ValueError after closing one session and opening another

[asiegel@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 0.93 (2020-03-24)
Description
Whenever I close a saved session file (.cxs) but leave ChimeraX open, I get these assorted ValueError messages when trying to open a new session (.cxs file). Oddly, if I shut ChimeraX down and reopen it and then try to open those exact same session files, everything works smoothly without errors.

Log:
UCSF ChimeraX version: 0.93 (2020-03-24)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "C:/Users/Alex/Google Drive/Shan
> Lab/HADDOCK/Best_3BodyDocking/SBDL18_CD254M_CD3_PRE.cxs"

Log from Thu Dec 17 13:24:32 2020UCSF ChimeraX version: 0.93 (2020-03-24)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open C:\ProgramData\ChimeraX\cpSRP43_PRE_colored.cxs format session

Log from Sat Dec 12 22:38:48 2020UCSF ChimeraX version: 0.93 (2020-03-24)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open C:\ProgramData\ChimeraX\cpSRP43_NMR.cxs format session

Log from Sat Dec 12 13:41:49 2020UCSF ChimeraX version: 0.93 (2020-03-24)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "C:\Users\Alex\Google Drive\Shan Lab\cpSRP43
> structures\cpSRP43_PRE.cxs" format session

Log from Sun Nov 15 22:59:07 2020UCSF ChimeraX version: 0.93 (2020-03-24)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open C:\Users\Alex\Desktop\cpSRP43-CD2-BTFMA.cxs format session

Log from Fri Sep 18 14:58:13 2020UCSF ChimeraX version: 0.93 (2020-03-24)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open C:\Users\Alex\Desktop\cpSRP43-CD2-BTFMA.cxs format session

Log from Sun Aug 30 16:37:13 2020UCSF ChimeraX version: 0.93 (2020-03-24)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "C:\Users\Alex\Google Drive\Shan Lab\cpSRP43 structures\200812 cpSRP43
> FL CD2 labels.cxs" format session

Log from Wed Aug 12 13:28:02 2020UCSF ChimeraX version: 0.93 (2020-03-24)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43 structures/200812 cpSRP43
> FL CD2 labels.cxs"

Log from Wed Aug 12 11:30:26 2020UCSF ChimeraX version: 0.93 (2020-03-24)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\Users\Alex\Desktop\Zoom call.cxs" format session

File not found: C:\Users\Alex\Desktop\Zoom call.cxs  

> open "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43
> structures/cpSRP43_composite.pdb"

Summary of feedback from opening C:/Users/Alex/Google Drive/Shan Lab/cpSRP43
structures/cpSRP43_composite.pdb  
---  
warning | Ignored bad PDB record found on line 2610  
END  
  
Chain information for cpSRP43_composite.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
F | No description available  
G | No description available  
  

> open "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43
> structures/cpSRP43_BTFA.py"

ChimeraX cannot open a regular Chimera session.  
An exporter from Chimera to ChimeraX is being worked on but is not ready at
this time.  

> open "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43
> structures/cpSRP43_alone.pdb"

Summary of feedback from opening C:/Users/Alex/Google Drive/Shan Lab/cpSRP43
structures/cpSRP43_alone.pdb  
---  
warnings | Ignored bad PDB record found on line 2938  
END  
  
Start residue of secondary structure not found: HELIX 1 1 SER A 117 TYR A 119
1 3  
Start residue of secondary structure not found: HELIX 2 2 ALA A 122 LYS A 138
1 17  
Start residue of secondary structure not found: HELIX 3 3 GLU A 141 GLN A 146
1 6  
Start residue of secondary structure not found: HELIX 4 4 ALA A 163 LEU A 170
1 8  
Start residue of secondary structure not found: HELIX 5 5 ASP A 173 GLU A 181
1 9  
47 messages similar to the above omitted  
  
cpSRP43_alone.pdb title:  
Crystal structure of the CPSRP54 tail bound to CPSRP43 [more info...]  
  
Chain information for cpSRP43_alone.pdb  
---  
Chain | Description  
2.1/A | signal recognition particle 43 kda protein, chloroplastic  
2.4/B | signal recognition particle 54 kda protein, chloroplastic  
2.5/B | signal recognition particle 54 kda protein, chloroplastic  
2.2/C | No description available  
2.3/E | No description available  
  

> close session

> open "C:\Users\Alex\Google Drive\Shan Lab\cpSRP43
> structures\cpSRP43_alone.pdb"

Summary of feedback from opening C:\Users\Alex\Google Drive\Shan Lab\cpSRP43
structures\cpSRP43_alone.pdb  
---  
warnings | Ignored bad PDB record found on line 2938  
END  
  
Start residue of secondary structure not found: HELIX 1 1 SER A 117 TYR A 119
1 3  
Start residue of secondary structure not found: HELIX 2 2 ALA A 122 LYS A 138
1 17  
Start residue of secondary structure not found: HELIX 3 3 GLU A 141 GLN A 146
1 6  
Start residue of secondary structure not found: HELIX 4 4 ALA A 163 LEU A 170
1 8  
Start residue of secondary structure not found: HELIX 5 5 ASP A 173 GLU A 181
1 9  
47 messages similar to the above omitted  
  
cpSRP43_alone.pdb title:  
Crystal structure of the CPSRP54 tail bound to CPSRP43 [more info...]  
  
Chain information for cpSRP43_alone.pdb  
---  
Chain | Description  
1.1/A | signal recognition particle 43 kda protein, chloroplastic  
1.4/B | signal recognition particle 54 kda protein, chloroplastic  
1.5/B | signal recognition particle 54 kda protein, chloroplastic  
1.2/C | No description available  
1.3/E | No description available  
  

> set bgColor white

> save session "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43 structures/200812
> cpSRP43 FL.cxs"

> select clear

> close session

> open "C:\Users\Alex\Desktop\Zoom call.cxs" format session

File not found: C:\Users\Alex\Desktop\Zoom call.cxs  

> open "C:\Users\Alex\Google Drive\Shan Lab\cpSRP43
> structures\cpSRP43_NMRnum.pdb"

Summary of feedback from opening C:\Users\Alex\Google Drive\Shan Lab\cpSRP43
structures\cpSRP43_NMRnum.pdb  
---  
warning | Ignored bad PDB record found on line 2498  
END  
  
Chain information for cpSRP43_NMRnum.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
Alignment identifier is 1.A  
Alignment identifier is 1.B  
Alignment identifier is 1.C  
Alignment identifier is 1.D  

> select clear

> color lightgray

> select clear

> select clear

> select clear

> select clear

> show sel cartoons

> hide sel atoms

> color sel green

> show sel cartoons

> hide sel atoms

> color sel purple

> color sel red

> select clear

> save session "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43 structures/200812
> cpSRP43 FL.cxs"

> select clear

> select /A:267

9 atoms, 8 bonds, 1 model selected  

> select up

67 atoms, 67 bonds, 1 model selected  

> select up

2227 atoms, 2266 bonds, 1 model selected  

> hide sel atoms

> save session "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43 structures/200812
> cpSRP43 FL.cxs"

> select clear

> select clear

> show sel atoms

> color sel black

> style sel ball

Changed 64 atom styles  

> style sel sphere

Changed 64 atom styles  

> style sel sphere

Changed 70 atom styles  

> show sel atoms

> color sel black

> hbonds sel

9 hydrogen bonds found  

> hbonds sel

9 hydrogen bonds found  

> select clear

> toolshed show H-Bonds

> hbonds

249 hydrogen bonds found  

> style sel stick

Changed 70 atom styles  

> save session "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43 structures/200812
> cpSRP43 FL CD2 labels.cxs"

