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#7990 closed defect (can't reproduce)

Crash using File→Open dialog on Windows and/or returning from function

Reported by:	chimerax-bug-report@…	Owned by:	pett
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-10-10.0.19044
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x8001010d

Thread 0x00000bac (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Current thread 0x00002b18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00002b18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chWindows fatal exception: code 0xi8001010em

erWindows fatal exception: acode 0xx8001010e\

oWindows fatal exception: pcode 0xe8001010en

_Windows fatal exception: ccode 0xo8001010em

mWindows fatal exception: acode 0xn8001010ed

\Windows fatal exception: dcode 0xi8001010ea

lWindows fatal exception: ocode 0xg8001010e.

py", line 135 in show_open_fileWindows fatal exception: _code 0xd8001010ei

aWindows fatal exception: lcode 0xo8001010eg


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

Thread 0x00002b18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_comWindows fatal exception: code 0xm8001010ea

nWindows fatal exception: dcode 0x\8001010ed

iWindows fatal exception: acode 0xl8001010eo

gWindows fatal exception: .code 0xp8001010ey

"Windows fatal exception: , line code 0x1358001010e in 

sWindows fatal exception: hcode 0xo8001010ew

_Windows fatal exception: ocode 0xp8001010ee

n_file_Windows fatal exception: dcode 0xi8001010ea

lWindows fatal exception: ocode 0xg8001010e


  File "C:\Program Files\ChimeraX 1.3\bWindows fatal exception: icode 0xn8001010e\

lWindows fatal exception: icode 0xb8001010e\

sWindows fatal exception: icode 0xt8001010ee

-Windows fatal exception: pcode 0xa8001010ec

kWindows fatal exception: acode 0xg8001010ee

sWindows fatal exception: \code 0xc8001010eh

iWindows fatal exception: mcode 0xe8001010er

axWindows fatal exception: Windows fatal exception: \code 0xo8001010ep

eWindows fatal exception: ncode 0x_8001010ec

ocode 0x8001010eWindows fatal exception: 

code 0xmWindows fatal exception: mcode 0x8001010ea

n8001010eWindows fatal exception: 

code 0xd8001010e\

dWindows fatal exception: icode 0xa8001010el

oWindows fatal exception: gcode 0x.8001010ep

yWindows fatal exception: "code 0x, line 8001010e107

 in 
Windows fatal exception:   File code 0x"Windows fatal exception: Ccode 0x:8001010e\

PWindows fatal exception: rcode 0xo8001010eg

ram8001010e

 FWindows fatal exception: icode 0xl8001010ee

sWindows fatal exception: \code 0xC8001010eh

iWindows fatal exception: mcode 0xeWindows fatal exception: r8001010ea

XWindows fatal exception:  code 0xcode 0x18001010e.

8001010e3

\Windows fatal exception: Windows fatal exception: code 0xcode 0xb8001010e8001010ei

nWindows fatal exception: 

\code 0xl8001010eWindows fatal exception: code 0xi8001010eb



\Windows fatal exception: sWindows fatal exception: icode 0xcode 0x8001010e8001010et

eWindows fatal exception: -code 0x

pWindows fatal exception: a8001010ecode 0xc

k8001010e

aWindows fatal exception: gcode 0xe8001010es

\Windows fatal exception: ccode 0xh8001010ei

merWindows fatal exception: acode 0xx8001010e\

uWindows fatal exception: iWindows fatal exception: \code 0xcode 0x8001010e8001010e



Windows fatal exception: code 0x8001010e

Windows fatal exception: gucode 0xi8001010e.

pWindows fatal exception: ycode 0x"8001010e, line 

301Windows fatal exception:  in code 0xe8001010ev

eWindows fatal exception: ncode 0xt8001010e_

lWindows fatal exception: ocode 0xo8001010ep


  File "CWindows fatal exception: :code 0x\8001010eP

rWindows fatal exception: ocode 0xg8001010er

am Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00002b18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00002b18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00002b18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00002b18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00002b18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00002b18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00002b18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00002b18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bWindows fatal exception: icode 0xn8001010e\

liWindows fatal exception: bcode 0x\8001010es

iWindows fatal exception: tcode 0xe8001010e-

pWindows fatal exception: acode 0xc8001010ek

aWindows fatal exception: gcode 0xe8001010es

\Windows fatal exception: ccode 0xh8001010ei

mWindows fatal exception: ecode 0xr8001010ea

x\ui\gui.py", line 301 in evenWindows fatal exception: tcode 0x8001010e_

lWindows fatal exception: ocode 0xo8001010ep


  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00002b18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packageWindows fatal exception: code 0xs\8001010ec

hWindows fatal exception: icode 0xm8001010ee

rWindows fatal exception: acode 0xx8001010e\

oWindows fatal exception: pcode 0xe8001010en

_Windows fatal exception: ccode 0xo8001010em

mWindows fatal exception: acode 0xn8001010ed

\Windows fatal exception: dcode 0xi8001010ea

log.pyWindows fatal exception: "code 0x, line 8001010e135

 in Windows fatal exception: scode 0xh8001010eo

w_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lWindows fatal exception: code 0xi8001010eb

\Windows fatal exception: scode 0xi8001010et

eWindows fatal exception: -code 0xp8001010ea

cWindows fatal exception: kcode 0xa8001010eg

eWindows fatal exception: scode 0x\8001010ec

hWindows fatal exception: imcode 0x8001010eer

axWindows fatal exception: \code 0xu8001010ei

\gui.Windows fatal exception: code 0xp8001010ey

", line Windows fatal exception: 301code 0x in 8001010ee

vent_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00002b18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_Windows fatal exception: code 0xd8001010ei

alWindows fatal exception: ocode 0xg8001010e


  File Windows fatal exception: "code 0xC8001010e:

\Windows fatal exception: Pcode 0xr8001010eo

gWindows fatal exception: rcode 0xa8001010em

 Windows fatal exception: Fcode 0xi8001010el

eWindows fatal exception: scode 0x\8001010eC

himeraXWindows fatal exception:  code 0x18001010e.

3Windows fatal exception: \code 0xb8001010ei

n\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\binWindows fatal exception: code 0x\8001010el

ibWindows fatal exception: \code 0xr8001010eu

nWindows fatal exception: pcode 0xy8001010e.

pWindows fatal exception: ycode 0x"8001010e, line 

87Windows fatal exception:  in code 0x_8001010er

uWindows fatal exception: ncode 0x_8001010ec

oWindows fatal exception: dcode 0xe8001010e


  File "C:Windows fatal exception: \code 0xP8001010ero

gWindows fatal exception: rcode 0xa8001010em

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

Thread 0x00002b18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "Windows fatal exception: code 0xC8001010e:

\Windows fatal exception: Pcode 0xr8001010eo

gWindows fatal exception: rcode 0xa8001010em

 Windows fatal exception: Fcode 0xi8001010el

eWindows fatal exception: scode 0x\8001010eC

hWindows fatal exception: icode 0xm8001010ee

rWindows fatal exception: acode 0xX8001010e 

1.3\bWindows fatal exception: icode 0x8001010en

\Windows fatal exception: lcode 0xi8001010eb

\site-packages\ChimeraX_main.py", line 1018 in Windows fatal exception: code 0xcode 0x
8001010e  File 

"Windows fatal exception: Ccode 0x:8001010e\

PWindows fatal exception: rcode 0xo8001010eg

rWindows fatal exception: acode 0xm8001010e

 Windows fatal exception: Fcode 0xi8001010el

es\ChimeraX 1.3\bWindows fatal exception: icode 0xn8001010e\

lWindows fatal exception: icode 0xb8001010e\

runpy.py"Windows fatal exception: code 0x, line 8001010e87

 in Windows fatal exception: _code 0xr8001010eu

nWindows fatal exception: _code 0xc8001010eo

dWindows fatal exception: ecode 0x
8001010e  File 

"Windows fatal exception: Ccode 0x:8001010e\

PWindows fatal exception: rcode 0xo8001010eg

rWindows fatal exception: acode 0xm8001010e 

FileWindows fatal exception: scode 0x\8001010eC

hWindows fatal exception: icode 0xm8001010ee

raX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00002b18 (most recent call first):
  File "C:\Program Files\ChimeraXWindows fatal exception:  code 0x18001010e.

