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Opened 4 years ago
Last modified 4 years ago
#6200 feedback defect
Crash using File→Open on Windows and/or in trigger.activate() — at Version 1
| 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 (last modified by )
The following bug report has been submitted:
Platform: Windows-10-10.0.19042
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x8001010e
Thread 0x00001eec (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 0x00001eec (most recent call first):
File "C:\Program Files\ChimeWindows fatal exception: rcode 0xa8001010eX
1.Windows fatal exception: 3code 0x\8001010eb
inWindows fatal exception: \code 0xl8001010ei
b\Windows fatal exception: scode 0xi8001010et
e-Windows fatal exception: pcode 0xa8001010ec
kaWindows fatal exception: gcode 0xe8001010es
\chiWindows fatal exception: mcode 0xe8001010er
axWindows fatal exception: \code 0xo8001010ep
enWindows fatal exception: _code 0xc8001010eo
mmand\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\ChimWindows fatal exception: ecode 0xr8001010ea
X 1.Windows fatal exception: 3code 0x\8001010eb
inWindows fatal exception: \code 0xl8001010ei
b\Windows fatal exception: rcode 0xu8001010en
pyWindows fatal exception: .code 0xp8001010ey
", line 197Windows fatal exception: in code 0x_8001010er
unWindows fatal exception: _code 0xm8001010eo
duWindows fatal exception: lcode 0xe8001010e_
asWindows fatal exception: _code 0xm8001010ea
in
Windows fatal exception: code 0x8001010e
Thread 0x00001eec (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 0x00001eec (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\biWindows fatal exception: ncode 0x\8001010el
ib\rWindows fatal exception: ucode 0xn8001010ep
y.Windows fatal exception: pcode 0xy8001010e"
, line 197 in Windows fatal exception: _code 0xr8001010eu
n_module_as_mWindows fatal exception: acode 0xi8001010en
Windows fatal exception: Windows fatal exception: code 0xcode 0x8001010e8001010e
Thread 0x00001eec (most recent call first):
Windows fatal exception: File code 0x8001010e"
CWindows fatal exception: :code 0x\8001010eP
roWindows fatal exception: gcode 0xr8001010ea
m 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\ChimeraXWindows fatal exception: 1code 0x.8001010e3
\bin\liWindows fatal exception: bcode 0x\8001010er
unpWindows fatal exception: ycode 0x.8001010ep
y"Windows fatal exception: , line code 0x878001010e in
_rWindows fatal exception: ucode 0xn8001010e_
coWindows fatal exception: dcode 0xe8001010e
File "Windows fatal exception: Ccode 0x:8001010e\
PrWindows fatal exception: ocode 0xg8001010er
am Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00001eec (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 0x00001eec (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\ChWindows fatal exception: icode 0xm8001010ee
raX Windows fatal exception: 1code 0x.8001010e3
\bWindows fatal exception: icode 0xn8001010e\
liWindows fatal exception: bcode 0x\8001010er
uWindows fatal exception: ncode 0xp8001010ey
.pWindows fatal exception: ycode 0x"8001010e, line
197 in Windows fatal exception: _code 0xr8001010eu
n_Windows fatal exception: mcode 0xo8001010ed
ulWindows fatal exception: ecode 0x_8001010ea
s_main
Windows fatal exception: code 0x8001010e
Thread 0x00001eec (most recent call first):
Windows fatal exception: File code 0x"8001010eC
:\PWindows fatal exception: rcode 0xo8001010eg
raWindows fatal exception: mcode 0x 8001010eF
ilWindows fatal exception: ecode 0xs8001010e\
ChWindows fatal exception: icode 0x8001010em
erWindows fatal exception: acode 0xX8001010e
1.Windows fatal exception: 3code 0x\8001010eb
inWindows fatal exception: \code 0xl8001010ei
b\Windows fatal exception: scode 0xi8001010et
e-packages\chimerax\open_command\dialog.py", line 135 in show_openWindows fatal exception: _code 0xf8001010ei
leWindows fatal exception: _code 0xd8001010ei
alWindows fatal exception: ocode 0xg8001010e
File "Windows fatal exception: Ccode 0x:8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x\8001010eP
roWindows fatal exception: gcode 0xr8001010ea
m Windows fatal exception: Fcode 0xi8001010el
esWindows fatal exception: \code 0xC8001010eh
imeraX 1.3\biWindows fatal exception: ncode 0x\8001010el
ib\Windows fatal exception: scode 0xi8001010et
e-Windows fatal exception: pcode 0xa8001010ec
kaWindows fatal exception: gcode 0xe8001010es
\cWindows fatal exception: hcode 0xi8001010em
erWindows fatal exception: acode 0xx8001010e\
opWindows fatal exception: ecode 0xn8001010e_
coWindows fatal exception: mcode 0xm8001010ea
ndWindows fatal exception: \code 0xd8001010ei
aWindows fatal exception: lcode 0xo8001010eg
.pyWindows fatal exception: "code 0x, line 8001010e107
in 8001010e
File "CWindows fatal exception: :code 0x\8001010eP
roWindows fatal exception: gcode 0xr8001010ea
m Windows fatal exception: Fcode 0xi8001010el
esWindows fatal exception: \code 0xC8001010eh
iWindows fatal exception: Windows fatal exception: mcode 0xcode 0xe8001010e8001010er
a
XWindows fatal exception: code 0x18001010e.
