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Opened 3 years ago
Closed 3 years ago
#7990 closed defect (can't reproduce)
Crash using File→Open dialog on Windows and/or returning from function
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Platform | Version: | |
| Keywords: | Cc: | 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 , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Platform |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash using File→Open dialog on Windows and/or returning from function |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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