3Windows fatal exception: \code 0xb8001010ei

nWindows fatal exception: \code 0xl8001010ei

bWindows fatal exception: \code 0xs8001010ei

tWindows fatal exception: ecode 0x-8001010ep

aWindows fatal exception: ccode 0xk8001010ea

gWindows fatal exception: ecode 0xs8001010e\

chiWindows fatal exception: mcode 0xe8001010er

aWindows fatal exception: xcode 0x\8001010eo

pen_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\Windows fatal exception: scode 0xi8001010et

eWindows fatal exception: -code 0xp8001010ea

cWindows fatal exception: kcode 0xa8001010eg

eWindows fatal exception: scode 0x\8001010ec

hWindows fatal exception: icode 0xm8001010ee

rWindows fatal exception: acode 0xx8001010e\

oWindows fatal exception: pcode 0xe8001010en

_cWindows fatal exception: ocode 0xm8001010em

aWindows fatal exception: ncode 0xd8001010e\

dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gWindows fatal exception: ucode 0xi8001010e.

pWindows fatal exception: ycode 0x"8001010e, line 

301Windows fatal exception:  in code 0xe8001010ev

eWindows fatal exception: ncode 0xt8001010e_

lWindows fatal exception: ocode 0xo8001010ep


Windows fatal exception:   File code 0x"8001010eC

:Windows fatal exception: \code 0xP8001010er

ogrWindows fatal exception: acode 0xm8001010e 

FWindows fatal exception: icode 0xl8001010ee

s\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.Windows fatal exception: 3code 0x\8001010eb

iWindows fatal exception: ncode 0x\8001010el

iWindows fatal exception: bcode 0x\8001010es

iWindows fatal exception: tcode 0xe8001010e-

pWindows fatal exception: acode 0xc8001010ek

aWindows fatal exception: gcode 0xe8001010es

\Windows fatal exception: Ccode 0xh8001010ei

merWindows fatal exception: acode 0xX8001010e_

mWindows fatal exception: acode 0xi8001010en

.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00002b18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00002b18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.pWindows fatal exception: ycode 0x"8001010e, line 

867Windows fatal exception:  in code 0xi8001010en

iWindows fatal exception: tcode 0x
8001010e  File 

"Windows fatal exception: Ccode 0x:8001010e\

PWindows fatal exception: rcode 0xo8001010eg

rWindows fatal exception: acode 0xm8001010e 

FWindows fatal exception: code 0xWindows fatal exception: 8001010ecode 0xiles\Chimera

8001010eWindows fatal exception: 

code 0x8001010e

Windows fatal exception: code 0xXWindows fatal exception:  8001010e1

code 0x.8001010e3

\bWindows fatal exception: Windows fatal exception: code 0xi8001010en

\lib\sicode 0x8001010et

e-Windows fatal exception: Windows fatal exception: code 0xp8001010ea

cWindows fatal exception: kcode 0xa8001010ecode 0x8001010eg



Windows fatal exception: eWindows fatal exception: scode 0x\8001010eC

hWindows fatal exception: icode 0xcode 0x8001010e8001010e



mWindows fatal exception: eWindows fatal exception: code 0xr8001010ea

XWindows fatal exception: code 0x_code 0xm8001010ea

iWindows fatal exception: ncode 0x.8001010e8001010e

Windows fatal exception: 

code 0xpWindows fatal exception: ycode 0x"Windows fatal exception: , line code 0x8001010e8001010e



1018 in Windows fatal exception: Windows fatal exception: 
8001010e  File 

"code 0xC8001010eWindows fatal exception: code 0x:8001010e

\Windows fatal exception: Pcode 0xr8001010eo

g

rWindows fatal exception: acode 0xWindows fatal exception: 8001010eWindows fatal exception: code 0xcode 0x8001010em8001010e

 Windows fatal exception: Fcode 0x

iWindows fatal exception: 

code 0xWindows fatal exception: 8001010ecode 0x

8001010eWindows fatal exception: 8001010e

lWindows fatal exception: e

sWindows fatal exception: code 0xcode 0x8001010e8001010e\

code 0x8001010eWindows fatal exception: Ccode 0x

h8001010e

Windows fatal exception: Windows fatal exception: icode 0xcode 0x8001010e8001010e



Windows fatal exception: Windows fatal exception: code 0x

code 0xWindows fatal exception: 8001010ecode 0xWindows fatal exception: 

code 0x8001010eWindows fatal exception: 8001010e



mWindows fatal exception: ecode 0xr8001010ea

X8001010eWindows fatal exception:  code 0xcode 0x

8001010e1Windows fatal exception: 

code 0x8001010e.Windows fatal exception: 8001010ecode 0x

3Windows fatal exception: \code 0xb8001010ei

n8001010e\



lWindows fatal exception: iWindows fatal exception: code 0xWindows fatal exception: 8001010ecode 0x

b8001010eWindows fatal exception: \code 0xcode 0xr8001010eu

nWindows fatal exception: Windows fatal exception: code 0x8001010e8001010e

pWindows fatal exception: ycode 0x.code 0xp8001010e





Windows fatal exception: ycode 0x"8001010eWindows fatal exception: , line 8001010ecode 0x



8001010eWindows fatal exception: 

code 0xWindows fatal exception: 8001010ecode 0x878001010e

 in 

_Windows fatal exception: Windows fatal exception: rcode 0xucode 0xn8001010e8001010e



_Windows fatal exception: Windows fatal exception: code 0xcode 0xcWindows fatal exception: o8001010ed

8001010ee


Windows fatal exception: code 0xcode 0x8001010e  File 

"Windows fatal exception: C8001010e:

code 0xWindows fatal exception: 8001010ecode 0x

8001010e\

Windows fatal exception: Windows fatal exception: code 0xcode 0xWindows fatal exception: 8001010ecode 0x

8001010e8001010e



Windows fatal exception: Windows fatal exception: PWindows fatal exception: rcode 0xo8001010ecode 0x

8001010eWindows fatal exception: 

code 0xcode 0x8001010eWindows fatal exception: 

8001010ecode 0xWindows fatal exception: 

code 0xg8001010e8001010e

Windows fatal exception: 

rcode 0xWindows fatal exception: Windows fatal exception: 8001010ea

mcode 0xWindows fatal exception: code 0x8001010e8001010e

code 0x

 Windows fatal exception: Fcode 0xi8001010el

e8001010eWindows fatal exception: sWindows fatal exception: \

code 0xcode 0x8001010eWindows fatal exception: 

code 0xWindows fatal exception: 8001010e8001010e



Windows fatal exception: Windows fatal exception: code 0xcode 0xcode 0x8001010e8001010eC

hWindows fatal exception: Windows fatal exception: code 0xcode 0x

8001010eWindows fatal exception: icode 0xm8001010ee8001010e

r

aWindows fatal exception: X

 18001010e.

code 0xWindows fatal exception: 8001010ecode 0x38001010e\



Windows fatal exception: Windows fatal exception: code 0xcode 0x8001010eb8001010ei

n

Windows fatal exception: Windows fatal exception: code 0xcode 0x8001010e\

lWindows fatal exception: icode 0xb8001010e\

8001010eWindows fatal exception: 

rWindows fatal exception: ucode 0xcode 0xn8001010ep

8001010eWindows fatal exception: 

yWindows fatal exception: .code 0xcode 0x8001010e8001010ep

yWindows fatal exception: 

code 0xWindows fatal exception: "code 0x, line 8001010e197

8001010eWindows fatal exception: 

code 0x in 8001010e_

rWindows fatal exception: Windows fatal exception: Windows fatal exception: code 0xu8001010encode 0x_8001010em

oWindows fatal exception: d

uWindows fatal exception: lcode 0xe8001010ecode 0x

8001010eWindows fatal exception: 

code 0xcode 0xWindows fatal exception: 8001010ecode 0x8001010e8001010e





Windows fatal exception: Windows fatal exception: _code 0xa8001010es

_mcode 0xa8001010eiWindows fatal exception: n


Windows fatal exception: code 0xcode 0x8001010eWindows fatal exception: 

code 0xThread 0x8001010e00002b18

 (most recent call first):
8001010eWindows fatal exception: 

code 0xWindows fatal exception:   File code 0x"8001010eC8001010e:



Windows fatal exception: code 0x\8001010eP

rogWindows fatal exception: rcode 0xa8001010em

 Windows fatal exception: Fcode 0xi8001010el

es\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00002b18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00002b18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00002b18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00002b18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00002b18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00002b18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00002b18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00002b18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00002b18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00002b18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00002b18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialoWindows fatal exception: code 0xg8001010e.

pyWindows fatal exception: "code 0x, line 8001010e107

 in Windows fatal exception: Windows fatal exception: 
code 0x  File 8001010e"

CWindows fatal exception: :code 0x\8001010eP

rWindows fatal exception: ocode 0xg8001010er

am FilesWindows fatal exception: \code 0xC8001010eh

iWindows fatal exception: mcode 0xe8001010er

aX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Windows fatal exception: code 0xF8001010ei

lWindows fatal exception: ecode 0xs8001010e\

CWindows fatal exception: hcode 0xi8001010em

eWindows fatal exception: rcode 0xa8001010eX

 Windows fatal exception: 1code 0x.8001010e3

\Windows fatal exception: bcode 0xi8001010en

\Windows fatal exception: lcode 0xi8001010eb

\siteWindows fatal exception: -code 0xp8001010ea

cWindows fatal exception: kcode 0xa8001010eg

es\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "CWindows fatal exception: :code 0x\8001010eP

rWindows fatal exception: ocode 0xg8001010er

aWindows fatal exception: mcode 0x 8001010eF

iWindows fatal exception: lcode 0xe8001010es

\Windows fatal exception: Ccode 0xh8001010ei

mWindows fatal exception: ecode 0xr8001010ea

XWindows fatal exception:  code 0x18001010e.

