id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17681 Reading volume data: OSError: Operation canceled chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.2-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Replace this text with list of actions that caused this problem to occur Log: UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Volumes/Groups/mosalaganti- > data/data/Kimberly/20250414_Krios_data_hela_DRP1/20250404_0047_s11g1_snapdrp1_mitotr/krios/TS_002/segmentation_new- > files/MEMBRANES.cxs format session Using preset: ArtiaX / Artiax Default Preset expands to these ChimeraX commands: set bgColor black lighting depthCue false camera ortho Log from Tue May 13 11:23:43 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Volumes/Groups/mosalaganti- > data/data/Kimberly/20250414_Krios_data_hela_DRP1/20250404_0047_s11g1_snapdrp1_mitotr/krios/TS_002/segmentation_new- > files/MEMBRANES.cxs Using preset: ArtiaX / Artiax Default Preset expands to these ChimeraX commands: set bgColor black lighting depthCue false camera ortho Log from Thu May 8 15:02:16 2025 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open S:/mosalaganti- > data/data/Kimberly/20250414_Krios_data_hela_DRP1/20250404_0047_s11g1_snapdrp1_mitotr/krios/TS_002/segmentation_new- > files/ER.smooth.obj S:/mosalaganti- > data/data/Kimberly/20250414_Krios_data_hela_DRP1/20250404_0047_s11g1_snapdrp1_mitotr/krios/TS_002/segmentation_new- > files/IMM.smooth.obj S:/mosalaganti- > data/data/Kimberly/20250414_Krios_data_hela_DRP1/20250404_0047_s11g1_snapdrp1_mitotr/krios/TS_002/segmentation_new- > files/LYSO.smooth.obj S:/mosalaganti- > data/data/Kimberly/20250414_Krios_data_hela_DRP1/20250404_0047_s11g1_snapdrp1_mitotr/krios/TS_002/segmentation_new- > files/OMM.smooth.obj Opened OBJ file ER.smooth.obj containing 1 objects, 5188908 triangles Opened OBJ file IMM.smooth.obj containing 1 objects, 2240158 triangles Opened OBJ file LYSO.smooth.obj containing 1 objects, 1219236 triangles Opened OBJ file OMM.smooth.obj containing 1 objects, 1733474 triangles > artiax start Using preset: ArtiaX / Artiax Default Preset expands to these ChimeraX commands: set bgColor black lighting depthCue false camera ortho > color #1 #aaddbbff > color #1 #adbca5ff > color #2 #ee0099ff > color #2 #ee88bbff > color #2 #e8b9abff > color #3 #ee0099ff > color #3 #e09891ff > color #3 #ee0099ff > color #3 #88cc55ff > color #3 #8c5f66ff > color #4 #ee0099ff > color #4 #e09891ff > color #1 #aaddbbff > color #1 #ddddffff > color #1 #ddfff7ff > color #4 #8c5f66ff > color #3 #884488ff > color #3 #84894aff > color #3 #aa66aaff > color #3 #a6a15eff > save S:/mosalaganti- > data/data/Kimberly/20250414_Krios_data_hela_DRP1/20250404_0047_s11g1_snapdrp1_mitotr/krios/TS_002/segmentation_new- > files/MEMBRANES.cxs ——— End of log from Thu May 8 15:02:16 2025 ——— opened ChimeraX session > set bgColor white > artiax start [Repeated 1 time(s)] > color #1 #66fde5ff > color #1 #1dfdf6ff > color #1 #55b6fdff > color #1 #526bfdff > color #1 #a5c9fdff > color #1 #5fa8fdff > color #1 #7698fdff > color #1 #a295fdff > color #1 #dbccfdff > color #1 #b4c4fdff > color #1 #8591bcff > color #2 #d8bab0ff > color #2 #d89087ff > color #2 #d85234ff > color #2 #948bd8ff > color #2 #bcd85aff > color #2 #4ad838ff > color #2 #646fd8ff > color #2 #604cd8ff > color #2 #96aed8ff > color #2 #c2d0d8ff > color #2 #0613d8ff > color #2 #3694d8ff > color #2 #3bbbd8ff > color #2 #33d8bdff > color #2 #6dd8aaff > color #2 #bad8d6ff > color #2 #d2d8d0ff > color #2 #d8a572ff > color #3 #848058ff > color #3 #e3dc98ff > color #3 #8fe370ff > color #3 #00e313ff > color #3 #a1e38eff > color #3 #bce38aff > color #3 #8ba766ff > color #3 #78a73fff > color #3 #96a725ff > color #3 #a7a00fff > color #3 #35a729ff > color #3 #216819ff > color #3 #1a5214ff > color #3 #1b5615ff > color #3 #2d5614ff > color #3 #2a5609ff > color #3 #365631ff > color #3 #3c5637ff > color #3 #425641ff > color #3 #325631ff > color #3 #518b50ff > color #3 #198b4bff > color #3 #218b19ff > color #3 #588b35ff > color #3 #4b8b25ff > color #3 #468b37ff > color #3 #5a8b53ff > color #3 #1e8b3cff > color #3 #528b4bff > color #3 #4d8246ff > color #3 #385f33ff > color #3 #55904dff > color #4 #6c5356ff > color #4 #9a767aff > color #4 #9a6326ff > color #4 #9a3c21ff > color #4 #9a3e79ff > color #4 #9a8069ff > color #4 #90639aff > color #4 #9a2250ff > color #4 #9a3c84ff > color #4 #884e9aff > color #4 #7e559aff > color #4 #7e6b9aff > color #4 #62399aff > color #4 #8f379aff > color #4 #9a5890ff > color #4 #d579c7ff > color #4 #d277c4ff > color #1 #c581bbff > color #1 #c595bfff > color #1 #c455c5ff > color #1 #c58ec3ff > color #1 #c5aac0ff > color #1 #c5779dff > color #1 #664ec5ff > color #1 #3145c5ff > color #1 #6075c5ff > color #1 #7c97ffff > color #2 #d982d6ff > color #2 #d9abc1ff > color #2 #d9bbbbff > color #2 #d9accfff > color #2 #d994d6ff > color #2 #a973a6ff > color #2 #f4a6efff > color #2 #ca7cf4ff > color #2 #f4e3edff > color #2 #f4cbc2ff > color #2 #f4a0a5ff > color #2 #f48994ff > color #2 #f0d7f4ff > color #2 #f4ebe8ff > color #2 #a889f4ff > color #2 #6159f4ff > color #2 #6691f4ff > color #2 #43eff4ff > color #2 #baf4e2ff > color #2 #c1d6f4ff > color #2 #c8c0f4ff > color #2 #c7c0f3ff > color #2 #a9a3cdff > color #2 #8a85a8ff > color #2 #a29cc5ff > color #4 #9e74d1ff > color #4 #9590d1ff > color #4 #6d3cd1ff > color #4 #542fa1ff > color #4 #746fa1ff > color #4 #7986a1ff > color #4 #5147a1ff > color #4 #6645a1ff > color #4 #714aa1ff > color #4 #8361a1ff > color #4 #794da1ff > color #4 #8d78a1ff > color #4 #7635a1ff > color #4 #a64ae2ff > color #4 #b38be2ff > color #4 #735a91ff > color #3 #9d8252ff > color #3 #9d6444ff > color #3 #9d616aff > color #1 #b9d2f9ff > color #1 #abb8f9ff > color #1 #dadef9ff > color #1 #c4f9f7ff > color #1 #d5e0f9ff > color #1 #d6f2f9ff > color #1 #ccf9ecff > color #1 #a0dbf9ff > color #1 #8ebbf9ff > color #1 #91bfffff > color #1 #5b78a0ff > color #1 #769cd0ff > color #1 #6c83d0ff > color #1 #85a1ffff > color #1 #69b9ffff > color #1 #53c9ffff > color #1 #cff1ffff > color #1 #d1d9ffff > color #1 #b2beffff > color #1 #c8b1ffff > color #1 #85f5ffff > color #1 #8effc1ff > color #1 #8dfff5ff > color #1 #6affe8ff > color #1 #70ffc3ff > color #1 #4cac83ff > color #1 #0fac81ff > color #1 #3098acff > color #1 #679bacff > color #1 #588492ff > color #1 #90d9f1ff > color #1 #72acbfff > color #1 #6da6bfff > color #1 #7dbabfff > color #1 #6da2bfff > color #1 #6495afff > color #4 #574a6aff > save /Users/edichaki/Desktop/image1.png supersample 3 > save /Volumes/Groups/mosalaganti- > data/data/Kimberly/20250414_Krios_data_hela_DRP1/20250404_0047_s11g1_snapdrp1_mitotr/krios/TS_002/segmentation_new- > files/MEMBRANES.cxs ——— End of log from Tue May 13 11:23:43 2025 ——— opened ChimeraX session > open /Volumes/Groups/mosalaganti- > data/data/Kimberly/20250414_Krios_data_hela_DRP1/20250404_0047_s11g1_snapdrp1_mitotr/krios/TS_002/Ribosome_template_match/Raw_tilt/reconstruction/deconv/TS_002.mrc_6.67Apx_invert.mrc Opened TS_002.mrc_6.67Apx_invert.mrc as #6, grid size 1024,1440,500, pixel 6.67,6.67,6.67, shown at step 1, values float32 > volume #6 level 255,0 level 255,0.8 level 255.1,1 > volume #6 level 255,0 level 255,0.7538 level 255.1,1 > volume #6 level 255,0 level 255,0.7538 level 255.1,0.2769 > volume #6 level 255,0.06154 level 255,0.7538 level 255.1,0.2769 > volume #6 level 255,0.06154 level 255,0.8154 level 255.1,0.2769 > volume #6 level 255,0.1077 level 255,0.8154 level 255.1,0.2769 > volume #6 level 255,0.1077 level 255,0.6154 level 255.1,0.2769 > volume #6 level 255,0.1231 level 255,0.6154 level 255.1,0.2769 [Repeated 1 time(s)] > volume #6 level 255,0.1077 level 255,0.6154 level 255.1,0.2769 > volume #6 level 255,0.09231 level 255,0.6154 level 255.1,0.2769 > volume #6 level 255,0.07692 level 255,0.6154 level 255.1,0.2769 [Repeated 1 time(s)] > volume #6 level 255,0.06154 level 255,0.6154 level 255.1,0.2769 > volume #6 level 255,0.04615 level 255,0.6154 level 255.1,0.2769 [Repeated 7 time(s)] > volume #6 level 255,0.06154 level 255,0.6154 level 255.1,0.2769 [Repeated 5 time(s)] > volume #6 level 255,0.07692 level 255,0.6154 level 255.1,0.2769 > volume #6 level 255,0.09231 level 255,0.6154 level 255.1,0.2769 > volume #6 level 255,0.1077 level 255,0.6154 level 255.1,0.2769 [Repeated 3 time(s)] > volume #6 level 255,0.1231 level 