id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3436 During undo, self._positions is None chimerax-bug-report@… Eric Pettersen "{{{ 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 }}} " defect closed normal Undo/Redo fixed chimera-programmers all ChimeraX