Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#4643 closed defect (fixed)

Mayhem after screen removed?

Reported by: chimerax-bug-report@… Owned by: pett
Priority: normal Milestone:
Component: UI Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.2 (2021-05-08 05:48:20 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
> view #2 clip false

> close #2

> close #3

> close #1

> open "/Users/akwl/OneDrive - University of
> Saskatchewan/Manuscripts/Crystal_2020_AL/Figures/Introduction/5xjc-
> assembly1.cif" "/Users/akwl/OneDrive - University of
> Saskatchewan/Manuscripts/Crystal_2020_AL/Figures/Introduction/6qdv-
> assembly1.cif"

5xjc-assembly1.cif title:  
Cryo-EM structure of the human spliceosome just prior to exon ligation at 3.6
angstrom [more info...]  
  
Chain information for 5xjc-assembly1.cif #1  
---  
Chain | Description  
A | Pre-mRNA-processing-splicing factor 8  
B | U5 snRNA  
C | 116 kDa U5 small nuclear ribonucleoprotein component  
D | U5 small nuclear ribonucleoprotein 200 kDa helicase  
E | U5 small nuclear ribonucleoprotein 40 kDa protein  
F | U6 snRNA  
G | pre-mRNA  
H | Homo sapiens small nuclear RNA (U2) gene  
I | Pre-mRNA-splicing factor SYF1  
J | Crooked neck-like protein 1  
K | Pre-mRNA-splicing factor SPF27  
L | Cell division cycle 5-like protein  
M | Pre-mRNA-splicing factor SYF2  
N | Protein BUD31 homolog  
O | Pre-mRNA-splicing factor RBM22  
P | Spliceosome-associated protein CWC15 homolog  
Q | Intron-binding protein aquarius  
R | SNW domain-containing protein 1  
S | Peptidyl-prolyl cis-trans isomerase-like 1  
T | Pleiotropic regulator 1  
U | Serine/arginine repetitive matrix protein 2  
V | Pre-mRNA-splicing factor CWC22 homolog  
W | Pre-mRNA-processing factor 17  
X | PRKR-interacting protein 1  
Y | ATP-dependent RNA helicase DHX8  
Z | Pre-mRNA-splicing factor SLU7  
a h | Small nuclear ribonucleoprotein Sm D3  
b i | Small nuclear ribonucleoprotein-associated proteins B and B'  
c j | Small nuclear ribonucleoprotein Sm D1  
d k | Small nuclear ribonucleoprotein Sm D2  
e l | Small nuclear ribonucleoprotein E  
f m | Small nuclear ribonucleoprotein F  
g n | Small nuclear ribonucleoprotein G  
o | U2 small nuclear ribonucleoprotein A'  
p | U2 small nuclear ribonucleoprotein B''  
q r s t | Pre-mRNA-processing factor 19  
u | Eukaryotic initiation factor 4A-III  
v | Protein mago nashi homolog 2  
w | RNA-binding protein 8A  
x | Protein CASC3  
  
Non-standard residues in 5xjc-assembly1.cif #1  
---  
ADP — (ADP)  
ATP — (ATP)  
GTP — (GTP)  
IHP — (IHP)  
MG — (MG)  
ZN — (ZN)  
  
6qdv-assembly1.cif title:  
Human post-catalytic P complex spliceosome [more info...]  
  
Chain information for 6qdv-assembly1.cif #2  
---  
Chain | Description  
2 | U2 snRNA  
5 | U5 snRNA  
6 | U6 snRNA  
7 | Eukaryotic initiation factor 4A-III  
8 | RNA-binding protein 8A  
9 | Protein mago nashi homolog 2  
A | Pre-mRNA-processing-splicing factor 8  
B | U5 small nuclear ribonucleoprotein 200 kDa helicase  
C | 116 kDa U5 small nuclear ribonucleoprotein component  
D | PRKR-interacting protein 1  
E | Ligated exons: MINX mRNA  
F | Cactin  
G | Protein FAM32A  
H | Pre-mRNA-splicing factor CWC22 homolog  
I | Intron lariat: MINX RNA  
J | Pleiotropic regulator 1  
K | SNW domain-containing protein 1  
L | Protein BUD31 homolog  
M | Pre-mRNA-splicing factor RBM22  
N | U5 small nuclear ribonucleoprotein 40 kDa protein  
O | Cell division cycle 5-like protein  
P | Spliceosome-associated protein CWC15 homolog  
R | Serine/arginine repetitive matrix protein 2  
S | Crooked neck-like protein 1  
T | Pre-mRNA-splicing factor SYF1  
U | Intron-binding protein aquarius  
V | ATP-dependent RNA helicase DHX8  
W | U2 small nuclear ribonucleoprotein A'  
Y | U2 small nuclear ribonucleoprotein B''  
Z | NF-kappa-B-activating protein  
b k | Small nuclear ribonucleoprotein-associated proteins B and B'  
c | Pre-mRNA-splicing factor SLU7  
d n | Small nuclear ribonucleoprotein Sm D3  
e p | Small nuclear ribonucleoprotein E  
f q | Small nuclear ribonucleoprotein F  
g r | Small nuclear ribonucleoprotein G  
h l | Small nuclear ribonucleoprotein Sm D1  
i | Peptidyl-prolyl cis-trans isomerase-like 1  
j m | Small nuclear ribonucleoprotein Sm D2  
o | Pre-mRNA-processing factor 17  
s | Pre-mRNA-splicing factor SPF27  
t u v w | Pre-mRNA-processing factor 19  
y | Pre-mRNA-splicing factor SYF2  
z | Replication stress response regulator SDE2  
  
