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Opened 21 months ago
Closed 21 months ago
#14537 closed defect (can't reproduce)
cannot select an axis to squeeze out which has size not equal to one
| Reported by: | 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-13.2-arm64-arm-64bit
ChimeraX Version: 1.8.dev202402020018 (2024-02-02 00:18:35 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.8.dev202402020018 (2024-02-02)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Successfully installed 'ChimeraX-NMRSTAR==1.0.2'
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/
Collecting ChimeraX-NMRSTAR==1.0.2
Downloading
https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxnmrstar/releases/1.0.2/ChimeraX_NMRSTAR-1.0.2-py3-none-
any.whl (7.2 kB)
Requirement already satisfied: ChimeraX-Core<2.0,>=1.6 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-NMRSTAR==1.0.2) (1.8.dev202402020018)
Requirement already satisfied: ChimeraX-Atomic~=1.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-NMRSTAR==1.0.2) (1.53)
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-NMRSTAR==1.0.2) (1.2.3)
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-NMRSTAR==1.0.2) (1.13.2)
Requirement already satisfied: pynmrstar~=3.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-NMRSTAR==1.0.2) (3.3.2)
Requirement already satisfied: ChimeraX-AtomicLibrary~=12.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Atomic~=1.0->ChimeraX-NMRSTAR==1.0.2) (12.1.10)
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Atomic~=1.0->ChimeraX-NMRSTAR==1.0.2) (2.0.1)
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Atomic~=1.0->ChimeraX-NMRSTAR==1.0.2) (1.3)
Requirement already satisfied: ChimeraX-Graphics~=1.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Atomic~=1.0->ChimeraX-NMRSTAR==1.0.2) (1.1.1)
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Atomic~=1.0->ChimeraX-NMRSTAR==1.0.2) (2.12.2)
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Atomic~=1.0->ChimeraX-NMRSTAR==1.0.2) (2.0.3)
Requirement already satisfied: ChimeraX-PDB~=2.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Atomic~=1.0->ChimeraX-NMRSTAR==1.0.2) (2.7.3)
Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Atomic~=1.0->ChimeraX-NMRSTAR==1.0.2) (1.0.4)
Requirement already satisfied: ChimeraX-Arrays~=1.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Atomic~=1.0->ChimeraX-NMRSTAR==1.0.2) (1.1)
Requirement already satisfied: ChimeraX-IO~=1.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-DataFormats~=1.0->ChimeraX-NMRSTAR==1.0.2) (1.0.1)
Requirement already satisfied: ChimeraX-SaveCommand~=1.4 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-DataFormats~=1.0->ChimeraX-NMRSTAR==1.0.2) (1.5.1)
Requirement already satisfied: ChimeraX-UI~=1.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-OpenCommand~=1.0->ChimeraX-NMRSTAR==1.0.2) (1.33.6)
Requirement already satisfied: requests<=3,>=2.21.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from pynmrstar~=3.0->ChimeraX-NMRSTAR==1.0.2) (2.31.0)
Requirement already satisfied: ChimeraX-Surface~=1.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-
NMRSTAR==1.0.2) (1.0.1)
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-UI~=1.0->ChimeraX-OpenCommand~=1.0->ChimeraX-
NMRSTAR==1.0.2) (1.2)
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-UI~=1.0->ChimeraX-OpenCommand~=1.0->ChimeraX-
NMRSTAR==1.0.2) (1.0)
Requirement already satisfied: charset-normalizer<4,>=2 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from requests<=3,>=2.21.0->pynmrstar~=3.0->ChimeraX-NMRSTAR==1.0.2)
(3.3.2)
Requirement already satisfied: idna<4,>=2.5 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from requests<=3,>=2.21.0->pynmrstar~=3.0->ChimeraX-NMRSTAR==1.0.2)
(3.6)
Requirement already satisfied: urllib3<3,>=1.21.1 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from requests<=3,>=2.21.0->pynmrstar~=3.0->ChimeraX-NMRSTAR==1.0.2)
(2.2.0)
Requirement already satisfied: certifi>=2017.4.17 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from requests<=3,>=2.21.0->pynmrstar~=3.0->ChimeraX-NMRSTAR==1.0.2)
(2023.11.17)
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX-
OpenCommand~=1.0->ChimeraX-NMRSTAR==1.0.2) (1.0.1)
Requirement already satisfied: ChimeraX-Map~=1.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.0->ChimeraX-NMRSTAR==1.0.2) (1.1.4)
Requirement already satisfied: ChimeraX-MapData~=2.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.0->ChimeraX-NMRSTAR==1.0.2) (2.0)
Requirement already satisfied: ChimeraX-StdCommands~=1.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.0->ChimeraX-NMRSTAR==1.0.2) (1.15)
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-NMRSTAR==1.0.2) (2.0.1)
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-NMRSTAR==1.0.2) (2.1.1)
Requirement already satisfied: ChimeraX-DistMonitor~=1.2 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-NMRSTAR==1.0.2) (1.4.1)
Requirement already satisfied: ChimeraX-Dssp~=2.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-NMRSTAR==1.0.2) (2.0)
Requirement already satisfied: ChimeraX-MapFit~=2.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-NMRSTAR==1.0.2) (2.0)
Installing collected packages: ChimeraX-NMRSTAR
Successfully installed ChimeraX-NMRSTAR-1.0.2
[notice] A new release of pip is available: 23.3.2 -> 24.0
[notice] To update, run:
/Applications/ChimeraX_Daily.app/Contents/MacOS/ChimeraX -m pip install
--upgrade pip
> open "/Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/Visualize
> tracking.cxc" format cmd
> close
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_0_arrows.bild
Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_0_arrows.bild
---
warnings | degenerate arrow on line 87
degenerate arrow on line 93
degenerate arrow on line 99
degenerate arrow on line 100
degenerate arrow on line 108
4 messages similar to the above omitted
Opened BILD data containing 208 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_0_chimerax_skeleton_blue.bild
Opened BILD data containing 473 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_1_chimerax_skeleton_red.bild
Opened BILD data containing 504 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_0/frame_0.tif
Opened frame_0.tif as #4, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #4 voxelSize 0.145,0.145,0.145
> volume flip #4 axis y
Opened frame_0.tif y flip as #5, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #4
> rename #5 id #4
> volume #4 color deep sky blue style image
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_1/frame_1.tif
Opened frame_1.tif as #5, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #5 voxelSize 0.145,0.145,0.145
> volume flip #5 axis y
Opened frame_1.tif y flip as #6, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #5
> rename #6 id #5
> volume #5 color tomato style image
> rename #1-5 id 1
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_1_arrows.bild
Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_1_arrows.bild
---
warnings | degenerate arrow on line 79
degenerate arrow on line 84
degenerate arrow on line 94
degenerate arrow on line 101
degenerate arrow on line 107
4 messages similar to the above omitted
Opened BILD data containing 196 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_1_chimerax_skeleton_blue.bild
Opened BILD data containing 504 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_2_chimerax_skeleton_red.bild
Opened BILD data containing 476 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_1/frame_1.tif
Opened frame_1.tif as #5, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #5 voxelSize 0.145,0.145,0.145
