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Opened 4 years ago
Closed 4 years ago
#5881 closed defect (fixed)
Save TIFF stack: ImageJ hyperstack shape and axes do not match
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.4.dev202110301952 (2021-10-30 19:52:32 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.4.dev202110301952 (2021-10-30)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/katekim/Dropbox/PKS13/POST NATURE 2ND REVIEWS/FIGURES/KS-
> substrate_dens2.cxs" format session
Opened denmod_KS_AT_sharpened_map.ccp4 as #5, grid size 209,117,160, pixel
0.835,0.835,0.835, shown at level 1.99, step 1, values float32
developer warning: container "attr_registration" snapshot methods are missing
include_state method
developer warning: container "custom_attr_preserver" snapshot methods are
missing include_state method
Log from Mon Jan 3 15:17:43 2022UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/harries/Dropbox/PKS13/POST NATURE 2ND REVIEWS/FIGURES/KS-
> substrate_dens2.cxs"
Exception ignored in: <function Framebuffer.__del__ at 0x118f92050>
Traceback (most recent call last):
File "/Applications/ChimeraX-1.1.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 2088, in __del__
% self.name)
chimerax.graphics.opengl.OpenGLError: OpenGL framebuffer "stereo camera" was
not deleted before graphics.Framebuffer destroyed
Exception ignored in: <function Framebuffer.__del__ at 0x118f92050>
Traceback (most recent call last):
File "/Applications/ChimeraX-1.1.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 2088, in __del__
% self.name)
chimerax.graphics.opengl.OpenGLError: OpenGL framebuffer "stereo camera" was
not deleted before graphics.Framebuffer destroyed
Log from Mon Jan 3 11:44:57 2022UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/harries/Dropbox/PKS13/POST NATURE 2ND REVIEWS/FIGURES/KS-
> substrate_dens2.cxs"
Log from Thu Dec 30 09:39:38 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/harries/Dropbox/PKS13/POST NATURE 2ND REVIEWS/FIGURES/KS-
> substrate_dens.cxs"
Log from Tue Dec 28 22:14:49 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open /Users/janetfiner-moore/KS-substrate_dens.cxs
Log from Tue Dec 28 19:21:24 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open /Users/janetfiner-moore/KS_Substrate_density.cxs
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Log from Mon Dec 27 14:32:40 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/harries/Dropbox/PKS13/MAPS and
> MODELS_UPDATED/COORDSwithHETATM/density_substrate.cxs"
Log from Mon Dec 27 13:32:19 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/harries/Dropbox/PKS13/MAPS AND
> MODELS_submit/KS_AT_conformer/KSAT_real_space_refined__Q__denmod_KS_AT_sharpened_map.pdb"
Chain information for
KSAT_real_space_refined__Q__denmod_KS_AT_sharpened_map.pdb #1
---
Chain | Description
A B | No description available
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> open "/Users/harries/Dropbox/PKS13/MAPS AND
> MODELS_submit/KS_AT_conformer/denmod_KS_AT_sharpened_map.ccp4"
Opened denmod_KS_AT_sharpened_map.ccp4, grid size 209,117,160, pixel
0.835,0.835,0.835, shown at level 4.5, step 1, values float32
> ui tool show "Show Volume Menu"
> transparency 50
> show target ab
> cartoon hide
> select H
13880 atoms, 1850 residues, 1 model selected
> hide sel target a
> help help:user
> select ::name="DCR"
102 atoms, 100 bonds, 2 residues, 1 model selected
> color sel purple
> color sel byhetero
> ui tool show "Side View"
> volume #2 level 2.657
> volume #2 level 2.045
> volume #2 level 2.096
> volume #2 level 2.198
> volume #2 level 2.249
> volume #2 level 2.3
> volume #2 level 2.249
> volume #2 level 2.198
> volume #2 level 2.147
> volume #2 level 1.994
> volume #2 level 1.943
> volume #2 level 1.739
> volume #2 level 1.483
> volume #2 level 1.483
> volume #2 level 1.177
> volume #2 level 0.6666
> volume #2 level 0.3603
> volume #2 level 0.002946
> volume #2 level 0.7686
> volume #2 level 0.8197
> volume #2 level 0.7686
> ui tool show "Side View"
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #2 level 1.61
> select clear
> volume #2 level 1.967
> open "/Users/harries/Dropbox/PKS13/MAPS and
> MODELS_UPDATED/COORDSwithHETATM/KS_wHET_real_space_refined.pdb"
Chain information for KS_wHET_real_space_refined.pdb #3
---
Chain | Description
A B | No description available
> hide #!1 models
> show #!1 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> volume #2 level 3.039
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> volume #2 level 1.916
