Opened 3 years ago

Closed 3 years ago

#8261 closed defect (can't reproduce)

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

Reported by: joewang@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Platform Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x8001010e

Thread 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005a30 (most recent call first):
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1276 in _choose_mtz_file
  File "C:\Users\cwang6\AppDatWindows fatal exception: acode 0x\8001010eL

ocalWindows fatal exception: \code 0xU8001010eC

SFWindows fatal exception: \code 0xC8001010eh

imWindows fatal exception: ecode 0xr8001010ea

X\1Windows fatal exception: .code 0x38001010e\

sitWindows fatal exception: ecode 0x-8001010ep

ackaWindows fatal exception: gcode 0xe8001010es

\chWindows fatal exception: icode 0xm8001010ee

raxWindows fatal exception: \code 0xi8001010es

olWindows fatal exception: dcode 0xe8001010e\

isWindows fatal exception: ocode 0xl8001010ed

e.py", line 1302 in _choose_reflections_file
  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-paWindows fatal exception: code 0xc8001010ek

ages\CWindows fatal exception: hcode 0xi8001010em

eraXWindows fatal exception: _code 0xm8001010e

aiWindows fatal exception: ncode 0x.8001010ep

y"Windows fatal exception: , line code 0x867 in 8001010ei

nitWindows fatal exception: 
code 0x  File 8001010e"

C:\Windows fatal exception: Pcode 0xr8001010eo

graWindows fatal exception: mcode 0x 8001010eF

ilWindows fatal exception: ecode 0xs8001010e\

ChWindows fatal exception: icode 0xm8001010eer

aXWindows fatal exception:  code 0x18001010e.

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 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005a30 (most recent call first):
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1276 in _choose_mtz_file
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1302 in _choose_reflections_file
  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 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005a30 (most recent call first):
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1276 in _choose_mtz_file
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1302 in _choose_reflections_file
  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 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005a30 (most recent call first):
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1276 in _choose_mtz_file
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1302 in _choose_reflections_file
  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 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005a30 (most recent call first):
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1276 in _choose_mtz_file
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1302 in _choose_reflections_file
  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 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005a30 (most recent call first):
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1276 in _choose_mtz_file
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1302 in _choose_reflections_file
  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 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005a30 (most recent call first):
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1276 in _choose_mtz_file
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1302 in _choose_reflections_file
  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 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005a30 (most recent call first):
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1276 in _choose_mtz_file
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1302 in _choose_reflections_file
  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 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005a30 (most recent call first):
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1276 in _choose_mtz_file
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1302 in _choose_reflections_file
  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 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005a30 (most recent call first):
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1276 in _choose_mtz_file
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1302 in _choose_reflections_file
  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 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005a30 (most recent call first):
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1276 in _choose_mtz_file
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1302 in _choose_reflections_file
  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 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005a30 (most recent call first):
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1276 in _choose_mtz_file
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1302 in _choose_reflections_file
  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 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _boWindows fatal exception: ocode 0x8001010et

strap

Windows fatal exception: Thread 0xcode 0x00005a308001010e (most recent call first):


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

UsWindows fatal exception: ecode 0xr8001010es

\cWindows fatal exception: wcode 0xa8001010en

gWindows fatal exception: 6code 0x\8001010eA

ppWindows fatal exception: Dcode 0xa8001010et

a\LWindows fatal exception: ocode 0xc8001010ea

l\Windows fatal exception: Ucode 0xC8001010eS

F\CWindows fatal exception: hcode 0xim8001010ee

raWindows fatal exception: Xcode 0x\8001010e1

.3\site-packages\chimerax\isolde\isolde.py", line 1276 in _choose_mtz_file
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1302 in _choose_reflections_file
  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 "CWindows fatal exception: :code 0x\8001010eP

rogramWindows fatal exception:  code 0xF8001010ei

lesWindows fatal exception: \code 0xC8001010eh

imWindows fatal exception: ecode 0xr8001010ea

X 1Windows fatal exception: .code 0x3\8001010eb

inWindows fatal exception: \code 0xl8001010ei

b\Windows fatal exception: rcode 0xu8001010e

nWindows fatal exception: pcode 0xy8001010e.

pyWindows fatal exception: "code 0x, line 8001010e87

 in _Windows fatal exception: rcode 0xu8001010en

_cWindows fatal exception: ocode 0xd8001010ee


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

Thread 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005a30 (most recent call first):
  File "C:\Users\cwang6\AppData\Local\Windows fatal exception: Ucode 0xC8001010eS

