id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2698 "OpenGL buffer ""None"" was not deleted before core.graphics.Buffer destroyed" chimerax-bug-report@… Tom Goddard "{{{ 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/gp10/Figure4-20191220.cxs Summary of feedback from opening /data/disk3/modeling/gp10/Figure4-20191220.cxs --- notes | 2 headers opened ChimeraX session > open /data/disk3/modeling/gp8/gp8-WCY-C12-cut-1.pdb /data/disk3/modeling/gp8/gp8-WCY-C12-cut-2.pdb Chain information for gp8-WCY-C12-cut-1.pdb #13.1 --- Chain | Description B D F H J L | No description available Chain information for gp8-WCY-C12-cut-2.pdb #13.2 --- Chain | Description A C E G I K | No description available > open /data/disk3/modeling/gp8/gp11-WCY-C12-cut-1.pdb /data/disk3/modeling/gp8/gp11-WCY-C12-cut-2.pdb Chain information for gp11-WCY-C12-cut-1.pdb #14.1 --- Chain | Description M O Q S W | No description available U | No description available Chain information for gp11-WCY-C12-cut-2.pdb #14.2 --- Chain | Description N P R X | No description available T V | No description available > lighting flat > hide #!14 models > show #!14 models > hide #!14 models > select #14 1572 atoms, 1584 bonds, 3 models selected > show #!14 models > hide #!11 models > show #!11 models > matchmaker #14 to #11 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 gp11-WCY-C12-cut.pdb, chain Q (#11) with gp11-WCY-C12-cut-1.pdb, chain Q (#14.1), sequence alignment score = 92.3 RMSD between 18 pruned atom pairs is 0.000 angstroms; (across all 18 pairs: 0.000) Matchmaker gp11-WCY-C12-cut.pdb, chain N (#11) with gp11-WCY-C12-cut-2.pdb, chain N (#14.2), sequence alignment score = 90.5 RMSD between 18 pruned atom pairs is 0.000 angstroms; (across all 18 pairs: 0.000) > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > matchmaker #13 to #10 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 gp8_WCY-C12-cut.pdb, chain A (#10) with gp8-WCY-C12-cut-1.pdb, chain B (#13.1), sequence alignment score = 1844.2 RMSD between 366 pruned atom pairs is 0.000 angstroms; (across all 366 pairs: 0.000) Matchmaker gp8_WCY-C12-cut.pdb, chain A (#10) with gp8-WCY-C12-cut-2.pdb, chain A (#13.2), sequence alignment score = 1844.2 RMSD between 366 pruned atom pairs is 0.000 angstroms; (across all 366 pairs: 0.000) > hide #!11 models > hide #!10 models > show #!10 models > hide #!10 models > hide #!13.2 models > hide #!13.1 models > lighting soft > ~select #14 Nothing selected > show #!13.2 models > select #13.2 17286 atoms, 17562 bonds, 1 model selected > show #!13.1 models > select #13.1 17286 atoms, 17562 bonds, 1 model selected > ~select #13.1 Nothing selected > select #13.1 17286 atoms, 17562 bonds, 1 model selected > ui mousemode rightMode ""rotate selected models"" > fitmap #13.1 inMap #17 Fit molecule gp8-WCY-C12-cut-1.pdb (#13.1) to map gp8-C12-clean.mrc (#17) using 17286 atoms average map value = 0.01961, steps = 80 shifted from previous position = 0.318 rotated from previous position = 3.02 degrees atoms outside contour = 5072, contour level = 0.01 Position of gp8-WCY-C12-cut-1.pdb (#13.1) relative to gp8-C12-clean.mrc (#17) coordinates: Matrix rotation and translation 0.00010619 -1.00000001 0.00000267 419.97678647 1.00000001 0.00010620 0.00000468 -0.01804600 -0.00000468 0.00000267 1.00000001 -0.01113844 Axis -0.00000101 0.00000367 1.00000000 Axis point 209.99741717 210.00167158 0.00000000 Rotation angle (degrees) 89.99391536 Shift along axis -0.01156098 > hide selAtoms > show selAtoms ribbons > show selAtoms surfaces > select #13.2 17286 atoms, 17562 bonds, 1 model selected > select #13.1 17286 atoms, 17562 bonds, 1 model selected > ~select #13.1 6 models selected > select #13.2 17286 atoms, 17562 bonds, 1 model selected > hide selAtoms > show selAtoms ribbons > show selAtoms surfaces > lighting flat > lighting soft > select #14 1572 atoms, 1584 bonds, 3 models selected > hide selAtoms > show selAtoms ribbons > show selAtoms ribbons > show selAtoms surfaces > select clear > save session /data/disk3/modeling/gp10/Figure4-20191221.cxs internal error: void QXcbWindow::setNetWmStateOnUnmappedWindow() called on mapped window Expected a keyword Expected a models specifier or a keyword Expected a keyword Expected a keyword > save /data/disk3/Paper-use/20191220-capsid.tif pixelSize 0.1 supersample 10 transparentBackground true > save /data/disk3/Paper-use/20191220-capsid.