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Opened 5 years ago
Closed 5 years ago
#3436 closed defect (fixed)
During undo, self._positions is None
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Undo/Redo | Version: | |
| Keywords: | Cc: | chimera-programmers | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Darwin-19.5.0-x86_64-i386-64bit
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/Bruce/Desktop/Radiation Inactivation/6m1d.pdb" format pdb
6m1d.pdb title:
ACE2-B0AT1 complex, open conformation [more info...]
Chain information for 6m1d.pdb #1
---
Chain | Description
A C | sodium-dependent neutral amino acid transporter B(0)AT1
B D | angiotensin-converting enzyme 2
> select /A:5-609
4799 atoms, 4942 bonds, 1 model selected
> select /A:5-609
4799 atoms, 4942 bonds, 1 model selected
> select /C:5-609
4799 atoms, 4942 bonds, 1 model selected
> select /B:21-768
6089 atoms, 6255 bonds, 1 model selected
> select /D:21-768
6089 atoms, 6255 bonds, 1 model selected
> select /A:5-609
4799 atoms, 4942 bonds, 1 model selected
> ui tool show Distances
Exactly two atoms must be selected!
> ui tool show Distances
> view clip false
> show target m
Exactly two atoms must be selected!
> ui tool show Distances
> ui tool show Distances
Exactly two atoms must be selected!
> ui tool show Distances
Exactly two atoms must be selected!
> toolshed show
Exactly two atoms must be selected!
> select
21776 atoms, 22394 bonds, 1 model selected
> select clear
Exactly two atoms must be selected!
> color sel bychain
> interfaces sel & ~solvent
0 buried areas:
Exactly two atoms must be selected!
> set bgColor white
> save /Users/Bruce/Desktop/image1.png supersample 3
> lighting simple
> lighting full
> lighting simple
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> ui tool show "Color Actions"
> color sel bychain
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> lighting simple
> lighting full
> lighting simple
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> view sel
Exactly two atoms must be selected!
> undo
> select disulfide
20 atoms, 10 bonds, 1 model selected
> show (sel-residues & sidechain) target ab
> color sel bychain
> color sel bypolymer
> color sel bychain
> color sel bypolymer
> preset "molecular surfaces" "chain id coloring (opaque)"
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color bychain targ s trans 0
> undo
> undo
> undo
> transparency (#!1 & sel) 50
> close
> open "/Users/Bruce/Desktop/Radiation Inactivation/6m1d.pdb" format pdb
6m1d.pdb title:
ACE2-B0AT1 complex, open conformation [more info...]
Chain information for 6m1d.pdb #1
---
Chain | Description
A C | sodium-dependent neutral amino acid transporter B(0)AT1
B D | angiotensin-converting enzyme 2
> preset "molecular surfaces" "chain id coloring (opaque)"
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color bychain targ s trans 0
> undo
> preset cartoons/nucleotides ribbons/slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> preset cartoons/nucleotides licorice/ovals
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> preset "initial styles" cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" "original look"
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset cartoons/nucleotides licorice/ovals
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> preset "initial styles" "original look"
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset cartoons/nucleotides ribbons/slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> color bychain
> preset "initial styles" cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "molecular surfaces" "chain id coloring (opaque)"
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color bychain targ s trans 0
> preset "molecular surfaces" "atomic coloring (transparent)"
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> preset "initial styles" "original look"
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> preset cartoons/nucleotides ribbons/slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> preset "overall look" interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