F\ChimeWindows fatal exception: rcode 0xa8001010eX

\1.Windows fatal exception: 3code 0x\8001010es

itWindows fatal exception: code 0xe8001010e-

pacWindows fatal exception: kcode 0xa8001010eg

esWindows fatal exception: \code 0xc8001010eh

imWindows fatal exception: ecode 0xr8001010ea

x\Windows fatal exception: icode 0xs8001010eo

ldWindows fatal exception: ecode 0x\8001010ei

soWindows fatal exception: lcode 0xd8001010ee

.pyWindows fatal exception: "code 0x, line 8001010e1276

 in _choose_mtz_file
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1302 in _choose_reflections_file
  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 code 0x
8001010e  File 

"C:\ProWindows fatal exception: gcode 0xr8001010ea

m Windows fatal exception: Fcode 0x8001010eil

esWindows fatal exception: \code 0xC8001010eh

imWindows fatal exception: ecode 0xr8001010ea

X Windows fatal exception: 1.3\bin\lib\runpy.pcode 0xy8001010e"

, line 87Windows fatal exception:  in code 0x_8001010er

un_Windows fatal exception: ccode 0xo8001010ed

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

ProWindows fatal exception: gcode 0xr8001010ea

m Windows fatal exception: Fcode 0x8001010e

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

Thread 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005a30 (most recent call first):
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1276 in _choose_mtz_file
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimWindows fatal exception: code 0x8001010ee

rax\isoldWindows fatal exception: ecode 0x\8001010ei

soldWindows fatal exception: ecode 0x.8001010ep

y"Windows fatal exception: , line code 0x13028001010e in 

_choWindows fatal exception: ocode 0xs8001010ee

_reWindows fatal exception: fcode 0xl8001010ee

ctWindows fatal exception: icode 0xo8001010en

s_Windows fatal exception: fcode 0xi8001010el

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

:Windows fatal exception: \code 0xP8001010er

ogrWindows fatal exception: acode 0xm8001010e 

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 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line Windows fatal exception: 574code 0x in 8001010e

wait
  File Windows fatal exception: code 0x"8001010eC

:Windows fatal exception: \code 0xP8001010er

oWindows fatal exception: gcode 0x8001010e

rWindows fatal exception: acode 0xm8001010e 

FilWindows fatal exception: ecode 0xs8001010e\

ChWindows fatal exception: icode 0xm8001010ee

rWindows fatal exception: acode 0xX8001010e 

1Windows fatal exception: .code 0x38001010e\

binWindows fatal exception: \code 0xl8001010ei

b\Windows fatal exception: tcode 0xh8001010er

eading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005a30 (most recent call first):
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1276 in _choose_mtz_file
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1Windows fatal exception: .code 0x38001010e\

siteWindows fatal exception: -code 0xp8001010ea

ckWindows fatal exception: acode 0xg8001010ee

s\cWindows fatal exception: hcode 0xi8001010eme

raxWindows fatal exception: \code 0xi8001010es

olWindows fatal exception: dcode 0xe8001010e\

isWindows fatal exception: ocode 0xl8001010ed

e.Windows fatal exception: pcode 0xy8001010e"

, line 1302Windows fatal exception:  in code 0x_8001010ec

hoWindows fatal exception: ocode 0xs8001010ee

_reWindows fatal exception: fcode 0xl8001010ee

ctions_file
  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 _ruWindows fatal exception: code 0xn8001010e_c

ode
  File "C:\Windows fatal exception: Pcode 0xr8001010eo

grWindows fatal exception: acode 0xm8001010e 

FiWindows fatal exception: code 0x8001010e

Windows fatal exception: code 0xl8001010ee

s\Windows fatal exception: Ccode 0xh8001010ei

meWindows fatal exception: rcode 0xa8001010eX

 1Windows fatal exception: .code 0x8001010e3

\bWindows fatal exception: icode 0xn8001010e\

liWindows fatal exception: bcode 0x\8001010er

unWindows fatal exception: pcode 0x8001010e

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

Thread 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.Windows fatal exception: pcode 0xy8001010e"

, line 574 in wWindows fatal exception: acode 0xi8001010et


  File Windows fatal exception: "code 0xC8001010e:

