id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4945 Volume mesh: masked_edges(): edge mask array size does not equal triangle array marco.salamina@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Darwin-19.6.0-x86_64-i386-64bit ChimeraX Version: 0.94 (2020-04-22) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- notes | available bundle cache has not been initialized yet Updating list of available bundles failed: Internal Server Error UCSF ChimeraX version: 0.94.dev202004220145 (2020-04-22) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open2 > /Users/marcosalamina/Downloads/cryosparc_P14_J161_003_volume_map_sharp.mrc > /Users/marcosalamina/Downloads/cryosparc_P14_J159_004_volume_map_sharp.mrc Opened cryosparc_P14_J161_003_volume_map_sharp.mrc, grid size 256,256,256, pixel 1.07, shown at level 0.126, step 1, values float32 Opened cryosparc_P14_J159_004_volume_map_sharp.mrc, grid size 256,256,256, pixel 1.07, shown at level 0.133, step 1, values float32 > volume #1 level 0.2612 > volume #2 level 0.436 > set bgColor white > select #2 2 models selected > ui mousemode rightMode ""translate selected models"" > undo > undo > volume #2 level 0.3223 > volume #1 level 0.4374 > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > volume #2 level 0.3792 > volume #1 level 0.5458 > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ~select #2 Nothing selected > volume #2 level 0.436 > volume #1 level 0.4916 > rock y 3 136 cycle 68 Unknown command: rock y 3 136 cycle 68 > rock y 3 136 cycle 68 Unknown command: rock y 3 136 cycle 68 > rock y 3 136 Unknown command: rock y 3 136 > help help:user > roll y 3 136 > roll y 3 120 > lighting soft > lighting flat > lighting full > lighting soft > graphics silhouettes false > graphics silhouettes true > roll y 3 120 > roll y 3 120 > roll x 3 120 > rock y 3 120 Unknown command: rock y 3 120 > wobble y 3 120 Unknown command: wobble y 3 120 > rock Unknown command: rock > volume #1 level 0.6001 > volume #2 level 0.4171 > select up Nothing selected > select up Nothing selected > select up Nothing selected > select up Nothing selected > roll x 3 120 > cd /Volumes/FastSSD/WorkSSD/CryoEM_paper_SSD/Figures/chimeraVideos Current working directory is: /Volumes/FastSSD/WorkSSD/CryoEM_paper_SSD/Figures/chimeraVideos > windowsize 400 300 > movie record supersample 3 > roll x 3 120 > movie stop > movie encode 2A_cdc25.mp4 quality higher Movie saved to 2A_cdc25.mp4 > close #1-2 > open2 > /Users/marcosalamina/Downloads/cryosparc_P14_J163_005_volume_map_sharp_local.mrc > /Users/marcosalamina/Downloads/cryosparc_P14_J162_005_volume_map_sharp_local.mrc Opened cryosparc_P14_J163_005_volume_map_sharp_local.mrc, grid size 256,256,256, pixel 1.07, shown at level 0.0776, step 1, values float32 Opened cryosparc_P14_J162_005_volume_map_sharp_local.mrc, grid size 256,256,256, pixel 1.07, shown at level 0.0832, step 1, values float32 > volume #1 level 0.1345 > volume #2 level 0.1791 > volume #1 level 0.2554 > volume #2 level 0.2856 > toolshed show ""Fit in Map"" Fit map cryosparc_P14_J163_005_volume_map_sharp_local.mrc in map cryosparc_P14_J162_005_volume_map_sharp_local.mrc using 79140 points correlation = 0.7141, correlation about mean = 0.3767, overlap = 1.481e+04 steps = 568, shift = 4.36, angle = 38.6 degrees Position of cryosparc_P14_J163_005_volume_map_sharp_local.mrc (#1) relative to cryosparc_P14_J162_005_volume_map_sharp_local.mrc (#2) coordinates: Matrix rotation and translation 0.78519979 -0.61028361 -0.10495329 129.10613582 0.59913788 0.79155256 -0.12032602 -36.54390143 0.15650904 0.03159847 0.98717094 -20.09351460 Axis 0.12186589 -0.20973143 0.97013475 Axis point 118.45230145 169.07994025 0.00000000 Rotation angle (degrees) 38.55946591 Shift along axis 3.90462171 Fit map cryosparc_P14_J163_005_volume_map_sharp_local.mrc in map cryosparc_P14_J162_005_volume_map_sharp_local.mrc using 79140 points correlation = 0.7141, correlation about mean = 0.3768, overlap = 1.481e+04 steps = 48, shift = 0.0228, angle = 0.166 degrees Position of cryosparc_P14_J163_005_volume_map_sharp_local.mrc (#1) relative to cryosparc_P14_J162_005_volume_map_sharp_local.mrc (#2) coordinates: Matrix rotation and translation 0.78342199 -0.61243073 -0.10572885 129.76475939 0.60127345 0.78992729 -0.12035414 -36.59429967 0.15722667 0.03071613 0.98708474 -20.05561236 Axis 0.12075788 -0.21019326 0.97017335 Axis point 118.60193397 169.17289571 0.00000000 Rotation angle (degrees) 38.71955118 Shift along axis 3.90457194 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > volume #2 level 0.3623 > volume #1 level 0.2895 > volume #1 level 0.2937 > lighting soft > lighting full > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > select #1 2 models selected > ui mousemode rightMode ""translate selected atoms"" > ui mousemode rightMode ""translate selected models"" > volume #2 level 0.3239 > ui mousemode rightMode ""rotate selected models"" > select