> style sel stick

Changed 8 atom styles  

> color sel black

> show sel atoms

Unknown command: :145  

> select :145

11 atoms, 10 bonds, 1 model selected  

> select :145,146

19 atoms, 18 bonds, 1 model selected  

Expected an objects specifier or a keyword  

> select :145,146

19 atoms, 18 bonds, 1 model selected  

> select :209,216,230,234,239,246,253,257,267

78 atoms, 69 bonds, 2 pseudobonds, 2 models selected  

> nucleotides sel tube/slab shape box

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel ladder

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel tube/slab shape box

> nucleotides sel tube/slab shape box

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> select clear

> toolshed show "Blast Protein"

> blastprotein /A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name
> bp1

Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr
or pdb for sequences similar to the given protein sequence  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service  
Opal job id: appBlastProtein2Service1597256347514386636114  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1597256347514386636114  
stdout.txt = standard output  
stderr.txt = standard error  
BlastProtein finished.  

> style stick

Changed 2494 atom styles  

> color bynucleotide

> graphics silhouettes true

> toolshed show "Side View"

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> lighting shadows false

> graphics silhouettes true

> lighting flat

> lighting flat

> lighting full

> lighting soft

> lighting simple

> lighting full

> lighting simple

> ui mousemode rightMode "mark maximum"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode select

> ui mousemode rightMode select

Drag select of 2 residues, 1 pseudobonds  
Drag select of 10 residues  

> select clear

> ui mousemode rightMode pivot

> ui mousemode rightMode pivot

> ui mousemode rightMode "translate selected atoms"

> ui mousemode rightMode "translate selected atoms"

> ui mousemode rightMode translate

> ui mousemode rightMode rotate

> ui mousemode rightMode select

> select clear

> select /A:44

9 atoms, 8 bonds, 1 model selected  

> select /A:43

8 atoms, 7 bonds, 1 model selected  

> select /A:61

9 atoms, 8 bonds, 1 model selected  

> save session "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43 structures/200812
> cpSRP43 FL CD2 labels.cxs"

> toolshed show Toolbar

> toolshed show "Basic Actions"

> hide /A target abp

> hide /A target abp

> show /A target abp

> hide /A target abp

> select :209,216,230,234,239,246,253,257,267

78 atoms, 69 bonds, 2 pseudobonds, 2 models selected  

> show sel atoms

> style sel stick

Changed 78 atom styles  

> style sel stick

Changed 78 atom styles  

> hide sel atoms

> style sel stick

Changed 78 atom styles  

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> style sel ball

Changed 78 atom styles  

> style sel sphere

Changed 78 atom styles  

> style sel stick

Changed 78 atom styles  

> show /A target abp

> hide sel atoms

> show sel atoms

> select clear

> hide atoms

> select :209,216,230,234,239,246,253,257,267

78 atoms, 69 bonds, 2 pseudobonds, 2 models selected  

> show sel atoms

> select clear

> save session "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43 structures/200812
> cpSRP43 FL CD2 labels.cxs"

opened ChimeraX session  

> color list

No custom colors.  
248 builtin colors: alice blue

, aliceblue

, antique white

, antiquewhite

, aqua

, aquamarine

, azure

, beige

, bisque

, black

, blanched almond

, blanchedalmond

, blue

, blue violet

, blueviolet

, brown

, burly wood

, burlywood

, cadet blue

, cadetblue

, chartreuse

, chocolate

, coral

, cornflower blue

, cornflowerblue

, cornsilk

, crimson

, cyan

, dark blue

, dark cyan

, dark goldenrod

, dark gray

, dark green

, dark grey

, dark khaki

, dark magenta

, dark olive green

, dark orange

, dark orchid

, dark red

, dark salmon

, dark sea green

, dark seagreen

, dark slate blue

, dark slate gray

, dark slate grey

, dark turquoise

, dark violet

, darkblue

, darkcyan

, darkgoldenrod

, darkgray

, darkgreen

, darkgrey

, darkkhaki

, darkmagenta

, darkolivegreen

, darkorange

, darkorchid

, darkred

, darksalmon

, darkseagreen

, darkslateblue

, darkslategray

, darkslategrey

, darkturquoise

, darkviolet

, deep pink

, deep sky blue

, deep skyblue

, deeppink

, deepskyblue

, dim gray

, dim grey

, dimgray

, dimgrey

, dodger blue

, dodgerblue

, fire brick

, firebrick

, floral white

, floralwhite

, forest green

, forestgreen

, fuchsia

, gainsboro

, ghost white

, ghostwhite

, gold

, goldenrod

, gray

, green

, green yellow

, greenyellow

, grey

, honeydew

, hot pink

, hotpink

, indian red

, indianred

, indigo

, ivory

, khaki

, lavender

, lavender blush

, lavenderblush

, lawn green

, lawngreen

, lemon chiffon

, lemonchiffon

, light blue

, light coral

, light cyan

, light goldenrod yellow

, light gray

, light green

, light grey

, light pink

, light salmon

, light sea green

, light seagreen

, light sky blue

, light skyblue

, light slate gray

, light slate grey

, light steel blue

, light yellow

, lightblue

, lightcoral

, lightcyan

, lightgoldenrodyellow

, lightgray

, lightgreen

, lightgrey

, lightpink

, lightsalmon

, lightseagreen

, lightskyblue

, lightslategray

, lightslategrey

, lightsteelblue

, lightyellow

, lime

, lime green

, limegreen

, linen

, magenta

, maroon

, medium aquamarine

, medium blue

, medium orchid

, medium purple

, medium sea green

, medium seagreen

, medium slate blue

, medium spring green

, medium turquoise

, medium violet red

, mediumaquamarine

, mediumblue

, mediumorchid

, mediumpurple

, mediumseagreen

, mediumslateblue

, mediumspringgreen

, mediumturquoise

, mediumvioletred

, midnight blue

, midnightblue

, mint cream

, mintcream

, misty rose

, mistyrose

, moccasin

, navajo white

, navajowhite

, navy

, old lace

, oldlace

, olive

, olive drab

, olivedrab

, orange

, orange red

, orangered

, orchid

, pale goldenrod

, pale green

, pale turquoise

, pale violet red

, palegoldenrod

, palegreen

, paleturquoise

, palevioletred

, papaya whip

, papayawhip

, peach puff

, peachpuff

, peru

, pink

, plum

, powder blue

, powderblue

, purple

, rebecca purple

, rebeccapurple

, red

, rosy brown

, rosybrown

, royal blue

, royalblue

, saddle brown

, saddlebrown

, salmon

, sandy brown

, sandybrown

, sea green

, seagreen

, seashell

, sienna

, silver

, sky blue

, skyblue

, slate blue

, slate gray

, slate grey

, slateblue

, slategray

, slategrey

, snow

, spring green

, springgreen

, steel blue

, steelblue

, tan

, teal

, thistle

, tomato

, transparent

, turquoise

, violet

, wheat

, white

, white smoke

, whitesmoke

, yellow

, yellow green

, and yellowgreen

.  