> undo
> set bgColor white
> color bychain
> preset cartoons/nucleotides ribbons/slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> view
> ui tool show "Color Actions"
> color bychain
> color bychain
> color bychain
> select disulfide
20 atoms, 10 bonds, 1 model selected
> show (#!1 & sel-residues & sidechain) target ab
> color sel bypolymer
> color sel bypolymer
> color sel bychain
> color sel byhetero
> rainbow sel
> color bfactor sel
20 atoms, 20 residues, 4 surfaces, atom bfactor range 184 to 1e+03
> color sel bychain
> color sel bychain
> undo
> undo
> undo
> color sel bychain
> mlp sel
Map values for surface "6m1d.pdb_A SES surface": minimum -27.09, mean -0.0378,
maximum 23.04
Map values for surface "6m1d.pdb_B SES surface": minimum -30.06, mean -2.94,
maximum 24.14
Map values for surface "6m1d.pdb_C SES surface": minimum -27.23, mean
-0.04426, maximum 24.26
Map values for surface "6m1d.pdb_D SES surface": minimum -29.82, mean -2.909,
maximum 24.47
> hbonds sel
0 hydrogen bonds found
> style sel sphere
Changed 20 atom styles
> style sel stick
Changed 20 atom styles
> ui mousemode right "link markers"
> preset "initial styles" "original look"
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> show sel atoms
> color sel bychain
> style sel stick
Changed 20 atom styles
> open /Users/Bruce/Downloads/3PH.cif
> preset cartoons/nucleotides ribbons/slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> preset cartoons/nucleotides ribbons/slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> color sel bychain
> select disulfide
20 atoms, 10 bonds, 1 model selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> ui tool show "Color Actions"
> color bychain
> hide #1.5#!1 target a
> hide #1.5#!1 target a
> color bychain
> color bychain
> color orange
> color bychain
> color lime
> color bychain
> color bypolymer
> color bychain
> hide surfaces
> hide surfaces
> hide atoms
> show atoms
> show atoms
> hide atoms
> show atoms
> show cartoons
> hide cartoons
> show cartoons
> show surfaces
> hide surfaces
> show atoms
> hide atoms
> show atoms
> hide atoms
> hide atoms
> show atoms
> hide atoms
> hide atoms
> show atoms
> show cartoons
> hide cartoons
> hide cartoons
> show cartoons
> style stick
Changed 21756 atom styles
> style ball
Changed 21756 atom styles
> style sphere
Changed 21756 atom styles
> style ball
Changed 21756 atom styles
> nucleotides tube/slab shape box
> nucleotides tube/slab shape box
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> nucleotides tube/slab shape box
> nucleotides ladder
> hide atoms
> nucleotides ladder
> nucleotides ladder
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> show atoms
> hide cartoons
> show cartoons
> hide atoms
> show atoms
> hide atoms
> color bychain
> color bychain
> color bypolymer
> color bychain
> hide #1.5 models
> show #1.5 models
> hide #1.1 models
> show #1.1 models
> select #1.1
4795 atoms, 1 model selected
> ~select #1.1
1 model selected
> select #1.1
4795 atoms, 1 model selected
> ~select #1.1
1 model selected
> select #1.1
4795 atoms, 1 model selected
> ~select #1.1
1 model selected
> hide #1.1 models
> show #1.1 models
> color bychain
> hide #1.1 models
> show #1.1 models
> show target m
> show target m
> show target m
> show target m
> show target m
> show target m
> show target m
> show target m
> view clip false
> view clip false
> view clip false
> view clip false
> show target m
> cartoon
> show target m
> show target m
> show target m
> show target m
> show target m
> view clip false
> view clip false
> view clip false
> view clip false
> view clip false
> view clip false
> view clip false
> select #1.1
4795 atoms, 1 model selected
> select #1.2
6083 atoms, 1 model selected
> select #1.3
4795 atoms, 1 model selected
> select #1.4
6083 atoms, 1 model selected
> select #1.3
4795 atoms, 1 model selected
> select #1.2
6083 atoms, 1 model selected
> select #1.1
4795 atoms, 1 model selected
> select #1.2
6083 atoms, 1 model selected
> view #1.2 clip false
No displayed objects specified.
