Delete status bar: wrapped C/C++ object of type QScreen has been deleted

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.2 (2021-05-08 05:48:20 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.2 (2021-05-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "/Users/jon/Documents/Documents/Lab
> Documents/HymanLab/TDP43_RNA_4BS2.cxs" format session

Log from Tue Jan 31 11:27:41 2023UCSF ChimeraX version: 1.2.2 (2021-05-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "/Users/jon/Documents/Documents/Lab
> Documents/HymanLab/TDP43_RNA_4BS2.cxs" format session

Log from Mon Jan 30 10:48:52 2023UCSF ChimeraX version: 1.2.2 (2021-05-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "/Users/jon/Documents/Documents/Lab
> Documents/HymanLab/TDP43_RNA_4BS2.cxs"

Log from Fri Jan 27 14:07:34 2023UCSF ChimeraX version: 1.2.2 (2021-05-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "/Users/jon/Documents/Documents/Lab
> Documents/HymanLab/TDP43_RNA_4BS2.cxs"

Log from Fri Jan 27 14:03:04 2023UCSF ChimeraX version: 1.2.2 (2021-05-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 4bs2

Summary of feedback from opening 4bs2 fetched from pdb  
---  
warning | Atom H is not in the residue template for GLY /A:96  
  
4bs2 title:  
NMR structure of human TDP-43 tandem RRMs in complex with UG-rich RNA [more
info...]  
  
Chain information for 4bs2  
---  
Chain | Description  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A
1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A | tar DNA-binding
protein 43  
1.1/B 1.2/B 1.3/B 1.4/B 1.5/B 1.6/B 1.7/B 1.8/B 1.9/B 1.10/B 1.11/B 1.12/B
1.13/B 1.14/B 1.15/B 1.16/B 1.17/B 1.18/B 1.19/B 1.20/B |
5'-R(*GP*up*GP*up*GP*ap*ap*up*GP*ap*ap*up)-3'  
  

> close session

> open 4bs2 format mmcif fromDatabase pdb

Summary of feedback from opening 4bs2 fetched from pdb  
---  
warning | Atom H is not in the residue template for GLY /A:96  
  
4bs2 title:  
NMR structure of human TDP-43 tandem RRMs in complex with UG-rich RNA [more
info...]  
  
Chain information for 4bs2  
---  
Chain | Description  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A
1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A | tar DNA-binding
protein 43  
1.1/B 1.2/B 1.3/B 1.4/B 1.5/B 1.6/B 1.7/B 1.8/B 1.9/B 1.10/B 1.11/B 1.12/B
1.13/B 1.14/B 1.15/B 1.16/B 1.17/B 1.18/B 1.19/B 1.20/B |
5'-R(*GP*up*GP*up*GP*ap*ap*up*GP*ap*ap*up)-3'  
  

> select #1.2/B

369 atoms, 400 bonds, 12 residues, 1 model selected  

> select #1.1

3143 atoms, 3204 bonds, 186 residues, 1 model selected  

> select #1

62860 atoms, 64080 bonds, 3720 residues, 21 models selected  

> ~select #1

Nothing selected  

> select #1.1

3143 atoms, 3204 bonds, 186 residues, 1 model selected  

> select ~sel

59717 atoms, 60876 bonds, 3534 residues, 20 models selected  

> delete atoms sel

> delete bonds sel

> set bgColor white

> nucleotides fill

> style nucleic stick

Changed 369 atom styles  

> select /A

2774 atoms, 2804 bonds, 174 residues, 1 model selected  

> color sel dark gray

> save "/Users/jon/Documents/Documents/Lab
> Documents/HymanLab/TDP43_RNA_4BS2.cxs"

——— End of log from Fri Jan 27 14:03:04 2023 ———

opened ChimeraX session  

> select nucleic-acid

369 atoms, 400 bonds, 12 residues, 1 model selected  

> cartoon hide sel

> ui tool show "Color Actions"

> color sel cornflower blue

> save "/Users/jon/Documents/Documents/Lab
> Documents/HymanLab/TDP43_RNA_4BS2.cxs"

——— End of log from Fri Jan 27 14:07:34 2023 ———

opened ChimeraX session  

> select guanine

48 atoms, 52 bonds, 4 residues, 1 model selected  

> color sel forest green

> select clear

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1.1/A  

> ui tool show "Show Sequence Viewer"