3\Windows fatal exception: bcode 0xi8001010en
\lWindows fatal exception: icode 0xb8001010e\
siWindows fatal exception: tcode 0xe8001010e-
paWindows fatal exception: ccode 0xk8001010ea
geWindows fatal exception: scode 0x\8001010ec
hiWindows fatal exception: mcode 0xe8001010er
axWindows fatal exception: \code 0xu8001010ei
\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.Windows fatal exception: 3code 0x\8001010eb
in\Windows fatal exception: lcode 0xi8001010eb
\sWindows fatal exception: icode 0xt8001010ee
-pWindows fatal exception: acode 0xc8001010ek
agWindows fatal exception: ecode 0xs8001010e\
ChWindows fatal exception: icode 0xm8001010ee
[had to delete a bunch of this to fit within ticket length limit]
Thread 0x00001eec (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 0x00001eec (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 0x00001eec (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 0x00001eec (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chiWindows fatal exception: mcode 0xe8001010er
ax\opWindows fatal exception: ecode 0xn8001010e_
coWindows fatal exception: mcode 0xm8001010ea
ndWindows fatal exception: \code 0xd8001010ei
alWindows fatal exception: ocode 0xg8001010e.
pyWindows fatal exception: "code 0x, line 8001010e135
in sWindows fatal exception: hcode 0xo8001010ew
_oWindows fatal exception: pcode 0xe8001010eWindows fatal exception: n
_code 0xfWindows fatal exception: icode 0xl8001010ee
8001010e_
dialWindows fatal exception: ocode 0xg8001010e
File "Windows fatal exception: Ccode 0x:8001010e\
PrWindows fatal exception: ocode 0xg8001010er
amWindows fatal exception: code 0xF8001010ei
leWindows fatal exception: scode 0x\8001010eC
hWindows fatal exception: iWindows fatal exception: mcode 0xecode 0x8001010e8001010e
rWindows fatal exception: acode 0xX8001010eWindows fatal exception:
code 0xWindows fatal exception: 1code 0x8001010e.8001010e
3
\Windows fatal exception: bcode 0xi8001010en
\lWindows fatal exception: icode 0xb8001010e\
siWindows fatal exception: tcode 0xe8001010e-
paWindows fatal exception: ccode 0xk8001010ea
geWindows fatal exception: scode 0x\8001010ec
hiWindows fatal exception: mcode 0xe8001010er
axWindows fatal exception: \code 0xo8001010ep
Windows fatal exception: ecode 0xn8001010e_
coWindows fatal exception: mcode 0xm8001010ea
ndWindows fatal exception: \code 0xd8001010ei
alWindows fatal exception: ocode 0xg8001010e.