> show #1.2 target m
> ~select #1.2
1 model selected
> ~select #1.5
Nothing selected
> select #1.1
4795 atoms, 1 model selected
> color (#!1 & sel) orange
> ~select #1.1
1 model selected
> select #1.1
4795 atoms, 1 model selected
> ~select #1.1
1 model selected
> select #1.1
4795 atoms, 1 model selected
> color (#!1 & sel) purple
> ~select #1.1
1 model selected
> select /B
6083 atoms, 6246 bonds, 1 model selected
> color (#!1 & sel) medium blue
> select /A
4795 atoms, 4936 bonds, 1 model selected
> color (#!1 & sel) orange
> select /B
6083 atoms, 6246 bonds, 1 model selected
> color (#!1 & sel) cornflower blue
> select /D
6083 atoms, 6246 bonds, 1 model selected
> color (#!1 & sel) lime
> select /C
4795 atoms, 4936 bonds, 1 model selected
> color (#!1 & sel) purple
> ~select #1.3
4936 bonds, 2 models selected
> select /A
4795 atoms, 4936 bonds, 1 model selected
> color (#!1 & sel) orange red
> ~select #1.1
4936 bonds, 2 models selected
> select clear
> ui tool show "Side View"
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting simple
> lighting soft
> lighting soft
> lighting full
> lighting simple
> lighting full
> lighting simple
> lighting full
> lighting simple
> lighting simple
> lighting full
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting full
> lighting simple
> lighting full
> lighting simple
> lighting soft
> lighting simple
> save /Users/Bruce/Downloads/ACE2_B0AT1_tetramer.cxs
> select protein
21756 atoms, 22364 bonds, 1 model selected
> cartoon (#!1 & sel)
> select clear
> show sidechain target ab
> undo
> ui tool show "Side View"
> select sidechain
13638 atoms, 11412 bonds, 1 model selected
> select clear
> select sideonly
10932 atoms, 8872 bonds, 1 model selected
> undo
> select sidechain
13638 atoms, 11412 bonds, 1 model selected
> select clear
> show target ab
> hide target a
> hide #* target a
> show target ab
> style ball
Changed 21756 atom styles
> style ringFill thin
Changed 2706 residue ring styles
> undo
> undo
> undo
> select clear
> select up
Nothing selected
> view
> undo
Alignment identifier is 1
Alignment identifier is 2
Exactly two atoms must be selected!
> ui tool show Distances
> select sidechain
13638 atoms, 11412 bonds, 1 model selected
> show (#!1 & sel-residues & sidechain) target ab
> undo
> hide (#!1 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!1 & sel-residues)
> show (#!1 & sel-residues & backbone) target ab
> undo
> undo
> select clear
> interfaces ~solvent
3 buried areas: B A 1042, D C 864, B D 738
> undo
> redo
> undo
> undo
> undo
> select clear
> help help:user/tools/distances.html
> ui tool show Distances
> preset "molecular surfaces" "atomic coloring (transparent)"
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> undo
> undo
> redo
> redo
> select clear
> preset cartoons/nucleotides ribbons/slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> view
> undo
> color byhetero
Exactly two atoms must be selected!
