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

[fatmaouf@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
Hello,

While saving as chimeraX session, I get the error in file attached. 
I don't face this problem each time I want to save as CXS file so I don't know the reason.
I have displayed a cmap and pdbs fitted in the map. I used tools/sequence viewer to hide a region from DNA. 
I already did save many files as CXS doing the same manipulation and didn't get any problem.

Thank you for your help,
Fadwa 

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open
> C:\\\Users\\\fatmaouf\\\Desktop\\\hemisome_box_ts14\\\ts14_hemisomebox_newfitting1605_split.cxs

Log from Sat May 14 17:59:08 2022UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open
> C:\\\Users\\\fatmaouf\\\Desktop\\\hemisome_box_ts14\\\ts14_hemisomebox_fittinglines_FIG.cxs

Log from Thu Feb 10 11:38:57 2022UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\\\Users\\\fatmaouf\\\Downloads\\\2pyo.pdb

2pyo.pdb title:  
Drosophila nucleosome core [more info...]  
  
Chain information for 2pyo.pdb #1  
---  
Chain | Description  
A E | histone H3  
B F | histone H4  
C G | histone H2A  
D H | histone H2B  
I | DNA (147-mer)  
J | DNA (147-mer)  
  
Non-standard residues in 2pyo.pdb #1  
---  
CL — chloride ion  
MN — manganese (II) ion  
  

> sequence chain #1/A#1/E

Alignment identifier is 1  

> select /H:28-122

753 atoms, 764 bonds, 95 residues, 1 model selected  

> hide sel target a

> select /H:28-122

753 atoms, 764 bonds, 95 residues, 1 model selected  

> select /D:28-122

753 atoms, 764 bonds, 95 residues, 1 model selected  

> select /H:28-122

753 atoms, 764 bonds, 95 residues, 1 model selected  

> select /G:11-119

824 atoms, 834 bonds, 109 residues, 1 model selected  

> hide sel target a

> select /F:15-102

708 atoms, 716 bonds, 88 residues, 1 model selected  

> hide sel target a

> select /E:37-135

816 atoms, 828 bonds, 99 residues, 1 model selected  

> hide sel target a

> select solvent

88 atoms, 88 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /I:-73-73

3011 atoms, 3378 bonds, 147 residues, 1 model selected  

> sequence chain #1/I

Alignment identifier is 1/I  

> sequence chain #1/I

Destroying pre-existing alignment with identifier 1/I  
Alignment identifier is 1/I  

> hide sel target a

> sequence chain #1/J

Alignment identifier is 1/J  

> hide sel target a

> hide sel target a

> hide sel target a

> open C:/Users/fatmaouf/Desktop/hemisome_box_ts14/hemisomemap.cmap

Opened hemisomemap.cmap, grid size 129,120,82, pixel 2, shown at level 0.0626,
step 1, values float32  

> select #1

12151 atoms, 12947 bonds, 3 pseudobonds, 1085 residues, 2 models selected  

> ui mousemode right "translate selected models"

> ui tool show "Map Coordinates"

> save C:/Users/fatmaouf/Desktop/hemisome_box_ts14/halfnucleosome.pdb
> displayedOnly true relModel #1

> open C:/Users/fatmaouf/Desktop/hemisome_box_ts14/halfnucleosome.pdb

Summary of feedback from opening
C:/Users/fatmaouf/Desktop/hemisome_box_ts14/halfnucleosome.pdb  
---  
warnings | Ignored bad PDB record found on line 6829  
END  
  
Start residue of secondary structure not found: HELIX 19 19 GLY E 44 SER E 57
1 14  
Start residue of secondary structure not found: HELIX 20 20 ARG E 63 ASP E 77
1 15  
Start residue of secondary structure not found: HELIX 21 21 GLN E 85 ALA E 114
1 30  
Start residue of secondary structure not found: HELIX 22 22 MET E 120 ARG E
131 1 12  
Start residue of secondary structure not found: HELIX 23 23 ASP F 24 ILE F 29
1 6  
23 messages similar to the above omitted  
Cannot find LINK/SSBOND residue DG (-34 )  
Cannot find LINK/SSBOND residue ASP (77 )  
  
halfnucleosome.pdb title:  
Drosophila nucleosome core [more info...]  
  
Chain information for halfnucleosome.pdb #3  
---  
Chain | Description  
A | histone H3  
B | histone H4  
C | histone H2A  
D | histone H2B  
I | DNA (147-mer)  
J | DNA (147-mer)  
  
Non-standard residues in halfnucleosome.pdb #3  
---  
CL — chloride ion  
MN — manganese (II) ion  
  

> hide #!3 models

> show #!3 models

> select #3

5896 atoms, 6266 bonds, 1 pseudobond, 540 residues, 2 models selected  

> hide #!1 models

> hide #!3 models

> show #!3 models

> volume #2 level 0.1241

> show #!1 models

> select #1

12151 atoms, 12947 bonds, 3 pseudobonds, 1085 residues, 2 models selected  

> save
> C:/Users/fatmaouf/Desktop/hemisome_box_ts14/ts14_hemisomebox_fitting.cxs
> includeMaps true

> show (#!1 & sel) target ab

> volume #2 level 0.1842

> hide #!2 models

> show #!2 models

> select #1/C

811 atoms, 821 bonds, 108 residues, 1 model selected  

> hide sel target a

> select #1/D

754 atoms, 764 bonds, 96 residues, 1 model selected  

> hide sel target a

> select #1/A

817 atoms, 828 bonds, 100 residues, 1 model selected  

> hide sel target a

> select #1/B

631 atoms, 638 bonds, 80 residues, 1 model selected  

> hide sel target a

> ui tool show "Show Sequence Viewer"

> sequence chain #1/I #3/I

Alignment identifier is 1  

> sequence chain #1/J #3/J

Alignment identifier is 2  
Seqview [ID: 1] region 2 chains [1-26] RMSD: 132.721  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/I