pyWindows fatal exception: "code 0x, line 8001010e107
in 8001010e
File "Windows fatal exception: Ccode 0x:8001010e\
PrWindows fatal exception: ocode 0xg8001010er
aWindows fatal exception: mcode 0x 8001010eF
ilWindows fatal exception: ecode 0xs8001010e\
ChWindows fatal exception: icode 0xm8001010ee
raWindows fatal exception: Xcode 0x 8001010e1
.3Windows fatal exception: \code 0xb8001010ei
n\Windows fatal exception: lcode 0xi8001010eb
\sWindows fatal exception: icode 0xt8001010ee
-pWindows fatal exception: acode 0xc8001010ek
agWindows fatal exception: ecode 0xs8001010e\Windows fatal exception: ccode 0xh8001010ei
m
Windows fatal exception: ecode 0xr8001010ea
x\Windows fatal exception: ucode 0xi8001010e\
guWindows fatal exception: icode 0x.8001010ep
y"Windows fatal exception: , line code 0x3018001010e in e
vWindows fatal exception: ecode 0xn8001010eWindows fatal exception: tcode 0x_8001010el
o
oWindows fatal exception: Windows fatal exception: pcode 0x
code 0x File 8001010e"
C:8001010eWindows fatal exception:
code 0x\8001010eWindows fatal exception:
Pcode 0xWindows fatal exception: r8001010ecode 0xo8001010e
gWindows fatal exception: rcode 0xa8001010em
FWindows fatal exception: icode 0xl8001010ee
s\Windows fatal exception: Ccode 0xh8001010ei
meWindows fatal exception: rcode 0xa8001010eX
1Windows fatal exception: .code 0x38001010e\
biWindows fatal exception: ncode 0x\8001010el
Windows fatal exception: icode 0xb8001010e\
siWindows fatal exception: tcode 0xe8001010e-
paWindows fatal exception: ccode 0xk8001010ea
geWindows fatal exception: scode 0x\8001010eC
hiWindows fatal exception: mcode 0xe8001010er
aXWindows fatal exception: _code 0xm8001010ea
inWindows fatal exception: .code 0xp8001010ey
", line Windows fatal exception: 867code 0x in 8001010ei
niWindows fatal exception: tcode 0x
8001010e File
"Windows fatal exception: Ccode 0x:8001010e\
PrWindows fatal exception: ocode 0xg8001010er
amWindows fatal exception: code 0xF8001010ei
leWindows fatal exception: scode 0x\8001010eC
hiWindows fatal exception: mcode 0xe8001010er
aXWindows fatal exception: code 0x18001010e.
3\Windows fatal exception: bcode 0xi8001010en
\lWindows fatal exception: icode 0xb8001010e\
siWindows fatal exception: tcode 0xe8001010e-
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 0x00001eec (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 0x00001eec (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 0x00001eec (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\triggerset.py", line 354 in activate_trigger
Windows fatal exception: access violation
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0xWindows fatal exception: 8001010ecode 0x
8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
===== Log before crash start =====
> open "C:\PDB\Hpar HphA corr.cxs" format session
opened ChimeraX session
> select /A:142-254
843 atoms, 856 bonds, 113 residues, 1 model selected
> cartoon hide sel
> save "C:/Users/Public/Desktop/Hpar zoom in.cxs"
[Errno 13] Permission denied: 'C:/Users/Public/Desktop/Hpar zoom
in.cxs.15560.tmp'
> close session
> open "C:\Dissertation\Hemophilin manuscript\Figures\Smal HphA.cxs" format
> session
opened ChimeraX session
> close session
> open "C:\PDB\Hpar HphA corr.cxs" format session
opened ChimeraX session
> color #1 #701b15 transparency 0
> color #1 #aa2920 transparency 0
> color #1 #c12f24 transparency 0
> color #1 #c16242 transparency 0
> color #1 #c1564e transparency 0
> color #1 #9c453f transparency 0
> select /A:95, 56,64,101
37 atoms, 34 bonds, 4 residues, 1 model selected
> color sel byelement
> select ligand