> volume flip #5 axis y
Opened frame_1.tif y flip as #6, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #5
> rename #6 id #5
> volume #5 color deep sky blue style image
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_2/frame_2.tif
Opened frame_2.tif as #6, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #6 voxelSize 0.145,0.145,0.145
> volume flip #6 axis y
Opened frame_2.tif y flip as #7, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #6
> rename #7 id #6
> volume #6 color tomato style image
> rename #2-6 id 2
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_2_arrows.bild
Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_2_arrows.bild
---
warnings | degenerate arrow on line 83
degenerate arrow on line 84
degenerate arrow on line 163
degenerate arrow on line 170
degenerate arrow on line 172
2 messages similar to the above omitted
Opened BILD data containing 205 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_2_chimerax_skeleton_blue.bild
Opened BILD data containing 476 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_3_chimerax_skeleton_red.bild
Opened BILD data containing 457 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_2/frame_2.tif
Opened frame_2.tif as #6, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #6 voxelSize 0.145,0.145,0.145
> volume flip #6 axis y
Opened frame_2.tif y flip as #7, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #6
> rename #7 id #6
> volume #6 color deep sky blue style image
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_3/frame_3.tif
Opened frame_3.tif as #7, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #7 voxelSize 0.145,0.145,0.145
> volume flip #7 axis y
Opened frame_3.tif y flip as #8, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #7
> rename #8 id #7
> volume #7 color tomato style image
> rename #3-7 id 3
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_3_arrows.bild
Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_3_arrows.bild
---
warnings | degenerate arrow on line 81
degenerate arrow on line 82
degenerate arrow on line 90
degenerate arrow on line 97
degenerate arrow on line 98
4 messages similar to the above omitted
Opened BILD data containing 190 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_3_chimerax_skeleton_blue.bild
Opened BILD data containing 457 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_4_chimerax_skeleton_red.bild
Opened BILD data containing 483 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_3/frame_3.tif
Opened frame_3.tif as #7, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #7 voxelSize 0.145,0.145,0.145
> volume flip #7 axis y
Opened frame_3.tif y flip as #8, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #7
> rename #8 id #7
> volume #7 color deep sky blue style image
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_4/frame_4.tif
Opened frame_4.tif as #8, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #8 voxelSize 0.145,0.145,0.145
> volume flip #8 axis y
Opened frame_4.tif y flip as #9, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #8
> rename #9 id #8
> volume #8 color tomato style image
> rename #4-8 id 4
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_4_arrows.bild
Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_4_arrows.bild
---
warnings | degenerate arrow on line 91
degenerate arrow on line 101
degenerate arrow on line 129
degenerate arrow on line 157
Opened BILD data containing 205 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_4_chimerax_skeleton_blue.bild
Opened BILD data containing 483 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_5_chimerax_skeleton_red.bild
Opened BILD data containing 491 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_4/frame_4.tif
Opened frame_4.tif as #8, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #8 voxelSize 0.145,0.145,0.145
> volume flip #8 axis y
Opened frame_4.tif y flip as #9, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #8
> rename #9 id #8
> volume #8 color deep sky blue style image
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_5/frame_5.tif
Opened frame_5.tif as #9, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #9 voxelSize 0.145,0.145,0.145
> volume flip #9 axis y
Opened frame_5.tif y flip as #10, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #9
> rename #10 id #9
> volume #9 color tomato style image
> rename #5-9 id 5
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_5_arrows.bild
Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_5_arrows.bild
---
warnings | degenerate arrow on line 85
degenerate arrow on line 86
degenerate arrow on line 97
degenerate arrow on line 110
degenerate arrow on line 133
4 messages similar to the above omitted
Opened BILD data containing 210 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_5_chimerax_skeleton_blue.bild
Opened BILD data containing 491 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_6_chimerax_skeleton_red.bild
Opened BILD data containing 496 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_5/frame_5.tif
Opened frame_5.tif as #9, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #9 voxelSize 0.145,0.145,0.145
> volume flip #9 axis y
Opened frame_5.tif y flip as #10, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #9
> rename #10 id #9
> volume #9 color deep sky blue style image
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_6/frame_6.tif
Opened frame_6.tif as #10, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #10 voxelSize 0.145,0.145,0.145
> volume flip #10 axis y
Opened frame_6.tif y flip as #11, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #10
> rename #11 id #10
> volume #10 color tomato style image
> rename #6-10 id 6
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_6_arrows.bild
Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_6_arrows.bild
---
warnings | degenerate arrow on line 60
degenerate arrow on line 73
degenerate arrow on line 90
degenerate arrow on line 109
degenerate arrow on line 128
4 messages similar to the above omitted
Opened BILD data containing 200 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_6_chimerax_skeleton_blue.bild
Opened BILD data containing 496 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_7_chimerax_skeleton_red.bild
Opened BILD data containing 465 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_6/frame_6.tif
Opened frame_6.tif as #10, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #10 voxelSize 0.145,0.145,0.145
> volume flip #10 axis y
Opened frame_6.tif y flip as #11, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #10
> rename #11 id #10
> volume #10 color deep sky blue style image
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_7/frame_7.tif
Opened frame_7.tif as #11, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #11 voxelSize 0.145,0.145,0.145
> volume flip #11 axis y
Opened frame_7.tif y flip as #12, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #11
> rename #12 id #11
> volume #11 color tomato style image
> rename #7-11 id 7
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_7_arrows.bild
Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_7_arrows.bild
---
warnings | degenerate arrow on line 94
degenerate arrow on line 144
degenerate arrow on line 177
Opened BILD data containing 200 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_7_chimerax_skeleton_blue.bild
Opened BILD data containing 465 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_8_chimerax_skeleton_red.bild
Opened BILD data containing 500 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_7/frame_7.tif