> sequence chain /B

Alignment identifier is 1.1/B  

> select /B:5

31 atoms, 33 bonds, 1 residue, 1 model selected  

> select /B:5

31 atoms, 33 bonds, 1 residue, 1 model selected  

> ui tool show Contacts

> ui tool show H-Bonds

> hbonds color #fa1e06

124 hydrogen bonds found  

> hide #1.1.1 models

> ui tool show H-Bonds

> hbonds color #fa1e06 intraModel false intraMol false intraRes false

0 hydrogen bonds found  

> show #1.1.1 models

> hide #1.1.1 models

> ~select #1.1.1

31 atoms, 33 bonds, 1 residue, 1 model selected  

> select backbone

1274 atoms, 1284 bonds, 186 residues, 1 model selected  

> select clear

> select ribose

192 atoms, 192 bonds, 12 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel wheat

> select clear

> select guanine

48 atoms, 52 bonds, 4 residues, 1 model selected  

> color sel forest green

> select ribose

192 atoms, 192 bonds, 12 residues, 1 model selected  

> color sel wheat

> undo

> color sel wheat target acsp

> color sel wheat target acsp

> color sel wheat target cspf

> nucleotides sel atoms

> style nucleic & sel stick

Changed 192 atom styles  

> select phosphonate

Nothing selected  

> select phosphate

55 atoms, 44 bonds, 12 residues, 1 model selected  

> color sel wheat target cspf

> color sel wheat

> select clear

> save "/Users/jon/Documents/Documents/Lab
> Documents/HymanLab/TDP43_RNA_4BS2.cxs"

> ui tool show "Show Sequence Viewer"

> sequence chain /B

Alignment identifier is 1.1/B  

> select /B:5

31 atoms, 33 bonds, 1 residue, 1 model selected  

> select /B:5

31 atoms, 33 bonds, 1 residue, 1 model selected  

> ui tool show Contacts

Illegal contacts 'color' attribute value (Color([0.9764706, 0.07058824,
0.11764706, 1.0])), leaving attribute unchanged  

> show #1.1.1 models

> select /A:256

17 atoms, 17 bonds, 1 residue, 1 model selected  

> show (sel-residues & sidechain) target ab

> select /A:104

11 atoms, 10 bonds, 1 residue, 1 model selected  

> save "/Users/jon/Documents/Documents/Lab
> Documents/HymanLab/TDP43_RNA_4BS2.cxs"

> show (sel-residues & sidechain) target ab

> select /A:149

20 atoms, 20 bonds, 1 residue, 1 model selected  

> show (sel-residues & sidechain) target ab

> select /A:181

22 atoms, 21 bonds, 1 residue, 1 model selected  

> show (sel-residues & sidechain) target ab

Back buffer dpr of 1 doesn't match <_NSViewBackingLayer: 0x7f81bb6af580>
contents scale of 2 - updating layer to match.  

Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x7f81bb6af580>
contents scale of 1 - updating layer to match.  

Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x7f81bb6af580>
contents scale of 1 - updating layer to match.  

Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x7f81bb6af580>
contents scale of 1 - updating layer to match.  

Back buffer dpr of 1 doesn't match <_NSViewBackingLayer: 0x7f81bb6af580>
contents scale of 2 - updating layer to match.  

Back buffer dpr of 1 doesn't match <_NSViewBackingLayer: 0x7f81bb6af580>
contents scale of 2 - updating layer to match.  

Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x7f81bb6af580>
contents scale of 1 - updating layer to match.  

Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x7f81bb6af580>
contents scale of 1 - updating layer to match.  

Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x7f81bb6af580>
contents scale of 1 - updating layer to match.  

Window position QRect(294,-448 654x459) outside any known screen, using
primary screen  

> save "/Users/jon/Documents/Documents/Lab
> Documents/HymanLab/TDP43_RNA_4BS2.cxs"

——— End of log from Mon Jan 30 10:48:52 2023 ———

opened ChimeraX session  

> select /A:179

14 atoms, 13 bonds, 1 residue, 1 model selected  

> show (sel-residues & sidechain) target ab

> select /A:180

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show (sel-residues & sidechain) target ab

> select /A:254

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show (sel-residues & sidechain) target ab

