Basic Actions: 'None' in restored model list

[yann.sterckx@…]

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-06-06)
Description
Dear,

I saved all of my prpgress in this session, but for some reason I do not understand, I can no longer open this session.

I would like to understand why this happened such that I don't lose hours of work again in the future. (the error message is listed below)

Many thanks and kind regards

Yann

Unable to restore session, resetting. Traceback (most recent call last): File "/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 596, in restore obj = sm.restore_snapshot(self, data) File "/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/basic_actions/statemgr.py", line 65, in restore_snapshot cmd.name_frozen(session, name, Objects(**value)) File "/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/basic_actions/cmd.py", line 51, in name_frozen if objects.empty(): File "/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/objects.py", line 199, in empty self._remove_deleted_models() File "/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/objects.py", line 127, in _remove_deleted_models mdel = [m for m in mset if m.deleted] File "/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/objects.py", line 127, in <listcomp> mdel = [m for m in mset if m.deleted] AttributeError: 'NoneType' object has no attribute 'deleted'

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  

> lighting depthCue false

> cartoon style strand thickness 0.6

> cartoon style helix thickness 0.6

> cartoon style coil thickness 0.2

> cartoon style protein xsection rectangle

> set silhouetteWidth 1.5

UCSF ChimeraX version: 0.9 (2019-06-06)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
/Users/yannsterckx/Desktop/Research_Projects/Chikungunya/Chikungunya_basigin.cxs

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 596, in restore  
obj = sm.restore_snapshot(self, data)  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/basic_actions/statemgr.py", line 65, in restore_snapshot  
cmd.name_frozen(session, name, Objects(**value))  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/basic_actions/cmd.py", line 51, in name_frozen  
if objects.empty():  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/objects.py", line 199, in empty  
self._remove_deleted_models()  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/objects.py", line 127, in _remove_deleted_models  
mdel = [m for m in mset if m.deleted]  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/objects.py", line 127, in <listcomp>  
mdel = [m for m in mset if m.deleted]  
AttributeError: 'NoneType' object has no attribute 'deleted'  
  
opened ChimeraX session  

> open
/Users/yannsterckx/Desktop/Research_Projects/Chikungunya/Chikungunya_basigin.cxs

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 596, in restore  
obj = sm.restore_snapshot(self, data)  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/basic_actions/statemgr.py", line 65, in restore_snapshot  
cmd.name_frozen(session, name, Objects(**value))  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/basic_actions/cmd.py", line 51, in name_frozen  
if objects.empty():  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/objects.py", line 199, in empty  
self._remove_deleted_models()  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/objects.py", line 127, in _remove_deleted_models  
mdel = [m for m in mset if m.deleted]  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/objects.py", line 127, in <listcomp>  
mdel = [m for m in mset if m.deleted]  
AttributeError: 'NoneType' object has no attribute 'deleted'  
  
opened ChimeraX session  

> open
/Users/yannsterckx/Desktop/Research_Projects/Chikungunya/Chikungunya_basigin.cxs

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 596, in restore  
obj = sm.restore_snapshot(self, data)  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/basic_actions/statemgr.py", line 65, in restore_snapshot  
cmd.name_frozen(session, name, Objects(**value))  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/basic_actions/cmd.py", line 51, in name_frozen  
if objects.empty():  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/objects.py", line 199, in empty  
self._remove_deleted_models()  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/objects.py", line 127, in _remove_deleted_models  
mdel = [m for m in mset if m.deleted]  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/objects.py", line 127, in <listcomp>  
mdel = [m for m in mset if m.deleted]  
AttributeError: 'NoneType' object has no attribute 'deleted'  
  
opened ChimeraX session  




OpenGL version: 4.1 ATI-1.68.20
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[Eric Pettersen]

Hi Yann,

The problem is that a surface was in a selection being tracked by the Basic Actions tool, and the session-restore code for surfaces had a bug in it. That code has been fixed, and the restore code for Basic Actions has been "bullet proofed" to handle sessions saved with the bad surface code. So if you get the daily build we think you will be able to restore your sessions.

--Eric

Eric Pettersen

UCSF Computer Graphics Lab

[Yann.Sterckx@…]

Dear Eric,

thanks for getting back to me and explaining what happened. Glad the bug could be fixed!

By the way: nice work on ChimeraX. I’m slowly moving from Chimera to X (getting more familiar with using the command line) and I’m enjoying the X experience!

Best wishes

Yann

[Eric Pettersen]

Dear Yann,

Glad you're liking "X" too. There's still lots of stuff that's Chimera-only, but we continue to chip away at the difference, and of course there's a lot of "X"-only stuff that's pretty neat. Some graphical interfaces are also slowly appearing. :-)

--Eric