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Opened 6 years ago
Closed 6 years ago
#3091 closed defect (fixed)
ToolInstance.delete(self) during session reset produces KeyError
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | Conrad Huang, Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Darwin-19.4.0-x86_64-i386-64bit
ChimeraX Version: 0.94 (2020-04-17)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 0.94.dev202004170644 (2020-04-17)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/jessejones/Documents/ChimeraX/Sessions/6NJ8 Review
> Fig3zoom2.cxs" format session
Log from Mon Apr 20 15:01:03 2020UCSF ChimeraX version: 0.94.dev202004170644
(2020-04-17)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/jessejones/Documents/ChimeraX/Sessions/T4 full3.cxs" format
> session
Log from Sat Apr 18 19:20:27 2020UCSF ChimeraX version: 0.94.dev202004170644
(2020-04-17)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/jessejones/Documents/ChimeraX/Sessions/T4 full2.cxs" format
> session
Log from Sat Apr 18 14:35:57 2020UCSF ChimeraX version: 0.94.dev202004170644
(2020-04-17)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Unknown command: fetch 6n68
> open 6n68
Fetching url http://files.rcsb.org/download/6n68.cif failed: HTTP Error 404:
Not Found
> open 6n63
Summary of feedback from opening 6n63 fetched from pdb
---
notes | Fetching compressed mmCIF 6n63 from
http://files.rcsb.org/download/6n63.cif
Fetching CCD GOA from http://ligand-expo.rcsb.org/reports/G/GOA/GOA.cif
Fetching CCD ACT from http://ligand-expo.rcsb.org/reports/A/ACT/ACT.cif
Fetching CCD FE from http://ligand-expo.rcsb.org/reports/F/FE/FE.cif
6n63 title:
Crystal structure of an Iron binding protein [more info...]
Chain information for 6n63 #1
---
Chain | Description
A | encapsulin cargo protein
Non-standard residues in 6n63 #1
---
ACT — acetate ion
FE — Fe (III) ion
GOA — glycolic acid (hydroxyacetic acid; hydroxyethanoic acid)
6n63 mmCIF Assemblies
---
1| author_and_software_defined_assembly
> sym #1 assembly 1
> view
> select #1/A#2/A
4798 atoms, 4704 bonds, 6 pseudobonds, 4 models selected
> select #1/A
2399 atoms, 2352 bonds, 3 pseudobonds, 2 models selected
> select #2/A
2399 atoms, 2352 bonds, 3 pseudobonds, 2 models selected
> hide sel atoms
> show sel atoms
> undo
> undo
> show sel surfaces
> color (#!2 & sel) yellow
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting soft
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> lighting simple
> lighting soft
> lighting full
> lighting shadows false
> select clear
Alignment identifier is 1
Seqview [ID: 1] region 2 chains [1-12] RMSD: 0.000
> hide #!2 surfaces
Seqview [ID: 1] region 2 chains [136-140] RMSD: 0.000
Seqview [ID: 1] region 2 chains [67-71] RMSD: 0.000
Seqview [ID: 1] region 2 chains [136-141] RMSD: 0.000
Seqview [ID: 1] region 2 chains [98-142] RMSD: 0.000
Seqview [ID: 1] region 2 chains [141-146] RMSD: 0.000
Seqview [ID: 1] region 2 chains [141-198] RMSD: 0.000
> show sel & #!2 surfaces
> show sel & #!2 surfaces
> hide sel & #!2 surfaces
> select #1/A#2/A
4798 atoms, 4704 bonds, 6 pseudobonds, 4 models selected
> show sel & #!2 surfaces
> select clear
> zoom 5
> zoom -2
> zoom -100
> zoom -100
> zoom -100
> zoom -100
> zoom -100
> zoom -100
> zoom -100
> zoom -100
> zoom -100
> zoom -100
> zoom -100
> zoom -100
> zoom -100
> zoom -100
> zoom -100
> zoom -100
> zoom -100
> zoom -100
> zoom -100
> zoom -100
> zoom -100
> zoom -1000
> select clear
> lighting simple
> lighting soft
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> save /Users/jessejones/Desktop/image9.png supersample 3
> select #1/A
2399 atoms, 2352 bonds, 3 pseudobonds, 2 models selected
> hide #!2 surfaces
> select #1/A
2399 atoms, 2352 bonds, 3 pseudobonds, 2 models selected
> select #2/A
2399 atoms, 2352 bonds, 3 pseudobonds, 2 models selected
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> show sel & #!2 surfaces
> select clear
> save2 "/Users/jessejones/Documents/ChimeraX/Sessions/6N63 surface.cxs"
> close session
> open 6n63
6n63 title:
Crystal structure of an Iron binding protein [more info...]
