Opened 5 months ago

Closed 5 months ago

#17681 closed defect (nonchimerax)

Reading volume data: OSError: Operation canceled

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

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>  
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 <listcomp>  
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

Change History (2)

comment:1 by Eric Pettersen, 5 months ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → volume redraw(?): Operation canceled

This was off an "artiax invert" command, but on the other hand the traceback is from a trigger handler and entirely within our own code, so initially assigning it to us, but its certainly possible it should be in the "Third Party" component and assigned to "artiax".

comment:2 by Tom Goddard, 5 months ago

Resolution: → nonchimerax
Status: assigned → closed
Summary: volume redraw(?): Operation canceled → Reading volume data: OSError: Operation canceled

This is an OSError operation canceled. Which I believe means the user sent SIGINT to ChimeraX probably by pressing ctrl-C in the terminal where ChimeraX was started. Possibly they did this because they were reading a 2 GB tomogram file from an external disk which may have been going too slowly.

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
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