Opened 3 years ago

Closed 3 years ago

#8822 closed defect (can't reproduce)

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

Reported by: 20210700031@… 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:        Linux-5.13.0-37-generic-x86_64-with-glibc2.31
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.
Fatal Python error: Segmentation fault

Current thread 0x00007fdf19780740 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/open_save.py", line 87 in get_path
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/map/session.py", line 252 in find
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/map/session.py", line 136 in absolute_path
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/map/session.py", line 379 in grid_data_from_state
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/map/session.py", line 219 in restore_snapshot
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/session.py", line 725 in restore
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/session.py", line 995 in open
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core_formats/__init__.py", line 26 in open
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 403 in remember_data_format
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 433 in collated_open
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 181 in provider_open
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2856 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 118 in cmd_open
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2856 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 36 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 846 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 87 in _run_code
  File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== 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 compare.cxs

QAccessibleTree::indexFromLogical: invalid index: -1 0 for
QTreeView(0x1b11fc0, name="treeView")  

Requested invalid tree cell: -1 0  


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

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

> open compare.cxs

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

Opened cryosparc_P3_J323_map.mrc as #1, grid size 256,256,256, pixel 1.57,
shown at level 0.848, step 1, values float32  
Opened cryosparc_P3_J306_003_volume_map.mrc as #3, grid size 256,256,256,
pixel 1.57, shown at level 0.775, step 1, values float32  
Opened emd_21374.map as #4, grid size 432,432,432, pixel 1.05, shown at level
0.5, step 1, values float32  
Opened emd_22907.map as #6, grid size 512,512,512, pixel 0.834, shown at level
6.52, step 1, values float32  
Log from Tue Apr 11 20:50:39 2023UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open cryosparc_P3_J323_map.mrc

Opened cryosparc_P3_J323_map.mrc as #1, grid size 256,256,256, pixel 1.57,
shown at level 0.522, step 1, values float32  

> volume #1 level 0.9666

> set bgColor white

> graphics silhouettes true

> lighting soft

> volume #1 level 0.7985

> open /home/jiangxinyi/Downloads/cryosparc_P3_J317_009_volume_map.mrc

Opened cryosparc_P3_J317_009_volume_map.mrc as #2, grid size 256,256,256,
pixel 1.57, shown at level 0.522, step 1, values float32  

> hide #!1 models

> volume #1 level 0.7206

> volume #2 level 0.6999

QSpiApplication::keyEventError "org.freedesktop.DBus.Error.NoReply" "Did not
receive a reply. Possible causes include: the remote application did not send
a reply, the message bus security policy blocked the reply, the reply timeout
expired, or the network connection was broken."  

> fitmap #1 inMap #2 search 20

Found 13 unique fits from 20 random placements having fraction of points
inside contour >= 0.100 (19 of 20).  
  
Correlations and times found:  
0.8853 (2), 0.8852 (3), 0.8454 (1), 0.8454 (1), 0.7537 (2), 0.7537 (2), 0.7537
(2), 0.7537 (1), 0.7536 (1), 0.7534 (1), 0.7534 (1), 0.7528 (1), 0.7263 (1)  
  
Best fit found:  
Fit map cryosparc_P3_J323_map.mrc in map cryosparc_P3_J317_009_volume_map.mrc
using 130247 points  
correlation = 0.8853, correlation about mean = 0.1949, overlap = 1.43e+05  
steps = 696, shift = 53.9, angle = 93.6 degrees  
Position of cryosparc_P3_J323_map.mrc (#1) relative to
cryosparc_P3_J317_009_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.07956883 0.99682926 -0.00047292 -15.23943265  
0.99682921 -0.07956855 0.00066113 16.48706099  
0.00062140 -0.00052403 -0.99999969 401.91733287  
Axis -0.73470284 -0.67838908 -0.00002924  
Axis point 0.00000000 15.38951493 200.95444478  
Rotation angle (degrees) 179.95378747  
Shift along axis 0.00006021  
  
Found 13 fits.  