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> select #3/A
6554 atoms, 6617 bonds, 442 residues, 1 model selected
> cartoon hide sel
> select #3/B
6554 atoms, 6617 bonds, 442 residues, 1 model selected
> cartoon hide sel
> select clear
> select #3/B
6554 atoms, 6617 bonds, 442 residues, 1 model selected
> hide sel target a
> select ::name="DCR"
204 atoms, 200 bonds, 4 residues, 2 models selected
> show sel target ab
> volume #2 level 2.937
> volume #2 level 1.967
> hide #3 models
> select #1:1101
102 atoms, 100 bonds, 2 residues, 1 model selected
> hide sel target a
> show #3 models
> ui tool show "Side View"
> select #3/A
6554 atoms, 6617 bonds, 442 residues, 1 model selected
> hide sel target a
> select ::name="DCR"
204 atoms, 200 bonds, 4 residues, 2 models selected
> ui tool show "Color Actions"
> color sel plum
> color sel byhetero
> color sel violet
> color sel byhetero
> color sel khaki
> color sel byhetero
> color sel light coral
> color sel byhetero
> color sel burly wood
> color sel tan
> color sel rosy brown
> color sel dim gray
> color sel dark magenta
> color sel orchid
> color sel byhetero
> color sel dark orchid
> color sel byhetero
> select clear
> save "/Users/harries/Dropbox/PKS13/MAPS and
> MODELS_UPDATED/COORDSwithHETATM/density_substrate.cxs"
opened ChimeraX session
> select #2
2 models selected
> select clear
> select #3/B:1101@C1
1 atom, 1 residue, 1 model selected
> ui tool show Distances
> distance #1/B:267@SG #3/B:1101@C1
Distance between KSAT_real_space_refined__Q__denmod_KS_AT_sharpened_map.pdb
#1/B CYS 267 SG and KS_wHET_real_space_refined.pdb #3/B DCR 1101 C1: 1.9Å
> distance style color #5d00ff
> distance style color #8300ff
> distance style color #8400ff
> distance style dashes 8
> distance style dashes 8
> distance style dashes 7
> distance style dashes 7
> distance style dashes 6
> distance style dashes 6
> distance style dashes 5
> distance style dashes 5
> distance style dashes 6
> distance style dashes 6
> distance style dashes 7
> distance style dashes 7
> distance style dashes 8
> distance style dashes 8
> distance style dashes 9
> distance style dashes 9
> distance style dashes 10
> distance style dashes 10
> distance style radius 0.19
> distance style radius 0.19
> distance style radius 0.18
> distance style radius 0.18
> distance style radius 0.17
> distance style radius 0.17
> select clear
> help help:user
> distance style symbol false
> view clip false
> view clip false
> undo
> undo
> ui tool show Distances
> style stick
Changed 41557 atom styles
> distance style decimalPlaces 0
> distance style decimalPlaces 0
> distance style decimalPlaces -1
Invalid "decimalPlaces" argument: Must be greater than or equal to 0
> distance style decimalPlaces 0
> toolshed show
> ~label
> distance style stick
Expected a keyword
> distance style dashes 11
> distance style dashes 11
> distance style dashes 10
> distance style dashes 10
> distance style dashes 9
> distance style dashes 9
> distance style dashes 8
> distance style dashes 8
> distance style dashes 7
> distance style dashes 7
> distance style dashes 6
> distance style dashes 6
> distance style dashes 5
> distance style dashes 5
> distance style dashes 4
> distance style dashes 4
> distance style dashes 3
> distance style dashes 3
> distance style dashes 2
> distance style dashes 2
> distance style dashes 1
> distance style dashes 1
> distance style dashes 0
> distance style dashes 0
> save "/Users/harries/Dropbox/PKS13/MAPS AND
> MODELS_submit/KS_AT_conformer/KS_substrate_density.png" width 1100 height
> 772 supersample 3
> save "/Users/harries/Dropbox/PKS13/POST NATURE 2ND
> REVIEWS/FIGURES/KS_Substrate_density.cxs"
opened ChimeraX session
> open /Users/janetfiner-moore/KSAT_real_space_refined-coot-2.pdb
Chain information for KSAT_real_space_refined-coot-2.pdb #2
---
Chain | Description
A B | No description available
> hide #3 models
> show #3 models
> hide #3 models
> select #2
28413 atoms, 28287 bonds, 4 pseudobonds, 2270 residues, 2 models selected
> show (#!2 & sel) target ab
> cartoon hide (#!2 & sel)
> ui tool show "Color Actions"
> color sel tan
> color sel byhetero
> select H
34221 atoms, 4570 residues, 3 models selected
> hide (#!1-2 & sel) target a
> select #2:1101
102 atoms, 100 bonds, 2 residues, 1 model selected
> show sel target ab
> color sel dark orchid
> color sel byhetero
> hide #!1 models
> hide #4 models
> open "/Users/janetfiner-moore/Dropbox/PKS13/MAPS AND
> MODELS_submit/KS_AT_conformer/denmod_KS_AT_sharpened_map.ccp4"
Opened denmod_KS_AT_sharpened_map.ccp4, grid size 209,117,160, pixel