255,0.6154 level 255.1,0.2769 [Repeated 1 time(s)] > volume #6 level 255,0.1385 level 255,0.6154 level 255.1,0.2769 > volume #6 level 254.9,0.1385 level 255,0.6154 level 255.1,0.2769 [Repeated 5 time(s)] > volume #6 level 254.9,0.1538 level 255,0.6154 level 255.1,0.2769 [Repeated 1 time(s)] > volume #6 level 254.9,0.1692 level 255,0.6154 level 255.1,0.2769 [Repeated 2 time(s)] > volume #6 level 254.9,0.1846 level 255,0.6154 level 255.1,0.2769 > volume #6 level 254.9,0.2 level 255,0.6154 level 255.1,0.2769 [Repeated 1 time(s)] > volume #6 level 254.9,0.2308 level 255,0.6154 level 255.1,0.2769 > volume #6 level 254.9,0.2615 level 255,0.6154 level 255.1,0.2769 > volume #6 level 254.9,0.2923 level 255,0.6154 level 255.1,0.2769 > volume #6 level 254.9,0.3077 level 255,0.6154 level 255.1,0.2769 > volume #6 level 254.9,0.3231 level 255,0.6154 level 255.1,0.2769 [Repeated 17 time(s)] > volume #6 level 255,0.3231 level 255,0.6154 level 255.1,0.2769 [Repeated 12 time(s)] > volume #6 level 255,0.3077 level 255,0.6154 level 255.1,0.2769 [Repeated 2 time(s)] > volume #6 level 255,0.2923 level 255,0.6154 level 255.1,0.2769 [Repeated 1 time(s)] > volume #6 level 255,0.2769 level 255,0.6154 level 255.1,0.2769 [Repeated 2 time(s)] > volume #6 level 255,0.2615 level 255,0.6154 level 255.1,0.2769 [Repeated 8 time(s)] > volume #6 level 255,0.2769 level 255,0.6154 level 255.1,0.2769 > volume #6 level 254.9,0.2769 level 255,0.6154 level 255.1,0.2769 > volume #6 level 254.9,0.2923 level 255,0.6154 level 255.1,0.2769 > volume #6 level 254.9,0.3077 level 255,0.6154 level 255.1,0.2769 [Repeated 3 time(s)] > volume #6 level 254.9,0.3231 level 255,0.6154 level 255.1,0.2769 [Repeated 5 time(s)] > volume #6 level 254.9,0.3077 level 255,0.6154 level 255.1,0.2769 [Repeated 2 time(s)] > volume #6 level 254.9,0.2769 level 255,0.6154 level 255.1,0.2769 [Repeated 7 time(s)] > volume #6 level 254.9,0.2615 level 255,0.6154 level 255.1,0.2769 [Repeated 3 time(s)] > volume #6 level 254.9,0.2462 level 255,0.6154 level 255.1,0.2769 [Repeated 10 time(s)] > volume #6 level 254.9,0.2462 level 255,0.6154 level 255.1,0.2154 > volume #6 level 255,0.2154 level 255,0.6154 level 255.1,0.2154 > volume #6 level 255,0.2154 level 255,0.7692 level 255.1,0.2154 > volume #6 level 255,0.2154 level 255,0.7692 level 255,0.09231 > cd .. Current working directory is: /Users/edichaki > close #6 > open /Volumes/Groups/mosalaganti- > data/data/Kimberly/20250414_Krios_data_hela_DRP1/20250404_0047_s11g1_snapdrp1_mitotr/krios/TS_002/Ribosome_template_match/Raw_tilt/reconstruction/deconv/TS_002.mrc_6.67Apx_invert.mrc Opened TS_002.mrc_6.67Apx_invert.mrc as #6, grid size 1024,1440,500, pixel 6.67,6.67,6.67, shown at step 1, values float32 > volume #6 level 255,0 level 255,0.8 level 255.1,1 > volume #6 level 255,0 level 255,0.8 level 255.1,0.2308 > volume #6 level 255,0 level 255,0.4462 level 255.1,0.2308 > volume #6 level 255,0.7538 level 255,0.4462 level 255.1,0.2308 > volume #6 level 255,0.7538 level 255,0.4462 level 255,0.2615 > volume #6 level 255,0.7538 level 254.9,0.04615 level 255,0.2615 > volume #6 level 255,0 level 254.9,0.04615 level 255,0.2615 > volume #6 level 255,0 level 254.9,0.04615 level 255,0.5692 > volume #6 level 255,0 level 254.9,0.1231 level 255,0.5692 > volume #6 level 255,0 level 254.9,0.3231 level 255,0.5692 > volume #6 level 255,0 level 255,0.2923 level 255,0.5692 > volume #6 level 255,0 level 255,0.2923 level 255,0.7385 > volume #6 level 255,0.2769 level 255,0.2923 level 255,0.7385 > volume #6 level 255,0.2769 level 255,0.2923 level 255,0.7538 > volume #6 level 255,0.2769 level 255,0.2 level 255,0.7538 > artiax invert [Repeated 3 time(s)] > artiax start > artiax invert [Repeated 1 time(s)]Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/triggerset.py"", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 4068, in _update_drawings v.update_drawings() File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 821, in update_drawings self._keep_displayed_data = self.displayed_matrices() ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1771, in displayed_matrices matrices.append(self.matrix(read_matrix)) ^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1254, in