QSpiApplication::keyEventError "org.freedesktop.DBus.Error.NoReply" "Did not
receive a reply. Possible causes include: the remote application did not send
a reply, the message bus security policy blocked the reply, the reply timeout
expired, or the network connection was broken."  

> hide #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!2 models

> show #!1 models

> hide #!2 models

> close #2

WARNING Qt AtSpiAdaptor: Accessible invalid: QAccessibleInterface(0x647aa40
invalid) "/org/a11y/atspi/accessible/2147484181"  

[Repeated 5 time(s)]

> open /home/jiangxinyi/Downloads/cryosparc_P3_J326_map.mrc

Opened cryosparc_P3_J326_map.mrc as #2, grid size 256,256,256, pixel 1.57,
shown at level 0.554, step 1, values float32  

WARNING Qt AtSpiAdaptor: Accessible invalid: QAccessibleInterface(0x638dab0
invalid) "/org/a11y/atspi/accessible/2147484174"  

[Repeated 13 time(s)]

WARNING Qt AtSpiAdaptor: Accessible invalid: QAccessibleInterface(0x15a6270
invalid) "/org/a11y/atspi/accessible/2147484177"  

[Repeated 6 time(s)]

WARNING Qt AtSpiAdaptor: Accessible invalid: QAccessibleInterface(0x638dab0
invalid) "/org/a11y/atspi/accessible/2147484174"  

[Repeated 6 time(s)]

> fitmap #1 inMap #2 search 20

Found 9 unique fits from 20 random placements having fraction of points inside
contour >= 0.100 (17 of 20).  
  
Correlations and times found:  
0.9923 (4), 0.992 (5), 0.992 (1), 0.7642 (2), 0.7578 (1), 0.7578 (1), 0.7576
(1), 0.7496 (1), 0.7408 (1)  
  
Best fit found:  
Fit map cryosparc_P3_J323_map.mrc in map cryosparc_P3_J326_map.mrc using
130247 points  
correlation = 0.9923, correlation about mean = 0.8741, overlap = 1.777e+05  
steps = 368, shift = 69.8, angle = 42.1 degrees  
Position of cryosparc_P3_J323_map.mrc (#1) relative to
cryosparc_P3_J326_map.mrc (#2) coordinates:  
Matrix rotation and translation  
1.00000002 -0.00000814 0.00013163 -0.03035981  
0.00000811 0.99999998 -0.00020832 0.06013743  
-0.00013163 0.00020835 0.99999998 0.00406354  
Axis 0.84493841 0.53384713 0.03295946  
Axis point 0.00000000 -18.42344301 271.78636234  
Rotation angle (degrees) 0.01412719  
Shift along axis 0.00658596  
  
Found 9 fits.  

QSpiApplication::keyEventError "org.freedesktop.DBus.Error.NoReply" "Did not
receive a reply. Possible causes include: the remote application did not send
a reply, the message bus security policy blocked the reply, the reply timeout
expired, or the network connection was broken."  

> volume #2 level 0.721

QSpiApplication::keyEventError "org.freedesktop.DBus.Error.NoReply" "Did not
receive a reply. Possible causes include: the remote application did not send
a reply, the message bus security policy blocked the reply, the reply timeout
expired, or the network connection was broken."  

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> volume #2 level 1.034

> volume #2 level 0.4549

> volume #2 level 0.1105

> show #!1 models

> volume #1 level 0.5203

> hide #!2 models

> volume #1 level 0.1698

> hide #!1 models

> show #!2 models

> volume #2 level 0.1

QSpiApplication::keyEventError "org.freedesktop.DBus.Error.NoReply" "Did not
receive a reply. Possible causes include: the remote application did not send
a reply, the message bus security policy blocked the reply, the reply timeout
expired, or the network connection was broken."  

> volume #2 level 0.17

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> volume #2 level 0.671

> volume #2 level 0.8484

> open
> /home/jiangxinyi/data/200kv/tribody/cryosparc_P3_J306_003_volume_map.mrc

Opened cryosparc_P3_J306_003_volume_map.mrc as #3, grid size 256,256,256,
pixel 1.57, shown at level 0.461, step 1, values float32  

> fitmap #3 inMap #2 search 20

Found 11 unique fits from 20 random placements having fraction of points
inside contour >= 0.100 (18 of 20).  
  