\PWindows fatal exception: rcode 0xo8001010eg

ramWindows fatal exception:  code 0xF8001010ei

leWindows fatal exception: s\code 0xC8001010eh

imerWindows fatal exception: acode 0xX8001010e 

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

inWindows fatal exception: \code 0xl8001010ei

b\tWindows fatal exception: hcode 0xr8001010ee

adWindows fatal exception: icode 0xn8001010eg

.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"Windows fatal exception: , line code 0x9308001010e in 

_booWindows fatal exception: tcode 0xstr8001010ea

p

Thread 0xWindows fatal exception: 00005a30code 0x (most recent call first):
8001010e  File 

"C:Windows fatal exception: \code 0xU8001010es

ersWindows fatal exception: \code 0xc8001010ew

anWindows fatal exception: gcode 0x68001010e\

ApWindows fatal exception: pcode 0xD8001010ea

taWindows fatal exception: \code 0xL8001010eo

caWindows fatal exception: lcode 0x\8001010eU

CSFWindows fatal exception: \code 0xC8001010eh

imWindows fatal exception: ecode 0xr8001010ea

X\1.3\site-packages\chimerax\isolde\isolde.py", line 1276 in _choose_mtz_file
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolWindows fatal exception: dcode 0xe8001010e\

isoWindows fatal exception: lcode 0xd8001010ee

.pyWindows fatal exception: "code 0x, line 8001010e1302

 in _cWindows fatal exception: hcode 0xo8001010eo

se_Windows fatal exception: rcode 0xe8001010ef

leWindows fatal exception: ccode 0xt8001010ei

onWindows fatal exception: scode 0x_8001010ef

ileWindows fatal exception: 
code 0x  File 8001010e"C

:\PWindows fatal exception: rcode 0xo8001010eg

ramWindows fatal exception:  code 0xF8001010ei

lesWindows fatal exception: \code 0xC8001010eh

imeraX 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 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005a30 (most recent call first):
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1276 in _choose_mtz_file
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1302 in _choose_reflections_file
  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 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005a30 (most recent call first):
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1276 in _choose_mtz_file
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1302 in _choose_reflections_file
  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 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005a30 (most recent call first):
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1276 in _choose_mtz_file
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1302 in _choose_reflections_file
  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 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005a30 (most recent call first):
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1276 in _choose_mtz_file
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1302 in _choose_reflections_file
  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 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005a30 (most recent call first):
  File "C:\Users\cwang6\AppData\LocWindows fatal exception: acode 0xl8001010e\

UCSF\ChiWindows fatal exception: mcode 0xe8001010er

aXWindows fatal exception: \code 0x18001010e.

3Windows fatal exception: \code 0xs8001010ei

teWindows fatal exception: -code 0xp8001010ea

ckaWindows fatal exception: gcode 0xe8001010es

\chiWindows fatal exception: mcode 0xe8001010er

axWindows fatal exception: \icode 0xs8001010eo

ldWindows fatal exception: ecode 0x\8001010ei

soWindows fatal exception: lcode 0xd8001010ee

.pyWindows fatal exception: "code 0x, line 8001010e1276

 in _choose_mtz_file
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1302 in _choose_reflections_file
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File Windows fatal exception: "code 0xC8001010e:

\Program Windows fatal exception: Fcode 0xi8001010el

eWindows fatal exception: scode 0x\8001010eC

hiWindows fatal exception: mcode 0xe8001010era

X Windows fatal exception: 1code 0x.38001010e\

biWindows fatal exception: ncode 0x\8001010el

ibWindows fatal exception: \code 0xs8001010ei

teWindows fatal exception: -code 0xp8001010ea

ckWindows fatal exception: acode 0xg8001010ee

s\Windows fatal exception: Ccode 0xh8001010ei

meWindows fatal exception: rcode 0xa8001010eX

_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 FWindows fatal exception: icode 0xl8001010ee

s\ChimWindows fatal exception: ecode 0xr8001010e

Windows fatal exception: acode 0xX8001010e 

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

inWindows fatal exception: \code 0xl8001010ei

b\Windows fatal exception: code 0xr8001010eu

npyWindows fatal exception: .code 0xp8001010ey

", line Windows fatal exception: 87code 0x in 8001010e_

ruWindows fatal exception: ncode 0x_8001010ec

odWindows fatal exception: ecode 0x
8001010e  File 

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

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

Thread 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\Windows fatal exception: Ccode 0xh8001010ei

meraWindows fatal exception: Xcode 0x 8001010e1

.3Windows fatal exception: \code 0xb8001010ei

n\lWindows fatal exception: icode 0x8001010eb

\tWindows fatal exception: hcode 0xr8001010ee

adWindows fatal exception: icode 0xn8001010eg

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

930 in Windows fatal exception: _code 0xb8001010eo

otWindows fatal exception: scode 0xt8001010er

apWindows fatal exception: 
code 0x
8001010eThread 0x

00005a30 (most recent call first):
  File Windows fatal exception: "code 0xC8001010e:

\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\isolde.py", line 1276 in _choose_mtz_file
  File "CWindows fatal exception: :code 0x\8001010eU

sersWindows fatal exception: \code 0xc8001010ew

anWindows fatal exception: gcode 0x6\8001010eA

ppWindows fatal exception: Dcode 0xa8001010et

a\Windows fatal exception: Lcode 0xo8001010ec

al\Windows fatal exception: Ucode 0xC8001010e

SFWindows fatal exception: \code 0xC8001010eh

imWindows fatal exception: ecode 0xr8001010ea

X\Windows fatal exception: 1code 0x.38001010e\

siWindows fatal exception: tcode 0xe8001010e-

paWindows fatal exception: ccode 0xk8001010ea

ges\chimerax\isolde\isolde.py", line 1302 in _choose_reflections_file
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimeWindows fatal exception: rcode 0xa8001010ex

\ui\Windows fatal exception: gcode 0xu8001010ei

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

301 in Windows fatal exception: ecode 0xv8001010ee

ntWindows fatal exception: _code 0xl8001010eo

opWindows fatal exception: 
code 0x  File 8001010e"

C:Windows fatal exception: \code 0xP8001010er

ogWindows fatal exception: rcode 0xa8001010em

 FWindows fatal exception: icode 0xl8001010ee

s\Windows fatal exception: Ccode 0xh8001010ei

meWindows fatal exception: rcode 0xa8001010eX

 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 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005a30 (most recent call first):
  File "C:\Users\cwang6\AppData\Local\UCSF\ChimeraX\1.3\site-packages\chimerax\isolde\molobject.py", line 1783 in _get_and_process_changes
Windows fatal exception: access violation

===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\\\Users\\\cwang6\\\Desktop\\\DNA\\\Coot\\\Central_ring.mrc

Opened Central_ring.mrc as #1, grid size 102,59,89, pixel 2.8,2.8,2.8, shown
at level 0.0131, step 1, values float32  

> open C:/Users/cwang6/Desktop/DNA/Coot/DNA_fit.pdb

Chain information for DNA_fit.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> ui tool show "Map Coordinates"

> volume #1 level 0.003536

> open D:/Projects/HBc_Mature/30_bp.pdb

Chain information for 30_bp.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> select #3

1912 atoms, 2060 bonds, 60 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #3,1,0,0,82.605,0,1,0,184.59,0,0,1,176.04

> view matrix models #3,1,0,0,70.601,0,1,0,135.69,0,0,1,201.69

> view matrix models #3,1,0,0,72.838,0,1,0,141.61,0,0,1,216.82

> view matrix models #3,1,0,0,75.709,0,1,0,138.89,0,0,1,210.46

> ui tool show "Fit in Map"

Fit molecule DNA_fit.pdb (#2) to map Central_ring.mrc (#1) using 19023 atoms  
average map value = 0.008043, steps = 2000  
shifted from previous position = 7.32  
rotated from previous position = 1.38 degrees  
atoms outside contour = 17055, contour level = 0.0035363  
  
Position of DNA_fit.pdb (#2) relative to Central_ring.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99971951 0.02364083 -0.00141926 -0.89468453  
-0.02363514 0.99971303 0.00390361 5.80958671  
0.00151114 -0.00386897 0.99999137 -2.79238077  
Axis -0.16192814 -0.06104968 -0.98491229  
Axis point 252.08041810 23.43488804 0.00000000  
Rotation angle (degrees) 1.37523600  
Shift along axis 2.54045130  
  
Fit molecule DNA_fit.pdb (#2) to map Central_ring.mrc (#1) using 19023 atoms  
average map value = 0.008004, steps = 2000  
shifted from previous position = 6.26  
rotated from previous position = 0.847 degrees  
atoms outside contour = 17059, contour level = 0.0035363  
  