Alignment identifier is 1/I  

> sequence chain #1/J

Alignment identifier is 1/J  

> select #3

5896 atoms, 6266 bonds, 1 pseudobond, 540 residues, 2 models selected  

> select #1

12151 atoms, 12947 bonds, 3 pseudobonds, 1085 residues, 2 models selected  

> ~select #1

Nothing selected  

> hide sel target a

> hide sel target a

> volume #2 level 0.1481

> select #2

2 models selected  

> select #1

12151 atoms, 12947 bonds, 3 pseudobonds, 1085 residues, 2 models selected  

> select #2

2 models selected  

> transparency #2.1 80

> set bgColor white

> select #1

12151 atoms, 12947 bonds, 3 pseudobonds, 1085 residues, 2 models selected  

> style sel stick

Changed 12151 atom styles  

> show sel cartoons

> select #3

5896 atoms, 6266 bonds, 1 pseudobond, 540 residues, 2 models selected  

> show sel cartoons

> style sel stick

Changed 5896 atom styles  

> select #1/C#1/G#3/C

2446 atoms, 2476 bonds, 325 residues, 2 models selected  

> hide sel atoms

> select #1/D#1/H#3/D

2262 atoms, 2292 bonds, 288 residues, 2 models selected  

> hide sel atoms

> select #1/A#1/E#3/A

2452 atoms, 2484 bonds, 1 pseudobond, 301 residues, 3 models selected  

> hide sel atoms

> select #1/B#1/F#3/B

1970 atoms, 1992 bonds, 248 residues, 2 models selected  

> hide sel atoms

> hide sel cartoons

> hide sel cartoons

> show sel cartoons

> select #1

12151 atoms, 12947 bonds, 3 pseudobonds, 1085 residues, 2 models selected  

> select #3

5896 atoms, 6266 bonds, 1 pseudobond, 540 residues, 2 models selected  

> select solvent

14 atoms, 14 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #3

5882 atoms, 6266 bonds, 526 residues, 1 model selected  

> select #1/C

811 atoms, 821 bonds, 108 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #1/D

754 atoms, 764 bonds, 96 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #1/A

817 atoms, 828 bonds, 100 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> undo

Undo failed, probably because structures have been modified.  

> select #1/B

631 atoms, 638 bonds, 80 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #1/E

818 atoms, 828 bonds, 1 pseudobond, 101 residues, 2 models selected  

> select #1/H

754 atoms, 764 bonds, 96 residues, 1 model selected  

> select #1/G

824 atoms, 834 bonds, 109 residues, 1 model selected  

> select #2

2 models selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/I

Alignment identifier is 1/I  

> sequence chain #1/J

Alignment identifier is 1/J  

> ~select #2

Nothing selected  

> set bgColor black

> delete atoms sel

> delete bonds sel

> delete atoms sel

> delete bonds sel

> volume #2 level 0.1136

> select #3

5882 atoms, 6266 bonds, 526 residues, 1 model selected  

> save
> C:/Users/fatmaouf/Desktop/hemisome_box_ts14/ts14_hemisomebox_fitting.cxs
> includeMaps true

> save C:/Users/fatmaouf/Desktop/hemisome_box_ts14/hemisome.obj

> set bgColor white

> ~select #3

Nothing selected  

> select #1

6025 atoms, 6403 bonds, 2 pseudobonds, 549 residues, 2 models selected  

> select #3

5882 atoms, 6266 bonds, 526 residues, 1 model selected  

> volume #2 level 0.04307

> volume #2 level 0.1061

> open C:/Users/fatmaouf/Desktop/hemisome_box_ts14/dnaline.pdb

Chain information for dnaline.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open C:/Users/fatmaouf/Desktop/hemisome_box_ts14/dnaline.pdb

Chain information for dnaline.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open C:/Users/fatmaouf/Desktop/hemisome_box_ts14/dnaline.pdb

Chain information for dnaline.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #5 models

> hide #4 models

> volume #2 level 0.1331

> open C:/Users/fatmaouf/Desktop/hemisome_box_ts14/dnaline2.pdb

Chain information for dnaline2.pdb #7  
---  
Chain | Description  
A B | No description available  
  

> open C:/Users/fatmaouf/Desktop/hemisome_box_ts14/dnaline2.pdb

Chain information for dnaline2.pdb #8  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #7 models

> close #7

> close #5

> close #4

> save
> C:/Users/fatmaouf/Desktop/hemisome_box_ts14/ts14_hemisomebox_fittinglines.cxs
> includeMaps true

> open C:/Users/fatmaouf/Desktop/hemisome_box_ts14/dnaline2.pdb

Chain information for dnaline2.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> close #8

> save
> C:/Users/fatmaouf/Desktop/hemisome_box_ts14/ts14_hemisomebox_fittinglines.cxs
> includeMaps true

> style sel stick

Changed 5882 atom styles  

> nucleotides sel ladder

> select #1

6025 atoms, 6403 bonds, 2 pseudobonds, 549 residues, 2 models selected  

> nucleotides sel ladder

> select #3

5882 atoms, 6266 bonds, 526 residues, 1 model selected  

> nucleotides sel ladder

> select #4

1271 atoms, 1424 bonds, 62 residues, 1 model selected  

> nucleotides sel ladder

> select #6

2255 atoms, 2528 bonds, 110 residues, 1 model selected  

> nucleotides sel ladder

> ~select #6

Nothing selected  

> select #6

2255 atoms, 2528 bonds, 110 residues, 1 model selected  

> close #6

> open C:/Users/fatmaouf/Desktop/hemisome_box_ts14/dnaline.pdb

Chain information for dnaline.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> view orient

> view orient

> ui tool show "Side View"

> ui mousemode right rotate

> ui mousemode right translate

> ui mousemode right rotate

> ui mousemode right translate

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\fatmaouf\Desktop\movie5.mp4

Movie saved to \C:Users\\...\Desktop\movie5.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\fatmaouf\Desktop\movie6.mp4

Movie saved to \C:Users\\...\Desktop\movie6.mp4  
  

> save C:\Users\fatmaouf\Desktop\image7.png supersample 3

> save C:\Users\fatmaouf\Desktop\image8.png supersample 3

> save C:\Users\fatmaouf\Desktop\image9.png supersample 3

> save C:\Users\fatmaouf\Desktop\image10.png supersample 3

> save C:\Users\fatmaouf\Desktop\image11.png supersample 3

> save C:\Users\fatmaouf\Desktop\image12.png supersample 3

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\fatmaouf\Desktop\movie7.mp4

Movie saved to \C:Users\\...\Desktop\movie7.mp4  
  

> select #1/I#1/J#3/I#3/J

5788 atoms, 6476 bonds, 1 pseudobond, 295 residues, 3 models selected  

> color (#!1,3 & sel) purple

> select #4/A#5/A

1760 atoms, 1972 bonds, 86 residues, 2 models selected  

> color sel purple

> select #4/B#5/B

1766 atoms, 1980 bonds, 86 residues, 2 models selected  

> color sel purple

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\fatmaouf\Desktop\movie8.mp4

Movie saved to \C:Users\\...\Desktop\movie8.mp4  
  

> select #5

2255 atoms, 2528 bonds, 110 residues, 1 model selected  

> ~select #5

Nothing selected  

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\fatmaouf\Desktop\movie9.mp4

