Opened 4 years ago

Closed 4 years ago

#6041 closed defect (duplicate)

Save TIFF stack: ImageJ hyperstack shape and axes do not match

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

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6yyt

Summary of feedback from opening 6yyt fetched from pdb  
---  
notes | Fetching compressed mmCIF 6yyt from
http://files.rcsb.org/download/6yyt.cif  
Fetching CCD ZN from http://ligand-expo.rcsb.org/reports/Z/ZN/ZN.cif  
  
6yyt title:  
Structure of replicating SARS-CoV-2 polymerase [more info...]  
  
Chain information for 6yyt #1  
---  
Chain | Description | UniProt  
A | nsp12 | R1AB_SARS2  
B D | nsp8 | R1AB_SARS2  
C | nsp7 | R1AB_SARS2  
P Q T U | RNA product |  
  
Non-standard residues in 6yyt #1  
---  
ZN — zinc ion  
  

> ui mousemode right zoom

> zoom 80

> zoom 10

> zoom default

Expected a number or a keyword  

> zoom 1

> zoom reset

Expected a number or a keyword  

> center

Unknown command: center  

> select #1

11375 atoms, 11714 bonds, 72 pseudobonds, 1354 residues, 4 models selected  

> view clip false

> select #1/A

6882 atoms, 7055 bonds, 10 pseudobonds, 855 residues, 3 models selected  

> zoom 1

> zoom 2

> zoom 0.1

> select #1/A:1

Nothing selected  

> zoom 2

[Repeated 2 time(s)]

> select #1/A

6882 atoms, 7055 bonds, 10 pseudobonds, 855 residues, 3 models selected  

> color #1 blue

> color #1 dark green

> color #1 cyan

> color #1 hot pink

> color #1 pink

> color #1,#2,#3 blue,pink,green

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color #1

> color #1/A pink

> color #1/B blue

> color #1/C green

> color #1/D purple

> style #1 stick

Changed 11375 atom styles  

> ~show #1/A stick

> hide #1/A stick

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> ~show #1/A

> show #1/A

> style #1/A ball

Changed 6882 atom styles  

> ribon #1/B

Unknown command: ribon #1/B  

> ribbon #1/B

> ~show #1

> ribbon #1

> ~select

Nothing selected  

> center #1

Unknown command: center #1  

> view clip false

> open emdb:11007

Summary of feedback from opening 11007 fetched from emdb  
---  
note | Fetching compressed map 11007 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-11007/map/emd_11007.map.gz  
  
Opened emdb 11007 as #2, grid size 240,240,240, pixel 0.834, shown at level
3.34, step 1, values float32  

> volume hide

> volume show

> volume hide

> volume show #1/A

Expected a keyword  

> volume show #1

Expected a keyword  

> volume #1/A

No volumes specified  

> volume show

> volume #2 level 4.862

> volume #2 level 3.624

> volume #2 level 3

> volume #2 step 2

> volume #2 step 4

> volume #2 step 16

> volume #2 step 1

> volume #2 style mesh

> volume #2 level 2

> 4

Unknown command: 4  

> volume #2 level 4

> volume #2 level 2

> volume #2 level 0.8

> volume #2 level 3

> ribbon #

> cartoon #

Expected an atoms specifier or a keyword  

> ribbon #1

> select #1

11375 atoms, 11714 bonds, 72 pseudobonds, 1354 residues, 4 models selected  

> color sel bychain

> ~select

Nothing selected  

> color zone #2 near #1 distance 5

> color zone #2 near sel & #3 distance 5

color zone: No atoms specified.  

> select #1

11375 atoms, 11714 bonds, 72 pseudobonds, 1354 residues, 4 models selected  

> color zone #2 near sel & #3 distance 5

color zone: No atoms specified.  

> color #2 near sel & #3 distance 5

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color sel bychain

> color zone #2 near sel & #1 distance 15

> ~ribbon

> ui mousemode right "translate selected models"