> color /A #ff11b8 target abp

> color /A #58fffa target abp

> color /A #cf3cff target abp

> show /A target c

> color /A #ffffff target c

> ui mousemode rightMode select

> ui mousemode rightMode pivot

> ui mousemode rightMode select

> ~hbonds

> hbonds

249 hydrogen bonds found  

> select :209,216,230,234,239,246,253,257,267

78 atoms, 69 bonds, 2 pseudobonds, 2 models selected  

> name frozen "single cys" sel

registering illegal selector name "single cys"  

> select clear

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1901, in <lambda>  
dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 588, in close_request  
tool_instance.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 496, in delete  
ToolInstance.delete(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 176, in delete  
self.session.tools.remove([self])  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 360, in remove  
del self._tool_instances[tid]  
KeyError: 7  
  
KeyError: 7  
  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 360, in remove  
del self._tool_instances[tid]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1901, in <lambda>  
dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 588, in close_request  
tool_instance.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 496, in delete  
ToolInstance.delete(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 176, in delete  
self.session.tools.remove([self])  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 360, in remove  
del self._tool_instances[tid]  
KeyError: 8  
  
KeyError: 8  
  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 360, in remove  
del self._tool_instances[tid]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1901, in <lambda>  
dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 588, in close_request  
tool_instance.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 496, in delete  
ToolInstance.delete(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 176, in delete  
self.session.tools.remove([self])  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 360, in remove  
del self._tool_instances[tid]  
KeyError: 9  
  
KeyError: 9  
  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 360, in remove  
del self._tool_instances[tid]  
  
See log for complete Python traceback.  
  

> select :209,216,230,234,239,246,253,257,267

78 atoms, 69 bonds, 2 pseudobonds, 2 models selected  

> name frozen "single cys" sel

registering illegal selector name "single cys"  

> name frozen "single cys" sel

registering illegal selector name "single cys"  

> name frozen "single cys" sel

registering illegal selector name "single cys"  

> name frozen singlecys sel

> name frozen singlecys sel

> color singlecys #ff3030 target abp

> color singlecys #00ff3b target abp

> select clear

> select /A:274

9 atoms, 8 bonds, 1 model selected  

> select clear

Drag select of 1 atoms, 5 residues, 1 bonds  

> select clear

> select /A:246

11 atoms, 10 bonds, 1 model selected  

> select /A:253

6 atoms, 5 bonds, 1 model selected  

> select /A:234

9 atoms, 8 bonds, 1 model selected  

> select clear

> save session "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43 structures/200812
> cpSRP43 FL CD2 labels.cxs"

Summary of feedback from opening C:\Users\Alex\Google Drive\Shan Lab\cpSRP43
structures\200812 cpSRP43 FL CD2 labels.cxs  
---  
warning | registering illegal selector name "single cys"  
  
opened ChimeraX session  

> save session C:/Users/Alex/Desktop/cpSRP43-CD2-BTFMA.cxs

> select /A:213

9 atoms, 8 bonds, 1 model selected  

> select up

142 atoms, 142 bonds, 1 model selected  

> select up

2227 atoms, 2266 bonds, 1 model selected  

> hide sel atoms

> ~hbonds

> select clear

> select :209,216,234,239,253,267

49 atoms, 43 bonds, 1 model selected  

> show sel atoms

> select clear

> save C:\Users\Alex\Desktop\image2.png supersample 3

> save session C:/Users/Alex/Desktop/cpSRP43-CD2-BTFMA.cxs

Summary of feedback from opening C:\Users\Alex\Desktop\cpSRP43-CD2-BTFMA.cxs  
---  
warning | registering illegal selector name "single cys"  
  
opened ChimeraX session  

> save C:\Users\Alex\Desktop\image4.png supersample 3

> select :260,257,239,219,212,188,192

64 atoms, 58 bonds, 1 model selected  

> select clear

> select :209,216,234,239,253,267

49 atoms, 43 bonds, 1 model selected  

> label sel residues

> label sel residues size 96

Expected a keyword  

Expected a keyword  

> label sel residues

Expected a keyword  

> label sel residues height 10

> label sel residues height 2

> select clear

> save session C:/Users/Alex/Desktop/cpSRP43-CD2-BTFMA.cxs

Summary of feedback from opening C:\Users\Alex\Desktop\cpSRP43-CD2-BTFMA.cxs  
---  
warning | registering illegal selector name "single cys"  
  
opened ChimeraX session  

> close #1.1

> select /A:213

9 atoms, 8 bonds, 1 model selected  

> select up

142 atoms, 142 bonds, 1 model selected  

> select up

2227 atoms, 2266 bonds, 1 model selected  

> hide sel atoms

> select clear

Unknown command: :90  

> select :46

8 atoms, 7 bonds, 1 model selected  

> select :46,60,71,76,131,148,161,209,222

81 atoms, 72 bonds, 1 model selected  

> style sel sphere

Changed 81 atom styles  

> show sel cartoons

> show sel atoms

> style sel stick

Changed 81 atom styles  

Expected an objects specifier or a keyword  

> select :46@CA,60,71,76,131,148,161,209,222

1 atom, 1 model selected  

> select :46@CA,60@CA,71@CA,76@CA,131@CA,148@CA,161@CA,20@CA9,222@CA

1 atom, 1 model selected  

> hide sel atoms

Expected an objects specifier or a keyword  

> select @CA :46,60,71,76,131,148,161,209,222

390 atoms, 72 bonds, 1 model selected  

> select :46,60,71,76,131,148,161,209,222@CA

10 atoms, 1 model selected  

> style sel sphere

Changed 10 atom styles  

> show sel atoms

> show sel atoms

> style sel sphere

Changed 10 atom styles  

> select :46,60,71,76,131,148,161,209,222

81 atoms, 72 bonds, 1 model selected  

> select :46,60,71,76,131,148,161,209,222@CA

10 atoms, 1 model selected  

> show sel atoms

> style sel sphere

Changed 10 atom styles  

> show sel atoms

> show sel cartoons

> style sel sphere

Changed 10 atom styles  

> style sel stick

Changed 10 atom styles  

> select #1:46,60,71,76,131,148,161,209,222@CA

10 atoms, 1 model selected  

> show sel atoms

> hide sel atoms

> show sel atoms

> color sel black

Expected an objects specifier or a keyword  

> select /A:46,60,71,76,131,148,161,209,222@CA

9 atoms, 1 model selected  

> show sel atoms

> style sel stick

Changed 9 atom styles  

> style sel sphere

Changed 9 atom styles  

> style sel sphere

Changed 9 atom styles  

> hide sel cartoons

> select clear


[had to nuke a lot of the log to fit it in the ticket]

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> open C:/ProgramData/ChimeraX/GUN4_cys.cxs

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\manager.py", line 259, in reset_state  
alignment._destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 501, in _destroy  
self._notify_observers("destroyed", None)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 541, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 459, in alignment_notification  
self.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 496, in delete  
ToolInstance.delete(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 175, in delete  
self.session.ui.remove_tool(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 316, in remove_tool  
self.main_window.remove_tool(tool_instance)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 728, in remove_tool  
tw._destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1806, in _destroy  
self.__toolkit.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1935, in destroy  
sbar.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\statusbar.py", line 50, in destroy  
v.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 391, in delete  
self.make_current()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 431, in make_current  
return self._opengl_context.make_current()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 128, in make_current  
qc = self._initialize_context()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 149, in _initialize_context  
qc.setScreen(self._screen)  
RuntimeError: wrapped C/C++ object of type QScreen has been deleted  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\manager.py", line 259, in reset_state  
alignment._destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 501, in _destroy  
self._notify_observers("destroyed", None)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 541, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 459, in alignment_notification  
self.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 496, in delete  
ToolInstance.delete(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 175, in delete  
self.session.ui.remove_tool(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 316, in remove_tool  
self.main_window.remove_tool(tool_instance)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 728, in remove_tool  
tw._destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1806, in _destroy  
self.__toolkit.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1935, in destroy  
sbar.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\statusbar.py", line 50, in destroy  
v.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 391, in delete  
self.make_current()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 431, in make_current  
return self._opengl_context.make_current()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 128, in make_current  
qc = self._initialize_context()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 149, in _initialize_context  
qc.setScreen(self._screen)  
RuntimeError: wrapped C/C++ object of type QScreen has been deleted  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 638, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2845, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 68, in open  
path_models = session.models.open(paths, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 729, in open  
session, filenames, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 504, in open_multiple_data  
models, status = open_data(session, fspec, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 457, in open_data  
models, status = open_func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 909, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 669, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 491, in delete  
self.alignment.detach_viewer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
  
See log for complete Python traceback.  
  