Opened frame_7.tif as #11, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #11 voxelSize 0.145,0.145,0.145
> volume flip #11 axis y
Opened frame_7.tif y flip as #12, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #11
> rename #12 id #11
> volume #11 color deep sky blue style image
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_8/frame_8.tif
Opened frame_8.tif as #12, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #12 voxelSize 0.145,0.145,0.145
> volume flip #12 axis y
Opened frame_8.tif y flip as #13, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #12
> rename #13 id #12
> volume #12 color tomato style image
> rename #8-12 id 8
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_8_arrows.bild
Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_8_arrows.bild
---
warnings | degenerate arrow on line 36
degenerate arrow on line 100
degenerate arrow on line 104
degenerate arrow on line 105
degenerate arrow on line 119
9 messages similar to the above omitted
Opened BILD data containing 213 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_8_chimerax_skeleton_blue.bild
Opened BILD data containing 500 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_9_chimerax_skeleton_red.bild
Opened BILD data containing 480 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_8/frame_8.tif
Opened frame_8.tif as #12, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #12 voxelSize 0.145,0.145,0.145
> volume flip #12 axis y
Opened frame_8.tif y flip as #13, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #12
> rename #13 id #12
> volume #12 color deep sky blue style image
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_9/frame_9.tif
Opened frame_9.tif as #13, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #13 voxelSize 0.145,0.145,0.145
> volume flip #13 axis y
Opened frame_9.tif y flip as #14, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #13
> rename #14 id #13
> volume #13 color tomato style image
> rename #9-13 id 9
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_9_arrows.bild
Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_9_arrows.bild
---
warnings | degenerate arrow on line 96
degenerate arrow on line 131
degenerate arrow on line 143
degenerate arrow on line 144
degenerate arrow on line 165
3 messages similar to the above omitted
Opened BILD data containing 210 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_9_chimerax_skeleton_blue.bild
Opened BILD data containing 480 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_10_chimerax_skeleton_red.bild
Opened BILD data containing 467 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_9/frame_9.tif
Opened frame_9.tif as #13, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #13 voxelSize 0.145,0.145,0.145
> volume flip #13 axis y
Opened frame_9.tif y flip as #14, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #13
> rename #14 id #13
> volume #13 color deep sky blue style image
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_10/frame_10.tif
Opened frame_10.tif as #14, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #14 voxelSize 0.145,0.145,0.145
> volume flip #14 axis y
Opened frame_10.tif y flip as #15, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #14
> rename #15 id #14
> volume #14 color tomato style image
> rename #10-14 id 10
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_10_arrows.bild
Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_10_arrows.bild
---
warnings | degenerate arrow on line 97
degenerate arrow on line 98
degenerate arrow on line 163
degenerate arrow on line 164
degenerate arrow on line 176
Opened BILD data containing 188 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_10_chimerax_skeleton_blue.bild
Opened BILD data containing 467 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_11_chimerax_skeleton_red.bild
Opened BILD data containing 451 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_10/frame_10.tif
Opened frame_10.tif as #14, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #14 voxelSize 0.145,0.145,0.145
> volume flip #14 axis y
Opened frame_10.tif y flip as #15, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #14
> rename #15 id #14
> volume #14 color deep sky blue style image
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_11/frame_11.tif
Opened frame_11.tif as #15, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #15 voxelSize 0.145,0.145,0.145
> volume flip #15 axis y
Opened frame_11.tif y flip as #16, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #15
> rename #16 id #15
> volume #15 color tomato style image
> rename #11-15 id 11
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_11_arrows.bild
Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_11_arrows.bild
---
warnings | degenerate arrow on line 77
degenerate arrow on line 85
degenerate arrow on line 94
degenerate arrow on line 119
degenerate arrow on line 120
4 messages similar to the above omitted
Opened BILD data containing 180 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_11_chimerax_skeleton_blue.bild
Opened BILD data containing 451 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_12_chimerax_skeleton_red.bild
Opened BILD data containing 404 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_11/frame_11.tif
Opened frame_11.tif as #15, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #15 voxelSize 0.145,0.145,0.145
> volume flip #15 axis y
Opened frame_11.tif y flip as #16, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #15
> rename #16 id #15
> volume #15 color deep sky blue style image
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_12/frame_12.tif
Opened frame_12.tif as #16, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #16 voxelSize 0.145,0.145,0.145
> volume flip #16 axis y
Opened frame_12.tif y flip as #17, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #16
> rename #17 id #16
> volume #16 color tomato style image
> rename #12-16 id 12
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_12_arrows.bild
Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_12_arrows.bild
---
warnings | degenerate arrow on line 140
degenerate arrow on line 152
degenerate arrow on line 176
degenerate arrow on line 179
Opened BILD data containing 181 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_12_chimerax_skeleton_blue.bild
Opened BILD data containing 404 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_13_chimerax_skeleton_red.bild
Opened BILD data containing 406 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_12/frame_12.tif
Opened frame_12.tif as #16, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #16 voxelSize 0.145,0.145,0.145
> volume flip #16 axis y
Opened frame_12.tif y flip as #17, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #16
> rename #17 id #16
> volume #16 color deep sky blue style image
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_13/frame_13.tif
Opened frame_13.tif as #17, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #17 voxelSize 0.145,0.145,0.145
> volume flip #17 axis y
Opened frame_13.tif y flip as #18, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #17
> rename #18 id #17
> volume #17 color tomato style image
> rename #13-17 id 13
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_13_arrows.bild
Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_13_arrows.bild
---
warnings | degenerate arrow on line 63
degenerate arrow on line 68
degenerate arrow on line 78
degenerate arrow on line 87
degenerate arrow on line 93
5 messages similar to the above omitted
Opened BILD data containing 171 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_13_chimerax_skeleton_blue.bild