Position of DNA_fit.pdb (#2) relative to Central_ring.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99981223 0.01483433 -0.01246793 1.59796532  
-0.01473297 0.99985798 0.00818259 3.48499170  
0.01258754 -0.00799737 0.99988879 -3.41009465  
Axis -0.38525970 -0.59659372 -0.70402478  
Axis point 225.57720406 -97.23091457 0.00000000  
Rotation angle (degrees) 1.20322918  
Shift along axis -0.29396466  
  
Fit molecule DNA_fit.pdb (#2) to map Central_ring.mrc (#1) using 19023 atoms  
average map value = 0.007931, steps = 2000  
shifted from previous position = 9.16  
rotated from previous position = 1.23 degrees  
atoms outside contour = 17083, contour level = 0.0035363  
  
Position of DNA_fit.pdb (#2) relative to Central_ring.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99997429 0.00454567 0.00554579 0.08172736  
-0.00462035 0.99989782 0.01352784 1.15789538  
-0.00548373 -0.01355312 0.99989312 -0.41109591  
Axis -0.88373276 0.35992601 -0.29911482  
Axis point 0.00000000 -19.43656047 -73.30197112  
Rotation angle (degrees) 0.87791535  
Shift along axis 0.46749640  
  
Fit molecule DNA_fit.pdb (#2) to map Central_ring.mrc (#1) using 19023 atoms  
average map value = 0.007969, steps = 2000  
shifted from previous position = 2.82  
rotated from previous position = 0.444 degrees  
atoms outside contour = 17088, contour level = 0.0035363  
  
Position of DNA_fit.pdb (#2) relative to Central_ring.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99995713 0.00917084 0.00127550 0.05736136  
-0.00919236 0.99979503 0.01803875 0.51076973  
-0.00110981 -0.01804970 0.99983647 -0.54416055  
Axis -0.88971153 0.05880670 -0.45271975  
Axis point 0.00000000 -24.24324749 -27.85595763  
Rotation angle (degrees) 1.16209420  
Shift along axis 0.22535385  
  
Fit molecule DNA_fit.pdb (#2) to map Central_ring.mrc (#1) using 19023 atoms  
average map value = 0.007942, steps = 2000  
shifted from previous position = 26.1  
rotated from previous position = 3.45 degrees  
atoms outside contour = 17066, contour level = 0.0035363  
  
Position of DNA_fit.pdb (#2) relative to Central_ring.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99777894 0.05557264 -0.03672701 0.37110379  
-0.05474739 0.99823284 0.02310660 5.53002446  
0.03794620 -0.02104457 0.99905816 -4.80422131  
Axis -0.31459667 -0.53207964 -0.78607900  
Axis point 108.18853593 -6.41470138 0.00000000  
Rotation angle (degrees) 4.02381367  
Shift along axis 0.71733602  
  
Fit molecule DNA_fit.pdb (#2) to map Central_ring.mrc (#1) using 19023 atoms  
average map value = 0.008013, steps = 2000  
shifted from previous position = 7.04  
rotated from previous position = 0.949 degrees  
atoms outside contour = 17054, contour level = 0.0035363  
  
Position of DNA_fit.pdb (#2) relative to Central_ring.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99861005 0.04732733 -0.02319661 -0.71806443  
-0.04668260 0.99852870 0.02758948 3.83435297  
0.02446822 -0.02646826 0.99935016 -2.33573300  
Axis -0.45634934 -0.40238110 -0.79362128  
Axis point 87.27532373 11.57874859 0.00000000  
Rotation angle (degrees) 3.39552807  
Shift along axis 0.63850448  
  

> close #2

Fit molecule 30_bp.pdb (#3) to map Central_ring.mrc (#1) using 1912 atoms  
average map value = 0.0161, steps = 68  
shifted from previous position = 9.89  
rotated from previous position = 6.85 degrees  
atoms outside contour = 282, contour level = 0.0035363  
  
Position of 30_bp.pdb (#3) relative to Central_ring.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99286468 0.11873215 0.01106407 85.71037134  
-0.11878095 0.99291298 0.00386107 146.13874937  
-0.01052723 -0.00514772 0.99993134 209.16541889  
Axis -0.03774695 0.09046791 -0.99518376  
Axis point 1415.49311940 -573.81225445 0.00000000  
Rotation angle (degrees) 6.85351029  
Shift along axis -198.17246728  
  
Fit molecule 30_bp.pdb (#3) to map Central_ring.mrc (#1) using 1912 atoms  
average map value = 0.0161, steps = 40  
shifted from previous position = 0.0887  
rotated from previous position = 1.17 degrees  
atoms outside contour = 284, contour level = 0.0035363  
  
