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#3074 closed defect (can't reproduce)

Mac Catalina prevent toolbar image save to desktop

Reported by:	chimerax-bug-report@…	Owned by:	Tom Goddard
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:        Darwin-19.4.0-x86_64-i386-64bit
ChimeraX Version: 0.94 (2020-04-17)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.94.dev202004170644 (2020-04-17)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> help help:quickstart

> open 6nj8

Summary of feedback from opening 6nj8 fetched from pdb  
---  
note | Fetching compressed mmCIF 6nj8 from
http://files.rcsb.org/download/6nj8.cif  
  
6nj8 title:  
Encapsulin iron storage compartment from Quasibacillus thermotolerans [more
info...]  
  
Chain information for 6nj8 #1  
---  
Chain | Description  
A B C D | Encapsulating protein for a DyP-type peroxidase  
E F G | targeting peptide  
  
6nj8 mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
  
  

> sym #1 assembly 1

> view

> hide #2 models

> show #1 models

> close

> open 6nj8 format mmCIF fromDatabase pdb

6nj8 title:  
Encapsulin iron storage compartment from Quasibacillus thermotolerans [more
info...]  
  
Chain information for 6nj8 #1  
---  
Chain | Description  
A B C D | Encapsulating protein for a DyP-type peroxidase  
E F G | targeting peptide  
  
6nj8 mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
  
  

> style stick

Changed 9059 atom styles  

> style sphere

Changed 9059 atom styles  

> style ball

Changed 9059 atom styles  

> style sphere

Changed 9059 atom styles  

> style sphere

Changed 9059 atom styles  

> style stick

Changed 9059 atom styles  

> style sphere

Changed 9059 atom styles  

> show cartoons

> style stick

Changed 9059 atom styles  

> style stick

Changed 9059 atom styles  

> hide cartoons

> hide cartoons

> show cartoons

> style sphere

Changed 9059 atom styles  

> style sphere

Changed 9059 atom styles  

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show atoms

> hide atoms

> show atoms

> hide atoms

> sym #1 assembly 1

> view

> select clear

Drag select of 23 residues  

> select clear

> show #2 surfaces

> color #!2 bychain

> color #!2 byhetero

> color #!2 byhetero

> hide #!2 atoms

> hide #!2 cartoons

> color #!2 bychain

> color bfactor #!2

9059 atoms, 1129 residues, 7 surfaces, atom bfactor range 51.1 to 117  

> mlp #!2

Map values for surface "6nj8 assembly 1_A SES surface": minimum -31.13, mean
-4.397, maximum 24.05  
Map values for surface "6nj8 assembly 1_B SES surface": minimum -29.92, mean
-4.451, maximum 23.02  
Map values for surface "6nj8 assembly 1_C SES surface": minimum -31.4, mean
-4.336, maximum 23.8  
Map values for surface "6nj8 assembly 1_D SES surface": minimum -27.96, mean
-4.521, maximum 22.3  
Map values for surface "6nj8 assembly 1_E SES surface": minimum -23.41, mean
-4.545, maximum 18.88  
Map values for surface "6nj8 assembly 1_F SES surface": minimum -23.76, mean
-4.235, maximum 18.82  
Map values for surface "6nj8 assembly 1_G SES surface": minimum -22.7, mean
-4.151, maximum 18.71  

> color bfactor #!2

9059 atoms, 1129 residues, 7 surfaces, atom bfactor range 51.1 to 117  

> color #!2 bychain

> color #2 cornflowerblue

> color #2 red

> undo

> select clear

> color #2 red

> undo

> preset "molecular surfaces" "ghostly white"

Changed 18118 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> preset "molecular surfaces" "atomic coloring (transparent)"

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color fromatoms targ s trans 70

  

> preset "molecular surfaces" "chain id coloring (opaque)"

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color bychain targ s trans 0

  

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> preset "overall look" interactive

Preset expands to these ChimeraX commands:

    
    
    ~set bg
    graphics silhouettes f

  

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> open http://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup

Opened 'http://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup' in
browser  

> open http://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup

Opened 'http://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup' in
browser  

> preset "molecular surfaces" "ghostly white"

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> preset "molecular surfaces" "atomic coloring (transparent)"

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color fromatoms targ s trans 70

  

> undo

> undo

> preset cartoons/nucleotides ribbons/slabs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> preset cartoons/nucleotides cylinders/stubs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> preset cartoons/nucleotides licorice/ovals

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh default arrows f x round width 1 thick 1
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides tube/slab shape ellipsoid

  

> preset cartoons/nucleotides cylinders/stubs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> preset "initial styles" "original look"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "initial styles" sticks

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "initial styles" cartoon

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "initial styles" "space-filling (chain colors)"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "initial styles" "space-filling (single color)"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> toolshed show "Cage Builder"

> hide #!2 models

> close #3

> close

> open 6nj8 format mmCIF fromDatabase pdb

6nj8 title:  
Encapsulin iron storage compartment from Quasibacillus thermotolerans [more
info...]  
  
