Opened 5 years ago

Closed 5 years ago

#3932 closed defect (not a bug)

Permission denied saving image

Reported by: 352884536@… Owned by: Eric Pettersen
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:        Windows-10-10.0.18362
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
PermissionError: [Errno 13] Permission denied: 'li2e+w.tif'

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

> open "E:\\\GHSR data collection\\\123.pdb"

Summary of feedback from opening E:\\\GHSR data collection\\\123.pdb  
---  
warnings | Ignored bad PDB record found on line 2040  
TER  
  
Ignored bad PDB record found on line 4641  
TER  
  
Ignored bad PDB record found on line 6419  
TER  
  
Ignored bad PDB record found on line 6856  
TER  
  
Ignored bad PDB record found on line 7830  
TER  
  
2 messages similar to the above omitted  
  
Chain information for 123.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
E | No description available  
G | No description available  
N | No description available  
R | No description available  
  

> set bgColor white

> save li2e.tif width 1000 height 1000 supersample 4 transparentBackground
> true

Traceback (most recent call last):  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\image_formats\\__init__.py", line 24, in save  
save_image(session, path, format_name, **kw)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\image_formats\save.py", line 115, in save_image  
i.save(path, format_name, **metadata)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-packages\PIL\Image.py", line
2131, in save  
fp = builtins.open(filename, "w+b")  
PermissionError: [Errno 13] Permission denied: 'li2e.tif'  
  
PermissionError: [Errno 13] Permission denied: 'li2e.tif'  
  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-packages\PIL\Image.py", line
2131, in save  
fp = builtins.open(filename, "w+b")  
  
See log for complete Python traceback.  
  

> save li2e.tif width 1000 height 1000 supersample 4 transparentBackground
> true

Traceback (most recent call last):  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\image_formats\\__init__.py", line 24, in save  
save_image(session, path, format_name, **kw)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\image_formats\save.py", line 115, in save_image  
i.save(path, format_name, **metadata)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-packages\PIL\Image.py", line
2131, in save  
fp = builtins.open(filename, "w+b")  
PermissionError: [Errno 13] Permission denied: 'li2e.tif'  
  
PermissionError: [Errno 13] Permission denied: 'li2e.tif'  
  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-packages\PIL\Image.py", line
2131, in save  
fp = builtins.open(filename, "w+b")  
  
See log for complete Python traceback.  
  

> save li2e.tif width 1000 height 1000 supersample 4 transparentBackground
> true

Traceback (most recent call last):  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\image_formats\\__init__.py", line 24, in save  
save_image(session, path, format_name, **kw)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\image_formats\save.py", line 115, in save_image  
i.save(path, format_name, **metadata)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-packages\PIL\Image.py", line
2131, in save  
fp = builtins.open(filename, "w+b")  
PermissionError: [Errno 13] Permission denied: 'li2e.tif'  
  
PermissionError: [Errno 13] Permission denied: 'li2e.tif'  
  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-packages\PIL\Image.py", line
2131, in save  
fp = builtins.open(filename, "w+b")  
  
See log for complete Python traceback.  
  
No known data format for file suffix '.'  

> save li2e.tif E:/ width 1000 height 1000 supersample 4 transparentBackground
> true

Expected a keyword  
Cannot determine format for 'E:/'  
Cannot determine format for '(E:)'  

> help help:user/preferences.html#background

> save li2e+w.tif width 1000 height 1000 supersample 4 transparentBackground
> true

Traceback (most recent call last):  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\image_formats\\__init__.py", line 24, in save  
save_image(session, path, format_name, **kw)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\image_formats\save.py", line 115, in save_image  
i.save(path, format_name, **metadata)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-packages\PIL\Image.py", line
2131, in save  
fp = builtins.open(filename, "w+b")  
PermissionError: [Errno 13] Permission denied: 'li2e+w.tif'  
  
PermissionError: [Errno 13] Permission denied: 'li2e+w.tif'  
  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-packages\PIL\Image.py", line
2131, in save  
fp = builtins.open(filename, "w+b")  
  
See log for complete Python traceback.  
  

> save li2e+w.tif width 1000 height 1000 supersample 4 transparentBackground
> true

Traceback (most recent call last):  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\image_formats\\__init__.py", line 24, in save  
save_image(session, path, format_name, **kw)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\image_formats\save.py", line 115, in save_image  
i.save(path, format_name, **metadata)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-packages\PIL\Image.py", line
2131, in save  
fp = builtins.open(filename, "w+b")  
PermissionError: [Errno 13] Permission denied: 'li2e+w.tif'  
  
PermissionError: [Errno 13] Permission denied: 'li2e+w.tif'  
  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-packages\PIL\Image.py", line
2131, in save  
fp = builtins.open(filename, "w+b")  
  
See log for complete Python traceback.  
  

> save li2e+w.tif width 1000 height 1000 supersample 4 transparentBackground
> true

Traceback (most recent call last):  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\image_formats\\__init__.py", line 24, in save  
save_image(session, path, format_name, **kw)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\image_formats\save.py", line 115, in save_image  
i.save(path, format_name, **metadata)  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-packages\PIL\Image.py", line
2131, in save  
fp = builtins.open(filename, "w+b")  
PermissionError: [Errno 13] Permission denied: 'li2e+w.tif'  
  
PermissionError: [Errno 13] Permission denied: 'li2e+w.tif'  
  
File "D:\chimera X\ChimeraX 1.0\bin\lib\site-packages\PIL\Image.py", line
2131, in save  
fp = builtins.open(filename, "w+b")  
  
See log for complete Python traceback.  
  

> save File "D:\chimera X\ChimeraX 1.0\bin\lib\site-packages\ li2e.tif width
> 1000 height 1000 supersample 4 transparentBackground true

Missing or invalid "restOfLine" argument: incomplete quoted text  
Cannot determine format for 'File'  
'D:\chimera X\ChimeraX 1.0\bin\lib\site-packages\' has only compression
suffix; cannot determine format from suffix  
Cannot determine format for 'E:\'  

> save li2e.tif E:\ width 1000 height 1000 supersample 4 transparentBackground
> true

Expected a keyword  

> save li2e.tif E:\ width 1000 height 1000 supersample 4 transparentBackground
> true

Expected a keyword  

> save li2e.tif E:/ width 1000 height 1000 supersample 4 transparentBackground
> true

Expected a keyword  




OpenGL version: 3.3.0 NVIDIA 442.74
OpenGL renderer: GeForce GTX 1650 SUPER/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: IPASON
Model:  
OS: Microsoft Windows 10 家庭中文版 (Build 18363)
Memory: 17,130,639,360
MaxProcessMemory: 137,438,953,344
CPU: 6 AMD Ryzen 5 3500X 6-Core Processor             "
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 Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Permission denied saving image

comment:2 by Eric Pettersen, 5 years ago

Resolution: → not a bug
Status: accepted → closed

Hi,

You are getting "Permission denied" because you are trying to save the image into a folder that you do not have write permission for. When ChimeraX starts up, its "current folder" should be your Desktop folder, so I don't know why you wouldn't have write permission for that. Regardless, to get around this you need to specify the folder you save the image to. There are several ways to do this:

1) You could use File→Save to save the image
2) You could use "browse" instead of a file name in the "save" command to get a file browser to choose the save location
3) You could specify the full path instead of just the file name (e.g. E:\image.tif)
4) You could use the "cd" command to change ChimeraX's "current folder" to someplace you have write permission for.

I hope this helps.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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