> select /A:105

12 atoms, 11 bonds, 1 residue, 1 model selected  

> show (sel-residues & sidechain) target ab

> select /A:255

16 atoms, 15 bonds, 1 residue, 1 model selected  

> show (sel-residues & sidechain) target ab

> undo

> select /A:197

24 atoms, 23 bonds, 1 residue, 1 model selected  

> show (sel-residues & sidechain) target ab

> select /A:176

22 atoms, 21 bonds, 1 residue, 1 model selected  

> show (sel-residues & sidechain) target ab

> undo

> select /A:147

20 atoms, 20 bonds, 1 residue, 1 model selected  

> show (sel-residues & sidechain) target ab

> lighting simple

> lighting simple

> lighting soft

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> lighting simple

> lighting soft

> lighting full

> lighting shadows false

> lighting simple

> lighting shadows true

> lighting soft

> select clear

> select H

1485 atoms, 186 residues, 1 model selected  

> hide sel target a

> select clear

> save "/Users/jon/Documents/Documents/Lab
> Documents/HymanLab/TDP43_RNA_4BS2.cxs"

> select O

347 atoms, 186 residues, 1 model selected  

> color sel red

> undo

> select clear

> select /A:172

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:173

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select add /A:172

35 atoms, 35 bonds, 2 residues, 1 model selected  

> select add /A:174

47 atoms, 46 bonds, 3 residues, 1 model selected  

> select add /A:175

58 atoms, 56 bonds, 4 residues, 1 model selected  

> show (sel-residues & sidechain) target ab

> select /A:145

22 atoms, 21 bonds, 1 residue, 1 model selected  

> show (sel-residues & sidechain) target ab

> select /A:114

22 atoms, 21 bonds, 1 residue, 1 model selected  

> show (sel-residues & sidechain) target ab

> save "/Users/jon/Documents/Documents/Lab
> Documents/HymanLab/TDP43_RNA_4BS2.cxs"

——— End of log from Tue Jan 31 11:27:41 2023 ———

opened ChimeraX session  

> select /A

2774 atoms, 2804 bonds, 174 residues, 1 model selected  

> hide sel target a

> select clear

> rotate -x 1 90

Unknown command: rotate -x 1 90  

> rotate x -1 90

Unknown command: rotate x -1 90  

> rotate x 1 90

Unknown command: rotate x 1 90  

> turn x 1 90

> turn x -1 90

> turn y 1 90

> wait

> turn y -1 90

> wait

> turn x 1 90

> wait

> turn x -1 90

> wait

> select /B:7

32 atoms, 34 bonds, 1 residue, 1 model selected  

> select /B:7

32 atoms, 34 bonds, 1 residue, 1 model selected  

> ui tool show "Color Actions"

> color sel teal

> select ribose

192 atoms, 192 bonds, 12 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel tan

> color sel wheat

> select phosphate

55 atoms, 44 bonds, 12 residues, 1 model selected  

> color sel red

> ui tool show "Color Actions"

> color sel tomato

> color sel fire brick

> select clear

> graphics silhouettes false

> graphics silhouettes true

> lighting full

> select /B:1

28 atoms, 30 bonds, 1 residue, 1 model selected  

> select /B:1

28 atoms, 30 bonds, 1 residue, 1 model selected  

> ui tool show "Color Actions"

> color sel wheat

> select /B:2

30 atoms, 31 bonds, 1 residue, 1 model selected  

> select /B:2

30 atoms, 31 bonds, 1 residue, 1 model selected  

> color sel wheat

> select /B:4

30 atoms, 31 bonds, 1 residue, 1 model selected  

> select /B:4

30 atoms, 31 bonds, 1 residue, 1 model selected  

> color sel wheat

> select /B:6

32 atoms, 34 bonds, 1 residue, 1 model selected  

> select /B:6

32 atoms, 34 bonds, 1 residue, 1 model selected  

> color sel wheat

> select /B:8

30 atoms, 31 bonds, 1 residue, 1 model selected  

> select /B:8

30 atoms, 31 bonds, 1 residue, 1 model selected  

> color sel wheat

> select /B:10-11

64 atoms, 69 bonds, 2 residues, 1 model selected  

> select /B:10-11

64 atoms, 69 bonds, 2 residues, 1 model selected  

> select /B:12

30 atoms, 31 bonds, 1 residue, 1 model selected  

> select /B:10-12

94 atoms, 101 bonds, 3 residues, 1 model selected  

> color sel wheat

> select phosphate

55 atoms, 44 bonds, 12 residues, 1 model selected  

> color sel fire brick

> select ::name="G"