0.835,0.835,0.835, shown at level 4.5, step 1, values float32
> transparency sel 50
> volume #5 level 4.495
> volume #5 level 4.444
> volume #5 level 4.393
> volume #5 level 4.24
> volume #5 level 4.087
> volume #5 level 3.882
> volume #5 level 3.831
> volume #5 level 3.678
> volume #5 level 3.474
> volume #5 level 3.168
> volume #5 level 2.913
> volume #5 level 2.708
> volume #5 level 2.453
> volume #5 level 2.147
> volume #5 level 1.943
> volume #5 level 1.687
> volume #5 level 1.483
> volume #5 level 1.381
> volume #5 level 1.33
> volume #5 level 1.381
> volume #5 level 1.432
> volume #5 level 1.483
No visible Surface models selected
> select #5
4 models selected
> transparency #5.1 50
> select clear
> save /Users/janetfiner-moore/KS-substrate_dens.cxs
opened ChimeraX session
> volume #5 level 1.994
> save /Users/janetfiner-moore/KS-substrate_dens.cxs
opened ChimeraX session
> select #3/A
6554 atoms, 6617 bonds, 442 residues, 1 model selected
> select #1/A#2/A#3/A
34527 atoms, 34873 bonds, 6 pseudobonds, 2296 residues, 5 models selected
> ui tool show "Color Actions"
> color sel tomato
> color sel byhetero
> color sel coral
> color sel sienna
> color sel indian red
> color sel byhetero
> select #2/B
14001 atoms, 14144 bonds, 2 pseudobonds, 929 residues, 2 models selected
> color sel crimson
> color sel red
> color sel byhetero
> color sel crimson
> color sel byhetero
> color sel red
> color sel crimson
> color sel red
> color sel byhetero
> ui tool show "Color Actions"
> color sel crimson
> color sel byhetero
> select ::name="DCR"
306 atoms, 300 bonds, 6 residues, 3 models selected
> color sel dark blue
> color sel byhetero
> select clear
> close #1
> close #3
> close #4
> save "/Users/harries/Dropbox/PKS13/POST NATURE 2ND REVIEWS/FIGURES/KS-
> substrate_dens2.cxs"
opened ChimeraX session
> select ::name="HOH"
412 atoms, 412 residues, 1 model selected
> color sel cyan
> select clear
> hide #!5 models
> select /A
14000 atoms, 14143 bonds, 2 pseudobonds, 929 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light coral
> color sel tomato
> color sel coral
> color sel indian red
> color sel tomato
> color sel byhetero
> color sel salmon
> color sel byhetero
> color sel orange red
> color sel tomato
> color sel light salmon
> color sel salmon
> color sel byhetero
> show #!5 models
> select clear
> save "/Users/harries/Dropbox/PKS13/POST NATURE 2ND REVIEWS/FIGURES/KS-
> substrate-dens.tif" width 1100 height 772 supersample 3
> save "/Users/harries/Dropbox/PKS13/POST NATURE 2ND REVIEWS/FIGURES/KS-
> substrate_dens2.cxs"
opened ChimeraX session
> select /A
14000 atoms, 14143 bonds, 2 pseudobonds, 929 residues, 2 models selected
> ui tool show "Color Actions"
> color sel pink
> color sel byhetero
> select /B
14001 atoms, 14144 bonds, 2 pseudobonds, 929 residues, 2 models selected
> color sel red
> color sel byhetero
> select ::name="DCR"
102 atoms, 100 bonds, 2 residues, 1 model selected
> color sel dark slate blue
> color sel dark blue
> color sel byhetero
> select clear
> save "/Users/harries/Dropbox/PKS13/POST NATURE 2ND REVIEWS/FIGURES/KS-
> substrate-dens-stereo.tif" width 1100 height 843 supersample 3
> save "/Users/harries/Dropbox/PKS13/POST NATURE 2ND REVIEWS/FIGURES/KS-
> substrate_dens2.cxs"
——— End of log from Mon Jan 3 15:17:43 2022 ———
opened ChimeraX session
> select #2/A:93-535
6432 atoms, 6493 bonds, 437 residues, 1 model selected
> color sel #f79292
> color sel byhetero
> select #2/B:93-535
6432 atoms, 6493 bonds, 437 residues, 1 model selected
> color sel #ff1616
> color sel byhetero
> select clear
> select ::name="HOH"
412 atoms, 412 residues, 1 model selected
> color sel cyan
> select clear
> select ::name="DCR"
102 atoms, 100 bonds, 2 residues, 1 model selected
> color sel medium blue
> color sel byhetero
> select clear
> save "/Users/katekim/Dropbox/PKS13/POST NATURE 2ND REVIEWS/FIGURES/KS-
> substrate_dens2_v2.cxs" includeMaps true
> save Fig2b.png pixelSize 0.05 supersample 24 transparentBackground false
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> save /Users/katekim/Desktop/Fig2b.tif models #5 format imagejtiff
Traceback (most recent call last):
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/__init__.py", line 167, in save
save_map(session, path, _name, **kw)
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 3971, in save_map
save_grid_data(grids, path, session, format_name, options)
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/fileformats.py", line 314, in save_grid_data
ff.save_func(garg, tpath, options = options, progress = p)