> select clear
> help help:user/menu.html#named-selections
> show target ab
> undo
> select /B
6083 atoms, 6246 bonds, 1 model selected
> undo
> hbonds
1844 hydrogen bonds found
> hbonds
1844 hydrogen bonds found
> hbonds
1844 hydrogen bonds found
> ~hbonds
> ~hbonds
> ~hbonds
> hbonds
1844 hydrogen bonds found
> hbonds
1844 hydrogen bonds found
> ~hbonds
> hbonds
1844 hydrogen bonds found
> select clear
> undo
> undo
> hide target a
> undo
> undo
> undo
> undo
> select clear
> undo
> undo
> undo
> undo
> undo
> undo
> select clear
> ~hbonds
> ui tool show "Show Sequence Viewer"
> sequence chain /A /C
Alignment identifier is 1
> ui mousemode right distance
> ui mousemode right "tape measure"
> marker segment #2 position 158,142.2,248.7 toPosition 166.2,167.9,247.1
> color yellow radius 0.1 label 27.05 labelHeight 2.705 labelColor yellow
> marker delete #2
> marker segment #2 position 157.8,148.1,230.2 toPosition 163.1,165.2,229.4
> color yellow radius 0.1 label 17.85 labelHeight 1.785 labelColor yellow
> select #2
2 atoms, 1 bond, 2 models selected
> ~select #2
Nothing selected
> ui mousemode right label
> label delete residues
> label delete residues
> label #1/B:57
> label #1/B:57
> label delete residues
> label height 5
> label height 4
> label height 5
> label height 5
> label delete residues
> label delete residues
> label #1/D:339
> label delete residues
> label #1/D:339
> ui mousemode right distance
> hide #1.5 models
> hide #!2 models
> show #!2 models
> ui mousemode right "move label"
> ui mousemode right "tape measure"
> marker delete #2
> marker segment #2 position 148.3,175.9,245.1 toPosition 138,150.1,243.3
> color yellow radius 0.1 label 27.79 labelHeight 2.779 labelColor yellow
> marker delete #2
> marker segment #2 position 144.2,144.9,249.2 toPosition 157.5,170,250.9
> color yellow radius 0.1 label 28.54 labelHeight 2.854 labelColor yellow
> marker delete #2
> marker segment #2 position 164.8,169.9,249.2 toPosition 159.2,147.5,259
> color yellow radius 0.1 label 25.02 labelHeight 2.502 labelColor yellow
> marker segment #2 position 164.8,169.9,249.2 toPosition 157.8,141.6,250.3
> color yellow radius 0.1 label 29.1 labelHeight 2.91 labelColor yellow
> marker delete #2
> marker segment #2 position 166.9,168,246.6 toPosition 160.3,141.8,247.3
> color yellow radius 0.1 label 26.99 labelHeight 2.699 labelColor yellow
> marker delete #2
> marker segment #2 position 166.9,168,246.6 toPosition 152.3,142.8,248.9
> color yellow radius 0.1 label 29.21 labelHeight 2.921 labelColor yellow
> ui mousemode right "tape measure"
> marker segment #2 position 153.8,164.3,183.5 toPosition 157.8,152.4,185.7
> color yellow radius 0.1 label 12.77 labelHeight 1.277 labelColor yellow
> marker delete #2
> marker segment #2 position 166.2,152.5,184.3 toPosition 157.8,152.4,185.7
> color yellow radius 0.1 label 8.603 labelHeight 0.8603 labelColor yellow
> ui mousemode right "move label"
> ui mousemode right "move label"
> ui mousemode right "tape measure"
> marker delete #2
> marker segment #2 position 157.1,161.1,186.5 toPosition 152.9,156.3,186.1
> color yellow radius 0.1 label 6.425 labelHeight 0.6425 labelColor yellow
> ui mousemode right "move label"
> label height 5
> label height 2
> undo
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/undo.py", line 185, in undo
inst.undo()
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/undo.py", line 388, in undo
self._update_owner(owner, attribute, old_value, option)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/undo.py", line 417, in _update_owner
setattr(owner, attribute, value)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 243, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 309, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 337, in set_display
dp = self.display_positions
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 350, in get_display_positions
dp = ones((len(self._positions),), bool)
TypeError: object of type 'NoneType' has no len()
undo failed: object of type 'NoneType' has no len():
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 350, in get_display_positions
dp = ones((len(self._positions),), bool)
See log for complete Python traceback.