Correlations and times found:  
0.9813 (3), 0.9813 (3), 0.7384 (1), 0.7384 (2), 0.7284 (1), 0.7284 (2), 0.7283
(2), 0.7282 (1), 0.728 (1), 0.7267 (1), 0.7032 (1)  
  
Best fit found:  
Fit map cryosparc_P3_J306_003_volume_map.mrc in map cryosparc_P3_J326_map.mrc
using 167748 points  
correlation = 0.9813, correlation about mean = 0.8269, overlap = 1.762e+05  
steps = 504, shift = 55.8, angle = 45.5 degrees  
Position of cryosparc_P3_J306_003_volume_map.mrc (#3) relative to
cryosparc_P3_J326_map.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.54413293 -0.83899900 0.00020599 478.88718291  
-0.83899901 0.54413288 -0.00018349 260.25049347  
0.00004184 -0.00027268 -0.99999996 396.16584607  
Axis -0.47743731 0.87866582 -0.00003879  
Axis point 310.15978077 0.00000000 198.07594041  
Rotation angle (degrees) 179.99464820  
Shift along axis 0.01923893  
  
Found 11 fits.  

QSpiApplication::keyEventError "org.freedesktop.DBus.Error.NoReply" "Did not
receive a reply. Possible causes include: the remote application did not send
a reply, the message bus security policy blocked the reply, the reply timeout
expired, or the network connection was broken."  

> hide #!2 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!3 models

> volume #3 level 0.848

QSpiApplication::keyEventError "org.freedesktop.DBus.Error.NoReply" "Did not
receive a reply. Possible causes include: the remote application did not send
a reply, the message bus security policy blocked the reply, the reply timeout
expired, or the network connection was broken."  

[Repeated 1 time(s)]

> volume #1 level 0.848

QSpiApplication::keyEventError "org.freedesktop.DBus.Error.NoReply" "Did not
receive a reply. Possible causes include: the remote application did not send
a reply, the message bus security policy blocked the reply, the reply timeout
expired, or the network connection was broken."  

> show #!1 models

> show #!2 models

> hide #!1 models

> hide #!2 models

> hide #!3 models

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!2 models

> show #!1 models

> hide #!1 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!3 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> volume #3 level 0.8317

> volume #3 level 0.7748

> open /home/jiangxinyi/data/200kv/tribody/7kkk-wts-tribody-fit.pdb

Chain information for 7kkk-wts-tribody-fit.pdb #4  
---  
Chain | Description  
A B C | No description available  
D E F | No description available  
  

WARNING Qt AtSpiAdaptor: Accessible invalid: QAccessibleInterface(0xd34e8a0
invalid) "/org/a11y/atspi/accessible/2147484609"  

[Repeated 5 time(s)]

> fitmap #4 inMap #2 search 20

Found 13 unique fits from 20 random placements having fraction of points
inside contour >= 0.100 (18 of 20).  
  
Average map values and times found:  
0.8273 (2), 0.8273 (4), 0.6823 (1), 0.677 (1), 0.677 (2), 0.6566 (1), 0.6557
(1), 0.5547 (1), 0.5469 (1), 0.5143 (1), 0.501 (1), 0.4974 (1), 0.4961 (1)  
  
Best fit found:  
Fit molecule 7kkk-wts-tribody-fit.pdb (#4) to map cryosparc_P3_J326_map.mrc
(#2) using 35070 atoms  
average map value = 0.8273, steps = 544  
shifted from previous position = 66.4  
rotated from previous position = 75.4 degrees  
atoms outside contour = 14913, contour level = 0.84837  
Position of 7kkk-wts-tribody-fit.pdb (#4) relative to
cryosparc_P3_J326_map.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.45463189 -0.89067830 0.00141311 409.12405535  
0.89066834 -0.45461775 0.00570849 132.49666210  
-0.00444202 0.00385388 0.99998267 43.45037809  
Axis -0.00104112 0.00328690 0.99999406  
Axis point 164.06398808 191.44576715 0.00000000  
Rotation angle (degrees) 117.04135455  
Shift along axis 43.45967402  
  
Found 13 fits.  

