Opened 4 years ago

Last modified 4 years ago

#6200 feedback defect

Crash using File→Open on Windows and/or in trigger.activate()

Reported by: esther.shin@… Owned by: pett
Priority: normal Milestone:
Component: Platform Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by pett) 

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 (4)

comment:1 by pett, 4 years ago

Cc: Tom Goddard added
Component: Unassigned → Platform
Description: modified (diff)
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash using File→Open on Windows and/or in trigger.activate()

comment:2 by pett, 4 years ago

Status: accepted → feedback

Hi Esther,

Thanks for reporting this problem. Were you using the File→Open dialog when this crash occurred?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

in reply to:  3 ; comment:3 by esther.shin@…, 4 years ago 

Hi Eric,

Yes that is correct. The screen froze and the chimera closed on its own afterwards


________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, February 18, 2022, 12:15 p.m.
Cc: Esther  Shin; goddard@cgl.ucsf.edu; pett@cgl.ucsf.edu
Subject: Re: [ChimeraX] #6200: Crash using File→Open on Windows and/or in trigger.activate()

[You don't often get email from chimerax-bugs-admin@cgl.ucsf.edu. Learn why this is important at http://aka.ms/LearnAboutSenderIdentification.]

#6200: Crash using File→Open on Windows and/or in trigger.activate()
------------------------------------+----------------------
          Reporter:  esther.shin@…  |      Owner:  pett
              Type:  defect         |     Status:  feedback
          Priority:  normal         |  Milestone:
         Component:  Platform       |    Version:
        Resolution:                 |   Keywords:
        Blocked By:                 |   Blocking:
Notify when closed:                 |   Platform:  all
           Project:  ChimeraX       |
------------------------------------+----------------------
Changes (by pett):

 * status:  accepted => feedback


Comment:

 Hi Esther,
         Thanks for reporting this problem.  Were you using the File→Open
 dialog when this crash occurred?

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab

--
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comment:4 by pett, 4 years ago

Hi Esther,

Thanks for confirming. Does this happen often, or was it more of a one-time thing? If it happens often, there are some things you could try out for us to see if it remedies the problem.

--Eric

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