matrix m = self.region_matrix(r, read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1278, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/griddata.py"", line 317, in matrix m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/mrc/mrc_grid.py"", line 50, in read_matrix m = self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/mrc/mrc_format.py"", line 287, in read_matrix matrix = read_array(self.path, self.data_offset, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/readarray.py"", line 70, in read_array file.close() OSError: [Errno 89] Operation canceled Error processing trigger ""graphics update"": OSError: [Errno 89] Operation canceled File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/readarray.py"", line 70, in read_array file.close() See log for complete Python traceback. 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. [Errno 89] Operation canceled Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/updateloop.py"", line 84, in draw_new_frame view.draw(check_for_changes = False) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/view.py"", line 188, in draw self._draw_scene(camera, drawings) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/view.py"", line 266, in _draw_scene draw_transparent(r, transparent_drawings) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/drawing.py"", line 1559, in draw_transparent r.draw_transparent( File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1312, in draw_transparent draw() File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/drawing.py"", line 1561, in lambda: _draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/drawing.py"", line 1567, in _draw_multiple d.draw(renderer, draw_pass) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/image3d.py"", line 933, in draw drawing = self._update_view_axis(renderer) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/image3d.py"", line 662, in _update_view_axis pd = self._update_2d_texture_planes(view_dir) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/image3d.py"", line 670, in _update_2d_texture_planes pd = self._texture_2d_planes(axis) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/image3d.py"", line 696, in _texture_2d_planes pd = self._make_planes(axis) ^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/image3d.py"", line 855, in _make_planes d = Texture2dPlanes(self, axis) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/image3d.py"", line 1355, in __init__ self._update_textures(planes) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/image3d.py"", line 1452, in _update_textures textures = [self._plane_texture(k, axis) for k, axis in planes] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/image3d.py"", line 1452, in textures = [self._plane_texture(k, axis) for k, axis in planes] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/image3d.py"", line 1459, in _plane_texture self._fill_plane_texture(k, axis, t) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/image3d.py"", line 1479, in _fill_plane_texture data = ir._color_plane(plane, axis) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/image3d.py"", line 298, in _color_plane m = self._matrix_plane(plane, axis) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/image3d.py"", line 272, in _matrix_plane m = self._data.matrix(ijk_origin, ijk_size, ijk_step) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/griddata.py"", line 317, in matrix m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/mrc/mrc_grid.py"", line 50, in read_matrix m = self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/mrc/mrc_format.py"", line 287, in read_matrix matrix = read_array(self.path, self.data_offset, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/readarray.py"", line 70, in read_array file.close() OSError: [Errno 89] Operation canceled Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/updateloop.py"", line 151, in _redraw_timer_callback self.session.ui.mouse_modes.mouse_pause_tracking() File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/mouse_modes/mousemodes.py"", line 504, in mouse_pause_tracking