> open 4XKB format mmCIF fromDatabase pdb

4xkb title:  
Crystal Structure of GENOMES UNCOUPLED 4 (GUN4) in Complex with
Deuteroporphyrin IX [more info...]  
  
Chain information for 4xkb #1  
---  
Chain | Description  
A | Ycf53-like protein  
  
Non-standard residues in 4xkb #1  
---  
DE9 — 3,3'-(3,7,12,17-tetramethylporphyrin-2,18-diyl)dipropanoic acid
(deuteroporphyrin IX)  
  
  

> open C:\ProgramData\ChimeraX\GUN4_cys.cxs format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 491, in delete  
self.alignment.detach_viewer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 491, in delete  
self.alignment.detach_viewer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 610, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 429, in defer  
cxcmd(session, topic)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 445, in cxcmd  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2845, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 68, in open  
path_models = session.models.open(paths, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 729, in open  
session, filenames, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 504, in open_multiple_data  
models, status = open_data(session, fspec, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 457, in open_data  
models, status = open_func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 909, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 669, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 491, in delete  
self.alignment.detach_viewer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
  
See log for complete Python traceback.  
  

> open 4XKB format mmCIF fromDatabase pdb

4xkb title:  
Crystal Structure of GENOMES UNCOUPLED 4 (GUN4) in Complex with
Deuteroporphyrin IX [more info...]  
  
Chain information for 4xkb #1  
---  
Chain | Description  
A | Ycf53-like protein  
  
Non-standard residues in 4xkb #1  
---  
DE9 — 3,3'-(3,7,12,17-tetramethylporphyrin-2,18-diyl)dipropanoic acid
(deuteroporphyrin IX)  
  
  
Alignment identifier is 1.A  

> select clear

> select clear

> select /A:191

5 atoms, 4 bonds, 1 model selected  

> style sel stick

Changed 5 atom styles  

> select /A:193

7 atoms, 7 bonds, 1 model selected  

> select clear

> select /A:194

5 atoms, 4 bonds, 1 model selected  

> style sel stick

Changed 5 atom styles  

> show sel atoms

> select clear

> ui mousemode rightMode rotate

> select /A:197

7 atoms, 6 bonds, 1 model selected  

> select /A:195

4 atoms, 3 bonds, 1 model selected  

> select /A:194

5 atoms, 4 bonds, 1 model selected  

> select /A:202

5 atoms, 4 bonds, 1 model selected  

> show sel atoms

> select /A:201

6 atoms, 5 bonds, 1 model selected  

> show sel atoms

> style sel stick

Changed 6 atom styles  

> style sel stick

Changed 6 atom styles  

> show sel atoms

> color sel red

> select clear

> open C:\ProgramData\ChimeraX\cpSRP43_PRE_colored.cxs format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 491, in delete  
self.alignment.detach_viewer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 491, in delete  
self.alignment.detach_viewer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 610, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 429, in defer  
cxcmd(session, topic)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 445, in cxcmd  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2845, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 68, in open  
path_models = session.models.open(paths, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 729, in open  
session, filenames, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 504, in open_multiple_data  
models, status = open_data(session, fspec, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 457, in open_data  
models, status = open_func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 909, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 669, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 491, in delete  
self.alignment.detach_viewer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
  
See log for complete Python traceback.  
  

> open "C:\Users\Alex\Google Drive\Shan Lab\cpSRP43
> structures\cpSRP43_PRE.cxs" format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 491, in delete  
self.alignment.detach_viewer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 491, in delete  
self.alignment.detach_viewer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 610, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 429, in defer  
cxcmd(session, topic)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 445, in cxcmd  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2845, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 68, in open  
path_models = session.models.open(paths, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 729, in open  
session, filenames, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 504, in open_multiple_data  
models, status = open_data(session, fspec, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 457, in open_data  
models, status = open_func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 909, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 669, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 491, in delete  
self.alignment.detach_viewer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
  
See log for complete Python traceback.  
  

> open C:\ProgramData\ChimeraX\cpSRP43_PRE_colored.cxs format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 491, in delete  
self.alignment.detach_viewer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 491, in delete  
self.alignment.detach_viewer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 610, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 429, in defer  
cxcmd(session, topic)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 445, in cxcmd  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2845, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 68, in open  
path_models = session.models.open(paths, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 729, in open  
session, filenames, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 504, in open_multiple_data  
models, status = open_data(session, fspec, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 457, in open_data  
models, status = open_func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 909, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 669, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 491, in delete  
self.alignment.detach_viewer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
  
See log for complete Python traceback.  
  

> open "C:\Users\Alex\Google Drive\Shan Lab\cpSRP43
> structures\cpSRP43_domains.cxs" format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 491, in delete  
self.alignment.detach_viewer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 491, in delete  
self.alignment.detach_viewer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 610, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 429, in defer  
cxcmd(session, topic)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 445, in cxcmd  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2845, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 68, in open  
path_models = session.models.open(paths, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 729, in open  
session, filenames, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 504, in open_multiple_data  
models, status = open_data(session, fspec, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 457, in open_data  
models, status = open_func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 909, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 669, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 491, in delete  
self.alignment.detach_viewer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
  
See log for complete Python traceback.  
  

> open "C:\Users\Alex\Google Drive\Shan Lab\cpSRP43
> structures\cpSRP43_domains.cxs" format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 491, in delete  
self.alignment.detach_viewer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 491, in delete  
self.alignment.detach_viewer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 610, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 429, in defer  
cxcmd(session, topic)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 445, in cxcmd  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2845, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 68, in open  
path_models = session.models.open(paths, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 729, in open  
session, filenames, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 504, in open_multiple_data  
models, status = open_data(session, fspec, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 457, in open_data  
models, status = open_func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 909, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 669, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 491, in delete  
self.alignment.detach_viewer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
  
See log for complete Python traceback.  
  

> open "C:\Users\Alex\Google Drive\Shan Lab\cpSRP43
> structures\cpSRP43_NMRnum.pdb"

Summary of feedback from opening C:\Users\Alex\Google Drive\Shan Lab\cpSRP43
structures\cpSRP43_NMRnum.pdb  
---  
warning | Ignored bad PDB record found on line 2498  
END  
  
Chain information for cpSRP43_NMRnum.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> open "C:\Users\Alex\Google Drive\Shan Lab\cpSRP43
> structures\cpSRP43_domains.cxs" format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 491, in delete  
self.alignment.detach_viewer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 491, in delete  
self.alignment.detach_viewer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 610, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 429, in defer  
cxcmd(session, topic)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 445, in cxcmd  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2845, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 68, in open  
path_models = session.models.open(paths, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 729, in open  
session, filenames, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 504, in open_multiple_data  
models, status = open_data(session, fspec, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 457, in open_data  
models, status = open_func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 909, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 669, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 491, in delete  
self.alignment.detach_viewer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
  
See log for complete Python traceback.  
  

