Opened 6 years ago

Closed 6 years ago

Last modified 6 years ago

#3052 closed defect (nonchimerax)

Toolbar icon image save → can't access Desktop

Reported by: jeremy.force@… Owned by: pett
Priority: normal Milestone:
Component: Platform Version:
Keywords: Cc: Greg Couch, Tom Goddard
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: 0.94 (2020-04-14)
Description
Unable to take snapshot of amino acid change with highlighted surrounding interactions in green

Log:
UCSF ChimeraX version: 0.94.dev202004140658 (2020-04-14)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/jf119/Downloads/3zbf 2.cif" format mmCIF

3zbf 2.cif title:  
Structure of Human ROS1 Kinase Domain in Complex with Crizotinib [more
info...]  
  
Chain information for 3zbf 2.cif #1  
---  
Chain | Description  
A | proto-oncogene tyrosine-protein kinase ros  
  
Non-standard residues in 3zbf 2.cif #1  
---  
VGH —
3-[(1R)-1-(2,6-dichloro-3-fluorophenyl)ethoxy]-5-(1-piperidin-4-yl-1H-pyrazol-4-yl)pyridin-2-amine
(crizotinib)  
  

> lighting soft

> toolshed show "Blast Protein"

> blastprotein /A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name
> bp1

Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr
or pdb for sequences similar to the given protein sequence  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service  
Opal job id: appBlastProtein2Service1587003720855-1159428074  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1587003720855-1159428074  
stdout.txt = standard output  
stderr.txt = standard error  
BlastProtein finished.  
Alignment identifier is bp1 [1]  
Associated 3zbf 2.cif chain A to 3ZBF_A with 0 mismatches  

> show target ab

> hide target a

> show target ab

> hide target a

> show sel target ab

> select sel :< 5

32 atoms, 29 bonds, 1 pseudobond, 2 models selected  

> select sel :< 5

164 atoms, 161 bonds, 1 pseudobond, 2 models selected  

> select /A:1953

6 atoms, 5 bonds, 1 model selected  

> toolshed show Rotamers

> swapaa interactive sel GLY rotLib Dunbrack

> swapaa sel GLY rotLib Dunbrack

Using Dunbrack library  
Swapping /A SER 1953 to GLY  
  

> swapaa interactive sel GLY rotLib Dunbrack

> swapaa sel GLY rotLib Dunbrack

Using Dunbrack library  
Swapping /A GLY 1953 to GLY  
  

> select sel :< 5

30 atoms, 27 bonds, 1 pseudobond, 2 models selected  

> undo

> undo

Undo failed, probably because structures have been modified.  

> select sel :< 5

30 atoms, 27 bonds, 1 pseudobond, 2 models selected  

> select sel :< 5

162 atoms, 159 bonds, 1 pseudobond, 2 models selected  

> show sel target ab

> undo

> toolshed show Rotamers

> select /A:1953

4 atoms, 3 bonds, 1 model selected  

> select sel :< 5

30 atoms, 27 bonds, 1 pseudobond, 2 models selected  

> select /A:1953

4 atoms, 3 bonds, 1 model selected  

> select sel :< 5

30 atoms, 27 bonds, 1 pseudobond, 2 models selected  

> select sel :< 5

162 atoms, 159 bonds, 1 pseudobond, 2 models selected  
Traceback (most recent call last):  
File
"/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/650C0982-D0EE-4DF7-94E9-A71387D79169/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/tool.py", line 162, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/650C0982-D0EE-4DF7-94E9-A71387D79169/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 453, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/650C0982-D0EE-4DF7-94E9-A71387D79169/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1634, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File
"/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/650C0982-D0EE-4DF7-94E9-A71387D79169/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File
"/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/650C0982-D0EE-4DF7-94E9-A71387D79169/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 1170, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File
"/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/650C0982-D0EE-4DF7-94E9-A71387D79169/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 375, in try_shortcut  
self.run_shortcut(keys)  
File
"/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/650C0982-D0EE-4DF7-94E9-A71387D79169/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 393, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File
"/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/650C0982-D0EE-4DF7-94E9-A71387D79169/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 312, in run  
f(s)  
File
"/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/650C0982-D0EE-4DF7-94E9-A71387D79169/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 1096, in save_image  
path = unused_file_name(directory, basename, suffix)  
File
"/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/650C0982-D0EE-4DF7-94E9-A71387D79169/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 1116, in unused_file_name  
files = listdir(dir)  
PermissionError: [Errno 1] Operation not permitted: '/Users/jf119/Desktop'  
  
PermissionError: [Errno 1] Operation not permitted: '/Users/jf119/Desktop'  
  
File
"/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/650C0982-D0EE-4DF7-94E9-A71387D79169/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 1116, in unused_file_name  
files = listdir(dir)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.8.24
OpenGL renderer: AMD Radeon Pro 455 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Attachments (2)

8846B4A0-E0C0-4FAD-BCB1-CDE987D8421F.png​ (692.4 KB ) - added by pett 6 years ago.
Added by email2trac
image001.png​ (692.4 KB ) - added by jeremy.force@… 6 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (6)

comment:1 by pett, 6 years ago

Cc: Greg Couch Tom Goddard added
Component: Unassigned → Platform
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Toolbar icon image save → can't access Desktop

in reply to:  2 ; comment:2 by pett, 6 years ago 

Hi Jeremy,
	The error is really because Mac OS Catalina isn’t allowing ChimeraX to access your Desktop, which is where it is trying to save the image.  You need to go to System Preferences, Security & Privacy category, and in the Privacy tab under Files and Folders allow ChimeraX to access your Desktop folder, as per the image below:

Added by email2trac

by pett, 6 years ago

Attachment: 8846B4A0-E0C0-4FAD-BCB1-CDE987D8421F.png​ added

Added by email2trac

comment:3 by pett, 6 years ago

Resolution: → nonchimerax
Status: accepted → closed

in reply to:  5 comment:4 by jeremy.force@…, 6 years ago 

Thank you!
Jeremy

From: Eric Pettersen <pett@cgl.ucsf.edu>
Reply-To: "ChimeraX-bugs@cgl.ucsf.edu" <ChimeraX-bugs@cgl.ucsf.edu>
Date: Thursday, April 16, 2020 at 1:14 PM
To: "ChimeraX-bugs@cgl.ucsf.edu" <ChimeraX-bugs@cgl.ucsf.edu>
Cc: "goddard@cgl.ucsf.edu" <goddard@cgl.ucsf.edu>, "gregc@cgl.ucsf.edu" <gregc@cgl.ucsf.edu>, A 1 <jeremy.force@duke.edu>
Subject: Re: [ChimeraX] #3052: Toolbar icon image save → can't access Desktop (was: ChimeraX bug report submission)

Hi Jeremy,
The error is really because Mac OS Catalina isn’t allowing ChimeraX to access your Desktop, which is where it is trying to save the image.  You need to go to System Preferences, Security & Privacy category, and in the Privacy tab under Files and Folders allow ChimeraX to access your Desktop folder, as per the image below:

[Screen Shot 2020-04-07 at 10.57.08 AM.png]

Added by email2trac

by jeremy.force@…, 6 years ago

Attachment: image001.png​ added

Added by email2trac

Note: See TracTickets for help on using tickets.