9/A

Alignment identifier is 9/A  

> select #9/A:586

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #9/A:586-587

19 atoms, 18 bonds, 2 residues, 1 model selected  

> select #9/A:585-586

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #9/A:585-587

28 atoms, 27 bonds, 3 residues, 1 model selected  

> select #5/A:583

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #5/A:583-585

21 atoms, 20 bonds, 3 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel deep sky blue

> select #5/A:586-587

18 atoms, 18 bonds, 2 residues, 1 model selected  

> select #5/A:586-587

18 atoms, 18 bonds, 2 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel turquoise

> select clear

> show #!12 models

> color zone #12 near #5 distance 7.92

> ui tool show "Color Zone"

> color zone #12 near #5 distance 1.32

> color zone #12 near #5 distance 5.34

> color zone #12 near #5 distance 5.51

> color zone #12 near #5 distance 5.96

> color zone #12 near #5 distance 5.26

> color zone #12 near #5 distance 6.76

> hide #!5 models

> save "D:/Structure analysis/figure/Japan/Japan color.bmp" width 656 height
> 566 supersample 3

> save "D:/Structure analysis/figure/all side view color.cxs"

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!1 models

> hide #!12 models

> show #!11 models

> color zone #11 near #1 distance 7.92

[Repeated 1 time(s)]

> ui tool show "Color Zone"

> color zone #11 near #1 distance 1.32

> color zone #11 near #1 distance 1.67

> color zone #11 near #1 distance 1.32

> color zone #11 near #1 distance 1.75

> color zone #11 near #1 distance 1.93

> color zone #11 near #1 distance 2.29

> color zone #11 near #1 distance 2.41

> color zone #11 near #1 distance 3.02

> color zone #11 near #1 distance 3.4

> color zone #11 near #1 distance 4.65

> color zone #11 near #1 distance 6.38

> color zone #11 near #1 distance 6.34

> color zone #11 near #1 distance 5.82

> color zone #11 near #1 distance 5.24

> color zone #11 near #1 distance 4.78

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> ui tool show "Color Zone"

> color zone #11 near #1 distance 1.32

> color zone #11 near #1 distance 7.54

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> color zone #11 near #1 distance 7.92

[Repeated 7 time(s)]

> ui tool show "Color Zone"

> color zone #11 near #1 distance 1.32

> color zone #11 near #1 distance 1.33

> color single #11

> color zone #11 near #1 distance 7.92

> hide #!11 models

> show #!11 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!2 models

> hide #!11 models

> show #!4 models

> ui tool show "Color Zone"

> color zone #4 near #2 distance 1.32

> color zone #4 near #2 distance 25.19

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!2 models

> save "D:/Structure analysis/figure/GD/GD color.bmp" width 687 height 566
> supersample 3

> save "D:/Structure analysis/figure/all side view color.cxs"

——— End of log from Fri Sep 23 17:05:41 2022 ———

opened ChimeraX session  




OpenGL version: 3.3.0 NVIDIA 516.54
OpenGL renderer: NVIDIA GeForce RTX 3050 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: LENOVO
Model: 82L5
OS: Microsoft Windows 11 家庭中文版 (Build 22000)
Memory: 14,877,257,728
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 5800H with Radeon Graphics         
OSLanguage: zh-CN
Locale: ('zh_CN', 'cp936')
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 Eric Pettersen, 3 years ago

Cc:	Tom Goddard added
Component:	Unassigned → Platform
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Crash using File→Open on Windows and/or in return statement

comment:2 by Eric Pettersen, 3 years ago

Resolution:	→ can't reproduce
Status:	accepted → closed

1.3

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