3\bWindows fatal exception: icode 0xn8001010e\

lWindows fatal exception: code 0xi8001010eb

\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00002b18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Windows fatal exception: Pcode 0xr8001010eo

gWindows fatal exception: rcode 0xa8001010em

 Windows fatal exception: Fcode 0xi8001010el

eWindows fatal exception: scode 0x\8001010eC

hWindows fatal exception: imcode 0xe8001010er

aWindows fatal exception: Xcode 0x 8001010e1

.Windows fatal exception: 3code 0x\8001010eb

in\lWindows fatal exception: icode 0xb8001010e\

sWindows fatal exception: icode 0xt8001010ee

-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_Windows fatal exception: code 0xm8001010eo

duWindows fatal exception: lcode 0xe8001010e_

aWindows fatal exception: scode 0x_8001010em

aWindows fatal exception: icode 0xn8001010e


Thread 0xWindows fatal exception: 00002b18code 0x (most recent call first):
8001010e  File 

"Windows fatal exception: Ccode 0x:8001010e\

PWindows fatal exception: rcode 0xo8001010eg

rWindows fatal exception: acode 0xm8001010e 

FWindows fatal exception: icode 0xl8001010ee

s\ChimeraWindows fatal exception: Xcode 0x 8001010e1

.Windows fatal exception: 3code 0x\8001010eb

in\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00002b18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00002b18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\drawing.py", line 365 in get_display
Windows fatal exception: access violation

===== Log before crash start =====
> cartoon #1#!2

> select /A:385

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

> show sel target ab

> select /A:385@HB2

1 atom, 1 residue, 1 model selected  

> select add /A:385@HB3

2 atoms, 1 residue, 1 model selected  

> hide sel target a

> select /A:441

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select /A:385@CB

1 atom, 1 residue, 1 model selected  

> select /A:385@CB

1 atom, 1 residue, 1 model selected  

> select clear

> select add /A:385@CB

1 atom, 1 residue, 1 model selected  

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> show sel target ab

> cartoon hide sel

> select /A:385@H

1 atom, 1 residue, 1 model selected  

> select add /A:385@HA

2 atoms, 1 residue, 1 model selected  

> hide sel target a


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "C:\\\Users\\\Dell-
> LeeLab\\\Desktop\\\Working_folder_2021dec\\\Konkuk_Uni files\\\Weekly report
> sampathkumar\\\11_Progress_report_Nov_2022_P450\\\P450TT_6LAA\\\OLD_images\\\02_system2_pathway2_version3.cxs"

Log from Thu Nov 10 11:33:54 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "C:\\\Users\\\Dell-
> LeeLab\\\Desktop\\\Working_folder_2021dec\\\Konkuk_Uni files\\\Weekly report
> sampathkumar\\\11_Progress_report_Nov_2022_P450\\\P450TT_6LAA\\\OLD_images\\\02_system2_pathway2_version2.cxs"

Log from Wed Nov 2 19:25:51 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "C:\\\Users\\\Dell-
> LeeLab\\\Desktop\\\Working_folder_2021dec\\\Konkuk_Uni files\\\Weekly report
> sampathkumar\\\11_Progress_report_Nov_2022_P450\\\02_system2_pathway2_version1.cxs"

Log from Wed Nov 2 16:26:42 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\\\Users\\\Dell-
> LeeLab\\\Desktop\\\Working_folder_2021dec\\\Konkuk_Uni files\\\Weekly report
> sampathkumar\\\03_pathways_6LAA\\\03_Pathways_images_for_31meeting_6LAA\\\System_I_6LAA\\\Crystal_structure_6laa.pdb"

Crystal_structure_6laa.pdb title:  
Crystal structure of full-length CYP116B46 from tepidiphilus thermophilus
[more info...]  
  
Chain information for Crystal_structure_6laa.pdb #1  
---  
Chain | Description  
A | CYP116B46  
  
Non-standard residues in Crystal_structure_6laa.pdb #1  
---  
CO3 — carbonate ion  
EDO — 1,2-ethanediol (ethylene glycol)  
FES — FE2/S2 (inorganic) cluster  
FMN — flavin mononucleotide (riboflavin monophosphate)  
HEM — protoporphyrin IX containing Fe (HEME)  
IMD — imidazole  
  

> select /A:801@FE1

1 atom, 1 residue, 1 model selected  

> select /A:801@FE2

1 atom, 1 residue, 1 model selected  

> select add /A:801@FE1

2 atoms, 1 residue, 1 model selected  

> style sel ball

Changed 2 atom styles  

> select ::name="CO3"

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

> hide sel target a

> select ::name="CO3"

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

> hide sel target a

> select /A:107

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

> select up

94 atoms, 94 bonds, 11 residues, 1 model selected  

> select up

6796 atoms, 6388 bonds, 1314 residues, 1 model selected  

> select protein

6108 atoms, 6252 bonds, 753 residues, 1 model selected  

> select up

6110 atoms, 6253 bonds, 754 residues, 1 model selected  

> select up

6112 atoms, 6256 bonds, 754 residues, 1 model selected  

> select up

6114 atoms, 6257 bonds, 755 residues, 1 model selected  

> select up

6155 atoms, 6302 bonds, 755 residues, 1 model selected  

> select ~sel

641 atoms, 86 bonds, 1 pseudobond, 559 residues, 2 models selected  

> hide (#!1 & sel) target a

> select ::name="FMN"

31 atoms, 33 bonds, 1 residue, 1 model selected  

> show sel target ab

> select clear

> select protein

6108 atoms, 6252 bonds, 753 residues, 1 model selected  

> hide sel target a

> select clear

> set bgColor white

Alignment identifier is 1/A  

> select
> /A:27-35,39-57,72-82,99-109,123-160,167-171,173-185,190-207,210-237,243-255,260-303,306-319,349-353,371-375,387-406,435-450,460-464,539-548,580-595,606-610,612-621,630-632,636-643,655-667,687-691,712-720,753-760

2960 atoms, 2992 bonds, 361 residues, 1 model selected  

> select /A:27

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

> select /A:27-462

3575 atoms, 3672 bonds, 436 residues, 1 model selected  

> select /A:463

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

> select /A:237-463

1837 atoms, 1884 bonds, 227 residues, 1 model selected  

> select /A:27

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

> select /A:27-463

3583 atoms, 3680 bonds, 437 residues, 1 model selected  

> color sel forest green

> color #1 #1f8b1d transparency 0

> color #1 #35f032 transparency 0

> color #1 #36f533 transparency 0

> color #1 #36f333 transparency 0

> undo

[Repeated 6 time(s)]

> hide #!1 models

> show #!1 models

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

43 atoms, 46 bonds, 1 residue, 1 model selected  

> select /A:693

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

> select /A:464-693

1850 atoms, 1892 bonds, 230 residues, 1 model selected  

> color sel magenta

> select clear

> select /A:693

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

> select /A:693-727

275 atoms, 278 bonds, 35 residues, 1 model selected  

> select /A:692

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

> select /A:692-779

693 atoms, 697 bonds, 88 residues, 1 model selected  

> color sel cyan

> select
> /A:27-35,39-57,72-82,99-109,123-160,167-171,173-185,190-207,210-237,243-255,260-303,306-319,349-353,371-375,387-406,435-450,460-464,539-548,580-595,606-610,612-621,630-632,636-643,655-667,687-691,712-720,753-760

2960 atoms, 2992 bonds, 361 residues, 1 model selected  

> select /A:689

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

> select /A:689-691

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

> select clear

[Repeated 1 time(s)]

> select /A:681

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

> select add /A:682

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

> select add /A:683

20 atoms, 18 bonds, 3 residues, 1 model selected  

> select add /A:684

26 atoms, 23 bonds, 4 residues, 1 model selected  

> select add /A:685

36 atoms, 33 bonds, 5 residues, 1 model selected  

> select add /A:686

44 atoms, 40 bonds, 6 residues, 1 model selected  

> select add /A:687

52 atoms, 47 bonds, 7 residues, 1 model selected  

> select add /A:688

59 atoms, 54 bonds, 8 residues, 1 model selected  

> select add /A:690

68 atoms, 62 bonds, 9 residues, 1 model selected  

> select add /A:689

73 atoms, 66 bonds, 10 residues, 1 model selected  

> select add /A:691

82 atoms, 74 bonds, 11 residues, 1 model selected  

> select add /A:692

93 atoms, 84 bonds, 12 residues, 1 model selected  

> color sel gray

> select clear

> select /A:451

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

> select up

71 atoms, 73 bonds, 9 residues, 1 model selected  

> color sel gray

> select clear

> select /A:464

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

> color sel lime

> select clear

[Repeated 1 time(s)]

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select /A:801@S1

1 atom, 1 residue, 1 model selected  

> select up

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

> color sel byhetero

> select /A:514

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

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> color sel blue

> select /A:802@C7M

1 atom, 1 residue, 1 model selected  

> select up

31 atoms, 33 bonds, 1 residue, 1 model selected  

> select up

6796 atoms, 6388 bonds, 1314 residues, 1 model selected  

> select clear

> select /A:514

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

> select clear

> select /A:802@C8M

1 atom, 1 residue, 1 model selected  

> select up

31 atoms, 33 bonds, 1 residue, 1 model selected  

> color sel blue

> color sel byhetero

> select /A:800@CMB

1 atom, 1 residue, 1 model selected  

> select up

43 atoms, 46 bonds, 1 residue, 1 model selected  

> color sel blue

> color sel byhetero

> select ::name="IMD"

