Opened 5 years ago

Closed 5 years ago

#3796 closed defect (fixed)

cannot write mode RGBA as JPEG

Reported by: yuhx0914@… 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:        Darwin-19.4.0-x86_64-i386-64bit
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /Users/yuhx/Desktop/PSIImonomer/ColorSubunits/ColorSubunits.cxs format
> session

Log from Sun Oct 4 22:14:28 2020UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /Users/yuhx/Desktop/1.cxs format session

Log from Sun Oct 4 22:04:09 2020UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/yuhx/Desktop/PSIImonomer/2.77831-fit-3wu2.pdb

Summary of feedback from opening
/Users/yuhx/Desktop/PSIImonomer/2.77831-fit-3wu2.pdb  
---  
warnings | Cannot find LINK/SSBOND residue CYS (19 )  
Cannot find LINK/SSBOND residue FME (1 )  
Cannot find LINK/SSBOND residue FME (1 )  
Cannot find LINK/SSBOND residue FME (1 )  
Cannot find LINK/SSBOND residue PRO (335 )  
67 messages similar to the above omitted  
  
2.77831-fit-3wu2.pdb title:  
Crystal structure analysis of photosystem II complex [more info...]  
  
Chain information for 2.77831-fit-3wu2.pdb #1  
---  
Chain | Description  
A | photosystem Q(B) protein  
B | protein CP-47  
C | photosystem II 44 kda reaction center protein  
D | photosystem II D2 protein  
E | PSII reaction center subunit V  
F | PSII reaction center subunit VI  
H | PSII-H  
I | photosystem II reaction center protein I  
J | PSII-J  
K | PSII-K  
L | photosystem II reaction center protein L  
M | PSII-M  
O | MSP  
T | photosystem II reaction center protein T  
U | photosystem II 12 kda extrinsic protein  
V | cytochrome C-550  
X | photosystem II reaction center protein X  
Y | photosystem II reaction center protein YCF12  
Z | PSII-Z  
  
Non-standard residues in 2.77831-fit-3wu2.pdb #1  
---  
BCR — β-carotene  
BCT — bicarbonate ion  
CA — calcium ion  
CLA — chlorophyll A  
DGD — digalactosyl diacyl glycerol (DGDG)  
FE2 — Fe (II) ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
HEM — protoporphyrin IX containing Fe (HEME)  
HTG — heptyl 1-thiohexopyranoside  
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole  
LMG — 1,2-distearoyl-monogalactosyl-diglyceride  
LMT — dodecyl-β-D-maltoside  
MG — magnesium ion  
OEX — Ca-MN4-O5 cluster  
PHO — pheophytin A  
PL9 —
2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone
(plastoquinone 9)  
RRX — (3R)-β,β-caroten-3-ol (β-cryptoxanthin)  
SO4 — sulfate ion  
SQD — 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-α-D-glucopyranosyl]-Sn-glycerol
(sulfoquinovosyldiacylglycerol)  
UNL — unknown ligand  
  

> style ball

Changed 25752 atom styles  

> style stick

Changed 25752 atom styles  

> set bgColor white

> style ball

Changed 25752 atom styles  

> style ball

Changed 25752 atom styles  

> style ball

Changed 25752 atom styles  

> color byelement

> color bychain

> style stick

Changed 25752 atom styles  

> color byelement

> show cartoons

> show cartoons

> hide cartoons

> open /Users/yuhx/Desktop/PSIImonomer/2.77831_postprocess_masked_invert.mrc

Opened 2.77831_postprocess_masked_invert.mrc, grid size 240,240,240, pixel
0.822, shown at level 0.0316, step 1, values float32  

> save sess session includeMaps true

Cannot determine format for 'sess'  

> save 1.cxs session includeMaps true

Expected a keyword  

> save session includeMaps true

Cannot determine format for 'session'  

> save formats session includeMaps true

Expected fewer arguments  

> save formats session includeMaps true

Expected fewer arguments  

> save 1 format session includeMaps true

opened ChimeraX session  

> select #0:201.V

Expected an objects specifier or a keyword  

> select #1:201.V

Expected an objects specifier or a keyword  

> hide #!1 models

> show #!1 models

> hide #!2 models

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> show #1.1 models

> show #!2 models

> volume zone #1 nearAtoms #2/A range 2 newMap true

no atoms specified for zone  

> volume zone #2 nearAtoms #1/A range 2 newMap true

> Volume #3 color #7FFFD4

Unknown command: Volume #3 color #7FFFD4  

> volume #3 color #7FFFD4

> save ColorSubunits format session includeMaps true

opened ChimeraX session  

> save 1 format tiff width 1000 height 750 pixelSize 0.4 supersample 4
> transparentBackground true

Unknown data format: 'tiff'  

> save 0 format tiff width 1000 height 750 pixelSize 0.4 supersample 4
> transparentBackground true

Unknown data format: 'tiff'  

> save 1 format session includeMaps true

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/safesave.py", line 97, in __exit__  
os.replace(self._tmp_filename, self.name)  
FileNotFoundError: [Errno 2] No such file or directory: '1.cxs.tmp' -> '1.cxs'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 275, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 834, in save  
output.close()  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/safesave.py", line 119, in close  
self.__exit__(None, None, None)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/safesave.py", line 109, in __exit__  
os.remove(self._tmp_filename)  
FileNotFoundError: [Errno 2] No such file or directory: '1.cxs.tmp'  
  
FileNotFoundError: [Errno 2] No such file or directory: '1.cxs.tmp'  
  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/safesave.py", line 109, in __exit__  
os.remove(self._tmp_filename)  
  
See log for complete Python traceback.  
  

> save 1.tif format tiff width 1000 height 750 pixelSize 0.4 supersample 4
> transparentBackground true

Unknown data format: 'tiff'  

> save 1.tif format tiff width 1000 height 750 pixelSize 0.4 supersample 4
> transparentBackground true

Unknown data format: 'tiff'  

> save 0 format tiff width 1000 height 750 | pixelSize 0.4 supersample 4
> transparentBackground true

Cannot determine format for '0'  

> save 0.tif format "tiff image" width 1000 height 750 | pixelSize 0.4
> supersample 4 transparentBackground true

Expected a keyword  

> save 0.tif format "tiff image" width 1000 height 750 | pixelSize 0.4
> supersample 4 transparentBackground true

Expected a keyword  

> save 0.tif format tiff

Unknown data format: 'tiff'  

> save 0 format tiff

Unknown data format: 'tiff'  

> save 0 format pdb

> save 0 format tiff

Unknown data format: 'tiff'  

> save 0 format tiff

Unknown data format: 'tiff'  

> select #1

25752 atoms, 26226 bonds, 185 pseudobonds, 3001 residues, 2 models selected  

> ~select #1

Nothing selected  

> select #2

2 models selected  

> select #1

25752 atoms, 26226 bonds, 185 pseudobonds, 3001 residues, 2 models selected  

> select #3

2 models selected  

> save 0 format tiff

Unknown data format: 'tiff'  

> save 0 format tiff

Unknown data format: 'tiff'  

> save 0.tiff

> save 1 format jepg width 1000 height 750 pixelSize 0.4 supersample 4
> transparentBackground truef

Unknown data format: 'jepg'  

> hide #!1 models

> ~select #3

Nothing selected  

> show #!2 models

> hide #!3 models

> hide #!2 models

> show #!3 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> hide #3.1 models

> save 1.tiff width 1000 height 750 pixelSize 0.4 supersample 4
> transparentBackground true

Cannot specify width or height if pixel_size is given  

> save 1.tiff pixelSize 0.4 supersample 4 transparentBackground true

> save 2.tiff pixelSize 1 supersample 4 transparentBackground true

> save 3.tiff pixelSize 0.1 supersample 4 transparentBackground true

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #3.1 models

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 47, in display  
self._current_option)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/manager.py", line 91, in
save_args_string_from_widget  
provider_info.format_name, self).save_args_string_from_widget(widget)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/__init__.py", line 189, in save_args_string_from_widget  
return widget.options_string()  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/options.py", line 35, in options_string  
raise UserError("No %s to save" % self._name.lower())  
AttributeError: 'SaveModelOptionWidget' object has no attribute '_name'  
  
AttributeError: 'SaveModelOptionWidget' object has no attribute '_name'  
  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/options.py", line 35, in options_string  
raise UserError("No %s to save" % self._name.lower())  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 47, in display  
self._current_option)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/manager.py", line 91, in
save_args_string_from_widget  
provider_info.format_name, self).save_args_string_from_widget(widget)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/__init__.py", line 189, in save_args_string_from_widget  
return widget.options_string()  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/options.py", line 35, in options_string  
raise UserError("No %s to save" % self._name.lower())  
AttributeError: 'SaveModelOptionWidget' object has no attribute '_name'  
  
AttributeError: 'SaveModelOptionWidget' object has no attribute '_name'  
  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/options.py", line 35, in options_string  
raise UserError("No %s to save" % self._name.lower())  
  
See log for complete Python traceback.  
  

> save 0.jpeg pixelSize 0.4 supersample 4 quality 100 transparentBackground
> true

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 275, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/image_formats/save.py", line 116, in save_image  
i.save(path, format_name, **metadata)  
File
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.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 0.jpeg pixelSize 0.4 supersample 4 transparentBackground true

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 275, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/image_formats/save.py", line 116, in save_image  
i.save(path, format_name, **metadata)  
File
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.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 0.jpg pixelSize 0.4 supersample 4 transparentBackground true

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 275, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/image_formats/save.py", line 116, in save_image  
i.save(path, format_name, **metadata)  
File
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.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 0.tif pixelSize 0.4 supersample 4 transparentBackground true

> save 0 format jpeg pixelSize 0.4 supersample 4 transparentBackground true

Unknown data format: 'jpeg'  

> show #!3 models

> hide #!2 models

> show #3.1 models

> hide #!3 models

> show #!3 models

> save 0.jpeg pixelSize 0.4 supersample 4 quality 100 transparentBackground
> true

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 275, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/image_formats/save.py", line 116, in save_image  
i.save(path, format_name, **metadata)  
File
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.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
"/Applications/ChimeraX-1.1.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 ATI-3.8.24
OpenGL renderer: AMD Radeon Pro 555X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,1
      Processor Name: 6-Core Intel Core i7
      Processor Speed: 2.6 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 12 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 1037.100.362.0.0 (iBridge: 17.16.14281.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.4 (19E287)
      Kernel Version: Darwin 19.4.0
      Time since boot: 20 days 14:53

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0000
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    Radeon Pro 555X:

      Chipset Model: Radeon Pro 555X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67ef
      Revision ID: 0x00e3
      ROM Revision: 113-C980AL-075
      VBIOS Version: 113-C97501P-005
      EFI Driver Version: 01.A1.075
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.0
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 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: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

Change History (3)

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 → cannot write mode RGBA as JPEG

comment:2 by Tom Goddard, 5 years ago

The error message "OSError: cannot write mode RGBA as JPEG" is because the JPEG file format does not support transparency. You were using the transparent background option to the save command. I've made it give a clearer error message.

comment:3 by Tom Goddard, 5 years ago

Resolution: → fixed
Status: assigned → closed

There was an earlier error in the Log using the file save dialog, possibly to save a map, without choosing a map to save from the menu. I fixed that error.

There was a third error in the long about 1.cxs.tmp does not exist when saving a session file. I believe the session 1.cxs was being saved to the Desktop and you deleted the 1.cxs.tmp file it was using to create that session before it finished. I guess the session was large so you had time to delete the tmp file while it was still saving. I am going to leave that as it is and see if anyone else runs into that problem.

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