74 atoms, 78 bonds, 1 residue, 1 model selected
> color sel byelement
> select Fe
1 atom, 1 residue, 1 model selected
> color sel forest green
> save C:/Users/Public/Desktop/Hparahph.cxs
[Errno 13] Permission denied: 'C:/Users/Public/Desktop/Hparahph.cxs.15560.tmp'
> select #1
2125 atoms, 2034 bonds, 4 pseudobonds, 381 residues, 2 models selected
> turn y -50
> turn y +50
> ~select #1
Nothing selected
> save "C:/PDB/Hpara HphA .cxs"
> save "C:/PDB/Hpar HphA_1.tif" width 1340 height 821 supersample 3
> transparentBackground true
> turn y -50
> save "C:/PDB/Hpar HphA_2 turn y-50.tif" width 1340 height 821 supersample 3
> select /A:142-254
843 atoms, 856 bonds, 113 residues, 1 model selected
> cartoon hide sel
> ui tool show Distances
> select /A:297@FE
1 atom, 1 residue, 1 model selected
> select add /A:101@NE2
2 atoms, 2 residues, 1 model selected
> distance /A:297@FE /A:101@NE2
> save "C:/PDB/Hpar HphA_3 zoom.tif" width 1340 height 821 supersample 3
> select /A:142-254
843 atoms, 856 bonds, 113 residues, 1 model selected
> cartoon sel
> select #1
2125 atoms, 2034 bonds, 5 pseudobonds, 381 residues, 3 models selected
> ~select #1
Nothing selected
> save "C:/PDB/Hpar HphA_2 turn y-50.tif" width 1340 height 821 supersample 3
> transparentBackground true
> select /A:142-254
843 atoms, 856 bonds, 113 residues, 1 model selected
> surface hidePatches sel
> cartoon hide sel
> save "C:/PDB/Hpar HphA_3 zoom.tif" width 1340 height 821 supersample 3
> transparentBackground true
> select /A:142-254
843 atoms, 856 bonds, 113 residues, 1 model selected
> cartoon sel
> turn y +50
> select #1
2125 atoms, 2034 bonds, 5 pseudobonds, 381 residues, 3 models selected
> ~select #1
Nothing selected
> save "C:/PDB/Hpara HphA_1_2.tif" width 1340 height 821 supersample 3
> transparentBackground true
> turn x +30
> turn x -30
> turn z -30
> turn z +30
> turn z -10
> turn z -5
> turn z -25
> turn z +25
> turn z -20
Must select one or more distances in the table
> ~distance /A:297@FE /A:101@NE2
> turn y -50
> ui tool show Distances
> select /A:297@FE
1 atom, 1 residue, 1 model selected
> select /A:297@FE
1 atom, 1 residue, 1 model selected
> select #1
2125 atoms, 2034 bonds, 4 pseudobonds, 381 residues, 2 models selected
> ~select #1
Nothing selected
> select /A:297@FE
1 atom, 1 residue, 1 model selected
> select add /A:101@NE2
2 atoms, 2 residues, 1 model selected
> distance /A:297@FE /A:101@NE2
Must select one or more distances in the table
> ~distance /A:297@FE /A:101@NE2
> select #1
2125 atoms, 2034 bonds, 4 pseudobonds, 381 residues, 2 models selected
> ~select #1
Nothing selected
> save "C:/PDB/Hpar HphA_2 turn y-50.tif" width 1340 height 821 supersample 3
> save "C:/PDB/Hpar HphA_2 turn y-50.tif" width 1340 height 821 supersample 3
> transparentBackground true
> select /A:142-254
843 atoms, 856 bonds, 113 residues, 1 model selected
> cartoon hide sel
> ui tool show Distances
> select /A:297@FE
1 atom, 1 residue, 1 model selected
> select add /A:101@NE2
2 atoms, 2 residues, 1 model selected
> distance /A:297@FE /A:101@NE2
> select #1
2125 atoms, 2034 bonds, 5 pseudobonds, 381 residues, 3 models selected
> ~select #1
Nothing selected
> save "C:/PDB/Hpar HphA_4 zoom.tif" width 1340 height 821 supersample 3
> transparentBackground true
> select /A:142-254
843 atoms, 856 bonds, 113 residues, 1 model selected
> cartoon sel
> cartoon hide sel
> close session
> open C:/PDB/TbpB_3ve1.pdb
TbpB_3ve1.pdb title:
The 2.9 angstrom crystal structure of transferrin binding protein B (TBPB)
from serogroup B M982 neisseria meningitidis In complex with human transferrin
[more info...]