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

> show sel target ab

> color sel blue

> select clear

> ui mousemode right clip

> ui mousemode right zone

> ui mousemode right "clip rotate"

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

43 atoms, 46 bonds, 1 residue, 1 model selected  

> select up

6796 atoms, 6388 bonds, 1314 residues, 1 model selected  

> select down

43 atoms, 46 bonds, 1 residue, 1 model selected  

> ui mousemode right clip

> ui mousemode right "clip rotate"

> select clear

> select /A:211

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

> select up

228 atoms, 232 bonds, 28 residues, 1 model selected  

> select up

6796 atoms, 6388 bonds, 1314 residues, 1 model selected  

> lighting soft

> lighting full

> lighting soft

> lighting full

> lighting simple

> help help:user

> transparency #1 50 target c

> transparency #1 10 target c

> transparency #1 80 target c

> select clear

> transparency #1 60 target c

> undo

[Repeated 4 time(s)]

> ui mousemode right clip

> cd "C:/Users/Dell-LeeLab/Desktop/Working_folder_2021dec/Konkuk_Uni
> files/Weekly report sampathkumar/11_Progress_report_Nov_2022_P450"

Current working directory is: C:\Users\Dell-
LeeLab\Desktop\Working_folder_2021dec\Konkuk_Uni files\Weekly report
sampathkumar\11_Progress_report_Nov_2022_P450  

> save "C:/Users/Dell-LeeLab/Desktop/Working_folder_2021dec/Konkuk_Uni
> files/Weekly report
> sampathkumar/11_Progress_report_Nov_2022_P450/01_6LAA_crystal_st.cxs"

> save "C:/Users/Dell-LeeLab/Desktop/Working_folder_2021dec/Konkuk_Uni
> files/Weekly report
> sampathkumar/11_Progress_report_Nov_2022_P450/01_crystal_structure.png"
> width 1070 height 836 supersample 3 transparentBackground true

> select /A:803@N1

1 atom, 1 residue, 1 model selected  

> select up

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

> hide sel target a

> transparency #1 90 target c

> transparency #1 80 target c

> select clear

> select add /A:802@C8

1 atom, 1 bond, 1 residue, 1 model selected  

> color sel lime

> undo

> select clear

> ui mousemode right select

> select /A:755

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

> select /A:802@C8

1 atom, 1 residue, 1 model selected  

> select /A:802@C8

1 atom, 1 residue, 1 model selected  

> color sel lime

> undo

> select clear

[Repeated 2 time(s)]

> select /A:801@FE2

1 atom, 1 residue, 1 model selected  

> select add /A:802@C8

2 atoms, 2 residues, 1 model selected  

> ui tool show Distances

> distance /A:801@FE2 /A:802@C8

Distance between /A FES 801 FE2 and FMN 802 C8: 9.272Å  

> distance style color red

> distance style decimalPlaces 0

> distance /A:801@FE2 /A:802@C8

Distance already exists; modify distance properties with 'distance style'  

> distance style symbol false

> distance style radius 0

> undo

[Repeated 9 time(s)]

> select /A:802@C8

1 atom, 1 residue, 1 model selected  

> undo

[Repeated 1 time(s)]

> select /A:802@C8

1 atom, 1 residue, 1 model selected  

> select clear

[Repeated 1 time(s)]

> distance style radius 0.1

Exactly two atoms must be selected!  

> ui mousemode right distance

> ui mousemode right "translate selected models"

> ui mousemode right label

> ui mousemode right select

> ui mousemode right zoom

> hide #!2 models

> show #!2 models

> hide #2.1 models

> select /A:726

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

> select /A:726

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

> select /A:725-726

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

> select /A:385,725-726

21 atoms, 19 bonds, 3 residues, 1 model selected  

> show sel target ab

> color sel blue

> color sel byhetero

> label sel text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> undo

[Repeated 1 time(s)]

> select /A:378,385,725-726

32 atoms, 30 bonds, 4 residues, 1 model selected  

> select /A:378,385,392,725-726

43 atoms, 40 bonds, 5 residues, 1 model selected  

> select /A:378,385,388,392,725-726

54 atoms, 50 bonds, 6 residues, 1 model selected  

> select /A:378,385,388,392,723-726

70 atoms, 66 bonds, 8 residues, 1 model selected  

> select /A:378,385,388,392,718,723-726

81 atoms, 76 bonds, 9 residues, 1 model selected  

> select /A:378,385,388,392,718,723-726,729

90 atoms, 84 bonds, 10 residues, 1 model selected  

> show sel target ab

> color sel byhetero

> label sel text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"

Height must be a number  

> label height 1

> label height 2

Height must be a number  

> label height 2

[Repeated 1 time(s)]

> label sel attribute label_one_letter_code

> label sel attribute label_specifier

> label sel attribute name

> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> label sel text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> label sel text " {0.label_one_letter_code} {0.number}{0.insertion_code}"

[Repeated 1 time(s)]

> lable height 1.5

Unknown command: lable height 1.5  

> lable height 1

Unknown command: lable height 1  

> label height 1.5

> select /A:378,385,388,392,718,723-726,729

90 atoms, 84 bonds, 10 residues, 1 model selected  

> select /A:378,385,388,392,718,723-726,729

90 atoms, 84 bonds, 10 residues, 1 model selected  

> select /A:378,385,388,392,718,723-726,729

90 atoms, 84 bonds, 10 residues, 1 model selected  

> select /A:378,385,388,392,718,723-726,729

90 atoms, 84 bonds, 10 residues, 1 model selected  

> select /A:378-392,718,723-726,729

166 atoms, 165 bonds, 21 residues, 1 model selected  

> select /A:378-392,718,723-726,729

166 atoms, 165 bonds, 21 residues, 1 model selected  

> select /A:378-392,718,723-726,729

166 atoms, 165 bonds, 21 residues, 1 model selected  

> select /A:392

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

> select /A:392

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

> select
> /A:27-35,39-57,72-82,99-109,123-160,167-171,173-185,190-207,210-237,243-255,260-303,306-319,349-353,371-375,387-406,435-450,460-464,539-548,580-595,606-610,612-621,630-632,636-643,655-667,687-691,712-720,753-760

2960 atoms, 2992 bonds, 361 residues, 1 model selected  

> select
> /A:59-61,68-70,86-87,164-166,323-328,332-334,337-339,344-348,410-411,431-433,466-477,480-486,501-505,512-516,527-532,553-560,571-577,597-604,624-628,648-654,673-678,694-698,703-707,737-742,745-746,762-764,769-770,774-777

1144 atoms, 1142 bonds, 136 residues, 1 model selected  

> select up

1146 atoms, 1143 bonds, 137 residues, 1 model selected  

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select add /A:724@CG1

3 atoms, 1 bond, 2 residues, 1 model selected  

> select up

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

> select add /A:726@OG

17 atoms, 14 bonds, 3 residues, 1 model selected  

> select up

22 atoms, 19 bonds, 3 residues, 1 model selected  

> select add /A:725@OE1

23 atoms, 19 bonds, 4 residues, 1 model selected  

> select up

31 atoms, 29 bonds, 4 residues, 1 model selected  

> select add /A:718@NH2

32 atoms, 29 bonds, 5 residues, 1 model selected  

> select up

42 atoms, 39 bonds, 5 residues, 1 model selected  

> select add /A:723@OE1

43 atoms, 39 bonds, 6 residues, 1 model selected  

> select up

51 atoms, 48 bonds, 6 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel blue target acspfl

> undo

> color sel blue target l

> select clear

[Repeated 1 time(s)]

> select /A:724@CG1

1 atom, 1 residue, 1 model selected  

> select up

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

> label sel text "V 725 *"

> label sel text V725*

> select clear

[Repeated 1 time(s)]

> ui mousemode right select

> select /A:725@OE1

1 atom, 1 residue, 1 model selected  

> select up

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

> label sel text Q725*

> select clear

> ui mousemode right select

> select /A:726@CB

1 atom, 1 residue, 1 model selected  

> select up

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

> label sel text S726

> ui mousemode right select

> select /A:729@OE1

1 atom, 1 residue, 1 model selected  

> select up

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

> label sel text E729

> select clear

> ui mousemode right select

> select /A:718@NE

1 atom, 1 residue, 1 model selected  

> select up

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

> label sel text R718

> select clear

> ui mousemode right select

> select /A:729@OE2

1 atom, 1 residue, 1 model selected  

> select up

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

> label sel text E729*

> select /A:392@CD

1 atom, 1 residue, 1 model selected  

> select up

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

> label sel text R392

> ui tool show "Color Actions"

> color sel forest green target l

> color sel lime target l

> color sel forest green target l

> ui mousemode right select

> select clear

> select /A:388@NH2

1 atom, 1 residue, 1 model selected  

> select up

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

> color sel forest green

> undo

> label sel text R388

> color sel forest green

> undo

> ui tool show "Color Actions"