Chain information for 6nj8 #1  
---  
Chain | Description  
A B C D | Encapsulating protein for a DyP-type peroxidase  
E F G | targeting peptide  
  
6nj8 mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
  
  

> sym #1 assembly 1

> view

> hide #2 cartoons

> hide #2 atoms

> show #2 surfaces

> lighting full

> lighting flat

> lighting full

> lighting shadows false

> lighting soft

> lighting simple

> lighting full

> lighting soft

> volume style image

No volumes specified  

> volume style surface

No volumes specified  

> volume hide

No volumes specified  

> volume planes z style image imageMode "full region"

No volumes specified  

> ui mousemode rightMode "mark maximum"

> ui mousemode rightMode clip

> select clear

> select #1/E#1/F#1/G#2/E#2/F#2/G

294 atoms, 288 bonds, 2 models selected  

> color (#!2 & sel) red

> select clear

> select #1/A#1/B#1/C#1/D#2/A#2/B#2/C#2/D

17824 atoms, 18208 bonds, 2 models selected  

> select clear

> select #1/A

2228 atoms, 2276 bonds, 1 model selected  

> select clear

> select #1/A#1/B#1/C#1/D#2/A#2/B#2/C#2/D

17824 atoms, 18208 bonds, 2 models selected  

> surface style (#!2 & sel) mesh

> color (#!2 & sel) darkgray

> hide sel & #!2 surfaces

> show sel & #!2 cartoons

> color (#!2 & sel) lightgray

> select clear

> lighting full

> ui mousemode rightMode "translate selected models"

Traceback (most recent call last):  
File
"/private/var/folders/yz/jm3v7qyn48g7t1w3tcwlv7d40000gn/T/AppTranslocation/BF0E18DD-0820-410F-AB97-5784F003FEF9/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/yz/jm3v7qyn48g7t1w3tcwlv7d40000gn/T/AppTranslocation/BF0E18DD-0820-410F-AB97-5784F003FEF9/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/yz/jm3v7qyn48g7t1w3tcwlv7d40000gn/T/AppTranslocation/BF0E18DD-0820-410F-AB97-5784F003FEF9/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1641, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File
"/private/var/folders/yz/jm3v7qyn48g7t1w3tcwlv7d40000gn/T/AppTranslocation/BF0E18DD-0820-410F-AB97-5784F003FEF9/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/yz/jm3v7qyn48g7t1w3tcwlv7d40000gn/T/AppTranslocation/BF0E18DD-0820-410F-AB97-5784F003FEF9/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 1212, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File
"/private/var/folders/yz/jm3v7qyn48g7t1w3tcwlv7d40000gn/T/AppTranslocation/BF0E18DD-0820-410F-AB97-5784F003FEF9/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/yz/jm3v7qyn48g7t1w3tcwlv7d40000gn/T/AppTranslocation/BF0E18DD-0820-410F-AB97-5784F003FEF9/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/yz/jm3v7qyn48g7t1w3tcwlv7d40000gn/T/AppTranslocation/BF0E18DD-0820-410F-AB97-5784F003FEF9/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/yz/jm3v7qyn48g7t1w3tcwlv7d40000gn/T/AppTranslocation/BF0E18DD-0820-410F-AB97-5784F003FEF9/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 1138, in save_image  
path = unused_file_name(directory, basename, suffix)  
File
"/private/var/folders/yz/jm3v7qyn48g7t1w3tcwlv7d40000gn/T/AppTranslocation/BF0E18DD-0820-410F-AB97-5784F003FEF9/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 1158, in unused_file_name  
files = listdir(dir)  
PermissionError: [Errno 1] Operation not permitted:
'/Users/jessejones/Desktop'  
  
PermissionError: [Errno 1] Operation not permitted:
'/Users/jessejones/Desktop'  
  
File
"/private/var/folders/yz/jm3v7qyn48g7t1w3tcwlv7d40000gn/T/AppTranslocation/BF0E18DD-0820-410F-AB97-5784F003FEF9/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 1158, in unused_file_name  
files = listdir(dir)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-14.5.22
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.

Change History (2)

comment:1 by Eric Pettersen, 6 years ago

Component:	Unassigned → Input/Output
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Mac Catalina prevent toolbar image save to desktop

comment:2 by Tom Goddard, 6 years ago

Resolution:	→ can't reproduce
Status:	assigned → closed

macOS Catalina asks permission to access Downloads, Desktop and Documents folders on a per-application basis. Possibly the user accidentally denied permission when this dialog appeared. But it is also possible macOS Catalina has a problem. I have on rare occasions seen it not show the permission dialog, The permissions can be checked in macOS system preferences under Security & Privacy / Files and Folders.

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