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/imagestack/imagej_write.py", line 19, in
write_imagej_tiff
_write_3d_tiff(grid_data, path)
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/imagestack/imagej_write.py", line 29, in
_write_3d_tiff
imwrite(path, array_zcyx, imagej=True, resolution=(1/xstep, 1/ystep),
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tifffile/tifffile.py", line 856, in imwrite
result = tif.write(data, shape, dtype, **kwargs)
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tifffile/tifffile.py", line 1640, in write
ijshape = imagej_shape(
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tifffile/tifffile.py", line 14066, in imagej_shape
raise ValueError('ImageJ hyperstack shape and axes do not match')
ValueError: ImageJ hyperstack shape and axes do not match
ValueError: ImageJ hyperstack shape and axes do not match
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tifffile/tifffile.py", line 14066, in imagej_shape
raise ValueError('ImageJ hyperstack shape and axes do not match')
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-14.7.21
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 650
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro14,2
Processor Name: Dual-Core Intel Core i5
Processor Speed: 3.1 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
Boot ROM Version: 447.60.3.0.0
SMC Version (system): 2.44f6
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H1615)
Kernel Version: Darwin 19.6.0
Time since boot: 2 days 3:24
Graphics/Displays:
Intel Iris Plus Graphics 650:
Chipset Model: Intel Iris Plus Graphics 650
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x5927
Revision ID: 0x0006
Metal: Supported, feature set macOS GPUFamily2 v1
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.5.30
cftime: 1.5.1.1
charset-normalizer: 2.0.7
ChimeraX-AddCharge: 1.1.5
ChimeraX-AddH: 2.1.10
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.1.6
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4.dev202110301952
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
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
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.3
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.3.1
ChimeraX-ModelPanel: 1.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.8
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.5
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.14
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.5.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.2.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.7.3
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.2
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.21
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.4
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.2
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.1.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (3)
comment:1 by , 4 years ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Save TIFF stack: ImageJ hyperstack shape and axes do not match |
comment:2 by , 4 years ago
Trying to save as an imagejtiff file caused the tifffile.py writing code to give an error about incorrect data dimensions
save /Users/katekim/Desktop/Fig2b.tif models #5 format imagejtiff
packages/chimerax/map_data/imagestack/imagej_write.py", line 29, in
_write_3d_tiff
imwrite(path, array_zcyx, imagej=True, resolution=(1/xstep, 1/ystep),
...
ValueError: ImageJ hyperstack shape and axes do not match
It appears the model #5 image data was a single image (1 channel, 1 time):
Opened denmod_KS_AT_sharpened_map.ccp4 as #5, grid size 209,117,160, pixel
0.835,0.835,0.835, shown at level 1.99, step 1, values float32
I can reproduce this error in ChimeraX 1.3 by just opening a map files and saving
open 1080 from emdb
save test.tif model #1 format imagejtiff
Should allow debugging and fixing this. My guess is the imagejtiff save is only working on multi-channel data but needs investigation.
comment:3 by , 4 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Fixed.
The call to tifffile.py imwrite() specified axis order metadata as ZYX in the metadata but handed it an array ZCYX. Apparently that worked in older tifffile.py but now it checks that the metadata matches the array size. I fixed the metadata to say the axis order is ZCYX.
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Reported by Kate Kim.
Also earlier: OpenGL framebuffer "stereo camera" was not deleted before graphics.Framebuffer destroyed