> color sel forest green target l

> select clear

> select /A:385@SG

1 atom, 1 residue, 1 model selected  

> select up

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

> cartoon hide sel

> color sel forest green

> undo

> label sel text C385

> ui tool show "Color Actions"

> color sel forest green target l

> select clear

> select /A:378@CD2

1 atom, 1 residue, 1 model selected  

> select up

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

> ui tool show "Color Actions"

> color sel forest green target l

> label sel text F378

> select clear

[Repeated 1 time(s)]

> ui mousemode right label

> label delete residues

> ui mousemode right label

[Repeated 1 time(s)]

> undo

[Repeated 1 time(s)]

> label delete residues

[Repeated 2 time(s)]

> ui mousemode right label

> label delete residues

> ui mousemode right label

> label delete residues

[Repeated 3 time(s)]

> undo

[Repeated 2 time(s)]

> ui mousemode right select

> undo

[Repeated 2 time(s)]

> ui mousemode right select

> color sel blue target l

> select clear[Repeated 1 time(s)]

Expected an objects specifier or a keyword  

> select /A:724@CG11 atom, 1 residue, 1 model selected

Expected a keyword  

> select up7 atoms, 6 bonds, 1 residue, 1 model selected

Expected an objects specifier or a keyword  

> label sel text "V 725 *"

> label sel text V725*

> select clear[Repeated 1 time(s)]

Expected an objects specifier or a keyword  

> ui mousemode right select

> select /A:725@OE11 atom, 1 residue, 1 model selected

Expected a keyword  

> select up9 atoms, 8 bonds, 1 residue, 1 model selected

Expected an objects specifier or a keyword  

> label sel text Q725*

> select clear

> ui mousemode right select

> select /A:726@CB1 atom, 1 residue, 1 model selected

Expected a keyword  

> select up6 atoms, 5 bonds, 1 residue, 1 model selected

Expected an objects specifier or a keyword  

> label sel text S726

> ui mousemode right select

> select /A:729@OE11 atom, 1 residue, 1 model selected

Expected a keyword  

> select up9 atoms, 8 bonds, 1 residue, 1 model selected

Expected an objects specifier or a keyword  

> label sel text E729

> select clear

> ui mousemode right select

> select /A:718@NE1 atom, 1 residue, 1 model selected

Expected a keyword  

> select up11 atoms, 10 bonds, 1 residue, 1 model selected

Expected an objects specifier or a keyword  

> label sel text R718

> select clear

> ui mousemode right select

> select /A:729@OE21 atom, 1 residue, 1 model selected

Expected a keyword  

> select up9 atoms, 8 bonds, 1 residue, 1 model selected

Expected an objects specifier or a keyword  

> label sel text E729*

> select /A:392@CD1 atom, 1 residue, 1 model selected

Expected a keyword  

> select up11 atoms, 10 bonds, 1 residue, 1 model selected

Expected an objects specifier or a keyword  

> label sel text R392

> ui tool show "Color Actions"

> color sel forest green target l

> color sel lime target l

> color sel forest green target l

> ui mousemode right select

> select clear

> select /A:388@NH21 atom, 1 residue, 1 model selected

Expected a keyword  

> select up11 atoms, 10 bonds, 1 residue, 1 model selected

Expected an objects specifier or a keyword  

> color sel forest green

> undo

> label sel text R388

> color sel forest green

> ui tool show "Build Structure"

> bond sel

Must specify two or more atoms  

> select /A:800@FE

1 atom, 1 residue, 1 model selected  

> select /A:800@FE

1 atom, 1 residue, 1 model selected  

> select add /A:385@SG

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select clear

> ui mousemode right label

> label delete residues

[Repeated 1 time(s)]

> select /A:385@SG

1 atom, 1 residue, 1 model selected  

> select /A:385@SG

1 atom, 1 residue, 1 model selected  

> selct up

Unknown command: selct up  

> select /A:378@CD2

1 atom, 1 residue, 1 model selected  

> select up

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

> color sel forest green

> select add /A:392@CG

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

> select up

22 atoms, 21 bonds, 2 residues, 1 model selected  

> select add /A:388@NH2

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

> select up

33 atoms, 31 bonds, 3 residues, 1 model selected  

> select add /A:385@O

34 atoms, 31 bonds, 4 residues, 1 model selected  

> select up

39 atoms, 36 bonds, 4 residues, 1 model selected  

> color sel forest green

> color sel byhetero

> select /A:83

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

> select /A:378@CD2

1 atom, 1 residue, 1 model selected  

> select up

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

> label sel text F378

> lable height 1.5

Unknown command: lable height 1.5  

> lable height 2

Unknown command: lable height 2  

> label height 2

> label height 1.5

> label color forestgreen

> ui mousemode right "move label"

> select clear

> select /A:392@NH2

1 atom, 1 residue, 1 model selected  

> label color navyblue

Invalid "color" argument: Expected one of 'auto' or 'default' or a color  

> label color red

> select residues R392 set lable R392

Invalid "residues" argument: Expected true or false (or 1 or 0)  

> select clear

> select /A:392@NH2

1 atom, 1 residue, 1 model selected  

> select up

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

> color sel red

> undo

> label sel text R392

> label height 1.5

> set label color red

Expected a keyword  

> label colour red

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> label color red

> ui mousemode right "move label"

> select /A:385@O

1 atom, 1 residue, 1 model selected  

> select up

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

> label sel text C385

> label height 1.5

> label color red

> ui mousemode right "move label"

> select clear

> select /A:388@NH2

1 atom, 1 residue, 1 model selected  

> select up

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

> label sel text R388

> label heigth 1.5

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> select /A:382

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

> select /A:382

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

> select /A:388@NH2

1 atom, 1 residue, 1 model selected  

> select up

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

> ui tool show "Color Actions"

> color sel red target l

Height must be a number  

> label height 1.5

> ui mousemode right "move label"

> select clear

> select /A:385@O

1 atom, 1 residue, 1 model selected  

> select up

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

> label sel text C385*

> select clear

> select /A:723@OE1

1 atom, 1 residue, 1 model selected  

> select up

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

> select add /A:718@NH1

10 atoms, 8 bonds, 2 residues, 1 model selected  

> select clear

> select /A:723@OE1

1 atom, 1 residue, 1 model selected  

> select up

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

> label sel text E723*

> label colour blue

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> label colou blue

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> label colou mediumblue

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> select clear

> select /A:718@NH1

1 atom, 1 residue, 1 model selected  

> select up

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

> select /A:723@OE1

1 atom, 1 residue, 1 model selected  

> select up

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

> color sel blue

> undo

> ui tool show "Color Actions"

> color sel blue target l

> label heigth 1.5

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  
Height must be a number  
[Repeated 1 time(s)]

> select clear

> ui mousemode right "move label"

> select /A:718@NH1

1 atom, 1 residue, 1 model selected  

> select up

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

> label sel text R718

Height must be a number  

> label heigth 1.5

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> label height 1.5

> select clear

> select /A:777

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

> select /A:718@NH1

1 atom, 1 residue, 1 model selected  

> select up

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

> ui tool show "Color Actions"

> color sel blue target l

> ui mousemode right "move label"

> select clear

> select /A:724@CG2

1 atom, 1 residue, 1 model selected  

> select up

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

> label sel text V724*

> color sel blue

> undo

> ui tool show "Color Actions"

> color sel blue target l

Height must be a number  

> ui mousemode right "move label"

> select /A:777

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

> select /A:726@CB

1 atom, 1 residue, 1 model selected  

> select up

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

> label sel text Q725*

> ui mousemode right "move label"

> select /A:725@CB

1 atom, 1 residue, 1 model selected  

> select /A:724@CG1

1 atom, 1 residue, 1 model selected  

> select up

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

> label sel text V724*

> select /A:725@OE1

1 atom, 1 residue, 1 model selected  

> select up

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

> label sel text Q725*

> select /A:777

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

> select /A:726@CB

1 atom, 1 residue, 1 model selected  

> select up

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

> label sel text S726

Height must be a number  

> label height 1.5

> select /A:725@OE1

1 atom, 1 residue, 1 model selected  

> select up

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

> select add /A:777

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

> select /A:729@CG

1 atom, 1 residue, 1 model selected  

> select up

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

> label sel text E729*

> label height 1.5

> select up

11 atoms, 9 bonds, 2 residues, 1 model selected  

> select add /A:726@CB

12 atoms, 9 bonds, 3 residues, 1 model selected  

> select up

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

> color sel blue

> undo

> ui tool show "Color Actions"

No target buttons for the coloring action are checked  

> color sel blue target l

> select clear

> ui mousemode right "move label"

> select /A:802@C7M

1 atom, 1 residue, 1 model selected  

> select up

31 atoms, 33 bonds, 1 residue, 1 model selected  

> label sel text FMN

> label height 1.5

> select /A:802@C8

1 atom, 1 residue, 1 model selected  

> label sel atoms text C8

> label height 1.5

> color sel red

> undo

> ui tool show "Color Actions"