Opened BILD data containing 406 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_14_chimerax_skeleton_red.bild
Opened BILD data containing 384 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_13/frame_13.tif
Opened frame_13.tif as #17, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #17 voxelSize 0.145,0.145,0.145
> volume flip #17 axis y
Opened frame_13.tif y flip as #18, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #17
> rename #18 id #17
> volume #17 color deep sky blue style image
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_14/frame_14.tif
Opened frame_14.tif as #18, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #18 voxelSize 0.145,0.145,0.145
> volume flip #18 axis y
Opened frame_14.tif y flip as #19, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #18
> rename #19 id #18
> volume #18 color tomato style image
> rename #14-18 id 14
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_14_arrows.bild
Opened BILD data containing 207 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_14_chimerax_skeleton_blue.bild
Opened BILD data containing 384 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_15_chimerax_skeleton_red.bild
Opened BILD data containing 384 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_14/frame_14.tif
Opened frame_14.tif as #18, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #18 voxelSize 0.145,0.145,0.145
> volume flip #18 axis y
Opened frame_14.tif y flip as #19, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #18
> rename #19 id #18
> volume #18 color deep sky blue style image
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_15/frame_15.tif
Opened frame_15.tif as #19, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #19 voxelSize 0.145,0.145,0.145
> volume flip #19 axis y
Opened frame_15.tif y flip as #20, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #19
> rename #20 id #19
> volume #19 color tomato style image
> rename #15-19 id 15
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_15_arrows.bild
Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_15_arrows.bild
---
warning | degenerate arrow on line 108
Opened BILD data containing 126 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_15_chimerax_skeleton_blue.bild
Opened BILD data containing 384 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_16_chimerax_skeleton_red.bild
Opened BILD data containing 303 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_15/frame_15.tif
Opened frame_15.tif as #19, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #19 voxelSize 0.145,0.145,0.145
> volume flip #19 axis y
Opened frame_15.tif y flip as #20, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #19
> rename #20 id #19
> volume #19 color deep sky blue style image
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_16/frame_16.tif
Opened frame_16.tif as #20, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #20 voxelSize 0.145,0.145,0.145
> volume flip #20 axis y
Opened frame_16.tif y flip as #21, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #20
> rename #21 id #20
> volume #20 color tomato style image
> rename #16-20 id 16
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_16_arrows.bild
Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_16_arrows.bild
---
warnings | degenerate arrow on line 55
degenerate arrow on line 103
Opened BILD data containing 124 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_16_chimerax_skeleton_blue.bild
Opened BILD data containing 303 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_17_chimerax_skeleton_red.bild
Opened BILD data containing 304 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_16/frame_16.tif
Opened frame_16.tif as #20, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #20 voxelSize 0.145,0.145,0.145
> volume flip #20 axis y
Opened frame_16.tif y flip as #21, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #20
> rename #21 id #20
> volume #20 color deep sky blue style image
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_17/frame_17.tif
Opened frame_17.tif as #21, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #21 voxelSize 0.145,0.145,0.145
> volume flip #21 axis y
Opened frame_17.tif y flip as #22, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #21
> rename #22 id #21
> volume #21 color tomato style image
> rename #17-21 id 17
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_17_arrows.bild
Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_17_arrows.bild
---
warnings | degenerate arrow on line 74
degenerate arrow on line 77
degenerate arrow on line 101
degenerate arrow on line 111
Opened BILD data containing 137 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_17_chimerax_skeleton_blue.bild
Opened BILD data containing 304 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_18_chimerax_skeleton_red.bild
Opened BILD data containing 302 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_17/frame_17.tif
Opened frame_17.tif as #21, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #21 voxelSize 0.145,0.145,0.145
> volume flip #21 axis y
Opened frame_17.tif y flip as #22, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #21
> rename #22 id #21
> volume #21 color deep sky blue style image
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_18/frame_18.tif
Opened frame_18.tif as #22, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #22 voxelSize 0.145,0.145,0.145
> volume flip #22 axis y
Opened frame_18.tif y flip as #23, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #22
> rename #23 id #22
> volume #22 color tomato style image
> rename #18-22 id 18
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_18_arrows.bild
Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_18_arrows.bild
---
warnings | degenerate arrow on line 94
degenerate arrow on line 127
Opened BILD data containing 132 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_18_chimerax_skeleton_blue.bild
Opened BILD data containing 302 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_19_chimerax_skeleton_red.bild
Opened BILD data containing 281 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_18/frame_18.tif
Opened frame_18.tif as #22, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #22 voxelSize 0.145,0.145,0.145
> volume flip #22 axis y
Opened frame_18.tif y flip as #23, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #22
> rename #23 id #22
> volume #22 color deep sky blue style image
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_19/frame_19.tif
Opened frame_19.tif as #23, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #23 voxelSize 0.145,0.145,0.145
> volume flip #23 axis y
Opened frame_19.tif y flip as #24, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #23
> rename #24 id #23
> volume #23 color tomato style image
> rename #19-23 id 19
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_19_arrows.bild
Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_19_arrows.bild
---
warnings | degenerate arrow on line 88
degenerate arrow on line 103
Opened BILD data containing 124 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_19_chimerax_skeleton_blue.bild
Opened BILD data containing 281 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_20_chimerax_skeleton_red.bild
Opened BILD data containing 291 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_19/frame_19.tif
Opened frame_19.tif as #23, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #23 voxelSize 0.145,0.145,0.145
> volume flip #23 axis y
Opened frame_19.tif y flip as #24, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #23
> rename #24 id #23
> volume #23 color deep sky blue style image