Chain information for TbpB_3ve1.pdb #1
---
Chain | Description | UniProt
A | TBP-2 | TBB1_NEIMB
B | serotransferrin | TRFE_HUMAN
C | TBP-2 | TBB1_NEIMB
D | serotransferrin | TRFE_HUMAN
Non-standard residues in TbpB_3ve1.pdb #1
---
CO3 — carbonate ion
FE — Fe (III) ion
GOL — glycerol (glycerin; propane-1,2,3-triol)
> select /B/D
10692 atoms, 10820 bonds, 13 pseudobonds, 1498 residues, 3 models selected
> cartoon hide (#!1 & sel)
> hide (#!1 & sel) target a
> select /C
4255 atoms, 4306 bonds, 8 pseudobonds, 571 residues, 2 models selected
> cartoon hide (#!1 & sel)
> hide (#!1 & sel) target a
> select /C
4255 atoms, 4306 bonds, 8 pseudobonds, 571 residues, 2 models selected
> cartoon (#!1 & sel)
> select /A
4282 atoms, 4331 bonds, 7 pseudobonds, 576 residues, 2 models selected
> hide (#!1 & sel) target a
> cartoon hide (#!1 & sel)
> ui tool show "Show Sequence Viewer"
> sequence chain /C
Alignment identifier is 1/C
> select /C:38
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide dashed lines
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide lines
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide missing segments
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide pseudobonds
> select #1
19229 atoms, 19457 bonds, 28 pseudobonds, 2645 residues, 3 models selected
> ~select #1
Nothing selected
> select /D
5347 atoms, 5412 bonds, 6 pseudobonds, 750 residues, 2 models selected
> cartoon (#!1 & sel)
> surface hidePatches (#!1 & sel)
> cartoon hide (#!1 & sel)
> select /A:320-350
237 atoms, 240 bonds, 31 residues, 1 model selected
> select /C:320-350
237 atoms, 240 bonds, 31 residues, 1 model selected
> select /C:190-350
1238 atoms, 1257 bonds, 1 pseudobond, 159 residues, 2 models selected
> select /C:126-350
1766 atoms, 1806 bonds, 1 pseudobond, 223 residues, 2 models selected
> select /C:242-350
824 atoms, 835 bonds, 1 pseudobond, 107 residues, 2 models selected
> color (#!1 & sel) forest green
> select /C:179-350
1336 atoms, 1360 bonds, 1 pseudobond, 170 residues, 2 models selected
> color (#!1 & sel) forest green
> select /C:38-178
1067 atoms, 1097 bonds, 1 pseudobond, 133 residues, 2 models selected
> color (#!1 & sel) blue
> select /C:542-691
962 atoms, 983 bonds, 2 pseudobonds, 127 residues, 2 models selected
> color (#!1 & sel) forest green
> select /C:374-541
850 atoms, 859 bonds, 3 pseudobonds, 106 residues, 2 models selected
> color (#!1 & sel) blue
> show pseudobonds
> hide pseudobonds
> undo
> color (#!1 & sel) blue
> select /A/C
8537 atoms, 8637 bonds, 15 pseudobonds, 1147 residues, 2 models selected
> hide (#!1 & sel) target a
> select /B/D
10692 atoms, 10820 bonds, 13 pseudobonds, 1498 residues, 3 models selected
> hide (#!1 & sel) target a
> save "C:/PDB/TbpB 3VE1.cxs"
> save C:/PDB/TbpB_3VE1.tif width 1340 height 821 supersample 3
> transparentBackground true
> close session
> open C:/PDB/NgoLbpB_7n88.pdb
NgoLbpB_7n88.pdb title:
The cryoem structure of LBPB from N. Gonorrhoeae In complex with lactoferrin
[more info...]
Chain information for NgoLbpB_7n88.pdb #1
---
Chain | Description | UniProt
A | lactoferrin-binding protein B | Q9Z4N2_NEIGO
B | lactotransferrin | TRFL_HUMAN
Non-standard residues in NgoLbpB_7n88.pdb #1
---
BCT — bicarbonate ion
FE — Fe (III) ion
> select /B
5238 atoms, 5364 bonds, 11 pseudobonds, 692 residues, 2 models selected
> cartoon hide (#!1 & sel)
> hide (#!1 & sel) target a
> select /A
4164 atoms, 4245 bonds, 4 pseudobonds, 532 residues, 2 models selected
> hide pseudobonds
> select #1
9402 atoms, 9609 bonds, 15 pseudobonds, 1224 residues, 3 models selected
> ~select #1
Nothing selected
> select /A:43-176
1073 atoms, 1094 bonds, 134 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /A:42-176
1080 atoms, 1101 bonds, 135 residues, 1 model selected
> color sel blue
> select /A:42-175
1073 atoms, 1094 bonds, 134 residues, 1 model selected
> select /A:176-337
1293 atoms, 1321 bonds, 162 residues, 1 model selected
> color sel forest green
> select /A:338-547
768 atoms, 778 bonds, 3 pseudobonds, 100 residues, 2 models selected
> color (#!1 & sel) blue
> select /A:547-704
1037 atoms, 1056 bonds, 1 pseudobond, 137 residues, 2 models selected
> color (#!1 & sel) forest green
> select #1
9402 atoms, 9609 bonds, 15 pseudobonds, 1224 residues, 3 models selected
> ~select #1
Nothing selected
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> save "C:/PDB/NgoLbpB 7n88.tif" width 1340 height 821 supersample 3
> transparentBackground true
> save C:/PDB/LbpB.cxs
> close session
> open C:/PDB/Kde_5ec6.pdb
Kde_5ec6.pdb title:
The apo crystal structure of haemoglobin receptor hpua from kingella
denitrificans [more info...]