self._mouse_pause() File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/mouse_modes/mousemodes.py"", line 645, in _mouse_pause m.pause(self._mouse_pause_position) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/mouse_modes/std_modes.py"", line 803, in pause p = self.view.picked_object(x, y) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/view.py"", line 837, in picked_object p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond = beyond, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/view.py"", line 869, in picked_object_on_segment p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/models.py"", line 143, in first_intercept pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/drawing.py"", line 1069, in first_intercept p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2, exclude=exclude) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/drawing.py"", line 1086, in first_intercept_children p = d.first_intercept(cxyz1, cxyz2, exclude=exclude) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1130, in first_intercept v = self.region_matrix((ijk,ijk,ijk_step)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1278, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/griddata.py"", line 317, in matrix m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/mrc/mrc_grid.py"", line 50, in read_matrix m = self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/mrc/mrc_format.py"", line 287, in read_matrix matrix = read_array(self.path, self.data_offset, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/readarray.py"", line 70, in read_array file.close() OSError: [Errno 89] Operation canceled OSError: [Errno 89] Operation canceled File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/readarray.py"", line 70, in read_array file.close() See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/updateloop.py"", line 151, in _redraw_timer_callback self.session.ui.mouse_modes.mouse_pause_tracking() File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/mouse_modes/mousemodes.py"", line 504, in mouse_pause_tracking self._mouse_pause() File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/mouse_modes/mousemodes.py"", line 645, in _mouse_pause m.pause(self._mouse_pause_position) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/mouse_modes/std_modes.py"", line 803, in pause p = self.view.picked_object(x, y) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/view.py"", line 837, in picked_object p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond = beyond, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/view.py"", line 869, in picked_object_on_segment p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/models.py"", line 143, in first_intercept pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/drawing.py"", line 1069, in first_intercept p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2, exclude=exclude) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/drawing.py"", line 1086, in first_intercept_children p = d.first_intercept(cxyz1, cxyz2, exclude=exclude) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1130, in first_intercept v = self.region_matrix((ijk,ijk,ijk_step)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1278, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/griddata.py"", line 317, in matrix m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/mrc/mrc_grid.py"", line 50, in read_matrix m = self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/mrc/mrc_format.py"", line 287, in read_matrix matrix = read_array(self.path, self.data_offset, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/readarray.py"", line 70, in read_array file.close() OSError: [Errno 89] Operation canceled OSError: [Errno 89] Operation canceled File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/readarray.py"", line 70, in read_array file.close() See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2176, in mousePressEvent cb(event) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2239, in select_data_cb d.redisplay_needed_cb() File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 316, in redisplay_needed_cb