Non-standard residues in 6qdv-assembly1.cif #2  
---  
ATP — (ATP)  
GTP — (GTP)  
IHP — (IHP)  
K — (K)  
MG — (MG)  
ZN — (ZN)  
  

> hide #!2 models

> select #1/F:1-97

2075 atoms, 2323 bonds, 44 pseudobonds, 97 residues, 2 models selected  

> select #1/F:1-97

2075 atoms, 2323 bonds, 44 pseudobonds, 97 residues, 2 models selected  

> show sel cartoons

> nucleotides (#!1 & sel) ladder

> color (#!1 & sel) red

> set bgColor white

> sequence chain #1/B

Alignment identifier is 1/B  

> select #1/B:8-104

1768 atoms, 1970 bonds, 54 pseudobonds, 84 residues, 3 models selected  

> show sel cartoons

> nucleotides (#!1 & sel) ladder

> color (#!1 & sel) blue

> select #1/G:-23-150

1551 atoms, 1721 bonds, 3 pseudobonds, 84 residues, 2 models selected  

> show sel cartoons

> nucleotides (#!1 & sel) ladder

> color (#!1 & sel) lime

> select #1/o:2-163

1282 atoms, 1299 bonds, 162 residues, 1 model selected  

> select #1/o:2-163

1282 atoms, 1299 bonds, 162 residues, 1 model selected  

> sequence chain #1/o

Alignment identifier is 1/o  

> select #1/p:3-96

760 atoms, 774 bonds, 94 residues, 1 model selected  

> select #1/H:1-184

2966 atoms, 3305 bonds, 80 pseudobonds, 140 residues, 3 models selected  

> show sel cartoons

> nucleotides (#!1 & sel) ladder

> color (#!1 & sel) cyan

> select #1/H:1-184

2966 atoms, 3305 bonds, 80 pseudobonds, 140 residues, 3 models selected  

> select #1/H:1-184

2966 atoms, 3305 bonds, 80 pseudobonds, 140 residues, 3 models selected  

> select #1/G:-23-150

1551 atoms, 1721 bonds, 3 pseudobonds, 84 residues, 2 models selected  

> select #1/G:-23-150

1551 atoms, 1721 bonds, 3 pseudobonds, 84 residues, 2 models selected  

> select clear

> toolshed show

> show sel cartoons

> show sel cartoons

> select #1/B:8-104

1768 atoms, 1970 bonds, 54 pseudobonds, 84 residues, 3 models selected  

> name frozen "U5 snRNA" sel

registering illegal selector name "U5 snRNA"  

> close #2

> select #2/6:1-97

Nothing selected  

> select #2/6:1-97

Nothing selected  

> select #2/6:1-97

Nothing selected  

> sequence chain #2/6

Chains must have same sequence  

> sequence chain #2/6

Chains must have same sequence  

> sequence chain #1/F

Alignment identifier is 1/F  

> select #1/F:1-97

2075 atoms, 2323 bonds, 44 pseudobonds, 97 residues, 2 models selected  

> select #1/F:1-97

2075 atoms, 2323 bonds, 44 pseudobonds, 97 residues, 2 models selected  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2888, in _update_current_size  
int(100.0 * window_width / screen_width),  
ZeroDivisionError: float division by zero  
  
Error processing trigger "resized":  
ZeroDivisionError: float division by zero  
  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2888, in _update_current_size  
int(100.0 * window_width / screen_width),  
  
See log for complete Python traceback.  
  

> close

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 635, in _mmap_mod_cb  
self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True)  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 392, in disassociate  
self.session.alignments.destroy_alignment(self)  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/manager.py", line 108, in destroy_alignment  
alignment._destroy()  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 603, in _destroy  
self._notify_observers(self.NOTE_DESTROYED, None)  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 652, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 474, in alignment_notification  
self.delete()  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 512, in delete  
ToolInstance.delete(self)  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 154, in delete  
self.session.ui.remove_tool(self)  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 345, in remove_tool  
self.main_window.remove_tool(tool_instance)  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 725, in remove_tool  
tw._destroy()  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2049, in _destroy  
self.__toolkit.destroy()  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2189, in destroy  
sbar.destroy()  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/statusbar.py", line 51, in destroy  
v.delete()  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 438, in delete  
self.make_current()  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 478, in make_current  
return self._opengl_context.make_current()  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 99, in make_current  
qc = self._initialize_context()  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context  
qc.setScreen(self._screen)  
RuntimeError: wrapped C/C++ object of type QScreen has been deleted  
  
