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#4128 closed defect (duplicate)

save JPEG with transparent background: cannot write mode RGBA as JPEG

Reported by:	chimerax-bug-report@…	Owned by:	Tom Goddard
Priority:	normal	Milestone:
Component:	Input/Output	Version:	1.0
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Darwin-19.4.0-x86_64-i386-64bit
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "/Users/Chelsy/OneDrive - GSK/Allergy Project/Structures/Der p
> 2/1A9V_NMR.cxs" format session

Log from Mon Jan 11 19:11:17 2021UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/Chelsy/OneDrive - GSK/Allergy Project/Structures/Der p
> 2/6oy4_w7A1.pdb"

6oy4_w7A1.pdb title:  
Crystal structure of complex between recombinant der P 2.0103 and fab fragment
of 7A1 [more info...]  
  
Chain information for 6oy4_w7A1.pdb #1  
---  
Chain | Description  
A | DER P 2.0103  
C | fab fragment of igg, heavy chain  
D | fab fragment of igg, light chain  
  
Non-standard residues in 6oy4_w7A1.pdb #1  
---  
SO4 — sulfate ion  
  

> select /A

904 atoms, 909 bonds, 6 pseudobonds, 2 models selected  

> select /C

1774 atoms, 1699 bonds, 1 model selected  

> style sel ball

Changed 1774 atom styles  

> style sel ball

Changed 1774 atom styles  

> style sel ball

Changed 1774 atom styles  

> style sel sphere

Changed 1774 atom styles  

> style sel sphere

Changed 1774 atom styles  

> style sel sphere

Changed 1774 atom styles  

> show sel atoms

> mlp sel

Map values for surface "6oy4_w7A1.pdb_C SES surface": minimum -29.1, mean
-6.886, maximum 24.37  

> hide sel atoms

> show sel surfaces

> color sel bychain

> show sel surfaces

> select /D

1739 atoms, 1693 bonds, 2 pseudobonds, 2 models selected  

> show sel surfaces

> select /A

904 atoms, 909 bonds, 6 pseudobonds, 2 models selected  

> volume hide

No volumes specified  

> volume style surface

No volumes specified  

> volume style mesh

No volumes specified  

> ui mousemode right "play map series"

> ui mousemode right "play map series"

> ui mousemode right "map eraser"

> ui mousemode right "map eraser"

> ui mousemode right "map eraser"

> ui mousemode right "move planes"

> ui mousemode right "move planes"

> ui mousemode right "tape measure"

> ui mousemode right "tape measure"

> ui mousemode right "tape measure"

> color (#!1 & sel) red

> lighting full

> set bgColor white

> save /Users/Chelsy/Desktop/image4.png supersample 3

> select

4417 atoms, 4301 bonds, 8 pseudobonds, 2 models selected  

> select clear

> save /Users/Chelsy/Desktop/image5.png supersample 3

> select /A

904 atoms, 909 bonds, 6 pseudobonds, 2 models selected  

> ui tool show "Color Actions"

> color sel fire brick

> select clear

> save /Users/Chelsy/Desktop/image6.png supersample 3

> open "/Users/Chelsy/OneDrive - GSK/Allergy Project/Structures/Der p
> 2/1ktj_crystal.pdb"

Summary of feedback from opening /Users/Chelsy/OneDrive - GSK/Allergy
Project/Structures/Der p 2/1ktj_crystal.pdb  
---  
notes | Combining 2 symmetry atoms into HOH /A:202 O  
Combining 2 symmetry atoms into HOH /B:187 O  
Combining 2 symmetry atoms into HOH /B:189 O  
  
1ktj_crystal.pdb title:  
X-ray structure of der P 2, the major house dust mite allergen [more info...]  
  
Chain information for 1ktj_crystal.pdb #2  
---  
Chain | Description  
A B | allergen der P 2  
  

> close session

> open "/Users/Chelsy/OneDrive - GSK/Allergy Project/Structures/Der p
> 2/1ktj_crystal.pdb" format pdb

Summary of feedback from opening /Users/Chelsy/OneDrive - GSK/Allergy
Project/Structures/Der p 2/1ktj_crystal.pdb  
---  
notes | Combining 2 symmetry atoms into HOH /A:202 O  
Combining 2 symmetry atoms into HOH /B:187 O  
Combining 2 symmetry atoms into HOH /B:189 O  
  
1ktj_crystal.pdb title:  
X-ray structure of der P 2, the major house dust mite allergen [more info...]  
  
