Session restore: destroying already-destroyed alignment

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-09-04)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.91 (2019-09-04)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/misasijn/Documents/OneDrive - National Institutes of
Health/Yeast Display Program/Coronavirus/John/VRC_Center Response/Structural
Models/Published/Spike/SpikeAndFabs.cxs" format session

opened ChimeraX session  

> save image /Users/misasijn/Desktop/DownTop.png width 2500 height 2500
supersample 3 transparentBackground true

> hide #!2 models

> show #!1 models

> select up

Nothing selected  

> select up

Nothing selected  

> select up

Nothing selected  

> save image /Users/misasijn/Desktop/OpenTop.png width 2500 height 2500
supersample 3 transparentBackground true

> turn -90,0,0

> turn -90,0,0

> turn -90,0,0

> turn -90,0,0

> turn -90,0,0

> save image /Users/misasijn/Desktop/Open.png width 2500 height 2500
supersample 3 transparentBackground true

> hide #!1 models

> show #!2 models

> select up

Nothing selected  

> select up

Nothing selected  

> select up

Nothing selected  

> save image /Users/misasijn/Desktop/DownSide.png width 2500 height 2500
supersample 3 transparentBackground true

> open "/Users/misasijn/Documents/OneDrive - National Institutes of
Health/Yeast Display Program/Coronavirus/John/VRC_Center Response/Structural
Models/Published/RBD/6M0J_WangandSan_RDB-ACE2/6m0j.pdb1"

6m0j.pdb1 title:  
Crystal structure of sars-cov-2 spike receptor-binding domain bound with ACE2
[more info...]  
  
Chain information for 6m0j.pdb1 #3  
---  
Chain | Description  
A | No description available  
E | No description available  
  
Non-standard residues in 6m0j.pdb1 #3  
---  
CL — chloride ion  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose  
ZN — zinc ion  
  

> hide #!2 models

> show #!1 models

> matchmaker #2/A to #1/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6vyb.pdb1, chain A (#1) with 6vxx.pdb1, chain A (#2), sequence
alignment score = 6078.8  
RMSD between 955 pruned atom pairs is 0.543 angstroms; (across all 957 pairs:
0.554)  
  

> matchmaker #3/A to #1/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6vyb.pdb1, chain A (#1) with 6m0j.pdb1, chain A (#3), sequence
alignment score = 57.6  
RMSD between 5 pruned atom pairs is 1.192 angstroms; (across all 180 pairs:
33.607)  
  

> matchmaker #3/E to #1/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6vyb.pdb1, chain A (#1) with 6m0j.pdb1, chain E (#3), sequence
alignment score = 1032.5  
RMSD between 166 pruned atom pairs is 0.737 angstroms; (across all 169 pairs:
0.841)  
  

> save session "/Users/misasijn/Documents/OneDrive - National Institutes of
Health/Yeast Display Program/Coronavirus/John/VRC_Center Response/Structural
Models/Published/Spike/SpikeAndFabs.cxs"

> ui mousemode rightMode zoom

> ui mousemode rightMode translate

> ui mousemode rightMode translate

> ui mousemode rightMode translate

> hide #!1 models

> open "/Users/misasijn/Documents/OneDrive - National Institutes of
Health/Yeast Display Program/Coronavirus/John/VRC_Center Response/Structural
Models/Published/Spike/SpikeAndFabs.cxs"

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 622, in restore  
self.reset()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 466, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/tools.py", line 313, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 499, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 325, in detach_viewer  
self.session.alignments.destroy_alignment(self)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/manager.py", line 108, in destroy_alignment  
del self._alignments[alignment.ident]  
KeyError: '1'  
  
Summary of feedback from opening /Users/misasijn/Documents/OneDrive - National
Institutes of Health/Yeast Display Program/Coronavirus/John/VRC_Center
Response/Structural Models/Published/Spike/SpikeAndFabs.cxs  
---  
notes | Exception ignored in: <function Buffer.__del__ at 0x1158f1560>  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "vcolor" was not
deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x1158f1560>  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "instance_placement"
was not deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x1158f1560>  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer
"instance_shift_and_scale" was not deleted before core.graphics.Buffer
destroyed  
Exception ignored in: <function Buffer.__del__ at 0x1158f1560>  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "vcolor" was not
deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x1158f1560>  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "instance_placement"
was not deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x1158f1560>  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer
"instance_shift_and_scale" was not deleted before core.graphics.Buffer
destroyed  
Exception ignored in: <function Buffer.__del__ at 0x1158f1560>  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "vcolor" was not
deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x1158f1560>  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "instance_placement"
was not deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x1158f1560>  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer
"instance_shift_and_scale" was not deleted before core.graphics.Buffer
destroyed  
Exception ignored in: <function Buffer.__del__ at 0x1158f1560>  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "vcolor" was not
deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x1158f1560>  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "instance_placement"
was not deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x1158f1560>  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer
"instance_shift_and_scale" was not deleted before core.graphics.Buffer
destroyed  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 622, in restore  
self.reset()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 466, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/tools.py", line 313, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 499, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 325, in detach_viewer  
self.session.alignments.destroy_alignment(self)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/manager.py", line 108, in destroy_alignment  
del self._alignments[alignment.ident]  
KeyError: '1'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 588, in _qt_safe  
run(session, "open " + " ".join([quote_if_necessary(p) for p in paths]))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2688, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/open.py", line 68, in open  
path_models = session.models.open(paths, format=format, name=name, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 637, in open  
session, filenames, format=format, name=name, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 479, in open_multiple_data  
models, status = open_data(session, fspec, format=format, name=name, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 435, in open_data  
models, status = open_func(*args, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 883, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 659, in restore  
self.reset()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 466, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/tools.py", line 313, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 495, in delete  
self.seq_canvas.destroy()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 552, in destroy  
header.destroy()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/headers/conservation.py", line 99, in destroy  
super().destroy()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/headers/header_sequence.py", line 73, in destroy  
self.alignment.remove_observer(self)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 451, in remove_observer  
self.observers.remove(observer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 451, in remove_observer  
self.observers.remove(observer)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.10.18
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[pett]

Lots of changes since 0.91