Position of 30_bp.pdb (#3) relative to Central_ring.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99280476 0.11939604 0.00912687 85.80021576  
-0.11923618 0.99273022 -0.01641486 146.14695633  
-0.01102039 0.01520850 0.99982361 209.19928772  
Axis 0.13091299 0.08340473 -0.98787926  
Axis point 1404.77156499 -834.87935579 0.00000000  
Rotation angle (degrees) 6.93712376  
Shift along axis -183.24192864  
  
Fit molecule 30_bp.pdb (#3) to map Central_ring.mrc (#1) using 1912 atoms  
average map value = 0.0161, steps = 40  
shifted from previous position = 0.0828  
rotated from previous position = 1.01 degrees  
atoms outside contour = 288, contour level = 0.0035363  
  
Position of 30_bp.pdb (#3) relative to Central_ring.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99270516 0.12032574 0.00762810 85.86540046  
-0.12000373 0.99219557 -0.03386809 146.13075833  
-0.01164377 0.03270562 0.99939720 209.22128739  
Axis 0.26616346 0.07704948 -0.96084358  
Axis point 1389.82982545 -998.56926777 0.00000000  
Rotation angle (degrees) 7.18431918  
Shift along axis -166.91540065  
  
Fit molecule 30_bp.pdb (#3) to map Central_ring.mrc (#1) using 1912 atoms  
average map value = 0.0161, steps = 28  
shifted from previous position = 0.0335  
rotated from previous position = 0.0871 degrees  
atoms outside contour = 286, contour level = 0.0035363  
  
Position of 30_bp.pdb (#3) relative to Central_ring.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99278794 0.11965303 0.00743386 85.86844296  
-0.11932227 0.99223106 -0.03520976 146.12829501  
-0.01158906 0.03406880 0.99935230 209.22351100  
Axis 0.27762421 0.07623171 -0.95766044  
Axis point 1396.54223683 -1017.20562755 0.00000000  
Rotation angle (degrees) 7.16749533  
Shift along axis -165.38631191  
  

> save C:/Users/cwang6/Desktop/DNA/Coot/30bp_fit.pdb relModel #1

> select clear

> color #1 #b2b2b29b models

Fit molecule 30_bp.pdb (#3) to map Central_ring.mrc (#1) using 1912 atoms  
average map value = 0.0161, steps = 40  
shifted from previous position = 0.0581  
rotated from previous position = 0.872 degrees  
atoms outside contour = 288, contour level = 0.0035363  
  
Position of 30_bp.pdb (#3) relative to Central_ring.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99276464 0.11992919 0.00594680 85.92779414  
-0.11948204 0.99155930 -0.05034071 146.13904934  
-0.01193393 0.04926595 0.99871440 209.24113589  
Axis 0.38321892 0.06879291 -0.92109217  
Axis point 1387.82747084 -1111.26054877 0.00000000  
Rotation angle (degrees) 7.46731079  
Shift along axis -149.74788462  
  

> ui tool show ISOLDE

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Chain information for 30_bp.pdb  
---  
Chain | Description  
2.2/A | No description available  
2.2/B | No description available  
  
Done loading forcefield  
Opened Central_ring.mrc as #2.1.1.1, grid size 102,59,89, pixel 2.8,2.8,2.8,
shown at step 1, values float32  


===== 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  

> open C:\\\Users\\\cwang6\\\Desktop\\\DNA\\\Coot\\\Central_ring.mrc

Opened Central_ring.mrc as #1, grid size 102,59,89, pixel 2.8,2.8,2.8, shown
at level 0.0131, step 1, values float32  




OpenGL version: 3.3.0 NVIDIA 471.68
OpenGL renderer: Quadro T2000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision 5540
OS: Microsoft Windows 10 Enterprise (Build 19044)
Memory: 34,040,631,296
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i9-9880H CPU @ 2.30GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
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-Clipper: 0.17.0
    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-ISOLDE: 1.3
    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-PDBImages: 1.1
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-Phenix: 0.3
    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
    MolecularDynamicsViewer: 1.4
    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
    Send2Trash: 1.8.0
    SEQCROW: 1.4.2
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

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

comment:2 by Eric Pettersen, 3 years ago

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

Hi Joseph,

Thanks for reporting this problem. We believe it is fixed in the ChimeraX 1.5 release, so if you upgrade to that then I believe you won't experience this problem anymore.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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