Chain information for 1ktj_crystal.pdb #1  
---  
Chain | Description  
A B | allergen der P 2  
  

> select /A

1075 atoms, 1007 bonds, 1 model selected  

> hide sel cartoons

> hide sel atoms

> style sel stick

Changed 1075 atom styles  

> style sel stick

Changed 1075 atom styles  

> style sel stick

Changed 1075 atom styles  

> show sel atoms

> hide sel atoms

> select /B

1062 atoms, 1007 bonds, 1 model selected  

> style sel stick

Changed 1062 atom styles  

> show sel atoms

> select clear

> select ::name="HOH"

167 atoms, 1 model selected  

> hide sel atoms

> lighting full

> lighting soft

> lighting simple

> lighting full

> save /Users/Chelsy/Desktop/image7.png supersample 3

> close session

> open "/Users/Chelsy/OneDrive - GSK/Allergy Project/Structures/Der p
> 2/1a9v_nmr.pdb"

1a9v_nmr.pdb title:  
Tertiary structure of the major house dust mite allergen der P 2, NMR, 10
structures [more info...]  
  
Chain information for 1a9v_nmr.pdb  
---  
Chain | Description  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A | mite allergen
der P 2  
  

> select #1.1/A

1983 atoms, 2005 bonds, 1 model selected  

> color sel orange red

> select #1.2/A

1983 atoms, 2005 bonds, 1 model selected  

> ui tool show "Color Actions"

> color sel red

> select #1.3/A

1983 atoms, 2005 bonds, 1 model selected  

> color sel crimson

> select #1.4/A

1983 atoms, 2005 bonds, 1 model selected  

> color sel dark red

> select #1.5/A

1983 atoms, 2005 bonds, 1 model selected  

> color sel fire brick

> select #1.6/A

1983 atoms, 2005 bonds, 1 model selected  

> color sel tomato

> select #1.7/A

1983 atoms, 2005 bonds, 1 model selected  

> color sel brown

> select #1.8/A

1983 atoms, 2005 bonds, 1 model selected  

> color sel chocolate

> select #1.10/A

1983 atoms, 2005 bonds, 1 model selected  

> color sel saddle brown

> select clear

> select #1.10/A

1983 atoms, 2005 bonds, 1 model selected  

> color sel saddle brown

> select #1.9/A

1983 atoms, 2005 bonds, 1 model selected  

> color sel indian red

> select clear

> marker segment #2 position 4.173,4.908,-3.783 toPosition -0.878,4.01,-8.418
> color yellow radius 0.1 label 6.914 labelHeight 0.6914 labelColor yellow

> undo

> select clear

> view

> lighting full

> marker segment #2 position 2.317,6.37,-0.378 toPosition -13.25,9.128,-2.425
> color yellow radius 0.1 label 15.94 labelHeight 1.594 labelColor yellow

> ui mousemode right "delete markers"

> ui mousemode right "move markers"

> ui mousemode right "delete markers"

> ui mousemode right "tape measure"

> marker delete #2

> marker segment #2 position -11.57,3.276,-7.704 toPosition
> -13.15,-10.56,-5.04 color yellow radius 0.1 label 14.18 labelHeight 1.418
> labelColor yellow

> ui mousemode right "play coordinates"

> ui mousemode right "tape measure"

> ui mousemode right "delete markers"

> ui mousemode right "map eraser"

> ui mousemode right "tape measure"

> ui mousemode right "crop volume"

> ui mousemode right "map eraser"

> ui mousemode right "delete markers"

> ui mousemode right "tape measure"

> marker delete #2

> ui mousemode right "tape measure"

> marker segment #2 position -2.987,-6.76,-2.71 toPosition
> -9.885,0.1438,-3.399 color yellow radius 0.1 label 9.784 labelHeight 0.9784
> labelColor yellow

> marker delete #2

> ui mousemode right "tape measure"

> ui mousemode right "crop volume"

> save /Users/Chelsy/Desktop/image8.png supersample 3

> save Derp2nmr.png transparentBackground true

> save Derp2nmr.png transparentBackground true

> save Derp2nmr.png transparentBackground true

> save "/Users/Chelsy/OneDrive - GSK/Allergy Project/Structures/Der p
> 2/1A9V_NMR.cxs"

opened ChimeraX session  

> save Derp2nmr.png transparentBackground true

> save Derp2nmr.png transparentBackground true

> save Derp2nmr.png pixelSize 1 transparentBackground true

> save Derp2nmr1.png transparentBackground true

> save Derp2nmr1.png transparentBackground true

> save Derp2nmr1.png transparentBackground true

> save Derp2nmr1.png transparentBackground true

> save Derp2nmr1.png transparentBackground true

> save Derp2nmr1.png transparentBackground true

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/Chelsy/Desktop/movie4.mp4

Movie saved to /Users/Chelsy/Desktop/movie4.mp4  
  

> save Derp2nmr1.png transparentBackground true

> save Derp2nmr1.png transparentBackground true

> save Derp2nmr1.png transparentBackground true

> save Derp2nmr1.png transparentBackground true

> save Derp2nmr1.png transparentBackground true

> save Derp2nmr1.png transparentBackground true

> set background white

Expected a keyword  

> save pic.png transparentBackground true

Cannot determine format for 'pic'  

> save pic.jpg transparentBackground true

Traceback (most recent call last):  
File
"/programs/i386-mac/chimerax/1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/PIL/JpegImagePlugin.py", line 612, in _save  
rawmode = RAWMODE[im.mode]  
KeyError: 'RGBA'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/programs/i386-mac/chimerax/1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute  
cmd.run(cmd_text)  
File
"/programs/i386-mac/chimerax/1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/programs/i386-mac/chimerax/1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/programs/i386-mac/chimerax/1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/programs/i386-mac/chimerax/1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File
"/programs/i386-mac/chimerax/1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/image_formats/__init__.py", line 24, in save  
save_image(session, path, format_name, **kw)  
File
"/programs/i386-mac/chimerax/1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/image_formats/save.py", line 115, in save_image  
i.save(path, format_name, **metadata)  
File
"/programs/i386-mac/chimerax/1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/PIL/Image.py", line 2134, in save  
save_handler(self, fp, filename)  
File
"/programs/i386-mac/chimerax/1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/PIL/JpegImagePlugin.py", line 614, in _save  
raise OSError("cannot write mode %s as JPEG" % im.mode)  
OSError: cannot write mode RGBA as JPEG  
  
OSError: cannot write mode RGBA as JPEG  
  
File
"/programs/i386-mac/chimerax/1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/PIL/JpegImagePlugin.py", line 614, in _save  
raise OSError("cannot write mode %s as JPEG" % im.mode)  
  
See log for complete Python traceback.  
  

> save pic.jpg transparentBackground true

Traceback (most recent call last):  
File
"/programs/i386-mac/chimerax/1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/PIL/JpegImagePlugin.py", line 612, in _save  
rawmode = RAWMODE[im.mode]  
KeyError: 'RGBA'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/programs/i386-mac/chimerax/1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute  
cmd.run(cmd_text)  
File
"/programs/i386-mac/chimerax/1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/programs/i386-mac/chimerax/1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/programs/i386-mac/chimerax/1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/programs/i386-mac/chimerax/1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File
"/programs/i386-mac/chimerax/1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/image_formats/__init__.py", line 24, in save  
save_image(session, path, format_name, **kw)  
File
"/programs/i386-mac/chimerax/1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/image_formats/save.py", line 115, in save_image  
i.save(path, format_name, **metadata)  
File
"/programs/i386-mac/chimerax/1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/PIL/Image.py", line 2134, in save  
save_handler(self, fp, filename)  
File
"/programs/i386-mac/chimerax/1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/PIL/JpegImagePlugin.py", line 614, in _save  
raise OSError("cannot write mode %s as JPEG" % im.mode)  
OSError: cannot write mode RGBA as JPEG  
  
OSError: cannot write mode RGBA as JPEG  
  
File
"/programs/i386-mac/chimerax/1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/PIL/JpegImagePlugin.py", line 614, in _save  
raise OSError("cannot write mode %s as JPEG" % im.mode)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-14.5.22
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,2
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 2.7 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 1037.100.359.0.0 (iBridge: 17.16.14263.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.4 (19E266)
      Kernel Version: Darwin 19.4.0
      Time since boot: 2 days 11:40

Graphics/Displays:

    Intel Iris Plus Graphics 655:

      Chipset Model: Intel Iris Plus Graphics 655
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea5
      Revision ID: 0x0001
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        BenQ BL2400:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 2AA00758SL0 
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Adapter Type: Apple USB-C Digital AV Adapter
          Automatically Adjust Brightness: No
          Adapter Firmware Version: 2.35

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Component:	Unassigned → Input/Output
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → save JPEG with transparent background: cannot write mode RGBA as JPEG
Version:	→ 1.0

comment:2 by Eric Pettersen, 5 years ago

Resolution:	→ duplicate
Status:	assigned → closed

Fixed (only) in the daily build.

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