121 atoms, 129 bonds, 4 residues, 1 model selected  

> color sel lime

> select clear

> select /B:1

28 atoms, 30 bonds, 1 residue, 1 model selected  

> select /B:1

28 atoms, 30 bonds, 1 residue, 1 model selected  

> color sel wheat

> select phosphate

55 atoms, 44 bonds, 12 residues, 1 model selected  

> color sel fire brick

> select clear

> turn y 1 90

> wait

> turn y -1 90

> wait

> turn x 1 90

> wait

> turn x -1 90

> wait

> save "/Users/jon/Documents/Documents/Lab
> Documents/HymanLab/TDP43_RNA_4BS2.cxs"

> turn y 1 90

> wait

> turn y -1 90

> wait

> turn x 1 90

> wait

> turn x -1 90

> wait

> turn y 1 90

> wait

> turn y -1 90

> wait

> turn x 1 90

> wait

> turn x -1 90

> wait

> select /B

369 atoms, 400 bonds, 12 residues, 1 model selected  

> select clear

> hide chain B;

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide chain B

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide /B cartoons

> hide /b cartoons

> hide /chain bonds cartoon

Expected ',' or a keyword  

> select Chain B

Expected an objects specifier or a keyword  

> select Chain B

Expected an objects specifier or a keyword  

> ~display ~ :.B

> hide ~ :.B

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> ~display ~ : .B

> hide ~ : .B

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> select : .B

Expected an objects specifier or a keyword  

> select: chain B

Unknown command: select: chain B  

> select /A:175

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show (sel-residues & sidechain) target ab

> select /A:172

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:172

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:173

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show (sel-residues & sidechain) target ab

> select H

1485 atoms, 186 residues, 1 model selected  

> hide sel target a

> select clear

> select /A:175

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select add /A:173

22 atoms, 20 bonds, 2 residues, 1 model selected  

> color sel gold target a

> select clear

> lighting simple

> lighting soft

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> lighting soft

> select: chain B []

Unknown command: select: chain B []  

> select chain B []

Expected an objects specifier or a keyword  

> select chain B [][]

Expected an objects specifier or a keyword  

> select chain B al

Expected an objects specifier or a keyword  

> select chain B all

Expected an objects specifier or a keyword  

> select Chain B

Expected an objects specifier or a keyword  

> select Chain B;

Expected an objects specifier or a keyword  

> select Chain B;

Expected an objects specifier or a keyword  

> select nucleic acid

Expected a keyword  

> select /B

369 atoms, 400 bonds, 12 residues, 1 model selected  

> select clear

> select chain: B

Expected an objects specifier or a keyword  

> select chain :B

Expected an objects specifier or a keyword  

> select chain B

Expected an objects specifier or a keyword  

> select chain B

Expected an objects specifier or a keyword  

> sel: chain B

Unknown command: sel: chain B  

> select: chain B

Unknown command: select: chain B  

> select chain B

Expected an objects specifier or a keyword  

> select chain B [atoms]

Expected an objects specifier or a keyword  

> selchain B

Unknown command: selchain B  

> selChain B

Unknown command: selChain B  

> selChainB

Unknown command: selChainB  

> selChainB

Unknown command: selChainB  

> select ChainB

Expected an objects specifier or a keyword  

> select Chain B

Expected an objects specifier or a keyword  

> movie record

> wait

wait requires a frame count argument unless motion is in progress  

> turn y 1 90

> wait

> turn y -1 90

> wait

> turn x 1 90

> wait

> turn x -1 90

> wait

> movie encode

Movie saved to /Users/jon/Desktop/movie.mp4  
  

> wait

wait requires a frame count argument unless motion is in progress  

> turn y 1 90

> wait

> turn y -1 90

> wait

> turn x 1 90

> wait

> turn x -1 90

> wait

> movie record

> wait

wait requires a frame count argument unless motion is in progress  

> turn y 1 90

> wait

> turn y -1 90

> wait

> turn x 1 90

> wait

> turn x -1 90

> wait

> movie encode

Movie saved to /Users/jon/Desktop/movie.mp4  
  

> select ribose

192 atoms, 192 bonds, 12 residues, 1 model selected  

> color sel wheat target a

> select clear

> save "/Users/jon/Documents/Documents/Lab
> Documents/HymanLab/TDP43_RNA_4BS2.cxs"