Movie saved to \C:Users\\...\Desktop\movie9.mp4  
  

> save C:\Users\fatmaouf\Desktop\image13.png supersample 3

> save C:\Users\fatmaouf\Desktop\image14.png supersample 3

> save C:\Users\fatmaouf\Desktop\image15.png supersample 3

> select #1/F#3/B

1339 atoms, 1354 bonds, 168 residues, 2 models selected  

> color sel light sea green

> select #1/E#3/A

1635 atoms, 1656 bonds, 1 pseudobond, 201 residues, 3 models selected  

> color (#!1,3 & sel) cyan

> select #1/F#3/B

1339 atoms, 1354 bonds, 168 residues, 2 models selected  

> color sel cyan

> select #1/E#3/A

1635 atoms, 1656 bonds, 1 pseudobond, 201 residues, 3 models selected  

> color (#!1,3 & sel) light sea green

> select #1/H#3/D

1508 atoms, 1528 bonds, 192 residues, 2 models selected  

> color sel blue

> select #1/G#3/C

1635 atoms, 1655 bonds, 217 residues, 2 models selected  

> color sel cornflower blue

> select #3

5882 atoms, 6266 bonds, 526 residues, 1 model selected  

> ~select #3

Nothing selected  

> save C:\Users\fatmaouf\Desktop\image16.png supersample 3

> save C:\Users\fatmaouf\Desktop\image17.png supersample 3

> save C:\Users\fatmaouf\Desktop\image18.png supersample 3

> save C:\Users\fatmaouf\Desktop\image19.png supersample 3

> save C:\Users\fatmaouf\Desktop\image20.png supersample 3

> save C:\Users\fatmaouf\Desktop\image21.png supersample 3

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\fatmaouf\Desktop\movie10.mp4

Movie saved to \C:Users\\...\Desktop\movie10.mp4  
  

> save C:\Users\fatmaouf\Desktop\image22.png supersample 3

> save C:\Users\fatmaouf\Desktop\image23.png supersample 3

> save C:\Users\fatmaouf\Desktop\image24.png supersample 3

> save C:\Users\fatmaouf\Desktop\image25.png supersample 3

> save C:\Users\fatmaouf\Desktop\image26.png supersample 3

> save
> C:/Users/fatmaouf/Desktop/hemisome_box_ts14/ts14_hemisomebox_fittinglines_FIG.cxs
> includeMaps true

opened ChimeraX session  

> hide #!3 models

> show #!3 models

> hide #!2 models

> hide #!1 models

> hide #4 models

> hide #5 models

> open C:/Users/fatmaouf/Downloads/2pyo.pdb

2pyo.pdb title:  
Drosophila nucleosome core [more info...]  
  
Chain information for 2pyo.pdb #6  
---  
Chain | Description  
A E | histone H3  
B F | histone H4  
C G | histone H2A  
D H | histone H2B  
I | DNA (147-mer)  
J | DNA (147-mer)  
  
Non-standard residues in 2pyo.pdb #6  
---  
CL — chloride ion  
MN — manganese (II) ion  
  

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!6 models

> show #!6 models

> hide #!1 models

> show #!1 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> view orient

> select #6

12239 atoms, 12947 bonds, 4 pseudobonds, 1173 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view orient

> show sel cartoons

> style sel stick

Changed 12239 atom styles  

> nucleotides sel ladder

> ~select #6

Nothing selected  

> select #6

12239 atoms, 12947 bonds, 4 pseudobonds, 1173 residues, 2 models selected  

> select #6/C#6/G

1652 atoms, 1655 bonds, 234 residues, 1 model selected  

> color sel blue

> select #6/D#6/H

1521 atoms, 1528 bonds, 205 residues, 1 model selected  

> color sel cyan

> hide sel atoms

> select #6/C#6/G

1652 atoms, 1655 bonds, 234 residues, 1 model selected  

> hide sel atoms

> select #6/A#6/E

1658 atoms, 1656 bonds, 2 pseudobonds, 224 residues, 2 models selected  

> hide sel atoms

> color (#!6 & sel) cornflower blue

> select #6/B#6/F

1362 atoms, 1354 bonds, 191 residues, 1 model selected  

> hide sel atoms

> color sel light sea green

> select #1/I#3/I

2893 atoms, 3236 bonds, 148 residues, 2 models selected  

> color sel purple

> select #6/I#6/J

6046 atoms, 6754 bonds, 2 pseudobonds, 319 residues, 2 models selected  

> color (#!6 & sel) purple

> select #6/C#6/G

1652 atoms, 1655 bonds, 234 residues, 1 model selected  

> color sel cornflower blue

> select #6/D#6/H

1521 atoms, 1528 bonds, 205 residues, 1 model selected  

> color sel blue

> select #6/B#6/F

1362 atoms, 1354 bonds, 191 residues, 1 model selected  

> color sel light sea green

> select #5

2255 atoms, 2528 bonds, 110 residues, 1 model selected  

> select #6/D#6/H

1521 atoms, 1528 bonds, 205 residues, 1 model selected  

> select #6/A#6/E

1658 atoms, 1656 bonds, 2 pseudobonds, 224 residues, 2 models selected  

> color (#!6 & sel) cyan

> select #4

1271 atoms, 1424 bonds, 62 residues, 1 model selected  

> select #6/C#6/G

1652 atoms, 1655 bonds, 234 residues, 1 model selected  

> color sel blue

> select #6/C#6/G

1652 atoms, 1655 bonds, 234 residues, 1 model selected  

> select #6/D#6/H

1521 atoms, 1528 bonds, 205 residues, 1 model selected  

> color sel cornflower blue

> color sel light sea green

> select #6/A#6/E

1658 atoms, 1656 bonds, 2 pseudobonds, 224 residues, 2 models selected  

> select #6/B#6/F

1362 atoms, 1354 bonds, 191 residues, 1 model selected  

> color sel cornflower blue

> select #4

1271 atoms, 1424 bonds, 62 residues, 1 model selected  

> select #6

12239 atoms, 12947 bonds, 4 pseudobonds, 1173 residues, 2 models selected  

> open C:/Users/fatmaouf/Downloads/2pyo.pdb

2pyo.pdb title:  
Drosophila nucleosome core [more info...]  
  