> open C:\Users\Alex\Desktop\cpSRP43-CD2-BTFMA.cxs format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 491, in delete  
self.alignment.detach_viewer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 491, in delete  
self.alignment.detach_viewer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 610, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 429, in defer  
cxcmd(session, topic)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 445, in cxcmd  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2845, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 68, in open  
path_models = session.models.open(paths, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 729, in open  
session, filenames, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 504, in open_multiple_data  
models, status = open_data(session, fspec, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 457, in open_data  
models, status = open_func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 909, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 669, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 491, in delete  
self.alignment.detach_viewer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 320, in detach_viewer  
self.viewers.remove(viewer)  
  
See log for complete Python traceback.  
  

> open "C:\Users\Alex\Google Drive\Shan Lab\cpSRP43
> structures\cpSRP43_NMRnum.pdb"

Summary of feedback from opening C:\Users\Alex\Google Drive\Shan Lab\cpSRP43
structures\cpSRP43_NMRnum.pdb  
---  
warning | Ignored bad PDB record found on line 2498  
END  
  
Chain information for cpSRP43_NMRnum.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> select up

2 atoms, 1 bond, 1 model selected  

> select up

6 atoms, 5 bonds, 1 model selected  

> select up

26 atoms, 25 bonds, 1 model selected  

> select up

79 atoms, 78 bonds, 1 model selected  

> select up

2494 atoms, 2536 bonds, 1 model selected  

> hide sel atoms

> show sel cartoons

> select /C:458


[had to nuke large parts of the log to fit it in the ticket]

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> ~display /B

> hide sel atoms

> hide sel atoms

> view front

> view back

> hide sel atoms

> hide sel atoms

> select clear

> hide sel atoms

> select clear

> save C:\Users\Alex\Desktop\image27.png supersample 3

> view front

> save C:\Users\Alex\Desktop\image28.png supersample 3

> hide sel atoms

> save C:\Users\Alex\Desktop\image29.png supersample 3

> select /A:209@CD1

1 atom, 1 model selected  

> toolshed show Distances

> distance /A:142@N /A:209@CD1

Distance between /A LEU 142 N and ILE 209 CD1: 30.140Å  

> view back

> select clear

> save session C:/ProgramData/ChimeraX/cpSRP43_PRE_colored.cxs

opened ChimeraX session  

> close session

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 939, in <lambda>  
close_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_close_cb(sess))  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 655, in file_close_cb  
run(session, 'close session')  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2845, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\close.py", line 60, in close_session  
session.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 491, in delete  
self.alignment.detach_viewer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 326, in detach_viewer  
self.session.alignments.destroy_alignment(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\manager.py", line 107, in destroy_alignment  
del self._alignments[alignment.ident]  
KeyError: '1.A'  
  
KeyError: '1.A'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\manager.py", line 107, in destroy_alignment  
del self._alignments[alignment.ident]  
  
See log for complete Python traceback.  
  

> open C:\ProgramData\ChimeraX\cpSRP43_PRE_colored.cxs format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 490, in delete  
self.seq_canvas.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 552, in destroy  
header.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\headers\conservation.py", line 99, in destroy  
super().destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\headers\header_sequence.py", line 77, in destroy  
self.alignment.remove_observer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 452, in remove_observer  
self.observers.remove(observer)  
ValueError: list.remove(x): x not in list  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 490, in delete  
self.seq_canvas.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 552, in destroy  
header.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\headers\conservation.py", line 99, in destroy  
super().destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\headers\header_sequence.py", line 77, in destroy  
self.alignment.remove_observer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 452, in remove_observer  
self.observers.remove(observer)  
ValueError: list.remove(x): x not in list  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 610, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 429, in defer  
cxcmd(session, topic)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 445, in cxcmd  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2845, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 68, in open  
path_models = session.models.open(paths, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 729, in open  
session, filenames, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 504, in open_multiple_data  
models, status = open_data(session, fspec, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 457, in open_data  
models, status = open_func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 909, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 669, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 490, in delete  
self.seq_canvas.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 552, in destroy  
header.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\headers\conservation.py", line 99, in destroy  
super().destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\headers\header_sequence.py", line 77, in destroy  
self.alignment.remove_observer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 452, in remove_observer  
self.observers.remove(observer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 452, in remove_observer  
self.observers.remove(observer)  
  
See log for complete Python traceback.  
  

> open C:\ProgramData\ChimeraX\cpSRP43_PRE_colored.cxs format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 490, in delete  
self.seq_canvas.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 552, in destroy  
header.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\headers\consensus.py", line 39, in destroy  
super().destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\headers\header_sequence.py", line 77, in destroy  
self.alignment.remove_observer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 452, in remove_observer  
self.observers.remove(observer)  
ValueError: list.remove(x): x not in list  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 490, in delete  
self.seq_canvas.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 552, in destroy  
header.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\headers\consensus.py", line 39, in destroy  
super().destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\headers\header_sequence.py", line 77, in destroy  
self.alignment.remove_observer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 452, in remove_observer  
self.observers.remove(observer)  
ValueError: list.remove(x): x not in list  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 610, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 429, in defer  
cxcmd(session, topic)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 445, in cxcmd  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2845, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 68, in open  
path_models = session.models.open(paths, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 729, in open  
session, filenames, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 504, in open_multiple_data  
models, status = open_data(session, fspec, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 457, in open_data  
models, status = open_func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 909, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 669, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 490, in delete  
self.seq_canvas.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 552, in destroy  
header.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\headers\consensus.py", line 39, in destroy  
super().destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\headers\header_sequence.py", line 77, in destroy  
self.alignment.remove_observer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 452, in remove_observer  
self.observers.remove(observer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 452, in remove_observer  
self.observers.remove(observer)  
  
See log for complete Python traceback.  
  

> open C:\ProgramData\ChimeraX\cpSRP43_PRE_CD2toAcidicFace_connected.cxs

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 490, in delete  
self.seq_canvas.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 552, in destroy  
header.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\headers\consensus.py", line 39, in destroy  
super().destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\headers\header_sequence.py", line 77, in destroy  
self.alignment.remove_observer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 452, in remove_observer  
self.observers.remove(observer)  
ValueError: list.remove(x): x not in list  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 490, in delete  
self.seq_canvas.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 552, in destroy  
header.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\headers\consensus.py", line 39, in destroy  
super().destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\headers\header_sequence.py", line 77, in destroy  
self.alignment.remove_observer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 452, in remove_observer  
self.observers.remove(observer)  
ValueError: list.remove(x): x not in list  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 610, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 429, in defer  
cxcmd(session, topic)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 445, in cxcmd  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2845, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 68, in open  
path_models = session.models.open(paths, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 729, in open  
session, filenames, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 504, in open_multiple_data  
models, status = open_data(session, fspec, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 457, in open_data  
models, status = open_func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 909, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 669, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 490, in delete  
self.seq_canvas.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 552, in destroy  
header.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\headers\consensus.py", line 39, in destroy  
super().destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\headers\header_sequence.py", line 77, in destroy  
self.alignment.remove_observer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 452, in remove_observer  
self.observers.remove(observer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 452, in remove_observer  
self.observers.remove(observer)  
  
See log for complete Python traceback.  
  

