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

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> display :112@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 :179@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

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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

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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

[Eric Pettersen]

Hi Alex,

I'm hoping you can upgrade to the 1.1 release and try again. There have been *many* bug fixes and improvements since the 0.93 release that you are using. Even if the problem you're having isn't fixed in the 1.1 release, the fact that you will be using much more recent code will make it much easier for us to find your problem in the current code base and fix it. Let me know what happens.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[Eric Pettersen]

Now in ticket #4074