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!8.1 models > show #!8.1 models > hide #!14.1 models > show #!14.1 models > hide #!14.1 models > show #!14.1 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > hide #!3 models > lighting soft > lighting flat > lighting simple > lighting full > lighting full > lighting full > lighting flat > lighting shadows true intensity 0.5 > lighting soft > lighting shadows true intensity 0.5 > lighting full > lighting flat > lighting soft > lighting shadows true intensity 0.5 > lighting flat > show #!3 models > transparency #3 80 > lighting soft > transparency #3 70 > view name capsid1 > save /data/disk3/Paper-use/20191220-capsid.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!3 models > transparency #8.1 70 > transparency #9 70 > show #!3 models > hide #!3 models > transparency #8 70 > show #!3 models > save /data/disk3/Paper-use/20191220-capsid-1.tif pixelSize 0.1 supersample 10 transparentBackground true > select #8 76410 atoms, 77460 bonds, 3 models selected > show selAtoms surfaces > select #9 37263 atoms, 37783 bonds, 1 model selected > show selAtoms surfaces > transparency #8 30 > transparency #8.1 70 > transparency #8.1 30 > transparency #9 30 > select clear > hide #!3 models > save /data/disk3/Paper-use/20191220-capsid-2.tif pixelSize 0.1 supersample 10 transparentBackground true > select #8 76410 atoms, 77460 bonds, 3 models selected > hide selAtoms ribbons > select #9 37263 atoms, 37783 bonds, 1 model selected > hide selAtoms ribbons > select clear > save /data/disk3/Paper-use/20191220-capsid-2.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!8 models > hide #!9 models > hide #!8.1 models > show #!8.1 models > hide #!8.1 models > show #!8.1 models > hide #!8.1 models > show #!30 models > hide #!30 models > show #!24 models > select #24 24500 atoms, 24844 bonds, 3 models selected > show selAtoms surfaces > transparency #24 30 > show #!8.1 models > show #!9 models > transparency #8.1 30 > transparency #8.1 30 > transparency #8.1 80 > transparency #9 80 > select clear > select clear > select #24 24500 atoms, 24844 bonds, 3 models selected > show selAtoms surfaces > ~select #24 10 models selected > select #24 24500 atoms, 24844 bonds, 3 models selected > ~select #24.1 11765 atoms, 11934 bonds, 12 models selected > select #24.1 12735 atoms, 12910 bonds, 1 model selected > show selAtoms surfaces > show selAtoms surfaces > hide #!24.1 models > show #!24.1 models > hide selAtoms > hide selAtoms ribbons > show selAtoms surfaces > show selAtoms surfaces > hide selAtoms surfaces > hide selAtoms surfaces > show selAtoms surfaces > transparency #24 30 > transparency #24 50 > transparency #24 80 > select #24.2 11765 atoms, 11934 bonds, 1 model selected > ~select #24.2 5 models selected > show selAtoms surfaces > select #12.3 2547 atoms, 2582 bonds, 1 model selected > ~select #12.3 1 model selected > select #12.3 2547 atoms, 2582 bonds, 1 model selected > ~select #12.3 Nothing selected > select #24.2 11765 atoms, 11934 bonds, 1 model selected > show selAtoms surfaces > show selAtoms surfaces > hide selAtoms ribbons > select clear > lighting flat > lighting full > lighting soft > lighting shadows true intensity 0.5 > lighting soft > save /data/disk3/Paper-use/20191220-capsid-3.tif pixelSize 0.1 supersample 10 transparentBackground true > hide selAtoms surfaces > select #8 76410 atoms, 77460 bonds, 3 models selected > show selAtoms ribbons > select #9 37263 atoms, 37783 bonds, 1 model selected > ~select #9 Nothing selected > show selAtoms surfaces > show selAtoms surfaces > select #13 34572 atoms, 35124 bonds, 3 models selected Exception ignored in: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 2421, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""None"" was not deleted before core.graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 2421, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""None"" was not deleted before core.graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 2421, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""None"" was not deleted before core.graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 2421, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""None"" was not deleted before core.graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 2421, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""None"" was not deleted before core.graphics.Buffer destroyed > hide selAtoms surfaces > select #14 1572 atoms, 1584 bonds, 3 models selected > hide selAtoms surfaces > select clear > show #!26 models > hide #!26 models > select #24 24500 atoms, 24844 bonds, 3 models selected Exception ignored in: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 2421, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""None"" was not deleted before core.graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 2421, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""None"" was not deleted before