> open C:\ProgramData\ChimeraX\cpSRP43_PRE_colored.cxs format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 490, in delete  
self.seq_canvas.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 552, in destroy  
header.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\headers\consensus.py", line 39, in destroy  
super().destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\headers\header_sequence.py", line 77, in destroy  
self.alignment.remove_observer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 452, in remove_observer  
self.observers.remove(observer)  
ValueError: list.remove(x): x not in list  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 490, in delete  
self.seq_canvas.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 552, in destroy  
header.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\headers\consensus.py", line 39, in destroy  
super().destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\headers\header_sequence.py", line 77, in destroy  
self.alignment.remove_observer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 452, in remove_observer  
self.observers.remove(observer)  
ValueError: list.remove(x): x not in list  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 610, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 429, in defer  
cxcmd(session, topic)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 445, in cxcmd  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2845, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 68, in open  
path_models = session.models.open(paths, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 729, in open  
session, filenames, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 504, in open_multiple_data  
models, status = open_data(session, fspec, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 457, in open_data  
models, status = open_func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 909, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 669, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 490, in delete  
self.seq_canvas.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 552, in destroy  
header.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\headers\consensus.py", line 39, in destroy  
super().destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\headers\header_sequence.py", line 77, in destroy  
self.alignment.remove_observer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 452, in remove_observer  
self.observers.remove(observer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 452, in remove_observer  
self.observers.remove(observer)  
  
See log for complete Python traceback.  
  

> open "C:/Users/Alex/Google Drive/Shan
> Lab/HADDOCK/Best_3BodyDocking/SBDL18_CD254M_CD3_cluster1_2.pdb"

Summary of feedback from opening C:/Users/Alex/Google Drive/Shan
Lab/HADDOCK/Best_3BodyDocking/SBDL18_CD254M_CD3_cluster1_2.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK FILENAME="complex_65w.pdb0"  
  
Ignored bad PDB record found on line 2  
REMARK ===============================================================  
  
Ignored bad PDB record found on line 3  
REMARK HADDOCK run for complex  
  
Ignored bad PDB record found on line 4  
REMARK initial structure: complex_65.pdb  
  
Ignored bad PDB record found on line 5  
REMARK ===============================================================  
  
30 messages similar to the above omitted  
  
Chain information for SBDL18_CD254M_CD3_cluster1_2.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> select /B:536

17 atoms, 16 bonds, 1 model selected  

> select up

49 atoms, 48 bonds, 1 model selected  

> select up

620 atoms, 629 bonds, 1 model selected  

> select down

49 atoms, 48 bonds, 1 model selected  

> style sel stick

Changed 49 atom styles  

> show sel atoms

> style sel stick

Changed 62 atom styles  

> show sel atoms

> show sel atoms

> select clear

> close session

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 939, in <lambda>  
close_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_close_cb(sess))  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 655, in file_close_cb  
run(session, 'close session')  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2845, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\close.py", line 60, in close_session  
session.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 490, in delete  
self.seq_canvas.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 552, in destroy  
header.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\headers\consensus.py", line 39, in destroy  
super().destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\headers\header_sequence.py", line 77, in destroy  
self.alignment.remove_observer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 452, in remove_observer  
self.observers.remove(observer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 452, in remove_observer  
self.observers.remove(observer)  
  
See log for complete Python traceback.  
  

> open "C:/Users/Alex/Google Drive/Shan
> Lab/HADDOCK/Best_3BodyDocking/SBDL18_CD2_CD3_cluster7_2_stitched.pdb"

Summary of feedback from opening C:/Users/Alex/Google Drive/Shan
Lab/HADDOCK/Best_3BodyDocking/SBDL18_CD2_CD3_cluster7_2_stitched.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK FILENAME="complex_186w.pdb0"  
  
Ignored bad PDB record found on line 2  
REMARK ===============================================================  
  
Ignored bad PDB record found on line 3  
REMARK HADDOCK run for complex  
  
Ignored bad PDB record found on line 4  
REMARK initial structure: complex_186.pdb  
  
Ignored bad PDB record found on line 5  
REMARK ===============================================================  
  
30 messages similar to the above omitted  
  
Chain information for SBDL18_CD2_CD3_cluster7_2_stitched.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open "C:/Users/Alex/Google Drive/Shan
> Lab/HADDOCK/Best_3BodyDocking/SBDL18_CD2_CD3_cluster7_2_stitched.pdb"

Summary of feedback from opening C:/Users/Alex/Google Drive/Shan
Lab/HADDOCK/Best_3BodyDocking/SBDL18_CD2_CD3_cluster7_2_stitched.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK FILENAME="complex_186w.pdb0"  
  
Ignored bad PDB record found on line 2  
REMARK ===============================================================  
  
Ignored bad PDB record found on line 3  
REMARK HADDOCK run for complex  
  
Ignored bad PDB record found on line 4  
REMARK initial structure: complex_186.pdb  
  
Ignored bad PDB record found on line 5  
REMARK ===============================================================  
  
30 messages similar to the above omitted  
  
Chain information for SBDL18_CD2_CD3_cluster7_2_stitched.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> close #1

> close

> open "C:/Users/Alex/Google Drive/Shan
> Lab/HADDOCK/Best_3BodyDocking/SBDL18_CD2_CD3_cluster7_2_stitched.pdb"

Summary of feedback from opening C:/Users/Alex/Google Drive/Shan
Lab/HADDOCK/Best_3BodyDocking/SBDL18_CD2_CD3_cluster7_2_stitched.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK FILENAME="complex_186w.pdb0"  
  
Ignored bad PDB record found on line 2  
REMARK ===============================================================  
  
Ignored bad PDB record found on line 3  
REMARK HADDOCK run for complex  
  
Ignored bad PDB record found on line 4  
REMARK initial structure: complex_186.pdb  
  
Ignored bad PDB record found on line 5  
REMARK ===============================================================  
  
30 messages similar to the above omitted  
  
Chain information for SBDL18_CD2_CD3_cluster7_2_stitched.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> select clear