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_20/frame_20.tif
Opened frame_20.tif as #24, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #24 voxelSize 0.145,0.145,0.145
> volume flip #24 axis y
Opened frame_20.tif y flip as #25, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #24
> rename #25 id #24
> volume #24 color tomato style image
> rename #20-24 id 20
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_20_arrows.bild
Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_20_arrows.bild
---
warnings | degenerate arrow on line 83
degenerate arrow on line 95
degenerate arrow on line 97
degenerate arrow on line 107
degenerate arrow on line 109
Opened BILD data containing 108 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_20_chimerax_skeleton_blue.bild
Opened BILD data containing 291 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_21_chimerax_skeleton_red.bild
Opened BILD data containing 273 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_20/frame_20.tif
Opened frame_20.tif as #24, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #24 voxelSize 0.145,0.145,0.145
> volume flip #24 axis y
Opened frame_20.tif y flip as #25, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #24
> rename #25 id #24
> volume #24 color deep sky blue style image
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_21/frame_21.tif
Opened frame_21.tif as #25, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #25 voxelSize 0.145,0.145,0.145
> volume flip #25 axis y
Opened frame_21.tif y flip as #26, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #25
> rename #26 id #25
> volume #25 color tomato style image
> rename #21-25 id 21
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_21_arrows.bild
Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_21_arrows.bild
---
warnings | degenerate arrow on line 90
degenerate arrow on line 91
degenerate arrow on line 93
degenerate arrow on line 104
Opened BILD data containing 116 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_21_chimerax_skeleton_blue.bild
Opened BILD data containing 273 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_22_chimerax_skeleton_red.bild
Opened BILD data containing 308 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_21/frame_21.tif
Opened frame_21.tif as #25, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #25 voxelSize 0.145,0.145,0.145
> volume flip #25 axis y
Opened frame_21.tif y flip as #26, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #25
> rename #26 id #25
> volume #25 color deep sky blue style image
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_22/frame_22.tif
Opened frame_22.tif as #26, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #26 voxelSize 0.145,0.145,0.145
> volume flip #26 axis y
Opened frame_22.tif y flip as #27, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #26
> rename #27 id #26
> volume #26 color tomato style image
> rename #22-26 id 22
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_22_arrows.bild
Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_22_arrows.bild
---
warnings | degenerate arrow on line 88
degenerate arrow on line 95
degenerate arrow on line 114
Opened BILD data containing 119 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_22_chimerax_skeleton_blue.bild
Opened BILD data containing 308 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_23_chimerax_skeleton_red.bild
Opened BILD data containing 242 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_22/frame_22.tif
Opened frame_22.tif as #26, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #26 voxelSize 0.145,0.145,0.145
> volume flip #26 axis y
Opened frame_22.tif y flip as #27, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #26
> rename #27 id #26
> volume #26 color deep sky blue style image
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_23/frame_23.tif
Opened frame_23.tif as #27, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #27 voxelSize 0.145,0.145,0.145
> volume flip #27 axis y
Opened frame_23.tif y flip as #28, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #27
> rename #28 id #27
> volume #27 color tomato style image
> rename #23-27 id 23
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_23_arrows.bild
Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_23_arrows.bild
---
warnings | degenerate arrow on line 73
degenerate arrow on line 76
Opened BILD data containing 111 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_23_chimerax_skeleton_blue.bild
Opened BILD data containing 242 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_24_chimerax_skeleton_red.bild
Opened BILD data containing 251 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_23/frame_23.tif
Opened frame_23.tif as #27, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #27 voxelSize 0.145,0.145,0.145
> volume flip #27 axis y
Opened frame_23.tif y flip as #28, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #27
> rename #28 id #27
> volume #27 color deep sky blue style image
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_24/frame_24.tif
Opened frame_24.tif as #28, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #28 voxelSize 0.145,0.145,0.145
> volume flip #28 axis y
Opened frame_24.tif y flip as #29, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #28
> rename #29 id #28
> volume #28 color tomato style image
> rename #24-28 id 24
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_24_arrows.bild
Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_24_arrows.bild
---
warnings | degenerate arrow on line 52
degenerate arrow on line 62
degenerate arrow on line 80
degenerate arrow on line 81
degenerate arrow on line 85
2 messages similar to the above omitted
Opened BILD data containing 107 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_24_chimerax_skeleton_blue.bild
Opened BILD data containing 251 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_25_chimerax_skeleton_red.bild
Opened BILD data containing 232 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_24/frame_24.tif
Opened frame_24.tif as #28, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #28 voxelSize 0.145,0.145,0.145
> volume flip #28 axis y
Opened frame_24.tif y flip as #29, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #28
> rename #29 id #28
> volume #28 color deep sky blue style image
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_25/frame_25.tif
Opened frame_25.tif as #29, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #29 voxelSize 0.145,0.145,0.145
> volume flip #29 axis y
Opened frame_25.tif y flip as #30, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #29
> rename #30 id #29
> volume #29 color tomato style image
> rename #25-29 id 25
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_25_arrows.bild
Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_25_arrows.bild
---
warnings | degenerate arrow on line 57
degenerate arrow on line 88
degenerate arrow on line 104
Opened BILD data containing 109 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_25_chimerax_skeleton_blue.bild
Opened BILD data containing 232 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_26_chimerax_skeleton_red.bild
Opened BILD data containing 251 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_25/frame_25.tif
Opened frame_25.tif as #29, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #29 voxelSize 0.145,0.145,0.145
> volume flip #29 axis y
Opened frame_25.tif y flip as #30, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #29
> rename #30 id #29
> volume #29 color deep sky blue style image
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_26/frame_26.tif