> select /B:6

32 atoms, 34 bonds, 1 residue, 1 model selected  

> select /B:6

32 atoms, 34 bonds, 1 residue, 1 model selected  

> color sel dim gray target a

> undo

> color sel lavender blush target a

> undo

> color sel slate gray target a

> undo

> color sel light gray target a

> undo

> select clear

> toolshed show

> wait

wait requires a frame count argument unless motion is in progress  

> turn y 1 90

> wait

> turn y -1 90

> wait

> turn x 1 90

> wait

> turn x -1 90

> wait

> wait

wait requires a frame count argument unless motion is in progress  

> turn y 1 90

> wait

> turn y -1 90

> wait

> turn x 1 90

> wait

> turn x -1 90

> wait

> wait

wait requires a frame count argument unless motion is in progress  

> turn y 1 90

> wait

> turn y -1 90

> wait

> turn x 1 90

> wait

> turn x -1 90

> wait

> movie record

> wait

wait requires a frame count argument unless motion is in progress  

> turn y 1 90

> wait

> turn y -1 90

> wait

> turn x 1 90

> wait

> turn x -1 90

> wait

> movie encode

Movie saved to /Users/jon/Desktop/movie.mp4  
  

> wait

wait requires a frame count argument unless motion is in progress  

> turn y 1 90

> wait

> turn y -1 90

> wait

> turn x 1 90

> wait

> turn x -1 90

> wait

> movie record

> wait

wait requires a frame count argument unless motion is in progress  

> turn y 1 90

> wait

> turn y -1 90

> wait

> turn x 1 90

> wait

> turn x -1 90

> wait

> movie encode

Movie saved to /Users/jon/Desktop/movie.mp4  
  

> movie record

> wait

wait requires a frame count argument unless motion is in progress  

> turn y 1 90

> wait

> turn y -1 90

> wait

> turn x 1 90

> wait

> turn x -1 90

> wait

> movie encode

Movie saved to /Users/jon/Desktop/movie.mp4  
  

> movie record

> wait

wait requires a frame count argument unless motion is in progress  

> turn y 1 90

> wait

> turn y -1 110

> wait

> turn x 1 110

> wait

> turn x -1 90

> wait

> movie encode

Movie saved to /Users/jon/Desktop/movie.mp4  
  

> movie record

> wait

wait requires a frame count argument unless motion is in progress  

> turn y 1 90

> wait

> turn y -1 90

> wait

> turn x 1 110

> wait

> turn x -1 110

> wait

> movie encode

Movie saved to /Users/jon/Desktop/movie.mp4  
  

> save "/Users/jon/Documents/Documents/Lab
> Documents/HymanLab/TDP43_RNA_4BS2.cxs"

> hide ligand

> hide chain B

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide 'chain B'

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide "chain B"

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide chain B [ala]

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide chain B [all]

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide chain B [atoms]

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide chain B [100]

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide nucleic

> show nucleic

> save "/Users/jon/Documents/Documents/Lab
> Documents/HymanLab/TDP43_RNA_4BS2_2.cxs"

> select H

1485 atoms, 186 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> hide nucleic

> show nucleic

> hide nucleic

> wait

wait requires a frame count argument unless motion is in progress  

> crossfade

> show nucleic

> hide nucleic

> crossfade

> show nucleic

> hide nucleic

> wait

wait requires a frame count argument unless motion is in progress  

> crossfade

> show nucleic

> wait

wait requires a frame count argument unless motion is in progress  

> hide nucleic

> wait

wait requires a frame count argument unless motion is in progress  

> crossfade

> show nucleic

> hide nucleic

> crossfade 60

> show nucleic

> hide nucleic

> crossfade 120

> show nucleic

> hide nucleic

> crossfade 120

> show nucleic

> wait

wait requires a frame count argument unless motion is in progress  

> turn y 1 90

> wait

> turn y -1 90

> wait

> turn x 1 90

> wait

> turn x -1 90

> wait

> movie encode

No frames have been recorded  

> hide nucleic

> crossfade 120

> show nucleic

> wait 120

> turn y 1 90

> wait

> turn y -1 90

> wait

> turn x 1 90

> wait

> turn x -1 90

> wait

> movie encode

No frames have been recorded  

> hide nucleic

> movie record

> wait

wait requires a frame count argument unless motion is in progress  

> crossfade 120

> show nucleic

> wait 120

> turn y 1 90

> wait

> turn y -1 90

> wait

> turn x 1 90

> wait

> turn x -1 90

> wait

> movie encode

Movie saved to /Users/jon/Desktop/movie.mp4  
  

> save "/Users/jon/Documents/Documents/Lab
> Documents/HymanLab/TDP43_RNA_4BS2_2.cxs"