Chain information for 6n63 #1
---
Chain | Description
A | encapsulin cargo protein
Non-standard residues in 6n63 #1
---
ACT — acetate ion
FE — Fe (III) ion
GOA — glycolic acid (hydroxyacetic acid; hydroxyethanoic acid)
6n63 mmCIF Assemblies
---
1| author_and_software_defined_assembly
> show surfaces
> color yellow
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> save /Users/jessejones/Desktop/image10.png supersample 3
> open 6nj8
Summary of feedback from opening 6nj8 fetched from pdb
---
note | Fetching compressed mmCIF 6nj8 from
http://files.rcsb.org/download/6nj8.cif
6nj8 title:
Encapsulin iron storage compartment from Quasibacillus thermotolerans [more
info...]
Chain information for 6nj8 #2
---
Chain | Description
A B C D | Encapsulating protein for a DyP-type peroxidase
E F G | targeting peptide
6nj8 mmCIF Assemblies
---
1| complete icosahedral assembly
2| icosahedral asymmetric unit
3| icosahedral pentamer
4| icosahedral 23 hexamer
5| icosahedral asymmetric unit, std point frame
> sym #2 assembly 1
> view
> hide #3 models
> show #3 models
> toolshed show "Side View"
> select #2/A#2/B#2/C#2/D#3/A#3/B#3/C#3/D
17824 atoms, 18208 bonds, 2 models selected
> color (#3 & sel) gray
> hide sel & #3 cartoons
> style sel & #3 ball
Changed 8912 atom styles
> hide sel & #3 cartoons
> hide sel & #3 atoms
> show sel & #3 surfaces
> color (#!3 & sel) lightgray
> color (#!3 & sel) gray
> select #2/E#2/F#2/G#3/E#3/F#3/G
294 atoms, 288 bonds, 2 models selected
> show sel & #!3 surfaces
> color (#!3 & sel) purple
> lighting soft
> lighting full
> lighting shadows false
> select clear
> save2 "/Users/jessejones/Documents/ChimeraX/Sessions/T4 full.cxs"
> select #2/A#2/B#2/C#2/D#3/A#3/B#3/C#3/D
17824 atoms, 18208 bonds, 2 models selected
> hide sel & #!3 surfaces
> select #2/E#2/F#2/G#3/E#3/F#3/G
294 atoms, 288 bonds, 2 models selected
> hide sel & #!3 surfaces
> color (#!3 & sel) purple
> hide sel & #!3 atoms
> show sel & #!3 cartoons
> color (#!3 & sel) purple
> hide sel & #!3 cartoons
> show sel & #!3 surfaces
> style sel & #!3 sphere
Changed 147 atom styles
> hide sel & #!3 surfaces
> show sel & #!3 atoms
> style sel & #!3 ball
Changed 147 atom styles
> show sel & #!3 surfaces
> interfaces sel & #!3 & ~solvent
0 buried areas:
> preset "initial styles" "space-filling (single color)"
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> undo
> transparency #3.5-8,12-14 50
> ui mousemode rightMode "mark surface"
> show sel & #!3 surfaces
> hide (#!3 & sel) target a
> select clear
> select #3/A
2228 atoms, 2276 bonds, 1 model selected
> select #2/A
2228 atoms, 2276 bonds, 1 model selected
> select #2/B
2228 atoms, 2276 bonds, 1 model selected
> select #2
9059 atoms, 9248 bonds, 1 model selected
> ~select #2
Nothing selected
> color #1.1#3.5-14#!1,3 purple
> color #1.1#3.5-14#!1,3 gray
> color #1.1#3.5-14#!1,3 darkgray
> select #3.12
1 model selected
> color #3.12 darkgray
> select #2/E#2/F#2/G#3/E#3/F#3/G
294 atoms, 288 bonds, 2 models selected
> color (#!3 & sel) purple
> select #1/A
2399 atoms, 2352 bonds, 3 pseudobonds, 2 models selected
> color (#!1 & sel) yellow
> hide (#!1 & sel) target a
> show sel surfaces
> select #2/A#2/B#2/C#2/D#3/A#3/B#3/C#3/D
17824 atoms, 18208 bonds, 2 models selected
> hide (#!3 & sel) target a
> show sel & #!3 surfaces
> select #2/E#2/F#2/G#3/E#3/F#3/G
294 atoms, 288 bonds, 2 models selected
> hide sel & #!3 surfaces
> show sel & #!3 atoms
> hide sel & #!3 atoms
> show sel & #!3 surfaces
> select #2/A#2/B#2/C#2/D#3/A#3/B#3/C#3/D
17824 atoms, 18208 bonds, 2 models selected
> hide sel & #!3 surfaces
> show sel & #!3 cartoons
> select clear
> undo
> color (#!3 & sel) gray
> color (#!3 & sel) lightgray
> select clear
> save /Users/jessejones/Desktop/image11.png supersample 3
> save2 "/Users/jessejones/Documents/ChimeraX/Sessions/T4 full2.cxs"
> sym #1 assembly 1
> view
> select #1/A#4/A
4798 atoms, 4704 bonds, 6 pseudobonds, 4 models selected
> hide sel & #!4 atoms
> show sel & #!4 surfaces
> color (#!4 & sel) yellow
> lighting soft
> lighting shadows true intensity 0.5
> select clear
> save2 "/Users/jessejones/Documents/ChimeraX/Sessions/T4 full2.cxs"
opened ChimeraX session
> select #4
2399 atoms, 2352 bonds, 3 pseudobonds, 2 models selected