Chain information for Kde_5ec6.pdb #1
---
Chain | Description | UniProt
A | HPUA | F0EX68_9NEIS
Non-standard residues in Kde_5ec6.pdb #1
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
> select /A
2565 atoms, 2283 bonds, 1 pseudobond, 629 residues, 2 models selected
> hide (#!1 & sel) target a
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /A:210-322
819 atoms, 834 bonds, 113 residues, 1 model selected
> color sel forest green
> select /A:185-322
963 atoms, 978 bonds, 1 pseudobond, 132 residues, 2 models selected
> color (#!1 & sel) forest green
> select /A:174-322
1050 atoms, 1066 bonds, 1 pseudobond, 143 residues, 2 models selected
> color (#!1 & sel) forest green
> select /A:15-173
1178 atoms, 1206 bonds, 159 residues, 1 model selected
> color sel blue
> select #1
2565 atoms, 2283 bonds, 1 pseudobond, 629 residues, 2 models selected
> ~select #1
Nothing selected
> save "C:/PDB/hpuA in Kingella.cxs"
> save "C:/PDB/HpuA 5EC6.tif" width 1340 height 821 supersample 3
> transparentBackground true
> close session
> open C:/PDB/NHBA_2lfu.pdb
NHBA_2lfu.pdb title:
The structure of A N. Meningitides protein targeted for vaccine development
[more info...]
Chain information for NHBA_2lfu.pdb
---
Chain | Description | UniProt
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A | putative
lipoprotein GNA2132 | Q9JPI1_NEIME
> select #1.1/A#1.2/A#1.3/A#1.4/A#1.5/A#1.6/A#1.7/A#1.8/A#1.9/A#1.10/A
23720 atoms, 24070 bonds, 1600 residues, 10 models selected
> cartoon hide sel
> select #1.1/A
2372 atoms, 2407 bonds, 160 residues, 1 model selected
> cartoon sel
> select #1
23720 atoms, 24070 bonds, 1600 residues, 11 models selected
> ~select #1.1
21348 atoms, 21663 bonds, 1440 residues, 10 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1.1/A #1.2/A #1.3/A #1.4/A #1.5/A #1.6/A #1.7/A #1.8/A
> #1.9/A #1.10/A
Alignment identifier is 1
> select /A:276-316
6090 atoms, 6160 bonds, 410 residues, 10 models selected
> select /A:276-315
5950 atoms, 6020 bonds, 400 residues, 10 models selected
> color sel blue
> select /A:316-435
17770 atoms, 18040 bonds, 1200 residues, 10 models selected
> color sel forest green
> select #1
23720 atoms, 24070 bonds, 1600 residues, 11 models selected
> ~select #1
Nothing selected
> save "C:/PDB/NHBA 2LFU.tif" width 1340 height 821 supersample 3
> transparentBackground true
> save "C:/PDB/NHBA 2LFU.cxs"
> close session
> open "C:\PDB\hpuA in Kingella.cxs" format session
opened ChimeraX session
> save "C:/PDB/HpuA 5EC6.tif" width 1340 height 821 supersample 3
> transparentBackground true
> close session
> open C:/PDB/fHbp3kvd.pdb
fHbp3kvd.pdb title:
Crystal structure of the neisseria meningitidis factor H binding protein, FHBP
(GNA1870) At 2.0 A resolution [more info...]