core.graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 2421, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""None"" was not deleted before core.graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 2421, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""None"" was not deleted before core.graphics.Buffer destroyed > hide selAtoms surfaces > show selAtoms ribbons > select clear > lighting soft > hide #!8 models > show #!8 models > select #8 76410 atoms, 77460 bonds, 3 models selected > hide selAtoms ribbons > select #9 37263 atoms, 37783 bonds, 1 model selected > hide selAtoms ribbons > select clear > lighting soft > lighting simple > lighting shadows true > lighting soft > lighting simple > lighting shadows true > lighting soft > lighting simple > select #13 34572 atoms, 35124 bonds, 3 models selected > show selAtoms surfaces Exception ignored in: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 2421, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""None"" was not deleted before core.graphics.Buffer destroyed > select #14 1572 atoms, 1584 bonds, 3 models selected > show selAtoms ribbons > show selAtoms surfaces > select clear > lighting soft > lighting shadows true intensity 0.5 > lighting flat > lighting full > lighting soft > lighting simple > lighting simple > lighting soft > transparency #8.1 50 > transparency #8.1 70 > transparency #9 70 > select clear > save /data/disk3/Paper-use/20191220-capsid-4.tif pixelSize 0.1 supersample 10 transparentBackground true > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting simple > lighting soft > lighting full > transparency #8.1 0 > transparency #9 70 > transparency #9 0 > hide #!24 models > hide #!24.1 models > show #!24.1 models > hide #!24.2 models > hide #!24.1 models > select #13 34572 atoms, 35124 bonds, 3 models selected > hide selAtoms surfaces > show selAtoms ribbons > select #14 1572 atoms, 1584 bonds, 3 models selected > hide selAtoms surfaces > show selAtoms ribbons > select clear > show #!24.1 models > show #!24.2 models > select #24 24500 atoms, 24844 bonds, 3 models selected > show selAtoms surfaces Exception ignored in: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 2421, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""None"" was not deleted before core.graphics.Buffer destroyed > hide #!9 models > show #!9 models > transparency #9 70 > transparency #8.1 70 > select clear > select #9/T:75@CB 1 atom, 1 model selected > view capsid1 > lighting soft > select clear > transparency #8.1 80 > transparency #8.1 80 > transparency #9 80 > save /data/disk3/Paper-use/20191220-capsid-5.tif pixelSize 0.1 supersample 10 transparentBackground true > show #!3 models > hide selAtoms surfaces > select #13 34572 atoms, 35124 bonds, 3 models selected > show selAtoms surfaces > select #14 1572 atoms, 1584 bonds, 3 models selected > show selAtoms surfaces > select clear > save /data/disk3/Paper-use/20191220-capsid.tif pixelSize 0.1 supersample 10 transparentBackground true > select #13 34572 atoms, 35124 bonds, 3 models selected > hide selAtoms surfaces > hide selAtoms surfaces > select #14 1572 atoms, 1584 bonds, 3 models selected > hide selAtoms surfaces > select #24 24500 atoms, 24844 bonds, 3 models selected > show selAtoms surfaces > transparency #24 80 > transparency #24 30 > hide selAtoms ribbons > select clear > select #24 24500 atoms, 24844 bonds, 3 models selected > hide selAtoms surfaces > show selAtoms ribbons > view capsid1 > save /data/disk3/Paper-use/20191220-capsid-1.tif pixelSize 0.1 supersample 10 transparentBackground true > ~select #24 10 models selected > save /data/disk3/Paper-use/20191220-capsid-2.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!24 models > select #8 76410 atoms, 77460 bonds, 3 models selected > select #9 37263 atoms, 37783 bonds, 1 model selected > select #8 76410 atoms, 77460 bonds, 3 models selected > show selAtoms ribbons > hide selAtoms ribbons > show selAtoms ribbons > select #9 37263 atoms, 37783 bonds, 1 model selected > show selAtoms ribbons > hide #!8.1 models > hide #!8 models > select clear > select #13 34572 atoms, 35124 bonds, 3 models selected > show selAtoms surfaces > select #14 1572 atoms, 1584 bonds, 3 models selected > show selAtoms surfaces > show selAtoms surfaces > select clear > save /data/disk3/Paper-use/20191220-capsid-3.tif pixelSize 0.1 supersample 10 transparentBackground true > show #!8.1 models > save /data/disk3/Paper-use/20191220-capsid-4.