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Opened 6 years ago
Closed 6 years ago
#2719 closed defect (duplicate)
Graphics problem drawing silhouettes
| 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: 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/gp17/Figure4-20200102.cxs opened ChimeraX session > lighting flat > hide #!23 models > show #!23 models > surface dust #32 size 50 > surface dust #23 size 50 > hide #!27 models > show #!27 models > surface dust #27 size 50 > hide #!27 models > show #!27 models > hide #!36 models > show #!36 models > hide #!38 models > lighting soft > lighting simple > hide #!36 models > hide #!27 models > show #!27 models > hide #!23 models > show #!23 models > hide #!23 models > show #!23 models > show #!10 models > hide #!10 models > close #10 > show #!5 models > hide #!5 models > show #!5 models > hide #!14 models > show #!14 models > select #5 2813 atoms, 2855 bonds, 1 model selected > show selAtoms ribbons > rainbow selAtoms > hide #!14 models > hide #!14.1 models > hide #!14.3 models > hide #!15 models > hide #!16 models > hide #!18 models > hide #!19 models > show #!21 models > hide #!20 models > hide #!21 models > hide #!27 models > hide #!26 models > hide #!23 models > show #!23 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > show #!22 models > hide #!22 models > show #!32 models > hide #!32 models > show #!32 models > surface dust #32 size 50 > hide #!32 models > show #!36 models > hide #!36 models > show #!36 models > hide #!36 models > show #!36 models > hide #!23 models > show #!23 models > surface dust #23 size 50 > surface dust #23 size 100 > open /data/disk3/modeling/gp17/fiber-c6-flip-trim.mrc Opened fiber-c6-flip-trim.mrc, grid size 680,680,680, pixel 1.05, shown at step 1, values float32 > select #10 3 models selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!23 models > show #!23 models > hide #!23 models > show #!23 models > fitmap #10 inMap #23 Fit map fiber-c6-flip-trim.mrc in map fiber-c6-flip.mrc using 49238 points correlation = 1, correlation about mean = 1, overlap = 0.5508 steps = 248, shift = 12.2, angle = 7.33 degrees Position of fiber-c6-flip-trim.mrc (#10) relative to fiber-c6-flip.mrc (#23) coordinates: Matrix rotation and translation 1.00000001 0.00000141 0.00000147 -0.00100350 -0.00000140 1.00000001 -0.00002934 0.00228254 -0.00000147 0.00002935 1.00000001 0.00308486 Axis 0.99760620 0.05000093 -0.04776797 Axis point 0.00000000 -103.44283079 79.54987765 Rotation angle (degrees) 0.00168532 Shift along axis -0.00103432 > hide #!10 models > show #!10 models > hide #!23 models > surface dust #10 size 50 > surface dust #10 size 100 > hide #!36 models > show #!36 models > hide #!36 models > show #!36 models > show #!33 models > hide #!33 models > show #!33 models > close #33 > surface dust #10 size 30 > surface dust #10 size 100 > transparency #10 100 > transparency #10 70 > transparency #10 60 > lighting soft > lighting soft > lighting simple > show #!26 models > show #!38 models > hide #!38 models > show #!38 models > hide #!38 models > show #!22 models > hide #!22 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > show #!32 models > hide #!32 models > lighting soft > show #!58 models > surface dust #58 size 100 > surface dust #58 size 10 > surface dust #58 size 50 > select clear > hide #!36 models > show #!36 models > hide #!36 models > show #!32 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!32 models > show #!23 models > hide #!23 models > show #!23 models > close #23 > select #10 3 models selected > select #10 3 models selected > hide #!10 models > show #!10 models > select clear > lighting soft > lighting full > lighting flat > lighting shadows true intensity 0.5 > lighting simple > lighting simple > lighting soft > lighting flat > lighting simple > lighting shadows true > view p3 > view name np3 > save image /data/disk3/Paper-use/2020-A001.tif pixelSize 0.1 supersample 10 transparentBackground true > show #!27 models > hide #!27 models > show #!27 models > hide #!27 models > hide #!58 models > show #!58 models > hide #!58 models > show #!58 models > hide #!58 models > show #!58 models > hide #!58 models > hide #!34 models > show #!34 models > hide #!26 models > show #!26 models > hide #!26 models > show #!26 models > hide #!26 models > hide #!5 models > show #!5 models > open /data/disk3/modeling/gp17/gp17-trimmer-c6-abc.pdb Chain information for gp17-trimmer-c6-abc.pdb #12 --- Chain | Description A D E F G H | No description available B I J