> color sel red target l

> undo

> select /A:763

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

> select /A:763

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

> select clear

[Repeated 4 time(s)]

> select /A:801@FE2

1 atom, 1 residue, 1 model selected  

> label sel atoms text Fe2

> label height 1.5

> ui tool show "Color Actions"

> color sel red target l

> ui mousemode right "move label"

> save "C:/Users/Dell-LeeLab/Desktop/Working_folder_2021dec/Konkuk_Uni
> files/Weekly report
> sampathkumar/11_Progress_report_Nov_2022_P450/02_6LAA_crystal_st_Pathway_nature_communication.cxs"

> save "C:/Users/Dell-LeeLab/Desktop/Working_folder_2021dec/Konkuk_Uni
> files/Weekly report
> sampathkumar/11_Progress_report_Nov_2022_P450/02_crystal_structure_pathway_naturecommunication.png"
> width 1068 height 836 supersample 3

> select /A:800@FE

1 atom, 1 residue, 1 model selected  

> select add /A:801@FE1

2 atoms, 2 residues, 1 model selected  

> ui tool show Distances

> distance /A:800@FE /A:801@FE1

Distance between /A HEM 800 FE and FES 801 FE1: 29  

> distance /A:800@FE /A:801@FE1

Distance already exists; modify distance properties with 'distance style'  

> distance style dashes 20

> distance style color #fa0000

> distance style color #fc0000

> distance style color #fd0000

> distance style color #fe0000

> distance style dashes 19

> distance style dashes 18

> distance style dashes 19

> distance style dashes 10

> distance style dashes 11

> distance style dashes 12

> distance style dashes 13

> distance style dashes 14

> distance style dashes 15

> distance style dashes 16

> distance style dashes 17

> distance style dashes 18

> distance style dashes 19

> distance style dashes 20

> select clear

> distance style color yellow

> distance style color #ff5500

> save "C:/Users/Dell-LeeLab/Desktop/Working_folder_2021dec/Konkuk_Uni
> files/Weekly report
> sampathkumar/11_Progress_report_Nov_2022_P450/02_crystal_structure_pathway_naturecommunication_v1.png"
> width 1068 height 836 supersample 3

> save "C:/Users/Dell-LeeLab/Desktop/Working_folder_2021dec/Konkuk_Uni
> files/Weekly report
> sampathkumar/11_Progress_report_Nov_2022_P450/02_6LAA_crystal_st_Pathway_nature_communication_V2.cxs"

> select clear

> open "C:/Users/Dell-LeeLab/Desktop/Working_folder_2021dec/Konkuk_Uni
> files/Weekly report
> sampathkumar/03_pathways_6LAA/03_Pathways_images_for_31meeting_6LAA/System_II_6LAA/6LAA_solv_system_2.pdb~"

Unrecognized file suffix '.pdb~'  

> open "C:/Users/Dell-LeeLab/Desktop/Working_folder_2021dec/Konkuk_Uni
> files/Weekly report
> sampathkumar/03_pathways_6LAA/03_Pathways_images_for_31meeting_6LAA/System_II_6LAA/17_A_inner_water.pdb"

Chain information for 17_A_inner_water.pdb #3  
---  
Chain | Description  
? | No description available  
  
Alignment identifier is 1/A  
Missing or invalid "chains" argument: only initial part "#3" of atom specifier
valid  
Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  
Missing or invalid "chains" argument: only initial part "#3" of atom specifier
valid  

> close session

> open "C:/Users/Dell-LeeLab/Desktop/Working_folder_2021dec/Konkuk_Uni
> files/Weekly report
> sampathkumar/11_Progress_report_Nov_2022_P450/17_A_inner_water.pdb"

Chain information for 17_A_inner_water.pdb #1  
---  
Chain | Description  
? | No description available  
  

> ui tool show "Show Sequence Viewer"

> sequence chain /?

Alignment identifier is 1/  

> select /*:1

16 atoms, 16 bonds, 1 residue, 1 model selected  

> select /*:1

16 atoms, 16 bonds, 1 residue, 1 model selected  

> select /*:753

20 atoms, 19 bonds, 1 residue, 1 model selected  

> select /*:1-753

12091 atoms, 12234 bonds, 754 residues, 1 model selected  

> help help:user

> help help:quickstart

> help help:devel

Missing or invalid "chains" argument: only initial part "#1" of atom specifier
valid  
Missing or invalid "chains" argument: only initial part "#1" of atom specifier
valid  
Missing or invalid "chains" argument: only initial part "#1" of atom specifier
valid  
Missing or invalid "chains" argument: only initial part "#1" of atom specifier
valid  
Missing or invalid "chains" argument: only initial part "#1" of atom specifier
valid  
Missing or invalid "chains" argument: only initial part "#1" of atom specifier
valid  

> select protein

12088 atoms, 12232 bonds, 753 residues, 1 model selected  

> show #!1 target m

> close session

> open "C:/Users/Dell-LeeLab/Desktop/Working_folder_2021dec/Konkuk_Uni
> files/Weekly report
> sampathkumar/11_Progress_report_Nov_2022_P450/17_A_inner_water.pdb"

Chain information for 17_A_inner_water.pdb #1  
---  
Chain | Description  
? | No description available  
  
Missing or invalid "chains" argument: only initial part "#1" of atom specifier
valid  

> renumber#/ start 1-753 start 27

Unknown command: renumber#/ start 1-753 start 27  

> renumber #1 start 1-753 start 27

Unknown command: renumber #1 start 1-753 start 27  

> renumber #1/ start 1-753 start 27

Unknown command: renumber #1/ start 1-753 start 27  

> toolshed show

> close session

> open "C:/Users/Dell-LeeLab/Desktop/Working_folder_2021dec/Konkuk_Uni
> files/Weekly report
> sampathkumar/11_Progress_report_Nov_2022_P450/17_A_inner_water_renumbered.pdb"

Chain information for 17_A_inner_water_renumbered.pdb #1  
---  
Chain | Description  
A | No description available  
  
Alignment identifier is 1/A  

> select /A:385

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

> select /A:385

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

> select /A:27

16 atoms, 16 bonds, 1 residue, 1 model selected  

> select /A:27-441

6674 atoms, 6767 bonds, 415 residues, 1 model selected  

> select /A:443

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select /A:27-443

6722 atoms, 6815 bonds, 417 residues, 1 model selected  

> select /A:27

16 atoms, 16 bonds, 1 residue, 1 model selected  

> select /A:27-448

6798 atoms, 6892 bonds, 422 residues, 1 model selected  

> select /A:462

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select /A:27-462

7046 atoms, 7143 bonds, 436 residues, 1 model selected  

> select /A:446

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

> select /A:27-446

6760 atoms, 6854 bonds, 420 residues, 1 model selected  

> select /A:438

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select /A:27-438

6631 atoms, 6723 bonds, 412 residues, 1 model selected  

> select /A:449

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select /A:27-449

6822 atoms, 6916 bonds, 423 residues, 1 model selected  

> select /A:450

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select /A:27-450

6841 atoms, 6935 bonds, 424 residues, 1 model selected  

> color sel lime

> select /A:451

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select /A:451-461

183 atoms, 185 bonds, 11 residues, 1 model selected  

> select /A:459

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select /A:451-459

149 atoms, 151 bonds, 9 residues, 1 model selected  

> color sel gray

> select /A:460

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select /A:460-564

1694 atoms, 1714 bonds, 105 residues, 1 model selected  

> select /A:566

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

> select /A:460-566

1725 atoms, 1745 bonds, 107 residues, 1 model selected  

> color sel magenta

> select /A:460

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select /A:460-647

3001 atoms, 3033 bonds, 188 residues, 1 model selected  

> select /A:680

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select /A:460-680

3556 atoms, 3594 bonds, 221 residues, 1 model selected  

> color sel magenta

> select /A:681

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

> select /A:681-700

320 atoms, 324 bonds, 20 residues, 1 model selected  

> select /A:692

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select /A:681-692

180 atoms, 182 bonds, 12 residues, 1 model selected  

> color sel gray

> select /A:693

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select /A:693-779

1362 atoms, 1366 bonds, 87 residues, 1 model selected  

> color sel cyan

> select protein

12088 atoms, 12232 bonds, 753 residues, 1 model selected  

> hide sel target a

> select ::name="WAT"

18 atoms, 12 bonds, 6 residues, 1 model selected  

> hide sel target a

> transparency #1 80 target c

> select /?:757@S

1 atom, 1 residue, 1 model selected  

> select add /?:760@FE2

2 atoms, 2 residues, 1 model selected  

> select add /?:759@FE1

3 atoms, 3 residues, 1 model selected  

> select add /?:758@S

4 atoms, 4 residues, 1 model selected  

> style sel ball

Changed 4 atom styles  

> select clear

> select add /?:758@S

1 atom, 1 residue, 1 model selected  

> select add /?:760@FE2

2 atoms, 2 residues, 1 model selected  

> select add /A:734

9 atoms, 6 bonds, 3 residues, 1 model selected  

> select clear

[Repeated 1 time(s)]