> ui mousemode right "tape measure"
> marker delete #2
> marker segment #2 position 156.9,160.8,175.1 toPosition 153.8,157.2,175.1
> color yellow radius 0.1 label 4.806 labelHeight 0.4806 labelColor yellow
> marker delete #2
> marker segment #2 position 156.9,160.8,175.1 toPosition 154.1,156.8,175.7
> color yellow radius 0.1 label 4.981 labelHeight 0.4981 labelColor yellow
> ui mousemode right "move label"
> label height 2
> ui mousemode right "tape measure"
> marker delete #2
> ui mousemode right "tape measure"
> marker segment #2 position 157.1,161.1,186.5 toPosition 153.3,156.1,186.2
> color yellow radius 0.1 label 6.311 labelHeight 0.6311 labelColor yellow
> label height 2
> ui mousemode right "move label"
> ui mousemode right "tape measure"
> marker delete #2
> marker segment #2 position 176.8,170.2,130.5 toPosition 175,172.9,149.4
> color yellow radius 0.1 label 19.23 labelHeight 1.923 labelColor yellow
> marker delete #2
> marker segment #2 position 137.8,157.8,135.5 toPosition 136.4,160.6,147.6
> color yellow radius 0.1 label 12.52 labelHeight 1.252 labelColor yellow
> marker delete #2
> ui mousemode right distance
> ui mousemode right distance
> ui mousemode right select
> select /C:159
9 atoms, 8 bonds, 1 model selected
> select /D:628
8 atoms, 7 bonds, 1 model selected
> select /C:158
8 atoms, 7 bonds, 1 model selected
> select /C:158
8 atoms, 7 bonds, 1 model selected
Drag select of 46 residues
Drag select of 6 residues
Drag select of 8 residues
Drag select of 8 residues
> select clear
> ui mousemode right "next docked"
> ui mousemode right "next docked"
> ui mousemode right "next docked"
> ui mousemode right zone
> ui mousemode right zone
> ui mousemode right zone
> ui mousemode right select
Drag select of 823 residues
> select clear
> select clear
> ui mousemode right select
Drag select of 1021 residues
> ui mousemode right zone
> zone /D:649
> zone label false
> zone /D:649 residueDistance 3.82 labelDistance 3.06 surfaceDistance 6.12
> zone /D:649 residueDistance 2.8 labelDistance 2.24 surfaceDistance 4.48
> zone /D:649 residueDistance 1.2 labelDistance 0.963 surfaceDistance 1.93
> zone label false
> zone /D:649 residueDistance 0.921 labelDistance 0.737 surfaceDistance 1.47
> zone /D:649 residueDistance 0.708 labelDistance 0.567 surfaceDistance 1.13
> zone /B:658
> zone label false
> zone /B:658 residueDistance 0.544 labelDistance 0.435 surfaceDistance 0.871
> zone /B:658 residueDistance 0.418 labelDistance 0.335 surfaceDistance 0.669
> zone /B:658 residueDistance 0.308 labelDistance 0.247 surfaceDistance 0.493
> zone /D:642
> zone /D:649
> zone /B:646
> zone label false
> zone /D:645
> zone label false
> zone /D:645 residueDistance 0.235 labelDistance 0.188 surfaceDistance 0.376
> zone /D:645 residueDistance 0.151 labelDistance 0.121 surfaceDistance 0.241
> zone /D:645 residueDistance 0.116 labelDistance 0.0928 surfaceDistance 0.186
> ui mousemode right zone
> ui mousemode right clip
> ui mousemode right clip
> ui mousemode right clip
> ui mousemode right clip
> ui mousemode right clip
> ui mousemode right zone
> zone /D:653
> ui mousemode right clip
> ui mousemode right zone
> zone label false
> ui mousemode right label
> label #1/B:646
> label delete residues
> label #1/D:642
> label #1/D:653
> label delete residues
> label #1/D:653
> label #1/B:653
> label #1/D:653
> ui mousemode right zone
> zone /D:653
> zone /D:656
> zone /D:642
> zone /D:645
> zone /D:646
> zone /D:649
> ui mousemode right zone
> ui mousemode right zone
> select clear
> select
21756 atoms, 22364 bonds, 2 models selected
> select clear
> zone label false
> zone clear
Alignment identifier is 1
Alignment identifier is 2
> interfaces ~solvent
3 buried areas: B A 1042, D C 864, B D 738
> undo
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/undo.py", line 185, in undo
inst.undo()
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/undo.py", line 388, in undo
self._update_owner(owner, attribute, old_value, option)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/undo.py", line 419, in _update_owner
getattr(owner, attribute)(value)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 200, in set_selected
Drawing.set_highlighted(self, sel)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 392, in set_highlighted
self._highlighted_positions = ones(len(self.positions), bool)
TypeError: object of type 'NoneType' has no len()
undo failed: object of type 'NoneType' has no len():
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 392, in set_highlighted
self._highlighted_positions = ones(len(self.positions), bool)
See log for complete Python traceback.