self.redisplay_needed() File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 342, in redisplay_needed self.show_using_dialog_settings(self.active_volume) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 384, in show_using_dialog_settings dr.show() File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 773, in show self._keep_displayed_data = self.displayed_matrices() if show else None ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1771, in displayed_matrices matrices.append(self.matrix(read_matrix)) ^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1254, in matrix m = self.region_matrix(r, read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1278, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/griddata.py"", line 317, in matrix m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/mrc/mrc_grid.py"", line 50, in read_matrix m = self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/mrc/mrc_format.py"", line 287, in read_matrix matrix = read_array(self.path, self.data_offset, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/readarray.py"", line 70, in read_array file.close() OSError: [Errno 89] Operation canceled OSError: [Errno 89] Operation canceled File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/readarray.py"", line 70, in read_array file.close() See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/updateloop.py"", line 151, in _redraw_timer_callback self.session.ui.mouse_modes.mouse_pause_tracking() File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/mouse_modes/mousemodes.py"", line 504, in mouse_pause_tracking self._mouse_pause() File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/mouse_modes/mousemodes.py"", line 645, in _mouse_pause m.pause(self._mouse_pause_position) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/mouse_modes/std_modes.py"", line 803, in pause p = self.view.picked_object(x, y) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/view.py"", line 837, in picked_object p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond = beyond, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/view.py"", line 869, in picked_object_on_segment p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/models.py"", line 143, in first_intercept pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/drawing.py"", line 1069, in first_intercept p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2, exclude=exclude) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/drawing.py"", line 1086, in first_intercept_children p = d.first_intercept(cxyz1, cxyz2, exclude=exclude) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1130, in first_intercept v = self.region_matrix((ijk,ijk,ijk_step)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1278, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/griddata.py"", line 317, in matrix m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/mrc/mrc_grid.py"", line 50, in read_matrix m = self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/mrc/mrc_format.py"", line 287, in read_matrix matrix = read_array(self.path, self.data_offset, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/readarray.py"", line 70, in read_array file.close() OSError: [Errno 89] Operation canceled OSError: [Errno 89] Operation canceled File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/readarray.py"", line 70, in read_array file.close() See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2176, in mousePressEvent cb(event) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/histogram.py"", line 366, in select_marker_cb cb(self.markers[i]) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2245, in selected_marker_cb self.select_data_cb() File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2239, in select_data_cb d.redisplay_needed_cb() File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 316, in redisplay_needed_cb self.redisplay_needed() File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 342, in redisplay_needed self.show_using_dialog_settings(self.active_volume) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 384, in show_using_dialog_settings dr.show() File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 