QSpiApplication::keyEventError "org.freedesktop.DBus.Error.NoReply" "Did not
receive a reply. Possible causes include: the remote application did not send
a reply, the message bus security policy blocked the reply, the reply timeout
expired, or the network connection was broken."  

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> transparency #2,4 60

> show surfaces

WARNING Qt AtSpiAdaptor: Accessible invalid: QAccessibleInterface(0xe957740
invalid) "/org/a11y/atspi/accessible/2147484778"  

[Repeated 5 time(s)]

> hide atoms

> volume #2 level 1.161

> volume #2 level 0.9162

> volume #2 level 0.5979

> volume #2 level 0.457

> open /home/jiangxinyi/data/negative_stain/tribody/flex_fit/mdff/3nb6-wts-
> flexfit.pdb

Chain information for 3nb6-wts-flexfit.pdb #5  
---  
Chain | Description  
A B C | No description available  
D E F | No description available  
  

> hide #!4 models

> hide #5 models

WARNING QAccessibleTable::indexOfChild invalid child QAccessible::Client ""  

> close #5

WARNING Qt AtSpiAdaptor: Accessible invalid: QAccessibleInterface(0x73be720
invalid) "/org/a11y/atspi/accessible/2147484832"  

[Repeated 5 time(s)]

> open /home/jiangxinyi/data/negative_stain/tribody/flex_fit/7kkk-wts-3nb6.pdb

Chain information for 7kkk-wts-3nb6.pdb #5  
---  
Chain | Description  
A B C | No description available  
D E F | No description available  
  

> fitmap #5 inMap #2 search 20

Found 15 unique fits from 20 random placements having fraction of points
inside contour >= 0.100 (18 of 20).  
  
Average map values and times found:  
0.9211 (2), 0.9211 (2), 0.6603 (1), 0.6603 (1), 0.6545 (1), 0.5836 (1), 0.5832
(1), 0.5682 (1), 0.567 (1), 0.5665 (2), 0.5535 (1), 0.5532 (1), 0.5476 (1),
0.5452 (1), 0.5138 (1)  
  
Best fit found:  
Fit molecule 7kkk-wts-3nb6.pdb (#5) to map cryosparc_P3_J326_map.mrc (#2)
using 31497 atoms  
average map value = 0.9211, steps = 356  
shifted from previous position = 74.2  
rotated from previous position = 46.6 degrees  
atoms outside contour = 5647, contour level = 0.457  
Position of 7kkk-wts-3nb6.pdb (#5) relative to cryosparc_P3_J326_map.mrc (#2)
coordinates:  
Matrix rotation and translation  
0.99867071 0.05118158 0.00610454 37.28648922  
-0.05116178 0.99868473 -0.00335673 54.67797581  
-0.00626832 0.00303995 0.99997572 43.72082988  
Axis 0.06193121 0.11979125 -0.99086557  
Axis point 1168.43828709 -739.86748838 0.00000000  
Rotation angle (degrees) 2.96026635  
Shift along axis -34.46232499  
  
Found 15 fits.  

QSpiApplication::keyEventError "org.freedesktop.DBus.Error.NoReply" "Did not
receive a reply. Possible causes include: the remote application did not send
a reply, the message bus security policy blocked the reply, the reply timeout
expired, or the network connection was broken."  

> transparency #2,5 40

> volume #2 level 1.015

> close #4

WARNING Qt AtSpiAdaptor: Accessible invalid: QAccessibleInterface(0x1bb96130
invalid) "/org/a11y/atspi/accessible/2147484865"  

[Repeated 1 time(s)]

WARNING Qt AtSpiAdaptor: Accessible invalid: QAccessibleInterface(0xcc63750
invalid) "/org/a11y/atspi/accessible/2147484917"  

WARNING Qt AtSpiAdaptor: Accessible invalid: QAccessibleInterface(0x1bb96130
invalid) "/org/a11y/atspi/accessible/2147484865"  

> hide #5 models

> open /home/jiangxinyi/data/200kv/tribody/emd_21374.map

Opened emd_21374.map as #4, grid size 432,432,432, pixel 1.05, shown at level
0.0186, step 2, values float32  

> volume #4 step 1

> volume #4 level -0.0217

> volume #4 level 0.5

QSpiApplication::keyEventError "org.freedesktop.DBus.Error.NoReply" "Did not
receive a reply. Possible causes include: the remote application did not send
a reply, the message bus security policy blocked the reply, the reply timeout
expired, or the network connection was broken."  