Chain information for 2pyo.pdb #7  
---  
Chain | Description  
A E | histone H3  
B F | histone H4  
C G | histone H2A  
D H | histone H2B  
I | DNA (147-mer)  
J | DNA (147-mer)  
  
Non-standard residues in 2pyo.pdb #7  
---  
CL — chloride ion  
MN — manganese (II) ion  
  

> view

> view orient

> select #7

12239 atoms, 12947 bonds, 4 pseudobonds, 1173 residues, 2 models selected  

> view orient

> style sel stick

Changed 12239 atom styles  

> nucleotides sel ladder

> show sel cartoons

> select #6/C#6/G#7/C#7/G

3304 atoms, 3310 bonds, 468 residues, 2 models selected  

> hide sel atoms

> color sel blue

> select #6/D#6/H#7/D#7/H

3042 atoms, 3056 bonds, 410 residues, 2 models selected  

> color sel light sea green

> hide sel cartoons

> select #6/A#6/E#7/A#7/E

3316 atoms, 3312 bonds, 4 pseudobonds, 448 residues, 4 models selected  

> color (#!6-7 & sel) cyan

> hide sel atoms

> select #6/D#6/H#7/D#7/H

3042 atoms, 3056 bonds, 410 residues, 2 models selected  

> hide sel atoms

> show sel cartoons

> select #6/B#6/F#7/B#7/F

2724 atoms, 2708 bonds, 382 residues, 2 models selected  

> color sel cornflower blue

> select #6/I#6/J#7/I#7/J

12092 atoms, 13508 bonds, 4 pseudobonds, 638 residues, 4 models selected  

> color (#!6-7 & sel) purple

> select #6/D#6/H#7/D#7/H

3042 atoms, 3056 bonds, 410 residues, 2 models selected  

> hide sel atoms

> select #6/C#6/G#7/C#7/G

3304 atoms, 3310 bonds, 468 residues, 2 models selected  

> hide sel atoms

> show sel cartoons

> select #6/A#6/E#7/A#7/E

3316 atoms, 3312 bonds, 4 pseudobonds, 448 residues, 4 models selected  

> show sel atoms

> hide sel atoms

> show sel cartoons

> select #6/B#6/F#7/B#7/F

2724 atoms, 2708 bonds, 382 residues, 2 models selected  

> show sel cartoons

> hide sel atoms

> hide #!3 models

> hide #!6 models

> show #!6 models

> hide #!1 models

> close #1

> close #3

> show #!2 models

> select #6

12239 atoms, 12947 bonds, 4 pseudobonds, 1173 residues, 2 models selected  

> ~select #6

Nothing selected  

> select #6

12239 atoms, 12947 bonds, 4 pseudobonds, 1173 residues, 2 models selected  

> hide #!6 models

> show #!6 models

> select #7

12239 atoms, 12947 bonds, 4 pseudobonds, 1173 residues, 2 models selected  

> select #6

12239 atoms, 12947 bonds, 4 pseudobonds, 1173 residues, 2 models selected  

> ~select #6

Nothing selected  

> select #6

12239 atoms, 12947 bonds, 4 pseudobonds, 1173 residues, 2 models selected  

> select #7

12239 atoms, 12947 bonds, 4 pseudobonds, 1173 residues, 2 models selected  

> ~select #7

Nothing selected  

> save
> C:/Users/fatmaouf/Desktop/hemisome_box_ts14/ts14_hemisomebox_newfitting1305.cxs
> includeMaps true

> select #6/C

821 atoms, 821 bonds, 118 residues, 1 model selected  

> hide sel cartoons

> select #6/D

763 atoms, 764 bonds, 105 residues, 1 model selected  

> undo

> undo

> select #6/G

831 atoms, 834 bonds, 116 residues, 1 model selected  

> hide sel cartoons

> select #6/D

763 atoms, 764 bonds, 105 residues, 1 model selected  

> select #6/H

758 atoms, 764 bonds, 100 residues, 1 model selected  

> hide sel cartoons

> select #6/E

833 atoms, 828 bonds, 2 pseudobonds, 116 residues, 2 models selected  

> hide sel cartoons

> select #6/F

724 atoms, 716 bonds, 104 residues, 1 model selected  

> hide sel cartoons

> ui tool show "Show Sequence Viewer"

> sequence chain #6/J

Alignment identifier is 6/J  

> sequence chain #6/I

Alignment identifier is 6/I  

> hide sel cartoons

> hide sel atoms

> hide sel cartoons

> hide sel atoms

> hide sel cartoons

> hide sel atoms

> hide sel cartoons

> hide sel atoms

> hide sel cartoons

> hide sel atoms

> hide sel cartoons

> hide sel atoms

> select #7

12239 atoms, 12947 bonds, 4 pseudobonds, 1173 residues, 2 models selected  

> select #6

12239 atoms, 12947 bonds, 4 pseudobonds, 1173 residues, 2 models selected  

> select ligand

Nothing selected  

> select solvent

176 atoms, 176 residues, 2 models selected  

> delete atoms sel

> delete bonds sel

> show #5 models

> show #4 models

> hide #4 models

> show #4 models

> hide #4 models

> show #4 models

> hide #4 models

> show #4 models

> hide #4 models

> show #4 models

> hide #4 models

> select #7

12151 atoms, 12947 bonds, 3 pseudobonds, 1085 residues, 2 models selected  

> hide #5 models

> show #5 models

> ~select #7

Nothing selected  

> select #7

12151 atoms, 12947 bonds, 3 pseudobonds, 1085 residues, 2 models selected  

> ~select #7

Nothing selected  

> select #7

12151 atoms, 12947 bonds, 3 pseudobonds, 1085 residues, 2 models selected  

> hide #!7 models

> show #!7 models

> ui tool show "Show Sequence Viewer"

> sequence chain #7/I

Alignment identifier is 7/I  

> sequence chain #7/J

Alignment identifier is 7/J  

> ~select #7

Nothing selected  

> select #7

12151 atoms, 12947 bonds, 3 pseudobonds, 1085 residues, 2 models selected  

> hide sel cartoons

> hide sel atoms

> hide sel cartoons

> hide sel atoms

> hide sel cartoons

> hide sel atoms

> hide sel cartoons

> hide sel atoms

> select #7

12151 atoms, 12947 bonds, 3 pseudobonds, 1085 residues, 2 models selected  

> ~select #7

Nothing selected  

> select #6/C

811 atoms, 821 bonds, 108 residues, 1 model selected  

> select #7/C

811 atoms, 821 bonds, 108 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> select #7/D

754 atoms, 764 bonds, 96 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select #7/A

817 atoms, 828 bonds, 100 residues, 1 model selected  

> hide sel cartoons

> select #7/B

631 atoms, 638 bonds, 80 residues, 1 model selected  

> hide sel cartoons

> select #7

12151 atoms, 12947 bonds, 3 pseudobonds, 1085 residues, 2 models selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #7/I