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!9 models > show #!9 models > hide #!8.1 models > show #!8.1 models > hide #!9 models > save /data/disk3/Paper-use/20191220-capsid-5.tif pixelSize 0.1 supersample 10 transparentBackground true > show #!9 models > hide #!8.1 models > sequence chain #9 Chains must have same sequence > sequence chain #9 Chains must have same sequence > sequence chain #9.1 Chains must have same sequence > sequence chain #9 Chains must have same sequence Unknown command: sequencing chain #9 > sequence chain #9 Chains must have same sequence Unknown command: sequence chains #9 > view capsid1 > select #9 37263 atoms, 37783 bonds, 1 model selected > show selAtoms surfaces > transparency #9 30 > view capsid1 > show #!8.1 models > select #8.1 38205 atoms, 38730 bonds, 1 model selected > show selAtoms surfaces > transparency #8.1 30 > hide #!9 models > show #!9 models > hide #!9 models > select #9 37263 atoms, 37783 bonds, 1 model selected > show #!9 models > ~select #9 15 models selected > hide selAtoms surfaces > select #9 37263 atoms, 37783 bonds, 1 model selected > hide selAtoms surfaces > hide selAtoms surfaces > show selAtoms ribbons > select clear > select #9 37263 atoms, 37783 bonds, 1 model selected > save /data/disk3/Paper-use/20191220-capsid-6.tif pixelSize 0.1 supersample 10 transparentBackground true > select clear > lighting flat > lighting simple > lighting soft > lighting flat > lighting shadows true intensity 0.5 > lighting full > lighting soft > set silhouettes false > lighting shadows true intensity 0.5 > select clear > hide #!8.1 models > show #!8.1 models > hide #!8.1 models > show #!8.1 models > hide #!8.1 models > show #!8.1 models > select #8.1 38205 atoms, 38730 bonds, 1 model selected > hide selAtoms surfaces > show selAtoms ribbons > lighting soft > lighting shadows true intensity 0.5 > lighting full > ~select #8.1 15 models selected > select #9 37263 atoms, 37783 bonds, 1 model selected > select #8.1 38205 atoms, 38730 bonds, 1 model selected > lighting soft > toolshed show ""Side View"" > lighting shadows true intensity 0.5 > lighting soft > lighting full > lighting flat > lighting shadows true intensity 0.5 > lighting simple > lighting shadows true > lighting full > lighting simple > lighting shadows true > select clear > lighting shadows false > lighting full > lighting shadows false > lighting full > lighting simple > lighting full > lighting simple > lighting shadows true > lighting soft > lighting shadows true intensity 0.5 > lighting simple > set silhouettes false > set silhouettes true > lighting shadows true > lighting shadows false > lighting soft > lighting shadows true intensity 0.5 > lighting soft > lighting simple > lighting soft > lighting shadows true intensity 0.5 > lighting full > lighting shadows false > lighting simple > lighting soft > lighting shadows true intensity 0.5 > lighting soft > lighting simple > lighting simple > lighting soft > lighting shadows true intensity 0.5 > lighting soft > lighting simple > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting flat > lighting simple > lighting shadows true > lighting shadows false > lighting shadows true > lighting soft > lighting soft > transparency #9 50 > transparency #3 50 > transparency #3 50 > transparency #3 40 > transparency #3 30 > transparency #3 60 > transparency #3 40 > select #3 2 models selected > select clear > lighting flat > lighting soft > view capsid1 > save /data/disk3/Paper-use/20191220-capsid.tif pixelSize 0.1 supersample 10 transparentBackground true Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/sideview/tool.py"", line 116, in exposeEvent self.render() File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/sideview/tool.py"", line 139, in render mvwin = self.view.render.use_shared_context(self, width, height) AttributeError: 'NoneType' object has no attribute 'use_shared_context' AttributeError: 'NoneType' object has no attribute 'use_shared_context' File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/sideview/tool.py"", line 139, in render mvwin = self.view.render.use_shared_context(self, width, height) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/sideview/tool.py"", line 116, in exposeEvent self.render() File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/sideview/tool.py"", line 139, in render mvwin = self.view.render.use_shared_context(self, width, height) AttributeError: 'NoneType' object has no attribute 'use_shared_context' AttributeError: 'NoneType' object has no attribute 'use_shared_context' File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/sideview/tool.py"", line 139, in render mvwin = self.view.render.use_shared_context(self, width, height) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 384.130 OpenGL renderer: Quadro K2200/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Graphics duplicate all ChimeraX