> fitmap #5 inMap #2 search 20

Found 11 unique fits from 20 random placements having fraction of points
inside contour >= 0.100 (19 of 20).  
  
Average map values and times found:  
0.9211 (3), 0.9211 (3), 0.9211 (2), 0.6603 (3), 0.6603 (1), 0.6545 (1), 0.6545
(2), 0.5499 (1), 0.5434 (1), 0.5203 (1), 0.2418 (1)  
  
Best fit found:  
Fit molecule 7kkk-wts-3nb6.pdb (#5) to map cryosparc_P3_J326_map.mrc (#2)
using 31497 atoms  
average map value = 0.9211, steps = 520  
shifted from previous position = 96.6  
rotated from previous position = 76.8 degrees  
atoms outside contour = 15958, contour level = 1.0154  
Position of 7kkk-wts-3nb6.pdb (#5) relative to cryosparc_P3_J326_map.mrc (#2)
coordinates:  
Matrix rotation and translation  
0.99867223 0.05115743 0.00605940 37.29706627  
-0.05113514 0.99868460 -0.00377990 54.76769833  
-0.00624480 0.00346503 0.99997453 43.65188574  
Axis 0.07014547 0.11912944 -0.99039779  
Axis point 1169.63901434 -745.45271972 0.00000000  
Rotation angle (degrees) 2.96019451  
Shift along axis -34.09206563  
  
Found 11 fits.  

QSpiApplication::keyEventError "org.freedesktop.DBus.Error.NoReply" "Did not
receive a reply. Possible causes include: the remote application did not send
a reply, the message bus security policy blocked the reply, the reply timeout
expired, or the network connection was broken."  

> fitmap #4 inMap #2 search 20

Found 16 unique fits from 20 random placements having fraction of points
inside contour >= 0.100 (19 of 20).  
  
Correlations and times found:  
0.8516 (1), 0.8516 (2), 0.8516 (1), 0.776 (1), 0.776 (2), 0.7648 (1), 0.7648
(2), 0.7644 (1), 0.7644 (1), 0.7644 (1), 0.7494 (1), 0.7482 (1), 0.7411 (1),
0.7362 (1), 0.7361 (1), 0.7223 (1)  
  
Best fit found:  
Fit map emd_21374.map in map cryosparc_P3_J326_map.mrc using 81003 points  
correlation = 0.8516, correlation about mean = 0.1703, overlap = 1.098e+05  
steps = 268, shift = 55.7, angle = 45.3 degrees  
Position of emd_21374.map (#4) relative to cryosparc_P3_J326_map.mrc (#2)
coordinates:  
Matrix rotation and translation  
-0.76419666 -0.64498306 -0.00053489 519.74885493  
-0.64498294 0.76419687 -0.00039087 174.07168882  
0.00066091 0.00004626 -0.99999977 434.46667719  
Axis 0.34333856 -0.93921170 0.00009915  
Axis point 291.61766148 0.00000000 217.32972479  
Rotation angle (degrees) 179.96352583  
Shift along axis 15.00273256  
  
Found 16 fits.  

QSpiApplication::keyEventError "org.freedesktop.DBus.Error.NoReply" "Did not
receive a reply. Possible causes include: the remote application did not send
a reply, the message bus security policy blocked the reply, the reply timeout
expired, or the network connection was broken."  