K L M | No description available C N O P Q R | No description available > hide #!12 models > show #!12 models > select #12 16878 atoms, 17130 bonds, 1 model selected > hide selAtoms > show selAtoms ribbons > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > matchmaker #12 to #5 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 gp16-abc-wcy.pdb, chain A (#5) with gp17-trimmer-c6-abc.pdb, chain A (#12), sequence alignment score = 589.9 RMSD between 119 pruned atom pairs is 0.000 angstroms; (across all 119 pairs: 0.000) > save session /data/disk3/modeling/gp17/Figure4-20200102.cxs > open /data/disk3/modeling/gp12/6R21-gp12.pdb Chain information for 6R21-gp12.pdb #23 --- Chain | Description b | No description available > hide #!23 models > close #23 > open /data/disk3/modeling/gp12/gp12-6R21-c12.pdb Chain information for gp12-6R21-c12.pdb #23 --- Chain | Description a b c d e f | No description available > select #23 37512 atoms, 38472 bonds, 6 pseudobonds, 2 models selected > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > fitmap #23 inMap #34 Fit molecule gp12-6R21-c12.pdb (#23) to map gp12-c6-clean.mrc (#34) using 37512 atoms average map value = 0.0239, steps = 84 shifted from previous position = 7.48 rotated from previous position = 6.16 degrees atoms outside contour = 13236, contour level = 0.017652 Position of gp12-6R21-c12.pdb (#23) relative to gp12-c6-clean.mrc (#34) coordinates: Matrix rotation and translation -0.48612521 0.87388917 -0.00001558 128.56389143 -0.87388917 -0.48612521 -0.00003857 495.60688297 -0.00004128 -0.00000513 0.99999999 -0.19233067 Axis 0.00001913 0.00001471 -1.00000000 Axis point 209.99829376 210.00360077 0.00000000 Rotation angle (degrees) 119.08621974 Shift along axis 0.20207812 > hide selAtoms > hide selAtoms surfaces > show selAtoms ribbons > hide #!34 models > select clear > lighting soft > lighting flat > lighting simple > lighting flat > lighting shadows true intensity 0.5 > save session /data/disk3/modeling/gp17/Figure4-20200102.cxs > lighting soft > hide #!5 models > show #!5 models > hide #!10 models > show #!10 models > show #!2 models > hide #!5 models > show #!5 models > hide #!12 models > hide #!23 models > lighting soft > lighting simple > lighting flat > lighting shadows true intensity 0.5 > lighting soft > lighting full > lighting soft > lighting simple > lighting shadows true > show #!13 models > hide #!13 models > show #!13 models > hide #!13 models > show #!58 models > hide #!58 models > show #!58 models > hide #!58 models > show #!58 models > hide #!58 models > show #!36 models > hide #!36 models > show #!36 models > hide #!36 models > open /data/disk3/modeling/gp17/fiber-arm-leg-flip.mrc Opened fiber-arm-leg-flip.mrc, grid size 360,360,360, pixel 1.05, shown at level 0.000123, step 2, values float32 > open /data/disk3/modeling/gp17/fiber-arm-leg-flip-trim.mrc Opened fiber-arm-leg-flip-trim.mrc, grid size 360,360,360, pixel 1.05, shown at level -1.93e-06, step 2, values float32 > select #33 2 models selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > hide #!33 models > show #!33 models > hide #!10 models > show #!10 models > fitmap #33 inMap #10 Fit map fiber-arm-leg-flip-trim.mrc in map fiber-c6-flip-trim.mrc using 176714 points correlation = 0.8664, correlation about mean = 0.4121, overlap = 7.743 steps = 120, shift = 8.38, angle = 5.12 degrees Position of fiber-arm-leg-flip-trim.mrc (#33) relative to fiber-c6-flip- trim.mrc (#10) coordinates: Matrix rotation and translation 0.20848474 -0.70446776 -0.67842409 681.32398813 0.30737581 0.70571461 -0.63834707 389.88263888 0.92846874 -0.07544553 0.36366708 65.35245919 Axis 0.28420708 -0.81131476 0.51087640 Axis point 330.29723777 0.00000000 656.32470661 Rotation angle (degrees) 82.01387932 Shift along axis -89.29340869 > select clear > transparency #10 80 > save session /data/disk3/modeling/gp17/Figure4-20200102.cxs > fitmap #33 inMap #10 Fit map fiber-arm-leg-flip-trim.mrc in map fiber-c6-flip-trim.mrc using 123135 points correlation = 0.8821, correlation about mean = 0.26, overlap = 6.966 steps = 40, shift = 0.0891, angle = 0.107 degrees Position of fiber-arm-leg-flip-trim.mrc (#33) relative to fiber-c6-flip- trim.mrc (#10) coordinates: Matrix rotation and translation 0.20977410 -0.70519005 -0.67727526 681.11343986 0.30747061 0.70512437 -0.63895338 390.14547152 0.92814688 -0.07420636 0.36474205 64.96597067 Axis 0.28517481 -0.81067442 0.51135341 Axis point 330.80605869 0.00000000 657.09218336 Rotation angle (degrees) 81.96255415 Shift along axis -88.82398286 > lighting soft > lighting simple > lighting flat > set silhouettes false > lighting full > set silhouettes true > lighting simple > transparency #10 70 > transparency #10 90 > lighting soft > lighting simple > lighting full > lighting shadows false > lighting full > lighting simple > select clear > transparency #10 70 > transparency #10 50 > transparency #10 70 > open /data/disk3/modeling/gp17/fiber-arm-leg-flip-trim.mrc Opened fiber-arm-leg-flip-trim.mrc, grid size 360,360,360, pixel 1.05, shown at level -1.93e-06, step 2, values float32 > hide #!33 models > show #!33 models > matchmaker #35 to #33 No 'to' model specified > hide #!35 models > show #!35 models > select #35 2 models selected > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > fitmap #35 inMap #33 Fit map fiber-arm-leg-flip-trim.mrc in map fiber-arm-leg-flip-trim.mrc using 21842 points correlation = 1, correlation about mean = 1, overlap = 3.161 steps = 148, shift = 10.6, angle = 9.74 degrees Position of fiber-arm-leg-flip-trim.mrc (#35) relative to fiber-arm-leg-flip- trim.mrc (#33) coordinates: Matrix rotation and translation 1.00000002 -0.00003123 -0.00010262 0.03862400 0.00003122 1.00000003 -0.00008398 0.00599304 0.00010262 0.00008398 1.00000002 -0.04641070 Axis 0.61643600 -0.75330341 0.22921743 Axis point 471.59793113 0.00000000 324.34528061 Rotation angle (degrees) 0.00780550 Shift along axis 0.00865650 > hide #!33 models > select #33 2 models selected > show #!33 models > close #33 > select clear > select clear > select clear > save session /data/disk3/modeling/gp17/Figure4-20200102.cxs > hide #!35 models > show #!35 models > hide #!35 models > show #!35 models > show #!58 models > show #!34 models > hide #!58 models > show #!58 models > show #!26 models > hide #!58 models > show #!58 models > hide #!58 models > show #!58 models > hide #!58 models > show #!58 models > hide #!58 models > show #!58 models > hide #!58 models > show #!58 models > show #!13 models > surface dust #13 size 50 > hide #!13 models > show #!13 models > hide #!58 models > save session /data/disk3/modeling/gp17/Figure4-20200102.cxs > hide #!35 models > show #!27 models > hide #!27 models > show #!27 models > hide #!27 models > show #!58 models > hide #!58 models > show #!36 models > hide #!36 models > show #!36 models > open /data/disk3/modeling/gp17/fiber-6-fromtail-clean-newmrc.mrc Opened fiber-6-fromtail-clean-newmrc.mrc, grid size 400,400,400, pixel 1.05, shown at level -5.69e-06, step 2, values float32 > hide #!33 models > show #!33 models > select #33 2 models selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > hide #!33 models > show #!33 models > hide #!33 models > show #!33 models > hide #!36 models > show #!36 models > hide #!26 models > show #!26 models > hide #!33 models > show #!33 models > hide #!33 models > show #!33 models > hide #!13 models > show #!13 models > fitmap #33 inMap #13 Fit map fiber-6-fromtail-clean-newmrc.mrc in map gp17-trimmer-clean- trimmed.mrc using 79799 points correlation = 0.9739, correlation about mean = 0.7697, overlap = 29.19 steps = 140, shift = 16.9, angle = 9.35 degrees Position of fiber-6-fromtail-clean-newmrc.mrc (#33) relative to gp17-trimmer- clean-trimmed.mrc (#13) coordinates: Matrix rotation and translation -0.99999997 -0.00012617 -0.00003727 420.03784710 0.00012617 -0.99999997 -0.00011585 419.99873360 -0.00003726 -0.00011585 0.99999997 0.02064007 Axis -0.00002211 -0.00004839 1.00000000 Axis point 210.00567639 210.01261592 0.00000000 Rotation angle (degrees) 179.99277122 Shift along axis -0.00897018 > hide #!26 models > show #!26 models > hide #!26 models > hide #!13 models > hide #!33 models > hide #!36 models > show #!58 models > hide #!58 models > show #!33 models > show #!36 models > show #!26 models > select clear > hide #!36 models > show #!36 models > hide #!36 models > show #!36 models > hide #!36 models > show #!36 models > hide #!33 models > show #!33 models > hide #!33 models > show #!33 models > save session /data/disk3/modeling/gp17/Figure4-20200102.cxs > surface dust #33 size 50 > hide #!33 models > show #!33 models > hide #!36 models > show #!36 models > hide #!36 models > show #!36 models > show #!32 models > hide #!36 models > show #!36 models > hide #!36 models > show #!36 models > show #!58 models > hide #!58 models > show #!21 models > hide #!21 models > show #!21 models > hide #!21 models > show #!35 models > hide #!35 models > show #!21 models > hide #!21 models > show #!22 models > hide #!22 models > show #!21 models > hide #!21 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!7 models > hide #!7 models > show #!6 models > hide #!6 models > show #!6 models > show #!3 models > hide #!3 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!5 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > hide #!34 models > show #!34 models > surface dust #34 size 50 > hide #!33 models > show #!33 models > hide #!36 models > show #!35 models > hide #!35 models > show #!36 models > hide #!36 models > show #!58 models > hide #!58 models > open /data/disk3/modeling/gp17/tail-fiber-c6-refined-trimmed-down1.mrc Opened tail-fiber-c6-refined-trimmed-down1.mrc, grid size 160,160,160, pixel 5.4, shown at level 6.99e-07, step 1, values float32 > hide #!37 models > show #!37 models > select #37 2 models selected > show #!38 models > close #37 > hide #!38 models > show #!38 models > fitmap #38 inMap #32 Fit map tail-fiber-c6-refined-trimmed-down1.mrc in map tail-adsorbed-new.mrc using 6647 points correlation = 0.752, correlation about mean = 0.1268, overlap = 7.899 steps = 64, shift = 9.05, angle = 3.31 degrees Position of tail-fiber-c6-refined-trimmed-down1.mrc (#38) relative to tail- adsorbed-new.mrc (#32) coordinates: Matrix rotation and translation 0.99999989 0.00046673 -0.00004699 0.01791939 -0.00046672 0.99999989 0.00003343 0.00393411 0.00004700 -0.00003341 1.00000000 0.14313202 Axis -0.07105885 -0.09993567 -0.99245327 Axis point -22.33999344 -16.51794562 0.00000000 Rotation angle (degrees) 0.02694485 Shift along axis -0.14371834 > show #!36 models > hide #!32 models > show #!32 models > hide #!32 models > show #!10 models > hide #!38 models > show #!38 models > hide #!38 models > view np3 > show #!35 models > hide #!35 models > hide #!36 models > show #!32 models > hide #!32 models > hide #!10 models > show #!35 models > hide #!35 models > show #!36 models > hide #!36 models > show #!38 models > hide #!38 models > show #!35 models > hide #!35 models > show #!27 models > hide #!27 models > show #!35 models > hide #!35 models > show #!36 models > hide #!33 models > show #!33 models > hide #!36 models > show #!36 models > show #!38 models > save session /data/disk3/modeling/gp17/Figure4-20200102.cxs > show #!32 models > hide #!32 models > show #!32 models > hide #!38 models > show #!38 models > hide #!38 models > show #!38 models > fitmap #38 inMap #32 Fit map tail-fiber-c6-refined-trimmed-down1.mrc in map tail-adsorbed-new.mrc using 5323 points correlation = 0.7632, correlation about mean = 0.09345, overlap = 7.149 steps = 64, shift = 9.09, angle = 3.29 degrees Position of tail-fiber-c6-refined-trimmed-down1.mrc (#38) relative to tail- adsorbed-new.mrc (#32) coordinates: Matrix rotation and translation 0.99999999 -0.00011356 0.00000485 0.00361846 0.00011356 0.99999998 0.00015545 -0.03626258 -0.00000487 -0.00015545 0.99999999 0.30188283 Axis -0.80724070 0.02522195 0.58968322 Axis point 0.00000000 1281.21240711 261.68180744 Rotation angle (degrees) 0.01103369 Shift along axis 0.17417966 internal error: void QXcbWindow::setNetWmStateOnUnmappedWindow() called on mapped window > save session /data/disk3/modeling/gp17/Figure4-20200102.cxs An error occurred in drawing the scene. Redrawing graphics is now stopped to avoid a continuous stream of error messages. To restart graphics use the command "graphics restart" after changing the settings that caused the error. Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/updateloop.py", line 72, in draw_new_frame view.draw(check_for_changes = False) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/view.py", line 164, in draw self._draw_scene(camera, drawings) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/view.py", line 234, in _draw_scene silhouette.finish_silhouette_drawing(r) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py", line 1623, in finish_silhouette_drawing fb = r.pop_framebuffer() File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py", line 624, in pop_framebuffer fb.activate() File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py", line 2077, in activate GL.glDrawBuffer(self._draw_buffer) File "src/errorchecker.pyx", line 53, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1282, description = b'invalid operation', baseOperation = glDrawBuffer, cArguments = (GL_BACK,) ) 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 → Graphics problem drawing silhouettes |
comment:2 by , 6 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Duplicate. Believed fixed about 4 months ago.