Error processing trigger "modified":  
RuntimeError: wrapped C/C++ object of type QScreen has been deleted  
  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context  
qc.setScreen(self._screen)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 635, in _mmap_mod_cb  
self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True)  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 392, in disassociate  
self.session.alignments.destroy_alignment(self)  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/manager.py", line 108, in destroy_alignment  
alignment._destroy()  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 603, in _destroy  
self._notify_observers(self.NOTE_DESTROYED, None)  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 652, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 474, in alignment_notification  
self.delete()  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 512, in delete  
ToolInstance.delete(self)  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 154, in delete  
self.session.ui.remove_tool(self)  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 345, in remove_tool  
self.main_window.remove_tool(tool_instance)  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 725, in remove_tool  
tw._destroy()  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2049, in _destroy  
self.__toolkit.destroy()  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2189, in destroy  
sbar.destroy()  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/statusbar.py", line 51, in destroy  
v.delete()  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 438, in delete  
self.make_current()  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 478, in make_current  
return self._opengl_context.make_current()  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 99, in make_current  
qc = self._initialize_context()  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context  
qc.setScreen(self._screen)  
RuntimeError: wrapped C/C++ object of type QScreen has been deleted  
  
Error processing trigger "modified":  
RuntimeError: wrapped C/C++ object of type QScreen has been deleted  
  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context  
qc.setScreen(self._screen)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 635, in _mmap_mod_cb  
self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True)  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 392, in disassociate  
self.session.alignments.destroy_alignment(self)  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/manager.py", line 108, in destroy_alignment  
alignment._destroy()  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 603, in _destroy  
self._notify_observers(self.NOTE_DESTROYED, None)  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 652, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 474, in alignment_notification  
self.delete()  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 512, in delete  
ToolInstance.delete(self)  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 154, in delete  
self.session.ui.remove_tool(self)  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 345, in remove_tool  
self.main_window.remove_tool(tool_instance)  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 725, in remove_tool  
tw._destroy()  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2049, in _destroy  
self.__toolkit.destroy()  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2189, in destroy  
sbar.destroy()  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/statusbar.py", line 51, in destroy  
v.delete()  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 438, in delete  
self.make_current()  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 478, in make_current  
return self._opengl_context.make_current()  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 99, in make_current  
qc = self._initialize_context()  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context  
qc.setScreen(self._screen)  
RuntimeError: wrapped C/C++ object of type QScreen has been deleted  
  
Error processing trigger "modified":  
RuntimeError: wrapped C/C++ object of type QScreen has been deleted  
  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context  
qc.setScreen(self._screen)  
  
See log for complete Python traceback.  
  

> open "/Users/akwl/OneDrive - University of
> Saskatchewan/Manuscripts/Crystal_2020_AL/Figures/U1/U1_4pjo_packing.pyc"

Python code was compiled for a different version of Python  

> open "/Users/akwl/OneDrive - University of
> Saskatchewan/Manuscripts/Crystal_2020_AL/Figures/U1/4pjo.pdb"

Chain information for 4pjo.pdb #1  
---  
Chain | Description  
1 2 | No description available  
3 | No description available  
4 | No description available  
A | No description available  
B P | No description available  
C | No description available  
D | No description available  
E S e s | No description available  
F | No description available  
G | No description available  
K n | No description available  
L M l | No description available  
N | No description available  
O | No description available  
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T f t | No description available  
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X Y x y | No description available  
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> style stick

Changed 26905 atom styles  

> ui tool show "Unit Cell"

> unitcell #1

> unitcell #1 cells 2,2,2

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/alignment_headers/rmsd.py", line 199, in _atomic_changes_cb  
if chain.structure in changes.modified_structures():  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, 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'  
  
Error processing trigger "changes":  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/alignment_headers/rmsd.py", line 199, in _atomic_changes_cb  
if chain.structure in changes.modified_structures():  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, 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'  
  
Error processing trigger "changes":  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/alignment_headers/rmsd.py", line 199, in _atomic_changes_cb  
if chain.structure in changes.modified_structures():  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, 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'  
  
Error processing trigger "changes":  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, 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 Metal - 71.5.9
OpenGL renderer: Apple M1
OpenGL vendor: AppleHardware:

    Hardware Overview:

      Model Name: Mac mini
      Model Identifier: Macmini9,1
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 4 MB
      Memory: 16 GB

Software:

    System Software Overview:

      System Version: macOS 11.3 (20E232)
      Kernel Version: Darwin 20.4.0
      Time since boot: 3 days 3:55

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        LED Cinema Display:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.4.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.3
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.2
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.2
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.4
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.7
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 1.1.1
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0

Change History (3)

comment:1 by pett, 4 years ago

Cc: Tom Goddard added
Component: Unassigned → UI
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Mayhem after screen removed?

comment:2 by pett, 4 years ago

Resolution: → fixed
Status: accepted → closed

Fixed the first error (dividing by a screen width/height of zero) and committed to develop and 1.2 branches. Pretty sure this is not worth a new 1.2 release.

comment:3 by Tom Goddard, 4 years ago

I put in code a week ago to avoid the "QScreen has been deleted" error in OpenGL initialization to handle an error closing a tool status bar after a screen had been disconnected. I did not put that fix in 1.2, too dangerous a change, and a rare error.

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