> wait

wait requires a frame count argument unless motion is in progress  

> crossfade 90

> show nucleic

> wait 120

> turn y 1 90

> wait

> turn y -1 90

> wait

> turn x 1 90

> wait

> turn x -1 90

> wait

> wait

wait requires a frame count argument unless motion is in progress  

> crossfade 90

> show nucleic

> wait 120

> turn y 1 90

> wait

> turn y -1 90

> wait

> turn x 1 90

> wait

> turn x -1 90

> wait

> hide nucleic

> wait

wait requires a frame count argument unless motion is in progress  

> crossfade 90

> show nucleic

> wait 120

> turn y 1 90

> wait

> turn y -1 90

> wait

> turn x 1 90

> wait

> turn x -1 90

> wait

> hide nucleic

> hide nucleic

> movie record

> wait

wait requires a frame count argument unless motion is in progress  

> crossfade 90

> show nucleic

> wait 120

> turn y 1 90

> wait

> turn y -1 90

> wait

> turn x 1 90

> wait

> turn x -1 90

> movie encode

Movie saved to /Users/jon/Desktop/movie.mp4  
  

> hide nucleic

> wait

wait requires a frame count argument unless motion is in progress  

> crossfade 90

> show nucleic

> wait 120

> turn y 1 90

> wait

> turn x 1 90

> wait

> turn x -1 90

> wait

> turn y -1 90

> hide nucleic

> wait

wait requires a frame count argument unless motion is in progress  

> crossfade 90

> show nucleic

> wait 120

> turn y 1 90

> wait

> turn x 1 90

> wait

> turn x -1 90

> wait

> turn y -1 90

> crossfade 90

> show nucleic

> wait 120

> turn y 1 90

> wait

> turn x 1 90

> wait

> turn x -1 90

> wait

> turn y -1 90

> hide nucleic

> crossfade 90

> show nucleic

> wait 120

> turn y 1 90

> wait

> turn x 1 90

> wait

> turn x -1 90

> wait

> turn y -1 90

> wait

> hide nucleic

> crossfade 90

> show nucleic

> wait 120

> turn y 1 90

> wait

> turn z 1 90

> wait

> turn x -1 90

> wait

> turn y -1 90

> wait

> hide nucleic

> crossfade 90

> show nucleic

> wait 120

> turn y 1 90

> wait

> turn x 1 90

> wait

> turn z 1 90

> wait

> turn y -1 90

> wait

> hide nucleic

> crossfade 90

> show nucleic

> wait 120

> turn y 1 90

> wait

> turn x 1 90

> wait

> turn z -1 90

> wait

> turn y -1 90

> wait

> hide nucleic

> crossfade 90

> show nucleic

> wait 120

> turn y 1 90

> wait

> turn x 1 90

> wait

> turn z -1 90

> wait

> turn y 1 90

> wait

> hide nucleic

> crossfade 90

> show nucleic

> wait 120

> turn y 1 90

> wait

> turn x 1 90

> wait

> turn z -1 90

> wait

> turn x -1 90

> wait

> hide nucleic

> wait

wait requires a frame count argument unless motion is in progress  

> crossfade 90

> show nucleic

> wait 120

> turn y 1 90

> wait

> turn x 1 90

> wait

> turn z -1 90

> wait

> turn x -1 90

> wait

> hide nucleic

> wait

wait requires a frame count argument unless motion is in progress  

> crossfade 90

> show nucleic

> wait 120

> turn y 1 90

> wait

> turn x 1 90

> wait

> turn z -1 90

> wait

> turn x -1 90

> wait

> hide nucleic

> wait

wait requires a frame count argument unless motion is in progress  

> crossfade 90

> show nucleic

> wait 120

> turn y 1 90

> wait

> turn x 1 90

> wait

> turn z -1 90

> wait

> turn x -1 90

> wait

> hide nucleic

> wait

wait requires a frame count argument unless motion is in progress  

> crossfade 90

> show nucleic

> wait 120

> turn y 1 90

> wait

> turn x 1 90

> wait

> turn z -1 90

> wait

> turn x -1 90

> wait

> hide nucleic

> wait

wait requires a frame count argument unless motion is in progress  

> movie record

> wait

wait requires a frame count argument unless motion is in progress  

> crossfade 90

> show nucleic

> wait 120

> turn y 1 90

> wait

> turn x 1 90

> wait

> turn z -1 90

> wait

> turn x -1 90

> wait

> movie encode

Movie saved to /Users/jon/Desktop/movie.mp4  
  

> wait

wait requires a frame count argument unless motion is in progress  

> hide nucleic

> wait

wait requires a frame count argument unless motion is in progress  

> movie record

> wait

wait requires a frame count argument unless motion is in progress  

> crossfade 90

> show nucleic

> wait 120

> turn y 1 90

> wait

> turn x 1 90

> wait

> turn z -1 90

> wait

> turn x -1 90

> wait

> turn y -5 360

> wait

> movie encode

Movie saved to /Users/jon/Desktop/movie.mp4  
  

> wait

wait requires a frame count argument unless motion is in progress  

> hide nucleic

> wait

wait requires a frame count argument unless motion is in progress  

> save "/Users/jon/Documents/Documents/Lab
> Documents/HymanLab/TDP43_RNA_4BS2_movie.cxs"

> close session

Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 932, in <lambda>  
close_action.triggered.connect(lambda *, s=self, sess=session:
s.file_close_cb(sess))  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 652, in file_close_cb  
run(session, 'close session')  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/std_commands/close.py", line 60, in close_session  
session.reset()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/manager.py", line 252, in reset_state  
alignment._destroy()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 603, in _destroy  
self._notify_observers(self.NOTE_DESTROYED, None)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 652, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 474, in alignment_notification  
self.delete()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 512, in delete  
ToolInstance.delete(self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 154, in delete  