> select #1/A:5

Nothing selected  

> transparency #2 50

> ribbon #1

> select #1

11375 atoms, 11714 bonds, 72 pseudobonds, 1354 residues, 4 models selected  

> view matrix models #1,1,0,0,-29.855,0,1,0,27.836,0,0,1,13.868

> ~select

Nothing selected  

> select #1

11375 atoms, 11714 bonds, 72 pseudobonds, 1354 residues, 4 models selected  

> view matrix models #1,1,0,0,-15.921,0,1,0,-5.1815,0,0,1,-5.8626

> view matrix models #1,1,0,0,-2.0657,0,1,0,-3.7635,0,0,1,-4.7844

> view matrix models #1,1,0,0,-1.124,0,1,0,-2.2325,0,0,1,-4.5269

> select up

11375 atoms, 11714 bonds, 72 pseudobonds, 1354 residues, 4 models selected  

> select up

11375 atoms, 11714 bonds, 72 pseudobonds, 1354 residues, 4 models selected  

> select up

11375 atoms, 11714 bonds, 72 pseudobonds, 1354 residues, 6 models selected  

> select down

11375 atoms, 11714 bonds, 72 pseudobonds, 1354 residues, 4 models selected  

> select down

72 pseudobonds, 3 models selected  

> select up

11375 atoms, 11714 bonds, 72 pseudobonds, 1354 residues, 4 models selected  

> ~select

Nothing selected  

> fitmap #1 inMap #2

Fit molecule 6yyt (#1) to map emdb 11007 (#2) using 11375 atoms  
average map value = 2.72, steps = 164  
shifted from previous position = 1.1  
rotated from previous position = 1.25 degrees  
atoms outside contour = 7445, contour level = 3  
  
Position of 6yyt (#1) relative to emdb 11007 (#2) coordinates:  
Matrix rotation and translation  
0.99976727 0.02067959 0.00614516 -3.38561244  
-0.02066334 0.99978286 -0.00269583 -0.63871040  
-0.00619958 0.00256823 0.99997748 -3.41843005  
Axis 0.12110602 0.28400546 -0.95114364  
Axis point -69.34644240 178.51494994 0.00000000  
Rotation angle (degrees) 1.24532287  
Shift along axis 2.66000271  
  

> volume style mesh

> volume style surface

> volume style image

> volume style mesh

> transparency 0

> volume style surface

> transparency 50

> volume style mesh

> volume showOutlineBox true

> volume showOutlineBox false

> volume show

> volume hide

> volume show

> volume #2 orthoplanes xyz positionPlanes 120,120,120 style image region all

> mousemode rightMode "move planes"

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

> volume zone #2 nearAtoms #1 range 5

> volume #2 orthoplanes xyz positionPlanes 120,120,120 style image region all

> mousemode rightMode "move planes"

> volume #2 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 100.1 tiltedSlabSpacing 0.834 tiltedSlabPlaneCount 10

> mousemode rightMode "rotate slab"

> volume planes z style image imageMode "full region"

> mousemode rightMode "move planes"

> volume style surface

> volume style mesh

> volume style image

> volume zone #2 nearAtoms #1 range 5

> volume style image

> volume hide

> volume show

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

> volume planes z style image imageMode "full region"

> mousemode rightMode "move planes"

> volume #2 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 100.1 tiltedSlabSpacing 0.834 tiltedSlabPlaneCount 10

> mousemode rightMode "rotate slab"

> volume #2 orthoplanes xyz positionPlanes 120,120,120 style image region all

> mousemode rightMode "move planes"

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

> volume zone #2 nearAtoms #1 range 5

> volume showOutlineBox false

> volume style image

> volume show

> fitmap #1 inMap #2

Fit molecule 6yyt (#1) to map emdb 11007 (#2) using 11375 atoms  
average map value = 2.719, steps = 48  
shifted from previous position = 0.0167  
rotated from previous position = 0.0229 degrees  
atoms outside contour = 7444, contour level = 3  
  
Position of 6yyt (#1) relative to emdb 11007 (#2) coordinates:  
Matrix rotation and translation  
0.99976354 0.02074553 0.00651856 -3.41773679  
-0.02072750 0.99978118 -0.00282130 -0.62256840  
-0.00657566 0.00268552 0.99997477 -3.38600255  
Axis 0.12561676 0.29869366 -0.94604573  
Axis point -69.22700883 179.62750876 0.00000000  
Rotation angle (degrees) 1.25597500  
Shift along axis 2.58803101  
  

> volume show

> volume hide

> volume show

> volume style surface

> volume style image

> volume style mesh

> color zone #2 near sel & #1 distance 15

color zone: No atoms specified.  