Alignment identifier is 7/I  

> sequence chain #7/J

Alignment identifier is 7/J  

> ~select #7

Nothing selected  

> hide sel cartoons

> hide sel atoms

> hide sel cartoons

> hide sel atoms

> show sel cartoons

> show sel atoms

> show sel cartoons

> hide sel atoms

> show sel atoms

> hide sel cartoons

> hide sel atoms

> hide sel cartoons

> hide sel atoms

> save
> C:/Users/fatmaouf/Desktop/hemisome_box_ts14/ts14_hemisomebox_newfitting1305_split.cxs
> includeMaps true

> save C:/Users/fatmaouf/Desktop/hemisome_box_ts14/hemisome_newfitting.obj

> open C:/Users/fatmaouf/Desktop/hemisome_box_ts14/dnalinenuc.pdb

Chain information for dnalinenuc.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> show sel cartoons

> nucleotides sel ladder

> style sel stick

Changed 140 atom styles  

> select #1

1312 atoms, 1470 bonds, 64 residues, 1 model selected  

> nucleotides sel ladder

> style sel stick

Changed 1312 atom styles  

> color sel purple

> hide sel cartoons

> hide sel atoms

> hide sel cartoons

> hide sel atoms

> save
> C:/Users/fatmaouf/Desktop/hemisome_box_ts14/ts14_hemisomebox_newfitting1605_split.cxs
> includeMaps true

opened ChimeraX session  

> open C:/Users/fatmaouf/Desktop/hemisome_box_ts14/dnalinenuc.pdb

Chain information for dnalinenuc.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> close #1

> save
> C:/Users/fatmaouf/Desktop/hemisome_box_ts14/ts14_hemisomebox_newfitting1605new_split.cxs
> includeMaps true

> select #7

12151 atoms, 12947 bonds, 3 pseudobonds, 1085 residues, 2 models selected  

> ~select #7

Nothing selected  

> select #7

12151 atoms, 12947 bonds, 3 pseudobonds, 1085 residues, 2 models selected  

> select #2

2 models selected  

> ~select #2

Nothing selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #6/J #7/J

Alignment identifier is 1  

> sequence chain #6/I #7/I

Alignment identifier is 2  
Seqview [ID: 1] region 2 chains [144-147] RMSD: 78.358  
  
Seqview [ID: 1] region 2 chains [138-147] RMSD: 102.208  
  

> hide sel cartoons

> hide sel atoms

Seqview [ID: 1] region 2 chains [1-6] RMSD: 75.175  
  
Seqview [ID: 2] region 2 chains [1-6] RMSD: 85.324  
  
Seqview [ID: 2] region 2 chains [1-10] RMSD: 96.432  
  

> hide sel cartoons

> hide sel atoms

Seqview [ID: 2] region 2 chains [11-14] RMSD: 144.903  
  
Seqview [ID: 1] region 2 chains [144-147] RMSD: 78.358  
  
Seqview [ID: 1] region 2 chains [36-39] RMSD: 199.089  
  
Seqview [ID: 1] region 2 chains [36-57] RMSD: 175.370  
  
Seqview [ID: 1] region 2 chains [58-61] RMSD: 122.545  
  

> hide sel cartoons

> hide sel atoms

Seqview [ID: 1] region 2 chains [86-90] RMSD: 121.024  
  
Seqview [ID: 1] region 2 chains [86-90] RMSD: 121.024  
  

> show sel cartoons

> show sel atoms

> select #3

1435 atoms, 1608 bonds, 70 residues, 1 model selected  

> color sel purple

> save
> C:/Users/fatmaouf/Desktop/hemisome_box_ts14/ts14_hemisomebox_newfitting1605FF.cxs
> includeMaps true

> show #4 models

> hide #4 models

> ~select #3

Nothing selected  

> hide #!7 models

> show #!7 models

> select #7

12151 atoms, 12947 bonds, 3 pseudobonds, 1085 residues, 2 models selected  

> ~select #7

Nothing selected  
Seqview [ID: 1] region 2 chains [86-90] RMSD: 121.024  
  

> hide sel cartoons

> hide sel atoms

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 2069, in <lambda>  
dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 607, in close_request  
tool_instance.delete()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 502, in delete  
ToolInstance.delete(self)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tools.py", line 154, in delete  
self.session.ui.remove_tool(self)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 321, in remove_tool  
self.main_window.remove_tool(tool_instance)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 706, in remove_tool  
tw._destroy()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1974, in _destroy  
self.__toolkit.destroy()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 2109, in destroy  
sbar.destroy()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\statusbar.py", line 50, in destroy  
v.delete()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 390, in delete  
self.make_current()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 430, in make_current  
return self._opengl_context.make_current()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 128, in make_current  
qc = self._initialize_context()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 149, in _initialize_context  
qc.setScreen(self._screen)  
RuntimeError: wrapped C/C++ object of type QScreen has been deleted  
  
RuntimeError: wrapped C/C++ object of type QScreen has been deleted  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 149, in _initialize_context  
qc.setScreen(self._screen)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 2069, in <lambda>  
dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 607, in close_request  
tool_instance.delete()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 502, in delete  
ToolInstance.delete(self)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tools.py", line 154, in delete  
self.session.ui.remove_tool(self)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 321, in remove_tool  
self.main_window.remove_tool(tool_instance)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 706, in remove_tool  
tw._destroy()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1974, in _destroy  
self.__toolkit.destroy()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 2109, in destroy  
sbar.destroy()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\statusbar.py", line 50, in destroy  
v.delete()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 390, in delete  
self.make_current()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 430, in make_current  
return self._opengl_context.make_current()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 128, in make_current  
qc = self._initialize_context()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 149, in _initialize_context  
qc.setScreen(self._screen)  
RuntimeError: wrapped C/C++ object of type QScreen has been deleted  
  
RuntimeError: wrapped C/C++ object of type QScreen has been deleted  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 149, in _initialize_context  
qc.setScreen(self._screen)  
  
See log for complete Python traceback.  
  