Opened frame_26.tif as #30, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #30 voxelSize 0.145,0.145,0.145
> volume flip #30 axis y
Opened frame_26.tif y flip as #31, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #30
> rename #31 id #30
> volume #30 color tomato style image
> rename #26-30 id 26
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_26_arrows.bild
Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_26_arrows.bild
---
warnings | degenerate arrow on line 82
degenerate arrow on line 89
degenerate arrow on line 95
degenerate arrow on line 106
Opened BILD data containing 111 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_26_chimerax_skeleton_blue.bild
Opened BILD data containing 251 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_27_chimerax_skeleton_red.bild
Opened BILD data containing 246 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_26/frame_26.tif
Opened frame_26.tif as #30, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #30 voxelSize 0.145,0.145,0.145
> volume flip #30 axis y
Opened frame_26.tif y flip as #31, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #30
> rename #31 id #30
> volume #30 color deep sky blue style image
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_27/frame_27.tif
Opened frame_27.tif as #31, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #31 voxelSize 0.145,0.145,0.145
> volume flip #31 axis y
Opened frame_27.tif y flip as #32, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #31
> rename #32 id #31
> volume #31 color tomato style image
> rename #27-31 id 27
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_27_arrows.bild
Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_27_arrows.bild
---
warnings | degenerate arrow on line 70
degenerate arrow on line 96
Opened BILD data containing 98 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_27_chimerax_skeleton_blue.bild
Opened BILD data containing 246 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_28_chimerax_skeleton_red.bild
Opened BILD data containing 247 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_27/frame_27.tif
Opened frame_27.tif as #31, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #31 voxelSize 0.145,0.145,0.145
> volume flip #31 axis y
Opened frame_27.tif y flip as #32, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #31
> rename #32 id #31
> volume #31 color deep sky blue style image
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_28/frame_28.tif
Opened frame_28.tif as #32, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #32 voxelSize 0.145,0.145,0.145
> volume flip #32 axis y
Opened frame_28.tif y flip as #33, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #32
> rename #33 id #32
> volume #32 color tomato style image
> rename #28-32 id 28
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_28_arrows.bild
Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_28_arrows.bild
---
warnings | degenerate arrow on line 87
degenerate arrow on line 88
Opened BILD data containing 105 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_28_chimerax_skeleton_blue.bild
Opened BILD data containing 247 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_29_chimerax_skeleton_red.bild
Opened BILD data containing 221 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_28/frame_28.tif
Opened frame_28.tif as #32, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #32 voxelSize 0.145,0.145,0.145
> volume flip #32 axis y
Opened frame_28.tif y flip as #33, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #32
> rename #33 id #32
> volume #32 color deep sky blue style image
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_29/frame_29.tif
Opened frame_29.tif as #33, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #33 voxelSize 0.145,0.145,0.145
> volume flip #33 axis y
Opened frame_29.tif y flip as #34, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #33
> rename #34 id #33
> volume #33 color tomato style image
> rename #29-33 id 29
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_29_arrows.bild
Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_29_arrows.bild
---
warnings | degenerate arrow on line 63
degenerate arrow on line 72
degenerate arrow on line 93
degenerate arrow on line 103
Opened BILD data containing 105 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_29_chimerax_skeleton_blue.bild
Opened BILD data containing 221 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_30_chimerax_skeleton_red.bild
Opened BILD data containing 230 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_29/frame_29.tif
Opened frame_29.tif as #33, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #33 voxelSize 0.145,0.145,0.145
> volume flip #33 axis y
Opened frame_29.tif y flip as #34, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #33
> rename #34 id #33
> volume #33 color deep sky blue style image
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_30/frame_30.tif
Opened frame_30.tif as #34, grid size 200,200,1, pixel 1, shown at step 1,
values uint8
> volume #34 voxelSize 0.145,0.145,0.145
> volume flip #34 axis y
Opened frame_30.tif y flip as #35, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8
> close #34
> rename #35 id #34
> volume #34 color tomato style image
> rename #30-34 id 30
> mseries slider #1-30
executed Visualize tracking.cxc
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.
cannot select an axis to squeeze out which has size not equal to one
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.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_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 265, in _draw_scene
draw_transparent(r, transparent_drawings)
File
"/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1294, in draw_transparent
draw()
File
"/Applications/ChimeraX_Daily.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_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 806, in draw
bi.draw(renderer, draw_pass)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1397, in draw
Image3d.draw(self, renderer, draw_pass)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 816, in draw
pd = self._update_planes(renderer)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 581, in _update_planes
pd = self._update_2d_texture_planes(view_dir)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 589, in _update_2d_texture_planes
pd = self._texture_2d_planes(axis)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 615, in _texture_2d_planes
pd = self._make_planes(axis)
^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 743, in _make_planes
d = Texture2dPlanes(self, axis)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1017, in __init__
self._update_textures(planes)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1089, in _update_textures
textures = [self._plane_texture(k, axis) for k,axis in planes]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1089, in <listcomp>
textures = [self._plane_texture(k, axis) for k,axis in planes]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1096, in _plane_texture
self._fill_plane_texture(k, axis, t)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1115, in _fill_plane_texture
data = ir._color_plane(plane, axis)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1411, in _color_plane
dp = ir._color_plane(k, axis, color_3d=color_3d, require_color=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 250, in _color_plane
m = self._matrix_plane(plane, axis)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 227, in _matrix_plane
p = squeeze(m, 2-axis) # Reduce from 3d array to 2d.
^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/fromnumeric.py", line 1558, in squeeze
return squeeze(axis=axis)
^^^^^^^^^^^^^^^^^^
ValueError: cannot select an axis to squeeze out which has size not equal to
one
Exception ignored in: <function Texture.__del__ at 0x106d919e0>
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 3076, in __del__
raise OpenGLError('OpenGL texture was not deleted before graphics.Texture
destroyed')
chimerax.graphics.opengl.OpenGLError: OpenGL texture was not deleted before
graphics.Texture destroyed
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/filehistory.py", line 84, in <lambda>
t.add_handler('frame drawn', lambda *args, s=self: s.capture_thumbnails_cb())
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/filehistory.py", line 96, in capture_thumbnails_cb
fs.capture_image(models, ses)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/filehistory.py", line 190, in capture_image
self.image = models_image(session, models, size)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/filehistory.py", line 248, in models_image
image = v.image(width, height)
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 450, in image
rgba = self.image_rgba(width=width, height=height, supersample=supersample,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 500, in image_rgba
self.draw(c, drawings, swap_buffers = False)
File
"/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 265, in _draw_scene
draw_transparent(r, transparent_drawings)
File
"/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1294, in draw_transparent
draw()
File
"/Applications/ChimeraX_Daily.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_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 806, in draw
bi.draw(renderer, draw_pass)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1397, in draw
Image3d.draw(self, renderer, draw_pass)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 816, in draw
pd = self._update_planes(renderer)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 581, in _update_planes
pd = self._update_2d_texture_planes(view_dir)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 589, in _update_2d_texture_planes
pd = self._texture_2d_planes(axis)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 615, in _texture_2d_planes
pd = self._make_planes(axis)
^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 743, in _make_planes
d = Texture2dPlanes(self, axis)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1017, in __init__
self._update_textures(planes)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1089, in _update_textures
textures = [self._plane_texture(k, axis) for k,axis in planes]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1089, in <listcomp>
textures = [self._plane_texture(k, axis) for k,axis in planes]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1096, in _plane_texture
self._fill_plane_texture(k, axis, t)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1115, in _fill_plane_texture
data = ir._color_plane(plane, axis)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1411, in _color_plane
dp = ir._color_plane(k, axis, color_3d=color_3d, require_color=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 250, in _color_plane
m = self._matrix_plane(plane, axis)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 227, in _matrix_plane
p = squeeze(m, 2-axis) # Reduce from 3d array to 2d.
^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/fromnumeric.py", line 1558, in squeeze
return squeeze(axis=axis)
^^^^^^^^^^^^^^^^^^
ValueError: cannot select an axis to squeeze out which has size not equal to
one
Error processing trigger "frame drawn":
ValueError: cannot select an axis to squeeze out which has size not equal to
one
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/fromnumeric.py", line 1558, in squeeze
return squeeze(axis=axis)
^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Exception ignored in: <function Texture.__del__ at 0x106d919e0>
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 3076, in __del__
raise OpenGLError('OpenGL texture was not deleted before graphics.Texture
destroyed')
chimerax.graphics.opengl.OpenGLError: OpenGL texture was not deleted before
graphics.Texture destroyed
> graphics restart
An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.
cannot select an axis to squeeze out which has size not equal to one
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.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_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 265, in _draw_scene
draw_transparent(r, transparent_drawings)
File
"/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1294, in draw_transparent
draw()
File
"/Applications/ChimeraX_Daily.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_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 806, in draw
bi.draw(renderer, draw_pass)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1397, in draw
Image3d.draw(self, renderer, draw_pass)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 816, in draw
pd = self._update_planes(renderer)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 581, in _update_planes
pd = self._update_2d_texture_planes(view_dir)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 589, in _update_2d_texture_planes
pd = self._texture_2d_planes(axis)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 615, in _texture_2d_planes
pd = self._make_planes(axis)
^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 743, in _make_planes
d = Texture2dPlanes(self, axis)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1017, in __init__
self._update_textures(planes)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1089, in _update_textures
textures = [self._plane_texture(k, axis) for k,axis in planes]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1089, in <listcomp>
textures = [self._plane_texture(k, axis) for k,axis in planes]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1096, in _plane_texture
self._fill_plane_texture(k, axis, t)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1115, in _fill_plane_texture
data = ir._color_plane(plane, axis)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1411, in _color_plane
dp = ir._color_plane(k, axis, color_3d=color_3d, require_color=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 250, in _color_plane
m = self._matrix_plane(plane, axis)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 227, in _matrix_plane
p = squeeze(m, 2-axis) # Reduce from 3d array to 2d.