773, in show self._keep_displayed_data = self.displayed_matrices() if show else None ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1771, in displayed_matrices matrices.append(self.matrix(read_matrix)) ^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1254, in matrix m = self.region_matrix(r, read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1278, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/griddata.py"", line 317, in matrix m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/mrc/mrc_grid.py"", line 50, in read_matrix m = self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/mrc/mrc_format.py"", line 287, in read_matrix matrix = read_array(self.path, self.data_offset, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/readarray.py"", line 70, in read_array file.close() OSError: [Errno 89] Operation canceled OSError: [Errno 89] Operation canceled File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/readarray.py"", line 70, in read_array file.close() See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2176, in mousePressEvent cb(event) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/histogram.py"", line 366, in select_marker_cb cb(self.markers[i]) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2245, in selected_marker_cb self.select_data_cb() File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2239, in select_data_cb d.redisplay_needed_cb() File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 316, in redisplay_needed_cb self.redisplay_needed() File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 342, in redisplay_needed self.show_using_dialog_settings(self.active_volume) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 384, in show_using_dialog_settings dr.show() File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 773, in show self._keep_displayed_data = self.displayed_matrices() if show else None ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1771, in displayed_matrices matrices.append(self.matrix(read_matrix)) ^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1254, in matrix m = self.region_matrix(r, read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume.py"", line 1278, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/griddata.py"", line 317, in matrix m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/mrc/mrc_grid.py"", line 50, in read_matrix m = self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/mrc/mrc_format.py"", line 287, in read_matrix matrix = read_array(self.path, self.data_offset, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/readarray.py"", line 70, in read_array file.close() OSError: [Errno 89] Operation canceled OSError: [Errno 89] Operation canceled File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map_data/readarray.py"", line 70, in read_array file.close() See log for complete Python traceback. OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M3 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: iMac Model Identifier: Mac15,5 Model Number: Z19M0001ULL/A Chip: Apple M3 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 24 GB System Firmware Version: 11881.61.3 OS Loader Version: 11881.61.3 Software: System Software Overview: System Version: macOS 15.2 (24C101) Kernel Version: Darwin 24.2.0 Time since boot: 8 days, 8 hours, 43 minutes Graphics/Displays: Apple M3: Chipset Model: Apple M3 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: iMac: Display Type: Built-In Retina LCD Resolution: Retina 4.5K (4480 x 2520) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL U2722DE: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-ArtiaX: 0.6.0 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 geomdl: 5.3.1 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 pandas: 2.2.3 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pyarrow: 20.0.0 pycollada: 0.8 pydantic: 2.11.4 pydantic_core: 2.33.2 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 starfile: 0.5.12 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing-inspection: 0.4.0 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Volume Data nonchimerax all ChimeraX