Chain information for fHbp3kvd.pdb #1
---
Chain | Description | UniProt
D | lipoprotein GNA1870 | Q6QCC2_NEIME
> ui tool show "Show Sequence Viewer"
> sequence chain /D
Alignment identifier is 1/D
> select /A:214-320
Nothing selected
> select /D:214-320
786 atoms, 797 bonds, 107 residues, 1 model selected
> color sel forest green
> select /D:79-213
1042 atoms, 1055 bonds, 135 residues, 1 model selected
> color sel blue
> select #1
2017 atoms, 1853 bonds, 431 residues, 1 model selected
> ~select #1
Nothing selected
> save C:/PDB/fHbp_3KVD.tif width 1340 height 821 supersample 3
> transparentBackground true
> save C:/PDB/fHbp_3kvd.cxs
> close session
> open "C:/PDB/Smal HphA.pdb"
Summary of feedback from opening C:/PDB/Smal HphA.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Date 2019-10-03 Time 19:09:57 EDT -0400 (1570144197.21 s)
Ignored bad PDB record found on line 2
REMARK PHENIX refinement
Ignored bad PDB record found on line 4
REMARK ****************** INPUT FILES AND LABELS
******************************
Ignored bad PDB record found on line 5
REMARK Reflections:
Ignored bad PDB record found on line 6
REMARK file name : /home/esther/Phenix/Sml_01/Smal_mature_01_hkl.mtz
52 messages similar to the above omitted
Chain information for Smal HphA.pdb #1
---
Chain | Description
A B | No description available
> ui tool show "Show Sequence Viewer"
> sequence chain /A /B
Alignment identifier is 1
> select /B
3218 atoms, 3252 bonds, 4 pseudobonds, 233 residues, 2 models selected
> cartoon hide (#!1 & sel)
> hide (#!1 & sel) target a
> select ::name="HOH"
405 atoms, 405 residues, 1 model selected
> hide sel target a
> select /A
3218 atoms, 3252 bonds, 4 pseudobonds, 233 residues, 2 models selected
> hide (#!1 & sel) target a
> select /A:130-232
1362 atoms, 1371 bonds, 103 residues, 1 model selected
> color sel forest green
> select /A:1-129
1783 atoms, 1804 bonds, 129 residues, 1 model selected
> color sel blue
> select #1
6841 atoms, 6504 bonds, 8 pseudobonds, 871 residues, 2 models selected
> ~select #1
Nothing selected
> save "C:/PDB/Smal HphA_similarity compare.cxs"
> save "C:/PDB/Smal HphA N and Cterm.tif" width 1340 height 821 supersample 3
> transparentBackground true
> open C:/PDB/fHbp_3kvd.cxs
opened ChimeraX session
> open "C:/PDB/Smal HphA.pdb"
Summary of feedback from opening C:/PDB/Smal HphA.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Date 2019-10-03 Time 19:09:57 EDT -0400 (1570144197.21 s)
Ignored bad PDB record found on line 2
REMARK PHENIX refinement
Ignored bad PDB record found on line 4
REMARK ****************** INPUT FILES AND LABELS
******************************
Ignored bad PDB record found on line 5
REMARK Reflections:
Ignored bad PDB record found on line 6
REMARK file name : /home/esther/Phenix/Sml_01/Smal_mature_01_hkl.mtz
52 messages similar to the above omitted
Chain information for Smal HphA.pdb #2
---
Chain | Description
A B | No description available
> ui tool show Matchmaker
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fHbp3kvd.pdb, chain D (#1) with Smal HphA.pdb, chain A (#2),
sequence alignment score = 93.7
RMSD between 32 pruned atom pairs is 0.902 angstroms; (across all 171 pairs:
18.316)
> matchmaker #1/D to #2/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Smal HphA.pdb, chain A (#2) with fHbp3kvd.pdb, chain D (#1),
sequence alignment score = 93.7
RMSD between 32 pruned atom pairs is 0.902 angstroms; (across all 171 pairs:
18.316)
> select #2/B
3218 atoms, 3252 bonds, 4 pseudobonds, 233 residues, 2 models selected
> cartoon hide (#!2 & sel)
> hide (#!2 & sel) target a
> select #2/A
3218 atoms, 3252 bonds, 4 pseudobonds, 233 residues, 2 models selected
> hide (#!2 & sel) target a
> select ::name="HOH"
594 atoms, 594 residues, 2 models selected
> hide sel target a
> ui tool show Matchmaker
> matchmaker #1:214-329 #2:130-232
Missing required "to" argument
> matchmaker #1:214,329 #2:130,232
Missing required "to" argument
> matchmaker /#1:214,329 #2:130,232