> select clear

> select clear

> select /A:222

8 atoms, 7 bonds, 1 model selected  

> hide sel cartoons

> show sel cartoons

> select clear

Expected a models specifier or a keyword  

> view name front

> select /B:361

12 atoms, 12 bonds, 1 model selected  

> select up

96 atoms, 99 bonds, 1 model selected  

> color sel green

> select clear

> color /A lightgray

> cartoon suppressBackboneDisplay false

> ~display

> color :240@n,a black target a

> display :240@n

> color :15@CG1,a #97FF00 target a

> display :15@CG1

> color :15@CG2,a #00FF00 target a

> display :15@CG2

> color :26@CG1,a #79FF00 target a

> display :26@CG1

> color :26@CG2,a #00FF00 target a

> display :26@CG2

> color :42@CG1,a #00FF00 target a

> display :42@CG1

> color :42@CG2,a #00FF00 target a

> display :42@CG2

> color :45@CD1,a #00FF00 target a

> display :45@CD1

> color :46@CD1,a #00FF00 target a

> display :46@CD1

> color :59@CD1,a #92FF00 target a

> display :59@CD1

> color :59@CD2,a #00FF00 target a

> display :59@CD2

> color :60@CD1,a #00FF00 target a

> display :60@CD1

> color :71@CG1,a #FFDB00 target a

> display :71@CG1

> color :71@CG2,a #00FF00 target a

> display :71@CG2

> color :76@CD1,a #00FF00 target a

> display :76@CD1

> color :80@CG1,a #35FF00 target a

> display :80@CG1

> color :81@CG1,a #00FF00 target a

> display :81@CG1

> color :81@CG2,a #B7FF00 target a

> display :81@CG2

> color :100@CD1,a #00FF00 target a

> display :100@CD1

> color :103@CD1,a #FF8200 target a

> display :103@CD1

> color :104@CD1,a #97FF00 target a

> display :104@CD1

> color :109@CG1,a #0CFF00 target a

> display :109@CG1

> color :112@CG1,a #00FF00 target a

> display :112@CG1

> color :112@CG2,a #00FF00 target a

> display :112@CG2

> color :121@CD1,a #00FF00 target a

> display :121@CD1

> color :121@CD2,a #00FF00 target a

> display :121@CD2

> color :123@CG1,a #00FF00 target a

> display :123@CG1

> color :126@CD1,a #85FF00 target a

> display :126@CD1

> color :132@CG1,a #45FF00 target a

> display :132@CG1

> color :134@CD1,a #FF8100 target a

> display :134@CD1

> color :135@CD1,a #00FF00 target a

> display :135@CD1

> color :142@CD1,a #FF5B00 target a

> display :142@CD1

> color :142@CD2,a #FF0000 target a

> display :142@CD2

> color :145@CD1,a #FF4500 target a

> display :145@CD1

> color :151@CD1,a #23FF00 target a

> display :151@CD1

> color :165@CG1,a #00FF00 target a

> display :165@CG1

> color :169@CD1,a #FF0000 target a

> display :169@CD1

> color :170@CG1,a #76FF00 target a

> display :170@CG1

> color :170@CG2,a #FF0000 target a

> display :170@CG2

> color :172@CD1,a #FF0000 target a

> display :172@CD1

> color :176@CD1,a #FF1100 target a

> display :176@CD1

> color :178@CG1,a #00FF00 target a

> display :178@CG1

> color :178@CG2,a #FF0000 target a

> display :178@CG2

> color :184@CD1,a #FF4F00 target a

> display :184@CD1

> color :187@CD1,a #FF0000 target a

> display :187@CD1

> color :193@CD1,a #FF7D00 target a

> display :193@CD1

> color :194@CD1,a #FF0000 target a

> display :194@CD1

> color :209@CD1,a #FF1100 target a

> display :209@CD1

> color :211@CD1,a #FFC800 target a

> display :211@CD1

> color :214@CG1,a #C5FF00 target a

> display :214@CG1

> color :215@CD1,a #FF2700 target a

> display :215@CD1

> color :217@CG1,a #FF0000 target a

> display :217@CG1

> color :217@CG2,a #FF0000 target a

> display :217@CG2

> color :218@CD1,a #FF3B00 target a

> display :218@CD1

> color :222@CG1,a #00FF00 target a

> display :222@CG1

> color :277@CG1,a #EDFF00 target a

> display :277@CG1

> color :281@CG1,a #58FF00 target a

> display :281@CG1

> color :281@CG2,a #00FF00 target a

> display :281@CG2

> color :282@CD1,a #51FF00 target a

> display :282@CD1

> color :286@CG1,a #08FF00 target a

> display :286@CG1

> color :286@CG2,a #66FF00 target a

> display :286@CG2

> color :293@CD1,a #03FF00 target a

> display :293@CD1

> color :296@CD1,a #4FFF00 target a

> display :296@CD1

> color :297@CG1,a #47FF00 target a

> display :297@CG1

> color :297@CG2,a #74FF00 target a

> display :297@CG2

> color :313@CG1,a #82FF00 target a

> display :313@CG1

> color :317@CD1,a #FFBE00 target a

> display :317@CD1

> color :317@CD2,a #FFB800 target a

> display :317@CD2

> color :318@CG1,a #23FF00 target a

> display :318@CG1

> color :319@CD1,a #FFA900 target a

> display :319@CD1

> color :319@CD2,a #FFAA00 target a

> display :319@CD2

> color :320@CD1,a #FFC900 target a

> display :320@CD1

> color :0@1,a #FF0000 target a

> display :0@1

> color :0@2,a #FF0000 target a

> display :0@2

> color :0@2,a #FF0000 target a

> display :0@2

> color :0@2,a #FF0000 target a

> display :0@2

> color :0@2,a #FF0000 target a

> display :0@2

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> style sphere

Changed 2800 atom styles  

> color :3@N,a #FF6000 target a

> display :3@N

> color :4@N,a #FF6700 target a

> display :4@N

> color :11@N,a #FF5D00 target a

> display :11@N

> color :12@N,a #FF8C00 target a

> display :12@N

> color :13@N,a #FF8300 target a

> display :13@N

> color :14@N,a #FF9B00 target a

> display :14@N

> color :15@N,a #FFEC00 target a

> display :15@N

> color :16@N,a #2EFF00 target a

> display :16@N

> color :19@N,a #FFE900 target a

> display :19@N

> color :20@N,a #FFFE00 target a

> display :20@N

> color :21@N,a #1FFF00 target a

> display :21@N

> color :22@N,a #7AFF00 target a

> display :22@N

> color :23@N,a #71FF00 target a

> display :23@N

> color :24@N,a #5DFF00 target a

> display :24@N

> color :25@N,a #53FF00 target a

> display :25@N

> color :26@N,a #43FF00 target a

> display :26@N

> color :28@N,a #ABFF00 target a

> display :28@N

> color :29@N,a #31FF00 target a

> display :29@N

> color :30@N,a #1DFF00 target a

> display :30@N

> color :31@N,a #2DFF00 target a

> display :31@N

> color :32@N,a #17FF00 target a

> display :32@N

> color :33@N,a #3BFF00 target a

> display :33@N

> color :34@N,a #3FFF00 target a

> display :34@N

> color :36@N,a #4BFF00 target a

> display :36@N

> color :37@N,a #56FF00 target a

> display :37@N

> color :40@N,a #FFEE00 target a

> display :40@N

> color :41@N,a #7EFF00 target a

> display :41@N

> color :42@N,a #67FF00 target a

> display :42@N

> color :43@N,a #10FF00 target a

> display :43@N

> color :44@N,a #FF4F00 target a

> display :44@N

> color :46@N,a #12FF00 target a

> display :46@N

> color :47@N,a #35FF00 target a

> display :47@N

> color :48@N,a #FFFF00 target a

> display :48@N

> color :49@N,a #38FF00 target a

> display :49@N

> color :50@N,a #D1FF00 target a

> display :50@N

> color :51@N,a #63FF00 target a

> display :51@N

> color :52@N,a #FFC100 target a

> display :52@N

> color :53@N,a #FFBB00 target a

> display :53@N

> color :54@N,a #F8FF00 target a

> display :54@N

> color :55@N,a #4EFF00 target a

> display :55@N

> color :56@N,a #2AFF00 target a

> display :56@N

> color :57@N,a #30FF00 target a

> display :57@N

> color :58@N,a #0AFF00 target a

> display :58@N

> color :59@N,a #36FF00 target a

> display :59@N

> color :60@N,a #23FF00 target a

> display :60@N

> color :61@N,a #00FF00 target a

> display :61@N

> color :62@N,a #11FF00 target a

> display :62@N

> color :63@N,a #04FF00 target a

> display :63@N

> color :64@N,a #12FF00 target a

> display :64@N

> color :65@N,a #0AFF00 target a

> display :65@N

> color :66@N,a #10FF00 target a

> display :66@N

> color :67@N,a #47FF00 target a

> display :67@N

> color :70@N,a #8BFF00 target a

> display :70@N

> color :71@N,a #5BFF00 target a

> display :71@N

> color :77@N,a #F9FF00 target a

> display :77@N

> color :78@N,a #5BFF00 target a

> display :78@N

> color :79@N,a #17FF00 target a

> display :79@N

> color :80@N,a #00FF00 target a

> display :80@N

> color :81@N,a #00FF00 target a

> display :81@N

> color :84@N,a #00FF00 target a

> display :84@N

> color :85@N,a #00FF00 target a

> display :85@N

> color :86@N,a #00FF00 target a

> display :86@N

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> display :0@N

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> display :0@N

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> display :0@N

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> display :0@N

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> display :0@N

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> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> ~display /B

