id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4128 save JPEG with transparent background: cannot write mode RGBA as JPEG chimerax-bug-report@… Tom Goddard "{{{ 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 }}} " defect closed normal Input/Output 1.0 duplicate all ChimeraX