self.session.ui.remove_tool(self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 345, in remove_tool  
self.main_window.remove_tool(tool_instance)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 725, in remove_tool  
tw._destroy()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2049, in _destroy  
self.__toolkit.destroy()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2189, in destroy  
sbar.destroy()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/statusbar.py", line 51, in destroy  
v.delete()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 438, in delete  
self.make_current()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 478, in make_current  
return self._opengl_context.make_current()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 99, in make_current  
qc = self._initialize_context()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context  
qc.setScreen(self._screen)  
RuntimeError: wrapped C/C++ object of type QScreen has been deleted  
  
RuntimeError: wrapped C/C++ object of type QScreen has been deleted  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context  
qc.setScreen(self._screen)  
  
See log for complete Python traceback.  
  

> open "/Users/jon/Documents/Documents/Lab
> Documents/HymanLab/TDP43_RNA_4BS2_movie.cxs" format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 679, in restore  
self.reset()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 679, in restore  
self.reset()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, 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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 324, in interceptRequest  
self._callback(info)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 85, in _intercept  
return interceptor(request_info, *args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 357, in intercept  
chimerax_intercept(*args, view=view, session=session)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 453, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 366, in thread_safe  
func(*args, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 444, in defer  
cxcmd(session, topic)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 462, in cxcmd  
run(session, cmd)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 179, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 422, in collated_open  
return func(*func_args, **func_kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 982, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 721, in restore  
self.reset()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
  
See log for complete Python traceback.  
  

> open "/Users/jon/Documents/Documents/Lab
> Documents/HymanLab/TDP43_RNA_4BS2_movie.cxs" format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 679, in restore  
self.reset()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 679, in restore  
self.reset()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, 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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 324, in interceptRequest  
self._callback(info)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 85, in _intercept  
return interceptor(request_info, *args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 357, in intercept  
chimerax_intercept(*args, view=view, session=session)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 453, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 366, in thread_safe  
func(*args, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 444, in defer  
cxcmd(session, topic)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 462, in cxcmd  
run(session, cmd)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 179, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 422, in collated_open  
return func(*func_args, **func_kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 982, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 721, in restore  
self.reset()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
  
See log for complete Python traceback.  
  

> open "/Users/jon/Documents/Documents/Lab
> Documents/HymanLab/TDP43_RNA_4BS2_movie.cxs" format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 679, in restore  
self.reset()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 679, in restore  
self.reset()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, 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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 324, in interceptRequest  
self._callback(info)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 85, in _intercept  
return interceptor(request_info, *args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 357, in intercept  
chimerax_intercept(*args, view=view, session=session)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 453, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 366, in thread_safe  
func(*args, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 444, in defer  
cxcmd(session, topic)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 462, in cxcmd  
run(session, cmd)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 179, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 422, in collated_open  
return func(*func_args, **func_kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 982, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 721, in restore  
self.reset()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
  
See log for complete Python traceback.  
  