^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/fromnumeric.py", line 1558, in squeeze
return squeeze(axis=axis)
^^^^^^^^^^^^^^^^^^
ValueError: cannot select an axis to squeeze out which has size not equal to
one
Exception ignored in: <function Texture.__del__ at 0x106d919e0>
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 3076, in __del__
raise OpenGLError('OpenGL texture was not deleted before graphics.Texture
destroyed')
chimerax.graphics.opengl.OpenGLError: OpenGL texture was not deleted before
graphics.Texture destroyed
> graphics restart
An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.
cannot select an axis to squeeze out which has size not equal to one
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.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_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 265, in _draw_scene
draw_transparent(r, transparent_drawings)
File
"/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1294, in draw_transparent
draw()
File
"/Applications/ChimeraX_Daily.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_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 806, in draw
bi.draw(renderer, draw_pass)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1397, in draw
Image3d.draw(self, renderer, draw_pass)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 816, in draw
pd = self._update_planes(renderer)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 581, in _update_planes
pd = self._update_2d_texture_planes(view_dir)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 589, in _update_2d_texture_planes
pd = self._texture_2d_planes(axis)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 615, in _texture_2d_planes
pd = self._make_planes(axis)
^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 743, in _make_planes
d = Texture2dPlanes(self, axis)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1017, in __init__
self._update_textures(planes)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1089, in _update_textures
textures = [self._plane_texture(k, axis) for k,axis in planes]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1089, in <listcomp>
textures = [self._plane_texture(k, axis) for k,axis in planes]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1096, in _plane_texture
self._fill_plane_texture(k, axis, t)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1115, in _fill_plane_texture
data = ir._color_plane(plane, axis)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1411, in _color_plane
dp = ir._color_plane(k, axis, color_3d=color_3d, require_color=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 250, in _color_plane
m = self._matrix_plane(plane, axis)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 227, in _matrix_plane
p = squeeze(m, 2-axis) # Reduce from 3d array to 2d.
^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/fromnumeric.py", line 1558, in squeeze
return squeeze(axis=axis)
^^^^^^^^^^^^^^^^^^
ValueError: cannot select an axis to squeeze out which has size not equal to
one
Exception ignored in: <function Texture.__del__ at 0x106d919e0>
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 3076, in __del__
raise OpenGLError('OpenGL texture was not deleted before graphics.Texture
destroyed')
chimerax.graphics.opengl.OpenGLError: OpenGL texture was not deleted before
graphics.Texture destroyed
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_0_arrows.bild
Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_0_arrows.bild
---
warnings | degenerate arrow on line 87
degenerate arrow on line 93
degenerate arrow on line 99
degenerate arrow on line 100
degenerate arrow on line 108
4 messages similar to the above omitted
Opened BILD data containing 208 objects
> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/test_data/post_analysis/motility/map_fragment_motility_frame_10.bild
Opened BILD data containing 1719 objects
> graphics restart
An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.
cannot select an axis to squeeze out which has size not equal to one
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.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_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 265, in _draw_scene
draw_transparent(r, transparent_drawings)
File
"/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1294, in draw_transparent
draw()
File
"/Applications/ChimeraX_Daily.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_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 806, in draw
bi.draw(renderer, draw_pass)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1397, in draw
Image3d.draw(self, renderer, draw_pass)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 816, in draw
pd = self._update_planes(renderer)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 581, in _update_planes
pd = self._update_2d_texture_planes(view_dir)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 589, in _update_2d_texture_planes
pd = self._texture_2d_planes(axis)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 615, in _texture_2d_planes
pd = self._make_planes(axis)
^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 743, in _make_planes
d = Texture2dPlanes(self, axis)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1017, in __init__
self._update_textures(planes)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1089, in _update_textures
textures = [self._plane_texture(k, axis) for k,axis in planes]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1089, in <listcomp>
textures = [self._plane_texture(k, axis) for k,axis in planes]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1096, in _plane_texture
self._fill_plane_texture(k, axis, t)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1115, in _fill_plane_texture
data = ir._color_plane(plane, axis)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1411, in _color_plane
dp = ir._color_plane(k, axis, color_3d=color_3d, require_color=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 250, in _color_plane
m = self._matrix_plane(plane, axis)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 227, in _matrix_plane
p = squeeze(m, 2-axis) # Reduce from 3d array to 2d.
^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/fromnumeric.py", line 1558, in squeeze
return squeeze(axis=axis)
^^^^^^^^^^^^^^^^^^
ValueError: cannot select an axis to squeeze out which has size not equal to
one
Exception ignored in: <function Texture.__del__ at 0x106d919e0>
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 3076, in __del__
raise OpenGLError('OpenGL texture was not deleted before graphics.Texture
destroyed')
chimerax.graphics.opengl.OpenGLError: OpenGL texture was not deleted before
graphics.Texture destroyed
OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac14,2
Model Number: Z15W0000NZP/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 8419.80.7
OS Loader Version: 8419.80.7
Software:
System Software Overview:
System Version: macOS 13.2 (22D49)
Kernel Version: Darwin 22.3.0
Time since boot: 21 hours, 22 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.0.3
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.15
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.3
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.53
ChimeraX-AtomicLibrary: 12.1.10
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.11
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8.dev202402020018
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4.1
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.9
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.2
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.2
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.15
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-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NMRSTAR: 1.0.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.2
ChimeraX-PDB: 2.7.3
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
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.2.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.15
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.6
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.8
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.1
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.5
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.43
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.3
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.1.0
lz4: 4.3.3
MarkupSafe: 2.1.4
matplotlib: 3.8.2
matplotlib-inline: 0.1.6
msgpack: 1.0.7
ndindex: 1.7
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.2.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.9.0
numpy: 1.26.3
openvr: 1.26.701
packaging: 23.2
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.3.2
pkginfo: 1.9.6
platformdirs: 4.2.0
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.3.0
pygments: 2.17.2
pynmrstar: 3.3.2
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3301
pyparsing: 3.1.1
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2024.1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.4
setuptools: 69.0.3
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 1.25.3
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.1
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.12.9
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.1
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.2.0
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.42.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 21 months ago
| Component: | Unassigned → Volume Data |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → cannot select an axis to squeeze out which has size not equal to one |
comment:2 by , 21 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
Duplicate of #14536.
As described in the previous ticket the problem is with one of your TIFF files which is being read in as a 2D array instead of 3D by the TIFF file reader tifffile.py. I won't be able to debug this without the file. Reading 2D tiff files works fine in my tests.
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Reported by Liese