> undo
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/undo.py", line 185, in undo
inst.undo()
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/undo.py", line 388, in undo
self._update_owner(owner, attribute, old_value, option)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/undo.py", line 417, in _update_owner
setattr(owner, attribute, value)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 243, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 202, in set_selected
self._selection_changed()
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 206, in _selection_changed
self.session.ui.thread_safe(self.session.triggers.activate_trigger,
AttributeError: 'NoneType' object has no attribute 'ui'
undo failed: 'NoneType' object has no attribute 'ui':
AttributeError: 'NoneType' object has no attribute 'ui'
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 206, in _selection_changed
self.session.ui.thread_safe(self.session.triggers.activate_trigger,
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-14.6.18
OpenGL renderer: Intel Iris OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: Mac mini
Model Identifier: Macmini7,1
Processor Name: Dual-Core Intel Core i5
Processor Speed: 2.6 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 3 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
Boot ROM Version: 248.0.0.0.0
SMC Version (system): 2.24f32
Software:
System Software Overview:
System Version: macOS 10.15.5 (19F101)
Kernel Version: Darwin 19.5.0
Time since boot: 7 days 14:59
Graphics/Displays:
Intel Iris:
Chipset Model: Intel Iris
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x0a2e
Revision ID: 0x0009
Metal: Supported, feature set macOS GPUFamily1 v4
Displays:
DELL U3014:
Resolution: 2560 x 1600
UI Looks like: 2560 x 1600 @ 60 Hz
Framebuffer Depth: 24-Bit Color (ARGB8888)
Display Serial Number: J3Y9N63G634L
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8
Attachments (1)
Change History (9)
comment:1 by , 5 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Undo/Redo |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → During undo, self._positions is None |
comment:2 by , 5 years ago
comment:3 by , 5 years ago
| Cc: | added; removed |
|---|
The user hid a model, closed the model, then tried to undo the hide, producing a confusing traceback.
Where in the code should we catch undo operations on closed models? I am soliciting opinions from Conrad, Eric and Greg. Maybe some code already does this.
In this case in std_commands/src/show.py the undo state is saved using
undo_state.add(m, "display", m.display, True)
That is very simple but leaves it to the undo code to reset the value of the m.display attribute which leads to an error when the model is closed. There are quite a lot of attributes of Model handled with undo this way. We could have the undo go specifically look for Model and check Model.deleted. Or the undo code could just look at whatever object it is about to set an attribute and if it has a "deleted" property that is True then don't set the attribute. Or the hardest to implement because it effects code in many places is change how the undo state for model changes is saved and put checking code in the code that is registering the undo operation.
comment:4 by , 5 years ago
It could be an optional keyword argument to undo_state.add() that defaults to looking for and checking a 'deleted' property of the object.
comment:5 by , 5 years ago
I've attached a version of undo.py that has the code I suggested in it. It does fix the problem. The _consistency_check() routine that was already in the code will catch this problem for Collections (since they change size as things get deleted), so the deleted check I put in for the 'S' (series) mode may not be necessary in all cases. The undo code could definitely be made more efficient for Collections, but since Collections are defined outside the core that is a bit of a sticky wicket.
Didn't document the deleted_check argument.
comment:6 by , 5 years ago
How about you take this ticket and make your undo changes? They sound reasonable to me.
follow-up: 6 comment:7 by , 5 years ago
| Owner: | changed from to |
|---|
comment:8 by , 5 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
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Hiding a model, then closing it, then trying to undo the hide produces this error. Need to protect against undo actions on closed models.