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Opened 6 years ago
Closed 6 years ago
#2678 closed defect (can't reproduce)
Probable redraw(?) hang
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Linux-4.4.0-170-generic-x86_64-with-debian-stretch-sid ChimeraX Version: 0.91 (2019-06-29) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- note | Updating list of available bundles failed: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired (_ssl.c:1056) Please register the custom scheme 'cxreg' via QWebEngineUrlScheme::registerScheme() before installing the custom scheme handler. UCSF ChimeraX version: 0.91 (2019-06-29) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /data/disk3/modeling/gp10/Figure4-20191125.cxs opened ChimeraX session > hide #!7.1 models > hide #!7 models > hide #!7.2 models > show #!7 models > show #!7.1 models > show #!7.2 models > show #!1 models > show #!2 models > hide #!2 models > hide #!1 models > show #!1 models > show #!2 models > hide #!1 models > hide #!2 models > show #!4 models > hide #!4 models > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > show #!2 models > hide #!7 models > hide #!7.2 models > hide #!7.1 models > show #!17 models > show #!16 models > hide #!16 models > hide #!17 models > show #!19 models > hide #!19 models > show #!20 models > hide #!20 models > show #!21 models > hide #!21 models > show #!20 models > lighting flat > lighting flat > hide #!20 models > show #!20 models > hide #!20 models > show #!20 models > surface dust #20 size 160 > surface dust #20 size 80 > lighting flat > hide #!2 models > hide #!25.2 models > hide #!25.1 models > show #!4 models > hide #!4 models > show #!3 models > show #!2 models > hide #!2 models > hide #!3 models > show #!3 models > close #3 > show #!16 models > hide #!16 models > show #!16 models > hide #!16 models > show #!6 models > close #6 > hide #!20 models > show #!20 models > show #!29 models > open /data/disk3/model-gp8-gp11-gp12-gp17/hexamer-hexamer-combine.mrc Opened hexamer-hexamer-combine.mrc, grid size 400,400,400, pixel 1.05, shown at level 0.00718, step 2, values float32 > hide #!20 models > show #!20 models > hide #!3 models > show #!3 models > select #3 2 models selected > ui mousemode rightMode "translate selected models" > ~select #3 Nothing selected > select #3 2 models selected > hide #!20 models > show #!20 models Must specify one map, got 0 > fitmap #3 inMap #20 Fit map hexamer-hexamer-combine.mrc in map hexamer-pentamer-combine.mrc using 80015 points correlation = 0.8505, correlation about mean = 0.7162, overlap = 41.92 steps = 60, shift = 3.38, angle = 0.468 degrees Position of hexamer-hexamer-combine.mrc (#3) relative to hexamer-pentamer- combine.mrc (#20) coordinates: Matrix rotation and translation 0.69670830 -0.71735454 -0.00006048 214.35039514 0.71735454 0.69670831 -0.00004119 -86.94133806 0.00007168 -0.00001468 1.00000000 3.17428002 Axis 0.00001848 -0.00009212 1.00000000 Axis point 209.99294111 210.02337409 0.00000000 Rotation angle (degrees) 45.83649629 Shift along axis 3.18624911 > lighting soft > select #3 2 models selected > select clear > hide #!25 models > show #!25 models > hide #!29 models > show #!29 models > show #!28 models > hide #!28 models > show #!28 models > save session /data/disk3/modeling/gp10/Figure4-20191210.cxs > hide #!28 models > show #!28 models > hide #!29 models > show #!29 models > hide #!29 models > show #!29 models > hide #!29 models > hide #!25 models > show #!25 models > hide #!28 models > show #!28 models > show #!29 models > hide #!28 models > show #!28 models > hide #!28 models > hide #!29 models > show #!25.1 models > hide #!25.1 models > show #!7.1 models > show #!7.2 models > hide #!7.2 models > show #!7.2 models > show #!24 models > hide #!24 models > hide #!7 models > hide #!7.1 models > show #!7.1 models > hide #!7.2 models > show #!7.2 models > hide #!3 models > show #!3 models > hide #!20 models > show #!20 models > hide #!20 models > surface dust #3 size 160 > show #!1 models > hide #!1 models > transparency #3 30 > transparency #3 80 > transparency #3 50 > transparency #3 20 > transparency #3 10 Missing or invalid "percent" argument: Expected a number > hide #!3 models > show #!20 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > show #!3 models > hide #!3 models > show #!3 models > hide #!7 models > show #!7 models > hide #!20 models > show #!20 models > save /data/disk3/Paper-use/SFigure1.tif pixelSize 0.1 supersample 10 transparentBackground true > save /data/disk3/Paper-use/SFigure2.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!3 models > hide #!20 models > show #!20 models > transparency #20 10 > transparency #20 50 > lighting soft > lighting simple > lighting full > transparency #20 10 > select #7 25470 atoms, 25820 bonds, 3 models selected > show selAtoms surfaces > select clear > save /data/disk3/Paper-use/SFigure3.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!20 models > show #!3 models > transparency #3 50 Missing or invalid "percent" argument: Expected a number > transparency #3 0 > transparency #3 30 > save /data/disk3/Paper-use/SFigure4.tif pixelSize 0.1 supersample 10 transparentBackground true > save /data/disk3/Paper-use/SFigure5.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!3 models > show #!20 models > save /data/disk3/Paper-use/SFigure6.tif pixelSize 0.1 supersample 10 transparentBackground true > select #7 25470 atoms, 25820 bonds, 3 models selected > hide selAtoms surfaces > select clear > hide #!20 models > show #!20 models > transparency #3 30 > show #!3 models > hide #!20 models > save /data/disk3/Paper-use/Capsid-S1.