clear > select #2 2 models selected > ui mousemode rightMode ""translate selected models"" > select clear > graphics silhouettes false > graphics silhouettes true > view > view > view orient > view orient > view orient > toolshed show ""Side View"" Empty filename passed to function > volume #1 level 0.5199 > volume #2 level 0.3303 > cd /Volumes/FastSSD/WorkSSD/CryoEM_paper_SSD/Figures/chimeraVideos Current working directory is: /Volumes/FastSSD/WorkSSD/CryoEM_paper_SSD/Figures/chimeraVideos > save 2A_CDC25Session includeMaps true compress gzip Invalid ""compress"" argument: Expected true or false (or 1 or 0) > save 2A_CDC25Session includeMaps true compress Missing ""compress"" keyword's argument > save 2ACdc25_VideoSession Missing filename suffix 2ACdc25_VideoSession > save 2ACdc25_VideoSession.csx Unrecognized file suffix '.csx' > save 2ACdc25_VideoSession.cxs > roll x 3 120 > movie record supersample 3 > roll x 3 120 > movie stop > movie encode 2Acdc25.mp4 quality higher Movie saved to 2Acdc25.mp4 > movie record supersample 3 > roll x 3 120 > movie stop > movie encode 2Acdc25.mp4 quality higher Movie saved to 2Acdc25.mp4 > save2 > /Volumes/FastSSD/WorkSSD/CryoEM_paper_SSD/Figures/chimeraVideos/2ACdc25_VideoSession.cxs > close session > open2 /Users/marcosalamina/Downloads/postprocess_pentamer_153.mrc Opened postprocess_pentamer_153.mrc, grid size 256,256,256, pixel 0.86, shown at level 0.0101, step 1, values float32 > open2 /Users/marcosalamina/Desktop/pentamer.pdb Summary of feedback from opening /Users/marcosalamina/Desktop/pentamer.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 ASP C 18 TYR C 32 1 15 Start residue of secondary structure not found: HELIX 2 2 ALA C 38 CYS C 53 1 16 Start residue of secondary structure not found: HELIX 3 3 GLY C 85 ASP C 106 1 22 Start residue of secondary structure not found: HELIX 4 4 SER C 114 CYS C 137 1 24 Start residue of secondary structure not found: HELIX 5 5 TYR C 139 TRP C 144 1 6 12 messages similar to the above omitted Cannot find LINK/SSBOND residue GLN (186 ) Cannot find LINK/SSBOND residue TPO (187 ) pentamer.pdb title: Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super- assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-cyclin A-CDK2-P27 [more info...] Chain information for pentamer.pdb #2 --- Chain | Description K | CKS-1 L | cyclin-dependent kinase 2 S | S-phase kinase-associated protein 1 T | S-phase kinase-associated protein 2 Y | cyclin-A2 > hide surfaces > show cartoons > hide surfaces > hide atoms > toolshed show ""Fit in Map"" Fit molecule pentamer.pdb (#2) to map postprocess_pentamer_153.mrc (#1) using 8556 atoms average map value = 0.007106, steps = 252 shifted from previous position = 4.1 rotated from previous position = 34.7 degrees atoms outside contour = 5690, contour level = 0.010138 Position of pentamer.pdb (#2) relative to postprocess_pentamer_153.mrc (#1) coordinates: Matrix rotation and translation 0.91854713 0.29885921 -0.25875537 3.45449576 -0.15555822 0.87501541 0.45842085 -23.49645645 0.36341823 -0.38082964 0.85023290 19.02963528 Axis -0.73665624 -0.54611593 -0.39886712 Axis point 0.00000000 30.61706410 56.39009916 Rotation angle (degrees) 34.72478380 Shift along axis 2.69671742 > select #2 8556 atoms, 8747 bonds, 12 pseudobonds, 2 models selected > ui mousemode rightMode ""rotate selected models"" > ~select #2 Nothing selected Fit molecule pentamer.pdb (#2) to map postprocess_pentamer_153.mrc (#1) using 8556 atoms average map value = 0.01212, steps = 216 shifted from previous position = 14.3 rotated from previous position = 30.8 degrees atoms outside contour = 3093, contour level = 0.010138 Position of pentamer.pdb (#2) relative to postprocess_pentamer_153.mrc (#1) coordinates: Matrix rotation and translation 0.96574800 0.15771731 -0.20604850 10.41716658 0.02949344 -0.85565103 -0.51671212 259.92682703 -0.25780008 0.49293663 -0.83099492 182.01230240 Axis 0.99075194 0.05078298 -0.12582401 Axis point 0.00000000 104.52840339 127.58969549 Rotation angle (degrees) 149.36703213 Shift along axis 0.61917040 > hide #!1 models > select /T:354 8 atoms, 7 bonds, 1 model selected > select up 77 atoms, 77 bonds, 1 model selected > select up 2536 atoms, 2585 bonds, 1 model selected > color sel orange > select /K:69 11 atoms, 11 bonds, 1 model selected > select up 64 atoms, 65 bonds, 1 model selected > select up 598 atoms, 618 bonds, 1 model selected > color sel red > select /S:28 9 atoms, 8 bonds, 1 model selected > select up 74 atoms, 73 bonds, 1 model selected > select up 1097 atoms, 1114 bonds, 1 model selected > color sel gray > select /Y:293 11 atoms, 10 bonds, 1 model selected > select up 141 atoms, 141 bonds, 1 model selected > select up 2046 atoms, 2093 bonds, 1 model selected > color sel cornflowerblue > select /L:141 8 atoms, 7 bonds, 1 model selected > select up 17 atoms, 16 bonds, 1 model selected > select up 2279 atoms, 2337 bonds, 1 model selected > color sel forestgreen > select clear > show #!1 models > color zone #1 near #3 distance 8 sharpEdges true update true > color zone #1 near #2 distance 8 sharpEdges true update true > volume #1 level 0.01072 > volume #1 level 0.009026 > volume #1 level 0.01745 > volume #1 level 0.01458 > volume #1 style mesh 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 ""/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 73, in draw_new_frame view.draw(check_for_changes = False) File ""/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/view.py"", line 166, in draw self._draw_scene(camera, drawings) File ""/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/view.py"", line 201, in _draw_scene shadow, multishadow = self._compute_shadowmaps(opaque_drawings + transparent_drawings, camera) File ""/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/view.py"", line 559, in _compute_shadowmaps shadow_enabled = r.shadow.use_shadow_map(camera, drawings, self._shadow_bounds) File ""/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/opengl.py"", line 1329, in use_shadow_map draw_depth(r, sdrawings, opaque_only = not r.material.transparent_cast_shadows) File ""/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py"", line 1439, in draw_depth draw_opaque(r, drawings) File ""/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py"", line 1420, in draw_opaque _draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS) File ""/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py"", line 1431, in _draw_multiple d.draw(renderer, draw_pass) File ""/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py"", line 716, in draw self.draw_self(renderer, draw_pass) File ""/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py"", line 723, in draw_self self._draw_geometry(renderer, opaque_only = any_transp) File ""/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py"", line 747, in _draw_geometry self._update_buffers() File ""/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py"", line 864, in _update_buffers ds.update_element_buffer(ta, style, tm, em) File ""/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py"", line 1640, in update_element_buffer self.elements = e = self.masked_elements(triangles, style, triangle_mask, edge_mask) File ""/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py"", line 1674, in masked_elements self.masked_edges = me = masked_edges(ta, **kw) TypeError: masked_edges(): edge mask array size does not equal triangle array size > volume #1 level 0.01265 > volume #1 level 0.01183 > graphics restart 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 ""/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 73, in draw_new_frame view.draw(check_for_changes = False) File ""/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/view.py"", line 166, in draw self._draw_scene(camera, drawings) File ""/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/view.py"", line 201, in _draw_scene shadow, multishadow = self._compute_shadowmaps(opaque_drawings + transparent_drawings, camera) File ""/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/view.py"", line 559, in _compute_shadowmaps shadow_enabled = r.shadow.use_shadow_map(camera, drawings, self._shadow_bounds) File ""/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/opengl.py"", line 1329, in use_shadow_map draw_depth(r, sdrawings, opaque_only = not r.material.transparent_cast_shadows) File ""/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py"", line 1439, in draw_depth draw_opaque(r, drawings) File ""/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py"", line 1420, in draw_opaque _draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS) File ""/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py"", line 1431, in _draw_multiple d.draw(renderer, draw_pass) File ""/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py"", line 716, in draw self.draw_self(renderer, draw_pass) File ""/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py"", line 723, in draw_self self._draw_geometry(renderer, opaque_only = any_transp) File ""/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py"", line 747, in _draw_geometry self._update_buffers() File ""/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py"", line 864, in _update_buffers ds.update_element_buffer(ta, style, tm, em) File ""/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py"", line 1640, in update_element_buffer self.elements = e = self.masked_elements(triangles, style, triangle_mask, edge_mask) File ""/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py"", line 1674, in masked_elements self.masked_edges = me = masked_edges(ta, **kw) TypeError: masked_edges(): edge mask array size does not equal triangle array size OpenGL version: 4.1 INTEL-14.7.13 OpenGL renderer: Intel(R) HD Graphics 6000 OpenGL vendor: Intel Inc. }}} " defect closed normal Volume Data fixed all ChimeraX