Opened 7 years ago

Closed 7 years ago

#1733 closed defect (fixed)

Sequence headers session-restore problem

Reported by: boschdu@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Sequence Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-18.2.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-02-06)
Description
attempting to load a recently saved ChimeraX session

Log:
UCSF ChimeraX version: 0.9 (2019-02-06)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/dustinbosch/OneDrive -
UW/N_fowleri_project/SSGCID_structures/NfGalpha12.cxs"

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 594, in restore  
obj = sm.restore_snapshot(self, data)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 590, in restore_snapshot  
inst.seq_canvas.restore_state(session, data['seq canvas'])  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 1120, in restore_state  
headers.append(header_class.session_restore(session, self.sv, header_state))  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/headers/header_sequence.py", line 164, in
session_restore  
inst = HeaderSequence(alignment)  
TypeError: __init__() missing 1 required positional argument:
'refresh_callback'  
  
opened ChimeraX session  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 229, in _actually_resize  
self._reformat()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 1027, in _reformat  
self.label_width, self.font_pixels, self.numbering_widths, self.letter_gaps())  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 1602, in __init__  
self.layout_lines(alignment.seqs, self.normal_label_color)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2244, in layout_lines  
self._layout_line(line, label_color, bli, end)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2194, in _layout_line  
font=self._label_font(line))  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2134, in _label_font  
if self.has_associated_structures(line):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2072, in
has_associated_structures  
and [chain for chain in line.match_maps.keys() if not
chain.structure.deleted]:  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2072, in <listcomp>  
and [chain for chain in line.match_maps.keys() if not
chain.structure.deleted]:  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  

> open "/Users/dustinbosch/OneDrive -
UW/N_fowleri_project/SSGCID_structures/NfGalpha10.cxs"

opened ChimeraX session  

> open "/Users/dustinbosch/OneDrive -
UW/N_fowleri_project/SSGCID_structures/NfGalpha12.cxs"

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 594, in restore  
obj = sm.restore_snapshot(self, data)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 590, in restore_snapshot  
inst.seq_canvas.restore_state(session, data['seq canvas'])  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 1120, in restore_state  
headers.append(header_class.session_restore(session, self.sv, header_state))  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/headers/header_sequence.py", line 164, in
session_restore  
inst = HeaderSequence(alignment)  
TypeError: __init__() missing 1 required positional argument:
'refresh_callback'  
  
opened ChimeraX session  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 229, in _actually_resize  
self._reformat()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 1027, in _reformat  
self.label_width, self.font_pixels, self.numbering_widths, self.letter_gaps())  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 1602, in __init__  
self.layout_lines(alignment.seqs, self.normal_label_color)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2244, in layout_lines  
self._layout_line(line, label_color, bli, end)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2194, in _layout_line  
font=self._label_font(line))  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2134, in _label_font  
if self.has_associated_structures(line):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2072, in
has_associated_structures  
and [chain for chain in line.match_maps.keys() if not
chain.structure.deleted]:  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2072, in <listcomp>  
and [chain for chain in line.match_maps.keys() if not
chain.structure.deleted]:  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.4.10
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Change History (2)

comment:1 by Eric Pettersen, 7 years ago

Component: Unassigned → Sequence
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Sequence headers session-restore problem

comment:2 by Eric Pettersen, 7 years ago

Resolution: → fixed
Status: accepted → closed

Hi Dustin,

Thanks for reporting this problem. It is fixed now and the fix will be available in the next daily build (build happens overnight, so should be available tomorrow morning).

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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