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!3 models > show #!20 models > transparency #20 50 > transparency #20 40 > lighting soft > lighting simple > lighting full > lighting flat > lighting shadows true intensity 0.5 > lighting soft > lighting simple > lighting full > transparency #20 50 > lighting simple > transparency #20 30 > save /data/disk3/Paper-use/Capsid-S2.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!7 models > hide #!7.1 models > show #!3 models > save /data/disk3/Paper-use/Capsid-S2.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!3 models > show #!3 models > hide #!7.2 models > show #!7.2 models > hide #!7.2 models > hide #!7 models > hide #!3 models > hide #!20 models > show #!3 models > show #!7.1 models > show #!7.2 models > hide #!7.1 models > show #!7.1 models > hide #!7.1 models > show #!7.1 models > hide #!7.2 models > show #!7.2 models > hide #!7.2 models > show #!7.2 models #7.2 Unknown command: sequence #7.2 Unknown command: sequence chain#7.2 > sequence chain #7.2 Alignment identifier is 1 2 headers > hide #!3 models > show #!3 models > select #7.1 12735 atoms, 12910 bonds, 1 model selected > ~select #7.1 5 models selected > select #7.1 12735 atoms, 12910 bonds, 1 model selected > ~select #7.1 5 models selected > select #7.1 12735 atoms, 12910 bonds, 1 model selected > ~select #7.1 5 models selected > show #!20 models > show #!30 models > hide #!30 models > hide #!25 models > hide #!7 models > show #!7 models > hide #!3 models > hide #!20 models > hide #!7.2 models > hide #!7.1 models > show #!7.1 models > select #7.2 12735 atoms, 12910 bonds, 1 model selected > ~select #7.2 5 models selected > select #7.1 12735 atoms, 12910 bonds, 1 model selected > rainbow selAtoms > show #!20 models > hide #!20 models > hide #!7.1 models > show #!7.2 models > show #!7.1 models > show #!30 models > select #30 12735 atoms, 12910 bonds, 1 model selected > rainbow selAtoms > hide #!30 models > show #!30 models > hide #!30 models > show #!25.2 models > hide #!25.2 models > show #!25.2 models > hide #!25.2 models > show #!25.2 models > hide #!25 models > show #!30 models > select #7.2 12735 atoms, 12910 bonds, 1 model selected > rainbow selAtoms > hide #!7.2 models > show #!7.2 models > ~select #7.2 5 models selected > hide #!7.2 models > hide #!7.1 models > hide #!7 models > hide #!25.2 models > hide #!30 models > open /data/disk3/modeling/gp10/3j7w-s-c5-simu.pdb Chain information for 3j7w-s-c5-simu.pdb #6 --- Chain | Description A B C D E | No description available > select #6 12740 atoms, 12915 bonds, 1 model selected > hide selAtoms > show selAtoms ribbons > show #!25 models > show #!25.1 models > show #!25.2 models > show #!24 models > hide #!24 models > show #!24 models Invalid "to" argument: invalid atoms specifier > matchmaker #6 to #24 Specify a single 'to' model only > hide #!6 models > show #!6 models > hide #!24 models > show #!24 models > hide #!24 models > show #!24 models > matchmaker #6 to #24 Specify a single 'to' model only > show #!30 models > hide #!30 models > show #!30 models > hide #!30 models > show #!31 models > hide #!31 models > show #!31 models > matchmaker #6 to #31 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 3j7w-C5-C6-pentamer.pdb, chain F (#31) with 3j7w-s-c5-simu.pdb, chain A (#6), sequence alignment score = 1686.2 RMSD between 305 pruned atom pairs is 0.001 angstroms; (across all 343 pairs: 8.553) > hide #!31 models > hide #!24 models > hide #!25 models > show #!25 models > hide #!25 models > show #!25 models > ~select #6 Nothing selected > select #6 12740 atoms, 12915 bonds, 1 model selected > ~select #6 Nothing selected > select #6 12740 atoms, 12915 bonds, 1 model selected > hide #!25 models > hide #!25.1 models > hide #!25.2 models > show #!25.1 models > hide #!25.1 models > show #!21 models > hide #!21 models > show #!21 models > show #!16 models > select #16 76410 atoms, 77460 bonds, 3 models selected > ~select #16 30 models selected > hide #!16 models > show #!29 models > hide #!29 models > show #!31 models > hide #!31 models > show #!58 models > hide #!58 models > show #!2 models > hide #!2 models > show #!3 models > show #!17 models > hide #!17 models > show #!16 models > hide #!16 models > show #!7.2 models > hide #!7.2 models > show #!7.1 models > hide #!7.1 models > show #!1 models > hide #!1 models > hide #!7 models > show #!7 models > hide #!7 models > hide #!6 models > show #!6 models > hide #!3 models > show #!3 models Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/updateloop.py", line 119, in _redraw_timer_callback def _redraw_timer_callback(self): KeyboardInterrupt KeyboardInterrupt File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/updateloop.py", line 119, in _redraw_timer_callback def _redraw_timer_callback(self): See log for complete Python traceback. Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/updateloop.py", line 119, in _redraw_timer_callback def _redraw_timer_callback(self): KeyboardInterrupt KeyboardInterrupt File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/updateloop.py", line 119, in _redraw_timer_callback def _redraw_timer_callback(self): See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 384.130 OpenGL renderer: Quadro K2200/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation
Change History (2)
comment:1 by , 6 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Probable redraw(?) hang |
comment:2 by , 6 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
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User typed ctrl-C apparently to the startup shell on Linux. No indication why.