> volume #2 level 1.146

> hide #!2 models

> show #!2 models

> open /home/jiangxinyi/data/200kv/tribody/emd_22907.map

Opened emd_22907.map as #6, grid size 512,512,512, pixel 0.834, shown at level
2.13, step 2, values float32  

> volume #6 step 1

> volume #6 level 6.525

> fitmap #6 inMap #2 search 20

Found 17 unique fits from 20 random placements having fraction of points
inside contour >= 0.100 (20 of 20).  
  
Correlations and times found:  
0.8992 (1), 0.8992 (1), 0.8992 (2), 0.8224 (2), 0.8224 (2), 0.7877 (1), 0.7609
(1), 0.7536 (1), 0.7535 (1), 0.7535 (1), 0.7535 (1), 0.7534 (1), 0.7534 (1),
0.7443 (1), 0.7441 (1), 0.7283 (1), 0.7247 (1)  
  
Best fit found:  
Fit map emd_22907.map in map cryosparc_P3_J326_map.mrc using 175597 points  
correlation = 0.8992, correlation about mean = 0.1503, overlap = 2.521e+06  
steps = 260, shift = 62.2, angle = 24.9 degrees  
Position of emd_22907.map (#6) relative to cryosparc_P3_J326_map.mrc (#2)
coordinates:  
Matrix rotation and translation  
-0.98953430 -0.14429787 0.00003615 443.03614378  
-0.14429787 0.98953428 -0.00034503 20.55941524  
0.00001402 -0.00034663 -0.99999996 417.21147679  
Axis -0.07224030 0.99738725 0.00005003  
Axis point 222.26378636 0.00000000 208.60399335  
Rotation angle (degrees) 179.99936448  
Shift along axis -11.47849517  
  
Found 17 fits.  

QSpiApplication::keyEventError "org.freedesktop.DBus.Error.NoReply" "Did not
receive a reply. Possible causes include: the remote application did not send
a reply, the message bus security policy blocked the reply, the reply timeout
expired, or the network connection was broken."  

> hide #!4 models

> show #!4 models

> hide #!2 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!4 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!6 models

> show #!1 models

> hide #!2 models

> transparency #1 40

> show #!6 models

> show #!3 models

> hide #!3 models

> show #!3 models

> transparency #1,3,6 40

> transparency #1,3,6 0

> hide #!6 models

> transparency #1,3 40

> hide #!1 models

> show #!6 models

> show #!2 models

> hide #!3 models

> volume #2 level 0.775

QSpiApplication::keyEventError "org.freedesktop.DBus.Error.NoReply" "Did not
receive a reply. Possible causes include: the remote application did not send
a reply, the message bus security policy blocked the reply, the reply timeout
expired, or the network connection was broken."  

> volume #2 level 0.8

QSpiApplication::keyEventError "org.freedesktop.DBus.Error.NoReply" "Did not
receive a reply. Possible causes include: the remote application did not send
a reply, the message bus security policy blocked the reply, the reply timeout
expired, or the network connection was broken."  

> volume #2 level 0.85

> show #!4 models

> hide #!6 models

> show #!6 models

> hide #!4 models

> hide #!2 models

> show #!2 models

> volume #2 level 0.9

> transparency #2,6 0

> hide #!2 models

> show #!2 models

> save /home/jiangxinyi/data/200kv/tribody/compare.cxs

——— End of log from Tue Apr 11 20:50:39 2023 ———

opened ChimeraX session  




OpenGL version: 3.3.0 NVIDIA 390.144
OpenGL renderer: NVS 310/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 8 Intel(R) Xeon(R) CPU E5-2609 0 @ 2.40GHz
Cache Size: 10240 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           31Gi       3.0Gi        10Gi        98Mi        17Gi        27Gi
	Swap:         2.0Gi          0B       2.0Gi

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GF119 [NVS 310] [10de:107d] (rev a1)	
	Subsystem: NVIDIA Corporation GF119 [NVS 310] [10de:094e]	
	Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
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-LinuxSupport: 1.0
    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
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    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
    line-profiler: 3.3.0
    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
    pexpect: 4.8.0
    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
    ptyprocess: 0.7.0
    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
    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

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,

We believe this problem is fixed in newer versions of ChimeraX, so if you upgrade to the current release I think things will work fine.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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