> hide sel atoms

> select clear

> view front

> select clear

> save session "C:/Users/Alex/Google Drive/Shan
> Lab/HADDOCK/SBDL18_CD2_CD3_PRE.cxs"

> save C:\Users\Alex\Desktop\image1.png supersample 3

> open "C:/Users/Alex/Google Drive/Shan
> Lab/HADDOCK/Best_3BodyDocking/SBDL18_CD254M_CD3_cluster1_2_stitched.pdb"

Summary of feedback from opening C:/Users/Alex/Google Drive/Shan
Lab/HADDOCK/Best_3BodyDocking/SBDL18_CD254M_CD3_cluster1_2_stitched.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK FILENAME="complex_65w.pdb0"  
  
Ignored bad PDB record found on line 2  
REMARK ===============================================================  
  
Ignored bad PDB record found on line 3  
REMARK HADDOCK run for complex  
  
Ignored bad PDB record found on line 4  
REMARK initial structure: complex_65.pdb  
  
Ignored bad PDB record found on line 5  
REMARK ===============================================================  
  
30 messages similar to the above omitted  
  
Chain information for SBDL18_CD254M_CD3_cluster1_2_stitched.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> close session

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 939, in <lambda>  
close_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_close_cb(sess))  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 655, in file_close_cb  
run(session, 'close session')  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2845, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\close.py", line 60, in close_session  
session.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 490, in delete  
self.seq_canvas.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 552, in destroy  
header.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\headers\consensus.py", line 39, in destroy  
super().destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\headers\header_sequence.py", line 77, in destroy  
self.alignment.remove_observer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 452, in remove_observer  
self.observers.remove(observer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 452, in remove_observer  
self.observers.remove(observer)  
  
See log for complete Python traceback.  
  

> open "C:/Users/Alex/Google Drive/Shan
> Lab/HADDOCK/Best_3BodyDocking/SBDL18_CD254M_CD3_cluster1_2_stitched.pdb"

Summary of feedback from opening C:/Users/Alex/Google Drive/Shan
Lab/HADDOCK/Best_3BodyDocking/SBDL18_CD254M_CD3_cluster1_2_stitched.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK FILENAME="complex_65w.pdb0"  
  
Ignored bad PDB record found on line 2  
REMARK ===============================================================  
  
Ignored bad PDB record found on line 3  
REMARK HADDOCK run for complex  
  
Ignored bad PDB record found on line 4  
REMARK initial structure: complex_65.pdb  
  
Ignored bad PDB record found on line 5  
REMARK ===============================================================  
  
30 messages similar to the above omitted  
  
Chain information for SBDL18_CD254M_CD3_cluster1_2_stitched.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> view front

> view name front

> select /B:361

12 atoms, 12 bonds, 1 model selected  

> select up

96 atoms, 99 bonds, 1 model selected  

> color sel green

> select /C:535

6 atoms, 5 bonds, 1 model selected  

> select up

49 atoms, 48 bonds, 1 model selected  

> select up

142 atoms, 143 bonds, 1 model selected  

> color sel red

> select clear

> color /A lightgray

> cartoon suppressBackboneDisplay false

> ~display

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> display :15@CG2

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> display :317@CD1

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> display :319@CD1

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> display :319@CD2

> color :320@CD1,a #FFC900 target a

> display :320@CD1

> ~display /B

> style sphere

Changed 2942 atom styles  

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> display :3@N

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> display :4@N

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> display :105@N

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> display :106@N

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> display :108@N

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> display :110@N

> color :112@N,a #FFA400 target a

> display :112@N

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> display :114@N

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> display :127@N

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> display :128@N

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> display :130@N

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> display :136@N

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> display :139@N

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> display :140@N

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> display :164@N

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> display :175@N

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> display :178@N

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> display :179@N

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> display :201@N

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> display :276@N

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> display :279@N

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> display :287@N

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> display :288@N

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> display :289@N

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> display :290@N

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> display :0@N

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> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

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> display :0@N

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> display :0@N

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> display :0@N

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> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

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> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

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> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

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> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> color :0@N,a #FF0000 target a

> display :0@N

> ~display /B

> hide sel atoms

> select clear

> select /A:223@N

1 atom, 1 model selected  

> hide sel cartoons

> show sel cartoons

> hide sel atoms

> select clear

> select /A:230@N

1 atom, 1 model selected  

> select clear

> save session "C:/Users/Alex/Google Drive/Shan
> Lab/HADDOCK/SBDL18_CD254M_CD3_PRE.cxs"

> select clear

> name view front

"front": invalid atom specifier  

> view name front

> save session "C:/Users/Alex/Google Drive/Shan
> Lab/HADDOCK/SBDL18_CD254M_CD3_PRE.cxs"

opened ChimeraX session  

> open "C:/Users/Alex/Google Drive/Shan
> Lab/HADDOCK/Best_3BodyDocking/SBDL18_CD254M_CD3_PRE.cxs"

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 491, in delete  
self.alignment.detach_viewer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 326, in detach_viewer  
self.session.alignments.destroy_alignment(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\manager.py", line 107, in destroy_alignment  
del self._alignments[alignment.ident]  
KeyError: '1.A'  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 491, in delete  
self.alignment.detach_viewer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 326, in detach_viewer  
self.session.alignments.destroy_alignment(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\manager.py", line 107, in destroy_alignment  
del self._alignments[alignment.ident]  
KeyError: '1.A'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 525, in dropEvent  
_open_dropped_file(self.session, p)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1607, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2845, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 68, in open  
path_models = session.models.open(paths, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 729, in open  
session, filenames, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 504, in open_multiple_data  
models, status = open_data(session, fspec, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 457, in open_data  
models, status = open_func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 909, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 669, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 469, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 313, in reset_state  
tool_inst.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 490, in delete  
self.seq_canvas.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 552, in destroy  
header.destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\headers\conservation.py", line 99, in destroy  
super().destroy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\headers\header_sequence.py", line 77, in destroy  
self.alignment.remove_observer(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 452, in remove_observer  
self.observers.remove(observer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 452, in remove_observer  
self.observers.remove(observer)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 391.40
OpenGL renderer: GeForce GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Microsoft Corporation
Model: Surface Book
OS: Microsoft Windows 10 Pro (Build 18363)
Memory: 17,101,541,376
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i7-6600U CPU @ 2.60GHz"

[Eric Pettersen]

Reported by Alex Siegel