> select /?:760@FE2

1 atom, 1 residue, 1 model selected  

> select add /?:759@FE1

2 atoms, 2 residues, 1 model selected  

> select add /?:757@S

3 atoms, 3 residues, 1 model selected  

> select add /?:758@S

4 atoms, 4 residues, 1 model selected  

> ui tool show "Build Structure"

> bond sel

Created 5 bonds  

> bond length /?:760@FE2/?:759@FE1 1.815

> bond length /?:760@FE2/?:759@FE1 1.76

> bond length /?:760@FE2/?:759@FE1 1.706

> bond length /?:760@FE2/?:759@FE1 1.65

> bond length /?:760@FE2/?:759@FE1 1.596

> bond length /?:760@FE2/?:759@FE1 1.65

> bond length /?:760@FE2/?:759@FE1 1.87

> bond length /?:760@FE2/?:759@FE1 2.254

> bond length /?:760@FE2/?:759@FE1 2.527

> bond length /?:760@FE2/?:759@FE1 2.637

> bond length /?:760@FE2/?:759@FE1 2.692

> bond length /?:760@FE2/?:759@FE1 2.746

> bond length /?:760@FE2/?:759@FE1 2.802

> bond length /?:760@FE2/?:759@FE1 2.856

> bond length /?:760@FE2/?:759@FE1 2.966

> bond length /?:760@FE2/?:759@FE1 3.021

> bond length /?:760@FE2/?:759@FE1 2.966

> bond length /?:760@FE2/?:759@FE1 2.911

> bond length /?:760@FE2/?:759@FE1 2.966

> select clear

> select /?:757@S

1 atom, 1 residue, 1 model selected  

> select add /?:758@S

2 atoms, 2 residues, 1 model selected  

> select add /A:714

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

> select clear

> select /?:757@S

1 atom, 1 residue, 1 model selected  

> select add /?:760@FE2

2 atoms, 5 bonds, 2 residues, 1 model selected  

> select add /?:759@FE1

3 atoms, 5 bonds, 3 residues, 1 model selected  

> style sel stick

Changed 3 atom styles  

> select /?:758@S

1 atom, 1 residue, 1 model selected  

> hide sel target a

> undo

> style sel stick

Changed 1 atom style  

> select clear

[Repeated 1 time(s)]

> select /?:754@FE

1 atom, 1 residue, 1 model selected  

> select add /?:754@NA

2 atoms, 1 residue, 1 model selected  

> select add /?:754@NB

3 atoms, 1 residue, 1 model selected  

> select add /?:754@NC

4 atoms, 1 residue, 1 model selected  

> select add /?:754@ND

5 atoms, 1 residue, 1 model selected  

> bond sel

Created 0 bonds  

> bond sel

Created 0 bonds  

> bond sel reasonable false

Created 10 bonds  

> bond sel

Created 0 bonds  

> ~bond sel

> bond sel

Created 0 bonds  

> bond sel

Created 0 bonds  

> select /?:754@FE

1 atom, 1 residue, 1 model selected  

> select /?:754@FE

1 atom, 1 residue, 1 model selected  

> select add /?:754@NB

2 atoms, 1 residue, 1 model selected  

> bond sel

Created 0 bonds  

> bond sel reasonable false

Created 1 bond  

> select /?:754@FE

1 atom, 1 residue, 1 model selected  

> select add /?:754@NA

2 atoms, 1 residue, 1 model selected  

> bond sel reasonable false

Created 1 bond  

> select /?:754@ND

1 atom, 1 residue, 1 model selected  

> select add /?:754@FE

2 atoms, 1 residue, 1 model selected  

> bond sel reasonable false

Created 1 bond  

> select /?:754@NC

1 atom, 1 residue, 1 model selected  

> select add /?:754@FE

2 atoms, 1 residue, 1 model selected  

> bond sel reasonable false

Created 1 bond  

> select /?:754@FE

1 atom, 1 residue, 1 model selected  

> color sel orange

> style sel sphere

Changed 1 atom style  

> style sel ball

Changed 1 atom style  

> style sel stick

Changed 0 atom styles  

> select add /?:754@FE

1 atom, 4 bonds, 1 residue, 1 model selected  

> select subtract /?:754@FE

3 bonds, 1 model selected  

> style sel stick

Changed 0 atom styles  

> select clear

> select add /?:754@O1A

1 atom, 1 residue, 1 model selected  

> select /?:754@FE

1 atom, 1 residue, 1 model selected  

> color sel #ff5500ff

> color sel #fd5400ff

> color sel #fc5400ff

> color sel #fa5300ff

> color sel #f95300ff

> color sel #f75200ff

> color sel #f15000ff

> color sel #dc4900ff

> color sel #da4900ff

> color sel #d84800ff

> color sel #d64700ff

> color sel #d54700ff

> color sel #c14000ff

> color sel #be3f00ff

> color sel #bd3f00ff

> color sel #ba3e00ff

> color sel #b63d00ff

> color sel #ab3900ff

> color sel #ac3900ff

> color sel #ad3a00ff

> color sel #af3a00ff

> color sel #b03b00ff

> color sel #b13b00ff

> color sel #b33c00ff

> color sel #b43c00ff

> color sel #b53c00ff

> color sel #b63d00ff

> color sel #b83d00ff

> color sel #b93e00ff

> color sel #ba3e00ff

> select clear

[Repeated 1 time(s)]

> select /?:754@CMA

1 atom, 1 residue, 1 model selected  

> select up

73 atoms, 80 bonds, 1 residue, 1 model selected  

> color sel blue

> color sel byhetero

> select /?:754@FE

1 atom, 1 residue, 1 model selected  

> color sel #be3f00ff

> color sel #bd3f00ff

> color sel #bc3f00ff

> color sel #ba3e00ff

> select clear

> select /?:755@C7M

1 atom, 1 residue, 1 model selected  

> select up

50 atoms, 52 bonds, 1 residue, 1 model selected  

> color sel blue

> color sel byhetero

> ~bond sel

> select /?:754@FE

1 atom, 1 residue, 1 model selected  

> style sel sphere

Changed 1 atom style  

> select clear

> save "C:/Users/Dell-LeeLab/Desktop/Working_folder_2021dec/Konkuk_Uni
> files/Weekly report
> sampathkumar/11_Progress_report_Nov_2022_P450/02_system2_withoutpathway_version1.cxs"

> select /?:760@FE2

1 atom, 1 residue, 1 model selected  

> select /?:760@FE2

1 atom, 1 residue, 1 model selected  

> select /?:760@FE2

1 atom, 1 residue, 1 model selected  

> select /?:760@FE2

1 atom, 1 residue, 1 model selected  

> select add /?:755@C8

2 atoms, 2 residues, 1 model selected  

> ui tool show Distances

> distance /?:760@FE2 /?:755@C8

Distance between /? FE2 760 FE2 and FMN 755 C8: 21  

> select /?:759@FE1

1 atom, 1 residue, 1 model selected  

> select add /?:754@FE

2 atoms, 2 residues, 1 model selected  

> distance /?:759@FE1 /?:754@FE

Distance between /? FE1 759 FE1 and HEM 754 FE: 18  

> select clear

> hide #2.1 models

> save "C:/Users/Dell-LeeLab/Desktop/Working_folder_2021dec/Konkuk_Uni
> files/Weekly report
> sampathkumar/11_Progress_report_Nov_2022_P450/02_system2_withoutpathway_version2.cxs"

> save "C:/Users/Dell-LeeLab/Desktop/Working_folder_2021dec/Konkuk_Uni
> files/Weekly report
> sampathkumar/11_Progress_report_Nov_2022_P450/02_system2_withoutpathway_version2.png"
> width 1068 height 836 supersample 3 transparentBackground true

> select /A:726

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

> select /A:726

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

> select /A:725-726

28 atoms, 27 bonds, 2 residues, 1 model selected  

> select /A:385,725-726

38 atoms, 36 bonds, 3 residues, 1 model selected  

> show sel target ab

> color sel byhetero

> select H

6060 atoms, 762 residues, 1 model selected  

> hide sel target a

> select /A:385@SG

1 atom, 1 residue, 1 model selected  

> select up

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

> cartoon hide sel

> select /?:754@FE

1 atom, 1 residue, 1 model selected  

> select /?:754@FE

1 atom, 1 residue, 1 model selected  

> select add /A:385@SG

2 atoms, 2 residues, 1 model selected  

> ui tool show "Build Structure"

> bond sel

Created 0 bonds  

> bond sel

Created 0 bonds  

> select /?:754@FE

1 atom, 1 residue, 1 model selected  

> select add /A:385@SG

2 atoms, 2 residues, 1 model selected  

> bond sel reasonable false

Created 1 bond  

> select /A:157

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select /A:725@OE1

1 atom, 1 residue, 1 model selected  

> select up

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select add /A:726@OG

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

> select up

28 atoms, 27 bonds, 2 residues, 1 model selected  

> select clear

[Repeated 1 time(s)]