> open "/Users/jon/Documents/Documents/Lab
> Documents/HymanLab/TDP43_RNA_4BS2_movie.cxs" format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 679, in restore  
self.reset()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 679, in restore  
self.reset()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, 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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 324, in interceptRequest  
self._callback(info)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 85, in _intercept  
return interceptor(request_info, *args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 357, in intercept  
chimerax_intercept(*args, view=view, session=session)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 453, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 366, in thread_safe  
func(*args, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 444, in defer  
cxcmd(session, topic)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 462, in cxcmd  
run(session, cmd)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 179, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 422, in collated_open  
return func(*func_args, **func_kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 982, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 721, in restore  
self.reset()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
  
See log for complete Python traceback.  
  

> open "/Users/jon/Documents/Documents/Lab
> Documents/HymanLab/TDP43_RNA_4BS2_movie.cxs"

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 679, in restore  
self.reset()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 679, in restore  
self.reset()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, 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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/dialog.py", line 155, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 179, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 422, in collated_open  
return func(*func_args, **func_kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 982, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 721, in restore  
self.reset()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
  
See log for complete Python traceback.  
  

> open "/Users/jon/Documents/Documents/Lab
> Documents/HymanLab/TDP43_RNA_4BS2_2.cxs" format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 679, in restore  
self.reset()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 679, in restore  
self.reset()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, 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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 324, in interceptRequest  
self._callback(info)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 85, in _intercept  
return interceptor(request_info, *args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 357, in intercept  
chimerax_intercept(*args, view=view, session=session)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 453, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 366, in thread_safe  
func(*args, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 444, in defer  
cxcmd(session, topic)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 462, in cxcmd  
run(session, cmd)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 179, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 422, in collated_open  
return func(*func_args, **func_kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 982, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 721, in restore  
self.reset()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
  
See log for complete Python traceback.  
  

> open "/Users/jon/Documents/Documents/Lab
> Documents/HymanLab/TDP43_RNA_4BS2_2.cxs" format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 679, in restore  
self.reset()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 679, in restore  
self.reset()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, 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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 324, in interceptRequest  
self._callback(info)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 85, in _intercept  
return interceptor(request_info, *args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 357, in intercept  
chimerax_intercept(*args, view=view, session=session)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 453, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 366, in thread_safe  
func(*args, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 444, in defer  
cxcmd(session, topic)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 462, in cxcmd  
run(session, cmd)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 179, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 422, in collated_open  
return func(*func_args, **func_kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 982, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 721, in restore  
self.reset()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
  
See log for complete Python traceback.  
  

> open "/Users/jon/Documents/Documents/Lab
> Documents/HymanLab/TDP43_RNA_4BS2.cxs" format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 679, in restore  
self.reset()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 679, in restore  
self.reset()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, 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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 324, in interceptRequest  
self._callback(info)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 85, in _intercept  
return interceptor(request_info, *args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 357, in intercept  
chimerax_intercept(*args, view=view, session=session)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 453, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 366, in thread_safe  
func(*args, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 444, in defer  
cxcmd(session, topic)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 462, in cxcmd  
run(session, cmd)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 179, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 422, in collated_open  
return func(*func_args, **func_kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 982, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 721, in restore  
self.reset()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
  
See log for complete Python traceback.  
  

> open "/Users/jon/Documents/Documents/Lab
> Documents/HymanLab/TDP43_RNA_4BS2.cxs" format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 679, in restore  
self.reset()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 679, in restore  
self.reset()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, 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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 324, in interceptRequest  
self._callback(info)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 85, in _intercept  
return interceptor(request_info, *args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 357, in intercept  
chimerax_intercept(*args, view=view, session=session)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 453, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 366, in thread_safe  
func(*args, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 444, in defer  
cxcmd(session, topic)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 462, in cxcmd  
run(session, cmd)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 179, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 422, in collated_open  
return func(*func_args, **func_kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 982, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 721, in restore  
self.reset()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-18.8.5
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro14,1
      Processor Name: Dual-Core Intel Core i7
      Processor Speed: 2,5 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 451.140.1.0.0
      OS Loader Version: 540.120.3~22
      SMC Version (system): 2.43f11

Software:

    System Software Overview:

      System Version: macOS 12.6 (21G115)
      Kernel Version: Darwin 21.6.0
      Time since boot: 9 days 4:52

Graphics/Displays:

    Intel Iris Plus Graphics 640:

      Chipset Model: Intel Iris Plus Graphics 640
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x5926
      Revision ID: 0x0006
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.4.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.3
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.2
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.2
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.4
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.7
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 1.1.1
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0

[Eric Pettersen]

1.2.2