Opened 5 years ago

Closed 5 years ago

#4253 closed defect (can't reproduce)

Permission denied saving image

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

Description

The following bug report has been submitted:
Platform:        Windows-8.1-6.3.9600
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
I cant save hidrophofic png image 

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 "C:\Users\GUILLERMO\Documents\ALEX HP\DENGUE\SEQUENCE
> ANALISYS\1okesinagua.pdb" format pdb

Summary of feedback from opening C:\Users\GUILLERMO\Documents\ALEX
HP\DENGUE\SEQUENCE ANALISYS\1okesinagua.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Accelrys Discovery Studio PDB file  
  
Ignored bad PDB record found on line 2  
REMARK Created: 2020-06-19T19:25:40Z  
  
Chain information for 1okesinagua.pdb #1  
---  
Chain | Description  
A B | No description available  
  

> close session

No such database 'C'  

> open "C:/Users/GUILLERMO/Documents/ALEX HP/DENGUE/PDB´s/1oke.pdb"

1oke.pdb title:  
Crystal structure of the dengue 2 virus envelope protein In complex with
N-octyl-β-D-glucoside [more info...]  
  
Chain information for 1oke.pdb #1  
---  
Chain | Description  
A B | dengue virus TYPE 2 major envelope protein E  
  
Non-standard residues in 1oke.pdb #1  
---  
BMA — β-D-mannopyranose  
BOG — octyl β-D-glucopyranoside  
FUL — β-L-fucopyranose (6-deoxy-β-L-galactose)  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose  
  

> select ::name="BOG"

40 atoms, 40 bonds, 1 model selected  

> color sel bychain

> select clear

> color bychain

> select ::name="BOG"

40 atoms, 40 bonds, 1 model selected  

> cofr sel

> view sel

Drag select of 8 atoms, 24 residues, 6 bonds  

> mlp sel

Map values for surface "1oke.pdb_B SES surface": minimum -32.54, mean -5.348,
maximum 26.25  

> hide sel surfaces

> show (#!1 & sel) target ab

> label (#!1 & sel) text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> select clear

Drag select of 150 atoms, 92 residues, 128 bonds  

> hide (#!1 & sel) target a

> ~label (#!1 & sel) residues

> select clear

> select ::name="BOG"

40 atoms, 40 bonds, 1 model selected  

> select ::name="BOG"

40 atoms, 40 bonds, 1 model selected  

> show sel target ab

> select clear

> select clear

> select ::name="BOG"

40 atoms, 40 bonds, 1 model selected  

> color sel orange

> cofr sel

> view sel

> select clear

> select /A

3145 atoms, 3165 bonds, 1 model selected  

> select /B

3183 atoms, 3165 bonds, 1 model selected  

> mlp sel

Map values for surface "1oke.pdb_B SES surface": minimum -32.54, mean -5.348,
maximum 26.25  

> select /B:198@CD2

1 atom, 1 model selected  

> select clear

> select ::name="BOG"

40 atoms, 40 bonds, 1 model selected  

> color sel orange red

> color sel red

> hbonds sel

10 hydrogen bonds found  

> ~hbonds

> select /B:193@CE1

1 atom, 1 model selected  

> select clear

> save "C:/Users/GUILLERMO/Documents/región BOG.png" width 1900 height 767
> supersample 3

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py",
line 1541, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "C:\Program Files\ChimeraX 1.0\bin\lib\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 "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\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 "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\image_formats\\__init__.py", line 24, in save  
save_image(session, path, format_name, **kw)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\image_formats\save.py", line 115, in save_image  
i.save(path, format_name, **metadata)  
File "C:\Program Files\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:
'C:/Users/GUILLERMO/Documents/región BOG.png'  
  
PermissionError: [Errno 13] Permission denied:
'C:/Users/GUILLERMO/Documents/región BOG.png'  
  
File "C:\Program Files\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.  
  

> set bgColor white

> set bgColor black

> hide cartoons

> show cartoons

> hide cartoons

> save C:/Users/GUILLERMO/Documents/BOG.png width 1900 height 767 supersample
> 3

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 162, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 363, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1607, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\toolbar\\__init__.py", line 38, in run_provider  
providers.run_provider(session, name)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 45, in run_provider  
what(session)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 27, in _file_save  
show_save_file_dialog(session)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\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 "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\image_formats\\__init__.py", line 24, in save  
save_image(session, path, format_name, **kw)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\image_formats\save.py", line 115, in save_image  
i.save(path, format_name, **metadata)  
File "C:\Program Files\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:
'C:/Users/GUILLERMO/Documents/BOG.png'  
  
PermissionError: [Errno 13] Permission denied:
'C:/Users/GUILLERMO/Documents/BOG.png'  
  
File "C:\Program Files\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.  
  




OpenGL version: 3.3.0 - Build 10.18.14.4029
OpenGL renderer: Intel(R) HD Graphics 5500
OpenGL vendor: Intel
Manufacturer: Hewlett-Packard
Model: HP ENVY x360 Convertible
OS: Microsoft Windows 8.1 Single Language (Build 9600)
Memory: 8,502,923,264
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-5200U CPU @ 2.20GHz"
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

Cc: Eric Pettersen added
Component: UnassignedInput/Output
Owner: set to Tom Goddard
Platform: all
Project: ChimeraX
Status: newassigned
Summary: ChimeraX bug report submissionPermission denied saving image

comment:2 by Eric Pettersen, 5 years ago

Resolution: can't reproduce
Status: assignedclosed

Really? Can't save to his own Documents folder?

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