> hide sel surfaces
> toolshed show "Side View"
> hide #!3 models
> show #!3 models
> lighting shadows false
> select #3/A
2228 atoms, 2276 bonds, 1 model selected
> hide sel cartoons
> select #3/B
2228 atoms, 2276 bonds, 1 model selected
> hide sel cartoons
> select #3/C
2228 atoms, 2276 bonds, 1 model selected
> hide sel cartoons
> save /Users/jessejones/Desktop/image17.png supersample 3
> undo
> undo
> undo
> undo
> select clear
> select #2/E#3/E
98 atoms, 96 bonds, 2 models selected
> select #2/F#3/F
98 atoms, 96 bonds, 2 models selected
> select #3.5
1 model selected
> select #3
9059 atoms, 9248 bonds, 4 models selected
> ~select #3
7 models selected
> select #3.5
1 model selected
> ~select #3.5
Nothing selected
> select #3.9
49 atoms, 1 model selected
> select #3.10
49 atoms, 1 model selected
> select #3.9
49 atoms, 1 model selected
> surface style (#!3 & sel) mesh
> hide sel surfaces
> show sel surfaces
> transparency (#!3 & sel) 50
> surface style (#!3 & sel) mesh
> transparency (#!3 & sel) 70
> undo
> undo
> transparency (#!3 & sel) 0
> select #3.10
49 atoms, 1 model selected
> transparency (#!3 & sel) 70
> show sel atoms
> style sel ball
Changed 49 atom styles
> color (#!3 & sel) byhetero
> select clear
> surface style #3-4 dot
> surface style #3-4 mesh
> transparency #3-4 30
> transparency #3-4 70
> transparency #3-4 80
> transparency #3-4 90
> surface style #3-4 solid
> save /Users/jessejones/Desktop/image18.png supersample 3
> save2 "/Users/jessejones/Documents/ChimeraX/Sessions/T4 full3.cxs"
opened ChimeraX session
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
> toolshed show "Side View"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode rotate
> ui mousemode rightMode select
> save2 "/Users/jessejones/Documents/ChimeraX/Sessions/6NJ8 Review
> Fig3zoom2.cxs"
> select clear
> select #1/A#2/A#3/A#4/A
9254 atoms, 9256 bonds, 6 pseudobonds, 6 models selected
> show sel & #!3-4 cartoons
> select clear
> save2 "/Users/jessejones/Documents/ChimeraX/Sessions/6NJ8 Review
> Fig3zoom2.cxs"
opened ChimeraX session
> close session
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 876, in <lambda>
close_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_close_cb(sess))
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 606, in file_close_cb
run(session, 'close session')
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 2848, 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/std_commands/close.py", line 60, in close_session
session.reset()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 471, 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/seqalign/manager.py", line 259, in reset_state
alignment._destroy()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 501, in _destroy
self._notify_observers("destroyed", None)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 541, in _notify_observers
recipient.alignment_notification(note_name, note_data)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 459, in alignment_notification
self.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 496, in delete
ToolInstance.delete(self)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/tools.py", line 176, in delete
self.session.tools.remove([self])
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/tools.py", line 360, in remove
del self._tool_instances[tid]
KeyError: 10
KeyError: 10
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/tools.py", line 360, in remove
del self._tool_instances[tid]
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-14.5.22
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.
Change History (3)
comment:1 by , 6 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ToolInstance.delete(self) during session reset produces KeyError |
comment:2 by , 6 years ago
| Cc: | added |
|---|
comment:3 by , 6 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Believe this is fixed the #2110 fix -- removed maintaining a numerical id for tools.
Note:
See TracTickets
for help on using tickets.
This might be #2110 in a different guise.
Can we get rid of tool_instance.id? Maintaining its properties (uniqueness and referability) is a pain in when restoring sessions. Blastprotein is the only thing that needs it.
Conrad?