> select /A:725@OE1

1 atom, 1 residue, 1 model selected  

> select up

17 atoms, 16 bonds, 1 residue, 1 model selected  

> label sel text S726

> select /A:726@OG

1 atom, 1 residue, 1 model selected  

> select up

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

> label sel text S726

> select /A:725@OE1

1 atom, 1 residue, 1 model selected  

> select up

17 atoms, 16 bonds, 1 residue, 1 model selected  

> label sel text Q725

> select /A:385@O

1 atom, 1 residue, 1 model selected  

> select up

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

> label sel text C385

> label height 1.5

> select /A:726

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

> select add /A:725@OE1

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

> select up

28 atoms, 27 bonds, 2 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel blue target l

> ui mousemode right "move label"

> select /A:385@O

1 atom, 1 residue, 1 model selected  

> select up

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

> ui tool show "Color Actions"

> color sel red target l

> select /?:759@FE1

1 atom, 1 residue, 1 model selected  

> label sel atoms

> label sel atoms text Fe1

> label height 1.5

> ui tool show "Color Actions"

> color sel red target l

> select clear

> select /?:760@FE2

1 atom, 1 residue, 1 model selected  

> label sel atoms text Fe2

> label height 1.5

> color sel red target l

> select /?:755@C8

1 atom, 1 residue, 1 model selected  

> label sel atoms text C8

> label height 1.5

> select /?:755@O4

1 atom, 1 residue, 1 model selected  

> select up

50 atoms, 52 bonds, 1 residue, 1 model selected  

> label sel text FMN

> label height 1.5

> select clear

> save "C:/Users/Dell-LeeLab/Desktop/Working_folder_2021dec/Konkuk_Uni
> files/Weekly report
> sampathkumar/11_Progress_report_Nov_2022_P450/02_system2_pathway1_version1.cxs"

> select /?:756@C4

1 atom, 1 residue, 1 model selected  

> select up

31 atoms, 30 bonds, 1 residue, 1 model selected  

> label sel text DEC

> label height 1.5

> select clear

> save "C:/Users/Dell-LeeLab/Desktop/Working_folder_2021dec/Konkuk_Uni
> files/Weekly report
> sampathkumar/11_Progress_report_Nov_2022_P450/02_system2_pathway1_version2.cxs"

> save "C:/Users/Dell-LeeLab/Desktop/Working_folder_2021dec/Konkuk_Uni
> files/Weekly report
> sampathkumar/11_Progress_report_Nov_2022_P450/02_system2_pathway1_version1.png"
> width 1068 height 836 supersample 3 transparentBackground true

> save "C:/Users/Dell-LeeLab/Desktop/Working_folder_2021dec/Konkuk_Uni
> files/Weekly report
> sampathkumar/11_Progress_report_Nov_2022_P450/02_system2_withoutpathway_version3.png"
> width 1068 height 836 supersample 3

> save "C:/Users/Dell-LeeLab/Desktop/Working_folder_2021dec/Konkuk_Uni
> files/Weekly report
> sampathkumar/11_Progress_report_Nov_2022_P450/02_system2_pathway1_version2.cxs"

> select /A:385@O

1 atom, 1 residue, 1 model selected  

> select up

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

> hide sel target a

> select /A:382

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

> select /A:382

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

> show sel target ab

> color sel forest green

> color sel lime

> color sel byhetero

> select H

6060 atoms, 762 residues, 1 model selected  

> hide sel target a

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> label sel text A382

> label height 1.5

> color sel byhetero

> ui tool show "Color Actions"

> color sel red target l

> select /A:383

17 atoms, 17 bonds, 1 residue, 1 model selected  

> select add /A:384

34 atoms, 33 bonds, 2 residues, 1 model selected  

> show sel target ab

> color sel byhetero

> select H

6060 atoms, 762 residues, 1 model selected  

> hide sel target a

> select /A:384@CD

1 atom, 1 residue, 1 model selected  

> select up

17 atoms, 16 bonds, 1 residue, 1 model selected  

> label sel text Q384

> label height 1.5

> select /A:383@NE2

1 atom, 1 residue, 1 model selected  

> select up

17 atoms, 17 bonds, 1 residue, 1 model selected  

> label sel text H283

> label height 1.5

> select /A:384@NE2

1 atom, 1 residue, 1 model selected  

> select up

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select add /A:383@CE1

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

> select up

34 atoms, 34 bonds, 2 residues, 1 model selected  

> color sel red target l

> select clear

> select /A:331

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

73 atoms, 80 bonds, 1 residue, 1 model selected  

> label sel text HEME

> label height 1.5

> select /?:754@FE

1 atom, 1 residue, 1 model selected  

> label sel atoms text Fe

> label height 1.5

> select clear

> save "C:/Users/Dell-LeeLab/Desktop/Working_folder_2021dec/Konkuk_Uni
> files/Weekly report
> sampathkumar/11_Progress_report_Nov_2022_P450/02_system2_pathway2_version1.cxs"

——— End of log from Wed Nov 2 16:26:42 2022 ———

opened ChimeraX session  

> ui mousemode right "move label"

> ui mousemode right label

> label delete residues

[Repeated 1 time(s)]

> ui mousemode right "move label"

> save "C:/Users/Dell-LeeLab/Desktop/Working_folder_2021dec/Konkuk_Uni
> files/Weekly report
> sampathkumar/11_Progress_report_Nov_2022_P450/02_system2_pathway2_version2.png"
> width 1341 height 836 supersample 3

> save "C:/Users/Dell-LeeLab/Desktop/Working_folder_2021dec/Konkuk_Uni
> files/Weekly report
> sampathkumar/11_Progress_report_Nov_2022_P450/02_system2_pathway2_version2.cxs"

——— End of log from Wed Nov 2 19:25:51 2022 ———

opened ChimeraX session  

> select /A:726@OG

1 atom, 1 residue, 1 model selected  

> select up

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

> select add /A:725@OE1

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

> select up

28 atoms, 27 bonds, 2 residues, 1 model selected  

> color sel #55ffffff

> color sel #55fefeff

> color sel #53fafaff

> color sel #50f1f1ff

> color sel #50f0f0ff

> color sel #50efefff

> color sel #4feeeeff

> color sel #4fececff

> color sel #4eebebff

> color sel #4eeaeaff

> color sel #4de8e8ff

> color sel #4de7e7ff

> color sel #4de6e6ff

> color sel #4ce5e5ff

> color sel #4ce3e3ff

> color sel #4be1e1ff

> color sel #4adfdfff

> color sel #4addddff

> color sel #49dcdcff

> transparency #1 85 target c

> color sel byhetero

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select add /A:382

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

> select up

27 atoms, 25 bonds, 2 residues, 1 model selected  

> select up

29 atoms, 26 bonds, 3 residues, 1 model selected  

> color sel #00ff00ff

> color sel #00fe00ff

> color sel #00fd00ff

> color sel #00fc00ff

> color sel #00f800ff

> color sel #00f300ff

> color sel #00f000ff

> color sel #00ee00ff

> color sel #00eb00ff

> color sel #00ea00ff

> color sel #00e800ff

> color sel #00e700ff

> color sel #00e500ff

> color sel #00e300ff

> color sel #00df00ff

> color sel #00de00ff

> color sel byhetero

> transparency #1 85 target c

> select clear

> select /?:754@FE

1 atom, 1 residue, 1 model selected  

> style sel ball

Changed 1 atom style  

> select clear

[Repeated 1 time(s)]

> cd "C:/Users/Dell-LeeLab/Desktop/Working_folder_2021dec/Konkuk_Uni
> files/Weekly report
> sampathkumar/11_Progress_report_Nov_2022_P450/P450TT_6LAA/OLD_images"

Current working directory is: C:\Users\Dell-
LeeLab\Desktop\Working_folder_2021dec\Konkuk_Uni files\Weekly report
sampathkumar\11_Progress_report_Nov_2022_P450\P450TT_6LAA\OLD_images  

> save "C:/Users/Dell-LeeLab/Desktop/Working_folder_2021dec/Konkuk_Uni
> files/Weekly report
> sampathkumar/11_Progress_report_Nov_2022_P450/P450TT_6LAA/OLD_images/02_system2_pathway2_version3.png"
> width 1341 height 836 supersample 3

> save "C:/Users/Dell-LeeLab/Desktop/Working_folder_2021dec/Konkuk_Uni
> files/Weekly report
> sampathkumar/11_Progress_report_Nov_2022_P450/P450TT_6LAA/OLD_images/02_system2_pathway2_version3.cxs"

——— End of log from Thu Nov 10 11:33:54 2022 ———

opened ChimeraX session  




OpenGL version: 3.3.0 NVIDIA 512.77
OpenGL renderer: NVIDIA GeForce GTX 1660 SUPER/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Inspiron 3891
OS: Microsoft Windows 10 Home (Build 19044)
Memory: 16,962,883,584
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11700F @ 2.50GHz
OSLanguage: ko-KR
Locale: ('en_IN', 'cp949')
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 pett, 3 years ago

Cc:	Tom Goddard added
Component:	Unassigned → Platform
Owner:	set to pett
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Crash using File→Open dialog on Windows and/or returning from function

comment:2 by pett, 3 years ago

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

1.3

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