> select #1

11375 atoms, 11714 bonds, 72 pseudobonds, 1354 residues, 4 models selected  

> color zone #2 near sel & #1 distance 15

> ~select

Nothing selected  

> lighting flat

> zoom 2

> lighting full

> lighting soft

> lighting full

> lighting soft

> lighting simple

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> graphics silhouettes false

> lighting flat

> volume #2 region 1,0,0,239,239,239

> select #1

11375 atoms, 11714 bonds, 72 pseudobonds, 1354 residues, 4 models selected  

> fitmap #1 inMap #2

Fit molecule 6yyt (#1) to map emdb 11007 (#2) using 11375 atoms  
average map value = 2.719, steps = 44  
shifted from previous position = 0.00524  
rotated from previous position = 0.00795 degrees  
atoms outside contour = 7447, contour level = 3  
  
Position of 6yyt (#1) relative to emdb 11007 (#2) coordinates:  
Matrix rotation and translation  
0.99976491 0.02072028 0.00638649 -3.40564757  
-0.02070282 0.99978179 -0.00278710 -0.62775940  
-0.00644284 0.00265423 0.99997572 -3.39820778  
Axis 0.12450305 0.29354795 -0.94780198  
Axis point -69.25549340 179.27537465 0.00000000  
Rotation angle (degrees) 1.25213798  
Shift along axis 2.61253704  
  

> volume #2 level 3.5

> volume #2 change image level -0.6069,0 level 3.337,0.8 level 28.57,1

> ~select

Nothing selected  

> zoom.5

Unknown command: zoom.5  

> zoom .5

> save /Users/joshuamitchell/Desktop/sample.tif models #2 format imagejtiff

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 165, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 381, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1284, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider  
providers.run_provider(session, name)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider  
what(session)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save  
show_save_file_dialog(session)  
File
"/Applications/ChimeraX-1.3.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
"/Applications/ChimeraX-1.3.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
"/Applications/ChimeraX-1.3.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
"/Applications/ChimeraX-1.3.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
"/Applications/ChimeraX-1.3.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
"/Applications/ChimeraX-1.3.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
"/Applications/ChimeraX-1.3.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
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/__init__.py", line 185, in save  
save_map(session, path, _name, **kw)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 3972, in save_map  
save_grid_data(grids, path, session, format_name, options)  
File
"/Applications/ChimeraX-1.3.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
"/Applications/ChimeraX-1.3.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
"/Applications/ChimeraX-1.3.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
"/Applications/ChimeraX-1.3.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
"/Applications/ChimeraX-1.3.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
"/Applications/ChimeraX-1.3.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
"/Applications/ChimeraX-1.3.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.  
  

> save /Users/joshuamitchell/Desktop/sample.tif models #2 format imagejtiff

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 165, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 381, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1284, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider  
providers.run_provider(session, name)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider  
what(session)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save  
show_save_file_dialog(session)  
File
"/Applications/ChimeraX-1.3.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
"/Applications/ChimeraX-1.3.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
"/Applications/ChimeraX-1.3.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
"/Applications/ChimeraX-1.3.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
"/Applications/ChimeraX-1.3.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
"/Applications/ChimeraX-1.3.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
"/Applications/ChimeraX-1.3.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
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/__init__.py", line 185, in save  
save_map(session, path, _name, **kw)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 3972, in save_map  
save_grid_data(grids, path, session, format_name, options)  
File
"/Applications/ChimeraX-1.3.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
"/Applications/ChimeraX-1.3.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
"/Applications/ChimeraX-1.3.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
"/Applications/ChimeraX-1.3.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
"/Applications/ChimeraX-1.3.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
"/Applications/ChimeraX-1.3.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
"/Applications/ChimeraX-1.3.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-18.2.10
OpenGL renderer: Intel(R) Iris(TM) Graphics 6100
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro12,1
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 2.7 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 3 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 428.40.10.0.0
      OS Loader Version: 540.40.4~45
      SMC Version (system): 2.28f7

Software:

    System Software Overview:

      System Version: macOS 12.0.1 (21A559)
      Kernel Version: Darwin 21.1.0
      Time since boot: 10 days 4:03

Graphics/Displays:

    Intel Iris Graphics 6100:

      Chipset Model: Intel Iris Graphics 6100
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x162b
      Revision ID: 0x0009
      Metal Family: Supported, Metal GPUFamily macOS 1
      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: Yes
          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: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    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: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    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: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    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-DistUI: 1.0
    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: 1.1.4
    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: 2.0.4
    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: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 1.7
    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: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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: 2.4.6
    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: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 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: 1.13.7
    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: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    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: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    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: 3.0.6
    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: 1.11.3
    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: 2.2.0
    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 (2)

comment:1 by Tom Goddard, 4 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Save TIFF stack: ImageJ hyperstack shape and axes do not match

Same as #5881. Fixed a while ago.

comment:2 by Tom Goddard, 4 years ago

Resolution: → duplicate
Status: assigned → closed
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