Problem restoring sequence regions

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.8.dev202404192135 (2024-04-19 21:35:01 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
developer warning: toolbar 'Medical Image' depends on non-existent 'map'  
UCSF ChimeraX version: 1.8.dev202404192135 (2024-04-19)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "D:/TSSM Ppaper/tssm-vgsc-18-mutations L925M-L1024V-F1534S-F1538I.cxs"

Region 'mismatches of 5x0m.cif, chain A' extends past end of alignment;
truncating  

[Repeated 16 time(s)]Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 757, in restore  
obj = sm.restore_snapshot(self, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seq_view\tool.py", line 827, in restore_snapshot  
inst._finalize_init(data['alignment'])  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seq_view\tool.py", line 181, in _finalize_init  
self._update_errors_gaps(seq)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seq_view\tool.py", line 924, in _update_errors_gaps  
self.region_manager.new_region(region_name, blocks=blocks, fill=fill,  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seq_view\region_browser.py", line 922, in new_region  
region = Region(self, init_blocks=clipped_blocks, name=name,
name_prefix=name_prefix,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seq_view\region_browser.py", line 65, in __init__  
self.add_blocks(init_blocks, make_cb=False)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seq_view\region_browser.py", line 90, in add_blocks  
for x1, y1, x2, y2 in self.seq_canvas.bbox_list(cover_gaps=self.cover_gaps,
*block):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 444, in bbox_list  
return self.lead_block.bbox_list(line1, line2, pos1, pos2, cover_gaps)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1769, in bbox_list  
return self.next_block.bbox_list(line1, line2, pos1, pos2, cover_gaps)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1769, in bbox_list  
return self.next_block.bbox_list(line1, line2, pos1, pos2, cover_gaps)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1769, in bbox_list  
return self.next_block.bbox_list(line1, line2, pos1, pos2, cover_gaps)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
[Previous line repeated 65 more times]  
AttributeError: 'NoneType' object has no attribute 'bbox_list'  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 757, in restore  
obj = sm.restore_snapshot(self, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seq_view\tool.py", line 827, in restore_snapshot  
inst._finalize_init(data['alignment'])  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seq_view\tool.py", line 181, in _finalize_init  
self._update_errors_gaps(seq)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seq_view\tool.py", line 924, in _update_errors_gaps  
self.region_manager.new_region(region_name, blocks=blocks, fill=fill,  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seq_view\region_browser.py", line 922, in new_region  
region = Region(self, init_blocks=clipped_blocks, name=name,
name_prefix=name_prefix,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seq_view\region_browser.py", line 65, in __init__  
self.add_blocks(init_blocks, make_cb=False)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seq_view\region_browser.py", line 90, in add_blocks  
for x1, y1, x2, y2 in self.seq_canvas.bbox_list(cover_gaps=self.cover_gaps,
*block):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 444, in bbox_list  
return self.lead_block.bbox_list(line1, line2, pos1, pos2, cover_gaps)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1769, in bbox_list  
return self.next_block.bbox_list(line1, line2, pos1, pos2, cover_gaps)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1769, in bbox_list  
return self.next_block.bbox_list(line1, line2, pos1, pos2, cover_gaps)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1769, in bbox_list  
return self.next_block.bbox_list(line1, line2, pos1, pos2, cover_gaps)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
[Previous line repeated 65 more times]  
AttributeError: 'NoneType' object has no attribute 'bbox_list'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 334, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2904, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 131, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2904, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 213, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 514, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 484, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 37, in open  
return cxs_open(session, data, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 1027, in open  
session.restore(stream, path=path, resize_window=resize_window,
combine=combine)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 765, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 552, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seqalign\manager.py", line 273, in reset_state  
alignment._destroy()  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 724, in _destroy  
self._notify_observers(self.NOTE_DESTROYED, None)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 823, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seq_view\tool.py", line 471, in alignment_notification  
self.delete()  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seq_view\tool.py", line 515, in delete  
get_triggers().remove_handler(self._atomic_changes_handler)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'SequenceViewer' object has no attribute
'_atomic_changes_handler'  
  
AttributeError: 'SequenceViewer' object has no attribute
'_atomic_changes_handler'  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\seq_view\tool.py", line 515, in delete  
get_triggers().remove_handler(self._atomic_changes_handler)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 30.0.101.3111
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows

Manufacturer: Dell Inc.
Model: Inspiron 3880
OS: Microsoft Windows 11 Home (Build 22631)
Memory: 12,620,349,440
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i5-10400 CPU @ 2.90GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    beautifulsoup4: 4.12.3
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    build: 1.2.1
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    cftime: 1.6.3
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    ChimeraX-AddCharge: 1.5.16
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
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