> save C:/Users/fatmaouf/Desktop/hemisome_box_ts14/testhemisome.pdb models
> #6-7 displayedOnly true relModel #6

> open C:/Users/fatmaouf/Desktop/hemisome_box_ts14/testhemisome.pdb

Summary of feedback from opening
C:/Users/fatmaouf/Desktop/hemisome_box_ts14/testhemisome.pdb  
---  
warnings | Ignored bad PDB record found on line 2916  
END  
  
Ignored bad PDB record found on line 4967  
END  
  
Start residue of secondary structure not found: HELIX 1 1 GLY A 44 SER A 57 1
14  
Start residue of secondary structure not found: HELIX 2 2 ARG A 63 ASP A 77 1
15  
Start residue of secondary structure not found: HELIX 3 3 GLN A 85 ALA A 114 1
30  
Start residue of secondary structure not found: HELIX 4 4 MET A 120 ARG A 131
1 12  
Start residue of secondary structure not found: HELIX 5 5 ASN B 25 ILE B 29 1
5  
51 messages similar to the above omitted  
Cannot find LINK/SSBOND residue DG (-34 )  
Cannot find LINK/SSBOND residue ASP (77 )  
Start residue of secondary structure not found: HELIX 1 1 GLY A 44 SER A 57 1
14  
Start residue of secondary structure not found: HELIX 2 2 ARG A 63 ASP A 77 1
15  
Start residue of secondary structure not found: HELIX 3 3 GLN A 85 ALA A 114 1
30  
Start residue of secondary structure not found: HELIX 4 4 MET A 120 ARG A 131
1 12  
Start residue of secondary structure not found: HELIX 5 5 ASN B 25 ILE B 29 1
5  
51 messages similar to the above omitted  
  
testhemisome.pdb title:  
Drosophila nucleosome core [more info...]  
  
Chain information for testhemisome.pdb  
---  
Chain | Description  
1.1/I | DNA (147-mer)  
1.2/I | DNA (147-mer)  
1.1/J | DNA (147-mer)  
1.2/J | DNA (147-mer)  
  

> hide #!6 models

> hide #!7 models

> hide #!1.1 models

> show #!1.1 models

> view orient

> close #1

> view orient

> show #!6 models

> show #!7 models

> save C:/Users/fatmaouf/Desktop/hemisome_box_ts14/testhemisome2.pdb models
> #6-7 displayedOnly true selectedOnly true relModel #2

> open C:/Users/fatmaouf/Desktop/hemisome_box_ts14/testhemisome2.pdb

Summary of feedback from opening
C:/Users/fatmaouf/Desktop/hemisome_box_ts14/testhemisome2.pdb  
---  
warnings | Ignored bad PDB record found on line 868  
END  
  
Ignored bad PDB record found on line 871  
END  
  

> view orient

> open C:/Users/fatmaouf/Desktop/hemisome_box_ts14/testhemisome2.pdb

Summary of feedback from opening
C:/Users/fatmaouf/Desktop/hemisome_box_ts14/testhemisome2.pdb  
---  
warnings | Ignored bad PDB record found on line 868  
END  
  
Ignored bad PDB record found on line 871  
END  
  

> hide #!6 models

> hide #!7 models

> show #!6 models

> show #!7 models

> open C:/Users/fatmaouf/Downloads/essai-Hemisome.cxs

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 150, in _qt_safe  
if data_format is None else " format " +
StringArg.unparse(data_format.nicknames[0])))  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 100, in cmd_open  
return Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 154, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 390, in collated_open  
return func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 925, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 608, in restore  
version = serialize.pickle_deserialize(stream)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\serialize.py", line 57, in pickle_deserialize  
return unpickler.load()  
_pickle.UnpicklingError: invalid load key, '\x04'.  
  
_pickle.UnpicklingError: invalid load key, '\x04'.  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\serialize.py", line 57, in pickle_deserialize  
return unpickler.load()  
  
See log for complete Python traceback.  
  

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

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

> hide #!7 models

> hide #!6 models

> hide #5 models

> hide #3 models

> show #!7 models

> show #!6 models

> show #5 models

> show #4 models

> show #3 models

> hide #4 models

> select #3

1435 atoms, 1608 bonds, 70 residues, 1 model selected  

> nucleotides sel ladder

> ~select #3

Nothing selected  

> save C:\Users\fatmaouf\Desktop\image5.png supersample 3

> save C:\Users\fatmaouf\Desktop\image6.png supersample 3

> open
> C:/Users/fatmaouf/Downloads/FittingFiles_AL/FittingFiles_AL/dna_hemisome.pdb

Chain information for dna_hemisome.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #3 models

> open
> C:/Users/fatmaouf/Downloads/FittingFiles_AL/FittingFiles_AL/Hemisome_AL2.obj

Opened OBJ file Hemisome_AL2.obj containing 10 objects, 638160 triangles  

> hide #8.10 models

> show #8.10 models

> hide #8.2 models

> hide #8.1 models

> show #8.1 models

> hide #8.1 models

> show #8.2 models

> hide #8.3 models

> show #8.3 models

> hide #8.2 models

> hide #!6 models

> show #!6 models

> select #6

12151 atoms, 12947 bonds, 3 pseudobonds, 1085 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> hide #8.3 models

> show #8.3 models

> hide #8.3 models

> hide #8.4 models

> hide #8.5 models

> show #8.5 models

> hide #8.5 models

> show #8.5 models

> hide #8.7 models

> show #8.7 models

> hide #8.7 models

> show #8.7 models

> hide #8.9 models

> show #8.9 models

> hide #8.9 models

> show #8.9 models

> hide #8.7 models

> show #8.7 models

> hide #8.7 models

> show #8.7 models

> hide #8.9 models

> show #8.9 models

> open
> C:/Users/fatmaouf/Downloads/FittingFiles_AL/FittingFiles_AL/dna_hemisome.pdb

Chain information for dna_hemisome.pdb #9  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #1 models

> hide #8.9 models

> select #7

12151 atoms, 12947 bonds, 3 pseudobonds, 1085 residues, 2 models selected  

> hide #8.10 models

> hide #8.8 models

> hide #8.7 models

> hide #8.6 models

> show #8.6 models

> select #9

1845 atoms, 2068 bonds, 90 residues, 1 model selected  

> color sel purple

> nucleotides sel ladder

> nucleotides sel stubs

> nucleotides sel ladder

> nucleotides sel stubs

> nucleotides sel ladder

> hide #8.5 models

> show #8.5 models

> open
> C:/Users/fatmaouf/Downloads/FittingFiles_AL/FittingFiles_AL/dna_hemisome.pdb

Chain information for dna_hemisome.pdb #10  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #9 models

> nucleotides #5,10#!6-7 ladder

> color #2,5-7,10#8.5-6#!8 purple

> undo

> select #10

2296 atoms, 2574 bonds, 112 residues, 1 model selected  

> nucleotides sel ladder

> color sel purple

> ui tool show "Show Sequence Viewer"

> sequence chain #10/B

Alignment identifier is 10/B  

> sequence chain #10/A

Alignment identifier is 10/A  

> ~select #10

Nothing selected  

> hide #!2 models

> hide sel cartoons

> hide sel atoms

> hide sel cartoons

> hide sel atoms

> hide sel cartoons

> hide sel atoms

> hide sel cartoons

> hide sel atoms

> hide sel cartoons

> hide sel atoms

> hide sel cartoons

> hide sel atoms

> show #!2 models

> save
> C:/Users/fatmaouf/Downloads/FittingFiles_AL/FittingFiles_AL/Hemisome_fittingAL_FF.cxs
> includeMaps true

