Various sequence-related session problems

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 0.91 (2019-10-10)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.91 (2019-10-10)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open E:/yinlab/43a2/1/fig/cx/fig3_8_densi.cxs

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py", line 653,
in restore  
obj = sm.restore_snapshot(self, data)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\seq-view\tool.py", line 601,
in restore_snapshot  
inst._finalize_init(data['alignment'])  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\seq-view\tool.py", line 174,
in _finalize_init  
self.seq_canvas = SeqCanvas(parent, self, self.alignment)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line
184, in __init__  
self.layout_alignment()  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line
787, in layout_alignment  
self.label_width, self.font_pixels, self.numbering_widths, self.letter_gaps())  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line
1601, in __init__  
self.layout_lines(alignment.seqs, self.normal_label_color)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line
2243, in layout_lines  
self._layout_line(line, label_color, bli, end)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line
2193, in _layout_line  
font=self._label_font(line))  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line
2133, in _label_font  
if self.has_associated_structures(line):  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line
2071, in has_associated_structures  
and [chain for chain in line.match_maps.keys() if not
chain.structure.deleted]:  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line
2071, in <listcomp>  
and [chain for chain in line.match_maps.keys() if not
chain.structure.deleted]:  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\atomic\attr_registration.py",
line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File "D:\ChimeraX\bin\lib\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'  
  
Traceback (most recent call last):  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py", line 653,
in restore  
obj = sm.restore_snapshot(self, data)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\seq-view\tool.py", line 601,
in restore_snapshot  
inst._finalize_init(data['alignment'])  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\seq-view\tool.py", line 174,
in _finalize_init  
self.seq_canvas = SeqCanvas(parent, self, self.alignment)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line
184, in __init__  
self.layout_alignment()  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line
787, in layout_alignment  
self.label_width, self.font_pixels, self.numbering_widths, self.letter_gaps())  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line
1601, in __init__  
self.layout_lines(alignment.seqs, self.normal_label_color)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line
2243, in layout_lines  
self._layout_line(line, label_color, bli, end)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line
2193, in _layout_line  
font=self._label_font(line))  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line
2133, in _label_font  
if self.has_associated_structures(line):  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line
2071, in has_associated_structures  
and [chain for chain in line.match_maps.keys() if not
chain.structure.deleted]:  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line
2071, in <listcomp>  
and [chain for chain in line.match_maps.keys() if not
chain.structure.deleted]:  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\atomic\attr_registration.py",
line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File "D:\ChimeraX\bin\lib\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'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 599, in
_qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]))  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\run.py", line
31, in run  
results = command.run(text, log=log)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2837, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\open.py", line
68, in open  
path_models = session.models.open(paths, format=format, name=name, **kw)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\models.py", line 649, in
open  
session, filenames, format=format, name=name, **kw)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\io.py", line 489, in
open_multiple_data  
models, status = open_data(session, fspec, format=format, name=name, **kw)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\io.py", line 445, in
open_data  
models, status = open_func(*args, **kw)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py", line 883,
in open  
session.restore(stream, path=path, resize_window=resize_window)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py", line 659,
in restore  
self.reset()  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py", line 466,
in reset  
sm.reset_state(container, self)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\seqalign\manager.py", line
263, in reset_state  
alignment._destroy()  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\seqalign\alignment.py", line
494, in _destroy  
self._notify_observers("destroyed", None)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\seqalign\alignment.py", line
531, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\seq-view\tool.py", line 460,
in alignment_notification  
self.delete()  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\seq-view\tool.py", line 490,
in delete  
self.region_browser.destroy()  
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'  
  
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'  
  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\seq-view\tool.py", line 490,
in delete  
self.region_browser.destroy()  
  
See log for complete Python traceback.  
  

> open E:/yinlab/43a2/structure/phe/lat4_phe_if.pdb

Summary of feedback from opening E:/yinlab/43a2/structure/phe/lat4_phe_if.pdb  
---  
warning | Ignored bad PDB record found on line 3175  
END  
  
Chain information for lat4_phe_if.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open
E:/yinlab/43a2/structure/phe/cryosparc_P18_J2201_006_volume_map_sharp_60.mrc

Opened cryosparc_P18_J2201_006_volume_map_sharp_60.mrc, grid size 300,300,300,
pixel 0.834, shown at level 0.121, step 2, values float32  

> select :159,166,187,184,465,335,100,103,489

74 atoms, 67 bonds, 1 model selected  

> volume zone #2 nearAtoms sel range 1.5

> lighting soft

> close session

Traceback (most recent call last):  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 886, in
<lambda>  
close_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_close_cb(sess))  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 616, in
file_close_cb  
run(session, 'close session')  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\run.py", line
31, in run  
results = command.run(text, log=log)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2837, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\std_commands\close.py", line
60, in close_session  
session.reset()  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py", line 466,
in reset  
sm.reset_state(container, self)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\seqalign\manager.py", line
263, in reset_state  
alignment._destroy()  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\seqalign\alignment.py", line
494, in _destroy  
self._notify_observers("destroyed", None)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\seqalign\alignment.py", line
531, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\seq-view\tool.py", line 460,
in alignment_notification  
self.delete()  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\seq-view\tool.py", line 490,
in delete  
self.region_browser.destroy()  
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'  
  
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'  
  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\seq-view\tool.py", line 490,
in delete  
self.region_browser.destroy()  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 417.77
OpenGL renderer: GeForce RTX 2060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Eric Pettersen]

version 0.91