Missing or invalid "matchAtoms" argument: invalid atoms specifier
> matchmaker #1:214,329 #2/A:130,232
Missing required "to" argument
> matchmaker #1:214,329 to #2/A:130,232
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Smal HphA.pdb, chain A (#2) with fHbp3kvd.pdb, chain D (#1),
sequence alignment score = 0
Fewer than 3 residues aligned; cannot match Smal HphA.pdb, chain A with
fHbp3kvd.pdb, chain D
> toolshed show
> ui tool show AlphaFold
> ui tool show ViewDockX
No suitable models found for ViewDockX
> ui tool show Matchmaker
> matchmaker #1/D to #2/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Smal HphA.pdb, chain A (#2) with fHbp3kvd.pdb, chain D (#1),
sequence alignment score = 93.7
RMSD between 32 pruned atom pairs is 0.902 angstroms; (across all 171 pairs:
18.316)
> matchmaker #1/D to #2/A pairing ss cutoffDistance 5.0
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 5
Matchmaker Smal HphA.pdb, chain A (#2) with fHbp3kvd.pdb, chain D (#1),
sequence alignment score = 93.7
RMSD between 39 pruned atom pairs is 1.548 angstroms; (across all 171 pairs:
18.325)
> matchmaker #1/D to #2/A pairing ss cutoffDistance none
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
No iteration
Matchmaker Smal HphA.pdb, chain A (#2) with fHbp3kvd.pdb, chain D (#1),
sequence alignment score = 93.7
RMSD between 171 atom pairs is 17.834 angstroms
> matchmaker #1/D to #2/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Smal HphA.pdb, chain A (#2) with fHbp3kvd.pdb, chain D (#1),
sequence alignment score = 93.7
RMSD between 32 pruned atom pairs is 0.902 angstroms; (across all 171 pairs:
18.316)
> matchmaker #1/D to #2/A pairing ss showAlignment true
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Smal HphA.pdb, chain A (#2) with fHbp3kvd.pdb, chain D (#1),
sequence alignment score = 93.7
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: fHbp3kvd.pdb #1/D, Smal
HphA.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 32 pruned atom pairs is 0.902 angstroms; (across all 171 pairs:
18.316)
> matchmaker #1/D to #2/A pairing ss cutoffDistance 5.0 showAlignment true
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 5
Matchmaker Smal HphA.pdb, chain A (#2) with fHbp3kvd.pdb, chain D (#1),
sequence alignment score = 93.7
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: fHbp3kvd.pdb #1/D, Smal
HphA.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 39 pruned atom pairs is 1.548 angstroms; (across all 171 pairs:
18.325)
> matchmaker #1/D to #2/A pairing ss showAlignment true
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Smal HphA.pdb, chain A (#2) with fHbp3kvd.pdb, chain D (#1),
sequence alignment score = 93.7
Alignment identifier is 3
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3
Hiding conservation header for alignment 3
Chains used in RMSD evaluation for alignment 3: fHbp3kvd.pdb #1/D, Smal
HphA.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
RMSD between 32 pruned atom pairs is 0.902 angstroms; (across all 171 pairs:
18.316)
> close session
> open "C:\PDB\TbpB 3VE1.cxs" format session
opened ChimeraX session
> close session
> open C:\PDB\LbpB.cxs format session
opened ChimeraX session
> close session
> open "C:\PDB\hpuA in Kingella.cxs" format session
opened ChimeraX session
> close session
> open "C:\PDB\NHBA 2LFU.cxs" format session
opened ChimeraX session
> close session
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 3.3.0 - Build 27.20.100.9415
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel
Manufacturer: SAMSUNG ELECTRONICS CO., LTD.
Model: 950XDA
OS: Microsoft Windows 10 Pro (Build 19042)
Memory: 16,838,230,016
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHz
OSLanguage: ko-KR
Locale: ('en_CA', '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 (1)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Platform |
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash using File→Open on Windows and/or in trigger.activate() |
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