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 656, in take_snapshot  
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tools.py", line 96, in take_snapshot  
data['shown'] = self.tool_window.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1908, in shown  
return self.__toolkit.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 2187, in shown  
return not self.dock_widget.isHidden()  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x00000211CD52A508> -> <chimerax.seq-view.tool.SequenceViewer object at
0x00000211E6999DC8>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 656, in take_snapshot  
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tools.py", line 96, in take_snapshot  
data['shown'] = self.tool_window.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1908, in shown  
return self.__toolkit.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 2187, in shown  
return not self.dock_widget.isHidden()  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x00000211CD52A508> -> <chimerax.seq-view.tool.SequenceViewer object at
0x00000211E6999DC8>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save
> C:/Users/fatmaouf/Downloads/FittingFiles_AL/FittingFiles_AL/hemisome_fittingAL_FF.cxs
> includeMaps true

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 656, in take_snapshot  
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tools.py", line 96, in take_snapshot  
data['shown'] = self.tool_window.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1908, in shown  
return self.__toolkit.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 2187, in shown  
return not self.dock_widget.isHidden()  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x00000211CD52A508> -> <chimerax.seq-view.tool.SequenceViewer object at
0x00000211E6999DC8>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 656, in take_snapshot  
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tools.py", line 96, in take_snapshot  
data['shown'] = self.tool_window.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1908, in shown  
return self.__toolkit.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 2187, in shown  
return not self.dock_widget.isHidden()  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x00000211CD52A508> -> <chimerax.seq-view.tool.SequenceViewer object at
0x00000211E6999DC8>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> hide #8.6 models

> hide #8.5 models

> show #3 models

> hide #3 models

> close #1

> show #3 models

> close #3

> show #4 models

> close #4

> show #9 models

> hide #9 models

> close #9

> select #10

2296 atoms, 2574 bonds, 112 residues, 1 model selected  

> ~select #10

Nothing selected  

> save C:/Users/fatmaouf/Downloads/FittingFiles_AL/FittingFiles_AL/hem_ff.cxs
> includeMaps true

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 656, in take_snapshot  
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tools.py", line 96, in take_snapshot  
data['shown'] = self.tool_window.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1908, in shown  
return self.__toolkit.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 2187, in shown  
return not self.dock_widget.isHidden()  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x00000211CD52A508> -> <chimerax.seq-view.tool.SequenceViewer object at
0x00000211E6999DC8>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 656, in take_snapshot  
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tools.py", line 96, in take_snapshot  
data['shown'] = self.tool_window.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1908, in shown  
return self.__toolkit.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 2187, in shown  
return not self.dock_widget.isHidden()  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x00000211CD52A508> -> <chimerax.seq-view.tool.SequenceViewer object at
0x00000211E6999DC8>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> hide #!8 models

> save C:/Users/fatmaouf/Downloads/FittingFiles_AL/FittingFiles_AL/test.cxs
> includeMaps true

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 656, in take_snapshot  
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tools.py", line 96, in take_snapshot  
data['shown'] = self.tool_window.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1908, in shown  
return self.__toolkit.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 2187, in shown  
return not self.dock_widget.isHidden()  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x00000211CD52A508> -> <chimerax.seq-view.tool.SequenceViewer object at
0x00000211E6999DC8>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 656, in take_snapshot  
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tools.py", line 96, in take_snapshot  
data['shown'] = self.tool_window.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1908, in shown  
return self.__toolkit.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 2187, in shown  
return not self.dock_widget.isHidden()  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x00000211CD52A508> -> <chimerax.seq-view.tool.SequenceViewer object at
0x00000211E6999DC8>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> close #2

> save C:/Users/fatmaouf/Downloads/FittingFiles_AL/FittingFiles_AL/test.cxs
> includeMaps true

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 656, in take_snapshot  
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tools.py", line 96, in take_snapshot  
data['shown'] = self.tool_window.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1908, in shown  
return self.__toolkit.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 2187, in shown  
return not self.dock_widget.isHidden()  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x00000211CD52A508> -> <chimerax.seq-view.tool.SequenceViewer object at
0x00000211E6999DC8>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 656, in take_snapshot  
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tools.py", line 96, in take_snapshot  
data['shown'] = self.tool_window.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1908, in shown  
return self.__toolkit.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 2187, in shown  
return not self.dock_widget.isHidden()  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x00000211CD52A508> -> <chimerax.seq-view.tool.SequenceViewer object at
0x00000211E6999DC8>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> show #!8 models

> hide #!8 models

> hide #5 models

> show #5 models

> ui tool show "Show Sequence Viewer"

> sequence chain #5/A

Alignment identifier is 5/A  

> sequence chain #5/B

Alignment identifier is 5/B  

> select #5

2255 atoms, 2528 bonds, 110 residues, 1 model selected  

> show #8.2 models

> hide #8.2 models

> select #10

2296 atoms, 2574 bonds, 112 residues, 1 model selected  

> ~select #10

Nothing selected  

> select #7

12151 atoms, 12947 bonds, 3 pseudobonds, 1085 residues, 2 models selected  

> select #6

12151 atoms, 12947 bonds, 3 pseudobonds, 1085 residues, 2 models selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #6/I #7/I

Alignment identifier is 1  

> sequence chain #6/J #7/J

Alignment identifier is 2  
Seqview [ID: 1] region 2 chains [144-147] RMSD: 84.412  
  

