Eventually parsing of save-image keyword 'transparentBackground' goes south

[vikrambabuk@…]

The following bug report has been submitted:
Platform:        Darwin-18.0.0-x86_64-i386-64bit
ChimeraX Version: 0.8 (2018-11-11)
Description
During the saving of high resolution image

Log:
UCSF ChimeraX version: 0.8 (2018-11-11)  
How to cite UCSF ChimeraX  

> open "/Users/vikramkasaragod/Desktop/Manuscripts/Revision_Neuron/PDB_Resu
bmission_Artemisinins/artesunate/ESRF20112017_CM132A1_combined_refine_113.pdb"

Summary of feedback from opening
/Users/vikramkasaragod/Desktop/Manuscripts/Revision_Neuron/PDB_Resu
bmission_Artemisinins/artesunate/ESRF20112017_CM132A1_combined_refine_113.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Date 2018-01-14 Time 17:42:21 CET +0100 (1515948141.57 s)  
  
Ignored bad PDB record found on line 2  
REMARK PHENIX refinement  
  
Ignored bad PDB record found on line 4  
REMARK ****************** INPUT FILES AND LABELS
******************************  
  
Ignored bad PDB record found on line 5  
REMARK Reflections:  
  
Ignored bad PDB record found on line 6  
REMARK file name :
/home/vikramkasaragod/Desktop/2017_11_20_ESRF/ccp4/combine_scaled_CM132A1_1.50A.mtz  
  
65 messages similar to the above omitted  
  
Chain information for ESRF20112017_CM132A1_combined_refine_113.pdb #1  
---  
Chain | Description  
A | No description available  
  

> style selAtoms ball

Changed 6925 atom styles  

> show selAtoms surfaces

> lighting soft

> hide selAtoms

> select :DRG

54 atoms, 57 bonds selected  

> style selAtoms ball

Changed 54 atom styles  

> show selAtoms

> color selAtoms byhetero

> color selAtoms bychain

> color selAtoms byhetero

> select H

3277 atoms selected  

> hide selAtoms

> set bgColor black

> set bgColor white

> set bgColor gray

> set bgColor white

> set silhouettes true

> set bgColor black

> set bgColor white

> save image filename format png transparentBackground true

> save image filename format png transparentBackground true

> save image filename format png transparentBackground true

> save image filename format png transparentBackground true

> ui mousemode rightMode translate

> ui mousemode rightMode zoom

> select :DRG

54 atoms, 57 bonds selected  

> color selAtoms byhetero

> color selAtoms bychain

> color selAtoms byhetero

> save image filename format png transparentBackground true

Expected a keyword  

Unknown command: transparentBackground true  

> save image filename format png transparentBackground true

Expected a keyword  

Expected a keyword  

Expected a keyword  

Expected a keyword  

Invalid "quality" argument: Expected an integer  

> save image filename format png width 115 height 160 pixelSize 300
transparentBackground true

Cannot specify width or height if pixel_size is given  

> save image filename format png pixelSize 300 transparentBackground true

Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/cmd_line/tool.py", line 220, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2581, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/io.py", line 198, in export  
result = self.export_func(session, path, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/image.py", line 150, in save_image  
i.save(path, fmt.pil_name, **metadata)  
AttributeError: 'NoneType' object has no attribute 'save'  
  
AttributeError: 'NoneType' object has no attribute 'save'  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/image.py", line 150, in save_image  
i.save(path, fmt.pil_name, **metadata)  
  
See log for complete Python traceback.  
  

> save image vikram format png pixelSize 300 transparentBackground true

Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/cmd_line/tool.py", line 220, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2581, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/io.py", line 198, in export  
result = self.export_func(session, path, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/image.py", line 150, in save_image  
i.save(path, fmt.pil_name, **metadata)  
AttributeError: 'NoneType' object has no attribute 'save'  
  
AttributeError: 'NoneType' object has no attribute 'save'  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/image.py", line 150, in save_image  
i.save(path, fmt.pil_name, **metadata)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.0.34
OpenGL renderer: Intel(R) Iris(TM) Graphics 650
OpenGL vendor: Intel Inc.

[pett]

Reported by Vikram Kasaragod

[Tom Goddard]

Specifying pixelSize 300 probably made the image have 0 size, since this option will set the image width and height so that one pixel is 300 Angstroms. Probably the user thought they were setting DPI and did not read the documentation about what pixelSize does.

[Tom Goddard]

User was using old ChimeraX -- mid-November version did a check for bad image size and gave an explanatory error instead of a traceback. I improved the error message to report the image size it was trying to save. Also it should try to save a 1 pixel by 1 pixel image if a very large pixelSize is specified, not 0 by 0, so I fixed that.