> select #7

12151 atoms, 12947 bonds, 3 pseudobonds, 1085 residues, 2 models selected  

> ~select #7

Nothing selected  

> select #6

12151 atoms, 12947 bonds, 3 pseudobonds, 1085 residues, 2 models selected  

> ~select #6

Nothing selected  
Seqview [ID: 1] region 2 chains [1-5] RMSD: 109.875  
  
Seqview [ID: 1] region 2 chains [131-147] RMSD: 111.839  
  
Seqview [ID: 1] region 2 chains [1-32] RMSD: 157.785  
  
Seqview [ID: 1] region 2 chains [24-30] RMSD: 191.491  
  
Seqview [ID: 1] region 2 chains [6-10] RMSD: 120.556  
  
Seqview [ID: 1] region 2 chains [117-123] RMSD: 192.683  
  
Seqview [ID: 1] region 2 chains [56-64] RMSD: 112.048  
  
Seqview [ID: 1] region 2 chains [41-55] RMSD: 168.385  
  
Seqview [ID: 1] region 2 chains [1-43] RMSD: 170.794  
  
Seqview [ID: 1] region 2 chains [40-44] RMSD: 191.420  
  
Seqview [ID: 1] region 2 chains [1-17] RMSD: 127.884  
  
Seqview [ID: 1] region 2 chains [1-15] RMSD: 125.355  
  

> hide sel cartoons

> hide sel atoms

Seqview [ID: 1] region 2 chains [122-147] RMSD: 134.679  
  
Seqview [ID: 2] region 2 chains [1-14] RMSD: 104.391  
  
Seqview [ID: 2] region 2 chains [121-147] RMSD: 148.984  
  
Seqview [ID: 2] region 2 chains [143-147] RMSD: 104.063  
  
Seqview [ID: 2] region 2 chains [134-140] RMSD: 132.096  
  

> hide sel cartoons

> hide sel atoms

> save C:/Users/fatmaouf/Downloads/FittingFiles_AL/FittingFiles_AL/test.cxs

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 656, in take_snapshot  
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tools.py", line 96, in take_snapshot  
data['shown'] = self.tool_window.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1908, in shown  
return self.__toolkit.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 2187, in shown  
return not self.dock_widget.isHidden()  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x00000211CD52A508> -> <chimerax.seq-view.tool.SequenceViewer object at
0x00000211E6999DC8>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 656, in take_snapshot  
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tools.py", line 96, in take_snapshot  
data['shown'] = self.tool_window.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1908, in shown  
return self.__toolkit.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 2187, in shown  
return not self.dock_widget.isHidden()  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x00000211CD52A508> -> <chimerax.seq-view.tool.SequenceViewer object at
0x00000211E6999DC8>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> close #8

> save C:/Users/fatmaouf/Downloads/FittingFiles_AL/FittingFiles_AL/test.cxs
> includeMaps true

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 656, in take_snapshot  
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tools.py", line 96, in take_snapshot  
data['shown'] = self.tool_window.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1908, in shown  
return self.__toolkit.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 2187, in shown  
return not self.dock_widget.isHidden()  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x00000211CD52A508> -> <chimerax.seq-view.tool.SequenceViewer object at
0x00000211E6999DC8>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 656, in take_snapshot  
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tools.py", line 96, in take_snapshot  
data['shown'] = self.tool_window.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1908, in shown  
return self.__toolkit.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 2187, in shown  
return not self.dock_widget.isHidden()  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x00000211CD52A508> -> <chimerax.seq-view.tool.SequenceViewer object at
0x00000211E6999DC8>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
No model chosen to save relative to  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 47, in display  
self._current_option)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\manager.py", line 91, in
save_args_string_from_widget  
provider_info.format_name, self).save_args_string_from_widget(widget)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\map\\__init__.py", line 189, in save_args_string_from_widget  
return widget.options_string()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\options.py", line 35, in options_string  
raise UserError("No %s to save" % self._name.lower())  
AttributeError: 'SaveModelOptionWidget' object has no attribute '_name'  
  
AttributeError: 'SaveModelOptionWidget' object has no attribute '_name'  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\options.py", line 35, in options_string  
raise UserError("No %s to save" % self._name.lower())  
  
See log for complete Python traceback.  
  

> save C:/Users/fatmaouf/Downloads/FittingFiles_AL/FittingFiles_AL/test.pdb
> displayedOnly true relModel #5

> save C:/Users/fatmaouf/Downloads/FittingFiles_AL/FittingFiles_AL/test.cxs
> includeMaps true

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 656, in take_snapshot  
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tools.py", line 96, in take_snapshot  
data['shown'] = self.tool_window.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1908, in shown  
return self.__toolkit.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 2187, in shown  
return not self.dock_widget.isHidden()  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x00000211CD52A508> -> <chimerax.seq-view.tool.SequenceViewer object at
0x00000211E6999DC8>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 656, in take_snapshot  
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tools.py", line 96, in take_snapshot  
data['shown'] = self.tool_window.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1908, in shown  
return self.__toolkit.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 2187, in shown  
return not self.dock_widget.isHidden()  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 162, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 363, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1273, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\toolbar\\__init__.py", line 38, in run_provider  
providers.run_provider(session, name)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 45, in run_provider  
what(session)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 27, in _file_save  
show_save_file_dialog(session)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x00000211CD52A508> -> <chimerax.seq-view.tool.SequenceViewer object at
0x00000211E6999DC8>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save
> "C:/Users/fatmaouf/Downloads/FittingFiles_AL/FittingFiles_AL/test_hemisome
> fitting.obj"

> open C:/Users/fatmaouf/Desktop/hemisome_box_ts14/hemisomemap.cmap

Opened hemisomemap.cmap, grid size 129,120,82, pixel 2, shown at level 0.0626,
step 1, values float32  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> ui tool show "Map Coordinates"

> transparency sel 80

> select #1

2 models selected  

> transparency #1.1 80

> ~select #1

Nothing selected  

> volume #1 level 0.1357

> save C:/Users/fatmaouf/Desktop/hemisome_box_ts14/testnewfitting.cxs
> includeMaps true

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 656, in take_snapshot  
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tools.py", line 96, in take_snapshot  
data['shown'] = self.tool_window.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1908, in shown  
return self.__toolkit.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 2187, in shown  
return not self.dock_widget.isHidden()  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x00000211CD52A508> -> <chimerax.seq-view.tool.SequenceViewer object at
0x00000211E6999DC8>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 656, in take_snapshot  
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tools.py", line 96, in take_snapshot  
data['shown'] = self.tool_window.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1908, in shown  
return self.__toolkit.shown  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 2187, in shown  
return not self.dock_widget.isHidden()  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x00000211CD52A508> -> <chimerax.seq-view.tool.SequenceViewer object at
0x00000211E6999DC8>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000211CD52A508> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000211E6999DC8>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> ui tool show Log

QWindowsNativeFileDialogBase::shellItem : Unhandled scheme: "data"  




OpenGL version: 3.3.0 NVIDIA 511.79
OpenGL renderer: Quadro RTX 8000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision 5820 Tower
OS: Microsoft Windows 10 Enterprise (Build 19044)
Memory: 274,543,923,200
MaxProcessMemory: 137,438,953,344
CPU: 28 Intel(R) Xeon(R) W-2275 CPU @ 3.30GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    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: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    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
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    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: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    gdcm: 2.8.8
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5+mkl
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pywin32: 228
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    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: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2
    WMI: 1.5.1
File attachment: log_chimeraXerror.txt

log_chimeraXerror.txt​

[fatmaouf@…]

Added by email2trac

[pett]

Hi Fadwa,

Thanks for reporting this problem. It has been fixed in more recent versions of ChimeraX, so if you upgrade to a newer version you shouldn't run into it anymore.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab