wrapped C/C++ object of type ChainListWidget has been deleted

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-12.2.1-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> /Users/ishikawamoe/Desktop/analysis/reference/VC_NQR_vs_CT_RNF/NQRvsRNF.cxs

Log from Tue Dec 6 18:49:48 2022UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/ishikawamoe/Desktop/analysis/reference/ours/7xk3_cryoNQR.pdb
> format pdb

7xk3_cryoNQR.pdb title:  
Cryo-em structure of Na+-pumping nadh-ubiquinone oxidoreductase from vibrio
cholerae, state 1 [more info...]  
  
Chain information for 7xk3_cryoNQR.pdb #1  
---  
Chain | Description | UniProt  
A | Na(+)-translocating nadh-quinone reductase subunit A | NQRA_VIBC3  
B | Na(+)-translocating nadh-quinone reductase subunit B | NQRB_VIBC3  
C | Na(+)-translocating nadh-quinone reductase subunit C | NQRC_VIBC3  
D | Na(+)-translocating nadh-quinone reductase subunit D | NQRD_VIBC3  
E | Na(+)-translocating nadh-quinone reductase subunit E | NQRE_VIBC3  
F | Na(+)-translocating nadh-quinone reductase subunit F | NQRF_VIBC3  
  
Non-standard residues in 7xk3_cryoNQR.pdb #1  
---  
CA — calcium ion  
FAD — flavin-adenine dinucleotide  
FES — FE2/S2 (inorganic) cluster  
FMN — flavin mononucleotide (riboflavin monophosphate)  
LMT — dodecyl-β-D-maltoside  
PEE — 1,2-dioleoyl-Sn-glycero-3-phosphoethanolamine (DOPE)  
RBF — riboflavin (riboflavine; vitamin B2)  
  

> set bgColor white

> hide cartoons

> select add #1

14841 atoms, 15181 bonds, 1905 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> select ::name="HIS"

280 atoms, 281 bonds, 28 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 280 atom styles  

> color sel orange

> color sel orange red

> select ::name="CYS"

126 atoms, 105 bonds, 21 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 126 atom styles  

> color sel yellow

> close

> open /Users/ishikawamoe/Desktop/analysis/reference/ours/7xk7_cryoNQR_KR.pdb

7xk7_cryoNQR_KR.pdb title:  
Cryo-em structure of Na+-pumping nadh-ubiquinone oxidoreductase from vibrio
cholerae, with korormicin [more info...]  
  
Chain information for 7xk7_cryoNQR_KR.pdb #1  
---  
Chain | Description | UniProt  
A | Na(+)-translocating nadh-quinone reductase subunit A | NQRA_VIBC3  
B | Na(+)-translocating nadh-quinone reductase subunit B | NQRB_VIBC3  
C | Na(+)-translocating nadh-quinone reductase subunit C | NQRC_VIBC3  
D | Na(+)-translocating nadh-quinone reductase subunit D | NQRD_VIBC3  
E | Na(+)-translocating nadh-quinone reductase subunit E | NQRE_VIBC3  
F | Na(+)-translocating nadh-quinone reductase subunit F | NQRF_VIBC3  
  
Non-standard residues in 7xk7_cryoNQR_KR.pdb #1  
---  
CA — calcium ion  
FAD — flavin-adenine dinucleotide  
FES — FE2/S2 (inorganic) cluster  
FMN — flavin mononucleotide (riboflavin monophosphate)  
IQT — korormicin  
LMT — dodecyl-β-D-maltoside  
PEE — 1,2-dioleoyl-Sn-glycero-3-phosphoethanolamine (DOPE)  
RBF — riboflavin (riboflavine; vitamin B2)  
  

> select add #1

15181 atoms, 15495 bonds, 2 pseudobonds, 1969 residues, 2 models selected  

> hide sel atoms

> show sel cartoons

> color (#!1 & sel) dark gray

> select ::name="HIS"

310 atoms, 312 bonds, 31 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 310 atom styles  

> color sel orange

> select ::name="CYS"

126 atoms, 105 bonds, 21 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 126 atom styles  

> color sel yellow

> select Ala

Expected an objects specifier or a keyword  

> select ala

Expected an objects specifier or a keyword  

> select residue:ala

Expected an objects specifier or a keyword  

> select residue:ala

Expected an objects specifier or a keyword  

> select ::name="CYS"

126 atoms, 105 bonds, 21 residues, 1 model selected  

> select ::name="ALA""GLY"

Expected an objects specifier or a keyword  

> select ::name="ALA"

830 atoms, 680 bonds, 166 residues, 1 model selected  

> select ::name="ALA,GLY"

Nothing selected  

> select ::name="ALA,GLY"

Nothing selected  

> select ::name="ALA,GLY"

Nothing selected  

> select ::name="ALA"

830 atoms, 680 bonds, 166 residues, 1 model selected  

> color sel black

> select ::name="GLY"

749 atoms, 585 bonds, 187 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 749 atom styles  

> color sel black

> select ::name="ILE"

1032 atoms, 913 bonds, 129 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 1032 atom styles  

> color sel black

> select ::name="LEU"

1504 atoms, 1327 bonds, 188 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 1504 atom styles  

> color sel black

> select ::name="PHE"

1221 atoms, 1230 bonds, 111 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 1221 atom styles  

> color sel purple

> select ::name="PRO"

595 atoms, 602 bonds, 85 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 595 atom styles  

> color sel purple

> select ::name="TRP"

434 atoms, 465 bonds, 31 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 434 atom styles  

> color sel medium blue

> color sel purple

> select ::name="TYR"

648 atoms, 650 bonds, 54 residues, 1 model selected  

> color sel hot pink

> select ::name="VAL"

1197 atoms, 1042 bonds, 171 residues, 1 model selected  

> color sel black

> select clear

> save "/Users/ishikawamoe/Desktop/analysis/reference/ours/7xk7_canonical
> residues.cxs"

> close session

> open /Users/ishikawamoe/Desktop/analysis/reference/ours/7xk7_cryoNQR_KR.pdb
> format pdb

7xk7_cryoNQR_KR.pdb title:  
Cryo-em structure of Na+-pumping nadh-ubiquinone oxidoreductase from vibrio
cholerae, with korormicin [more info...]  
  
Chain information for 7xk7_cryoNQR_KR.pdb #1  
---  
Chain | Description | UniProt  
A | Na(+)-translocating nadh-quinone reductase subunit A | NQRA_VIBC3  
B | Na(+)-translocating nadh-quinone reductase subunit B | NQRB_VIBC3  
C | Na(+)-translocating nadh-quinone reductase subunit C | NQRC_VIBC3  
D | Na(+)-translocating nadh-quinone reductase subunit D | NQRD_VIBC3  
E | Na(+)-translocating nadh-quinone reductase subunit E | NQRE_VIBC3  
F | Na(+)-translocating nadh-quinone reductase subunit F | NQRF_VIBC3  
  
Non-standard residues in 7xk7_cryoNQR_KR.pdb #1  
---  
CA — calcium ion  
FAD — flavin-adenine dinucleotide  
FES — FE2/S2 (inorganic) cluster  
FMN — flavin mononucleotide (riboflavin monophosphate)  
IQT — korormicin  
LMT — dodecyl-β-D-maltoside  
PEE — 1,2-dioleoyl-Sn-glycero-3-phosphoethanolamine (DOPE)  
RBF — riboflavin (riboflavine; vitamin B2)  
  

> select add #1

15181 atoms, 15495 bonds, 2 pseudobonds, 1969 residues, 2 models selected  

> show sel atoms

> hide sel atoms

> show sel cartoons

> open
> /Users/ishikawamoe/Desktop/analysis/reference/rnf/7zc6_cryo_rnf_ermler.pdb

7zc6_cryo_rnf_ermler.pdb title:  
Na+ - translocating ferredoxin: nad+ reductase (RNF) of C. Tetanomorphum [more
info...]  
  
Chain information for 7zc6_cryo_rnf_ermler.pdb #2  
---  
Chain | Description  
A | RNFA  
B | RNFB  
C | RNFC  
D | RNFD  
E | RNFE  
G | RNFG  
  
Non-standard residues in 7zc6_cryo_rnf_ermler.pdb #2  
---  
FE — Fe (III) ion  
FMN — flavin mononucleotide (riboflavin monophosphate)  
RBF — riboflavin (riboflavine; vitamin B2)  
SF4 — iron/sulfur cluster  
  

> select add #2

26609 atoms, 27150 bonds, 35 pseudobonds, 3494 residues, 5 models selected  

> select subtract #1

11428 atoms, 11655 bonds, 33 pseudobonds, 1525 residues, 3 models selected  

> hide sel atoms

> show sel cartoons

> ui tool show Matchmaker

> matchmaker #!2 to #1/B pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7xk7_cryoNQR_KR.pdb, chain B (#1) with 7zc6_cryo_rnf_ermler.pdb,
chain D (#2), sequence alignment score = 543.2  
RMSD between 203 pruned atom pairs is 1.027 angstroms; (across all 296 pairs:
4.989)  
  

> matchmaker #!2 to #1/B pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7xk7_cryoNQR_KR.pdb, chain B (#1) with 7zc6_cryo_rnf_ermler.pdb,
chain D (#2), sequence alignment score = 543.2  
RMSD between 203 pruned atom pairs is 1.027 angstroms; (across all 296 pairs:
4.989)  
  

> color (#!2 & sel) light gray

> select add #1

26609 atoms, 27150 bonds, 35 pseudobonds, 3494 residues, 5 models selected  

> select subtract #2

15181 atoms, 15495 bonds, 2 pseudobonds, 1969 residues, 2 models selected  

> color (#!1 & sel) dim gray

> select subtract #1

Nothing selected  

> select add #2

11428 atoms, 11655 bonds, 33 pseudobonds, 1525 residues, 3 models selected  

> select add #1

26609 atoms, 27150 bonds, 35 pseudobonds, 3494 residues, 5 models selected  

> color (#!1-2 & sel) red

> select subtract #2

15181 atoms, 15495 bonds, 2 pseudobonds, 1969 residues, 2 models selected  

> select subtract #1

Nothing selected  

> select add #2

11428 atoms, 11655 bonds, 33 pseudobonds, 1525 residues, 3 models selected  

> color (#!2 & sel) light gray

> select subtract #2

Nothing selected  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> select add #2

11428 atoms, 11655 bonds, 33 pseudobonds, 1525 residues, 3 models selected  

> color (#!2 & sel) blue

> select subtract #2

Nothing selected  

> select #1/B:192

9 atoms, 8 bonds, 1 residue, 1 model selected  

> color sel orange

> show sel atoms

> style sel stick

Changed 9 atom styles  

> select #1/B:151

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

> show sel atoms

> style sel stick

Changed 11 atom styles  

> color sel yellow

> save /Users/ishikawamoe/Desktop/analysis/NQRvsRNF.cxs

——— End of log from Tue Dec 6 18:49:48 2022 ———

opened ChimeraX session  

> select add #2

11439 atoms, 11665 bonds, 33 pseudobonds, 1526 residues, 4 models selected  

> select add #1

26609 atoms, 27150 bonds, 35 pseudobonds, 3494 residues, 5 models selected  

> show sel atoms

> style sel stick

Changed 26609 atom styles  

> view sel

> view

[Repeated 1 time(s)]

> select subtract #1

11428 atoms, 11655 bonds, 33 pseudobonds, 1525 residues, 3 models selected  

> select subtract #2

Nothing selected  

> select #1/A

3433 atoms, 3480 bonds, 463 residues, 1 model selected  

> select #1/A/C/D/E/F

11729 atoms, 11954 bonds, 2 pseudobonds, 1535 residues, 2 models selected  

> hide sel cartoons

[Repeated 1 time(s)]

> hide sel atoms

> select add #1

15181 atoms, 15495 bonds, 2 pseudobonds, 1969 residues, 2 models selected  

> select add #2

26609 atoms, 27150 bonds, 35 pseudobonds, 3494 residues, 5 models selected  

> hide sel atoms

> select subtract #1

11428 atoms, 11655 bonds, 33 pseudobonds, 1525 residues, 3 models selected  

> select subtract #2

Nothing selected  

> select #2/D

2339 atoms, 2403 bonds, 306 residues, 1 model selected  

> select #2/A/C/B/E/F

7711 atoms, 7857 bonds, 33 pseudobonds, 1031 residues, 3 models selected  

> hide sel atoms

[Repeated 1 time(s)]

> hide sel cartoons

> select #2/A/C/B/E/F/G

9089 atoms, 9252 bonds, 33 pseudobonds, 1219 residues, 3 models selected  

> hide sel cartoons

> ui tool show "Show Sequence Viewer"

> sequence chain #2/D

Alignment identifier is 2/D  

> ui tool show "Fit in Map"

> ui tool show Matchmaker

> matchmaker #!2 to #1/B pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7xk7_cryoNQR_KR.pdb, chain B (#1) with 7zc6_cryo_rnf_ermler.pdb,
chain D (#2), sequence alignment score = 543.2  
RMSD between 203 pruned atom pairs is 1.027 angstroms; (across all 296 pairs:
4.989)  
  

> select add #2

11428 atoms, 11655 bonds, 33 pseudobonds, 1525 residues, 3 models selected  

> color (#!2 & sel) light gray

> color (#!2 & sel) gray

> select #1/B:1-42

336 atoms, 348 bonds, 41 residues, 1 model selected  

> select ~sel

26273 atoms, 26801 bonds, 35 pseudobonds, 3453 residues, 5 models selected  

> ui tool show "Color Actions"

> color (#!1-2 & sel) #ff7e79ff

> select subtract #2

14845 atoms, 15146 bonds, 2 pseudobonds, 1928 residues, 2 models selected  

> select add #1

15181 atoms, 15495 bonds, 2 pseudobonds, 1969 residues, 2 models selected  

> select subtract #1

Nothing selected  

> select add #2

11428 atoms, 11655 bonds, 33 pseudobonds, 1525 residues, 3 models selected  

> color (#!2 & sel) gray

> select subtract #2

Nothing selected  

> select add #2

11428 atoms, 11655 bonds, 33 pseudobonds, 1525 residues, 3 models selected  

> select add #1

26609 atoms, 27150 bonds, 35 pseudobonds, 3494 residues, 5 models selected  

> select subtract #2

15181 atoms, 15495 bonds, 2 pseudobonds, 1969 residues, 2 models selected  

> show sel cartoons

> hide sel cartoons

> undo

[Repeated 1 time(s)]

> select subtract #1

Nothing selected  

> save /Users/ishikawamoe/Desktop/image1.png supersample 3

> ui tool show "Show Sequence Viewer"

> sequence chain #1/B

Alignment identifier is 1/B  

> save "/Users/ishikawamoe/Desktop/analysis/reference/VC_NQR_vs_CT_RNF/NqrB vs
> RnfD.cxs"

> close #2

> close

> open /Users/ishikawamoe/Desktop/analysis/P19_NADH/P19_J70_model.pdb

Chain information for P19_J70_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> open /Users/ishikawamoe/Desktop/analysis/reference/ours_NQR/7xk3_cryoNQR.pdb

7xk3_cryoNQR.pdb title:  
Cryo-em structure of Na+-pumping nadh-ubiquinone oxidoreductase from vibrio
cholerae, state 1 [more info...]  
  
Chain information for 7xk3_cryoNQR.pdb #2  
---  
Chain | Description | UniProt  
A | Na(+)-translocating nadh-quinone reductase subunit A | NQRA_VIBC3 1-446  
B | Na(+)-translocating nadh-quinone reductase subunit B | NQRB_VIBC3 1-415  
C | Na(+)-translocating nadh-quinone reductase subunit C | NQRC_VIBC3 1-257  
D | Na(+)-translocating nadh-quinone reductase subunit D | NQRD_VIBC3 1-210  
E | Na(+)-translocating nadh-quinone reductase subunit E | NQRE_VIBC3 1-198  
F | Na(+)-translocating nadh-quinone reductase subunit F | NQRF_VIBC3 1-408  
  
Non-standard residues in 7xk3_cryoNQR.pdb #2  
---  
CA — calcium ion  
FAD — flavin-adenine dinucleotide  
FES — FE2/S2 (inorganic) cluster  
FMN — flavin mononucleotide (riboflavin monophosphate)  
LMT — dodecyl-β-D-maltoside  
PEE — 1,2-dioleoyl-Sn-glycero-3-phosphoethanolamine (DOPE)  
RBF — riboflavin (riboflavine; vitamin B2)  
  

> ui tool show Matchmaker

> matchmaker #2 to #1/B pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker P19_J70_model.pdb, chain B (#1) with 7xk3_cryoNQR.pdb, chain B
(#2), sequence alignment score = 1293.3  
RMSD between 384 pruned atom pairs is 0.455 angstroms; (across all 387 pairs:
0.563)  
  

> matchmaker #2 to #1/B pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker P19_J70_model.pdb, chain B (#1) with 7xk3_cryoNQR.pdb, chain B
(#2), sequence alignment score = 1293.3  
RMSD between 384 pruned atom pairs is 0.455 angstroms; (across all 387 pairs:
0.563)  
  

> view

[Repeated 1 time(s)]

> select add #1

14842 atoms, 15180 bonds, 2 pseudobonds, 1905 residues, 2 models selected  

> select add #2

29683 atoms, 30361 bonds, 2 pseudobonds, 3810 residues, 3 models selected  

> hide sel atoms

> show sel cartoons

> cartoon style (#2#!1 & sel) modeHelix tube sides 20

> select subtract #1

14841 atoms, 15181 bonds, 1905 residues, 1 model selected  

> select add #1

29683 atoms, 30361 bonds, 2 pseudobonds, 3810 residues, 3 models selected  

> select subtract #2

14842 atoms, 15180 bonds, 2 pseudobonds, 1905 residues, 2 models selected  

> color (#!1 & sel) red

> select add #2

29683 atoms, 30361 bonds, 2 pseudobonds, 3810 residues, 3 models selected  

> select subtract #1

14841 atoms, 15181 bonds, 1905 residues, 1 model selected  

> color sel gray

> select #1/E:90-120

251 atoms, 257 bonds, 31 residues, 1 model selected  

> select add #1

14842 atoms, 15180 bonds, 2 pseudobonds, 1905 residues, 2 models selected  

> select add #2

29683 atoms, 30361 bonds, 2 pseudobonds, 3810 residues, 3 models selected  

> select subtract #1

14841 atoms, 15181 bonds, 1905 residues, 1 model selected  

> select subtract #2

Nothing selected  

> select #1/A/B/C/F#2/A/B/C/F

23460 atoms, 24007 bonds, 1 pseudobond, 3001 residues, 3 models selected  

> hide sel cartoons

> open /Users/ishikawamoe/Desktop/analysis/P20_solNQR_NADH-
> Na+/cryosparc_P20_J217_flex_map_Fdown.mrc

Opened cryosparc_P20_J217_flex_map_Fdown.mrc as #3, grid size 300,300,300,
pixel 0.88, shown at level 0.00259, step 2, values float32  

> hide #!1 models

> hide #2 models

> select add #1

26570 atoms, 27183 bonds, 2 pseudobonds, 3405 residues, 3 models selected  

> select add #2

29683 atoms, 30361 bonds, 2 pseudobonds, 3810 residues, 3 models selected  

> select subtract #2

14842 atoms, 15180 bonds, 2 pseudobonds, 1905 residues, 2 models selected  

> select subtract #1

Nothing selected  

> select add #3

2 models selected  

> view

> volume #3 step 1

> select subtract #3

Nothing selected  

> volume #3 level 0.002538

> save /Users/ishikawamoe/Desktop/image2.png supersample 3

> show #!1 models

> show #2 models

> hide #!3 models

> open
> /Users/ishikawamoe/Desktop/analysis/P19_NADH/cryosparc_P19_J70_008_volume_map_sharp.mrc

Opened cryosparc_P19_J70_008_volume_map_sharp.mrc as #4, grid size
320,320,320, pixel 0.88, shown at level 0.2, step 2, values float32  

> open
> /Volumes/ISHIMOE4/NQR/cryo/oxidant/cryosparc_P16_J82_004_volume_map_sharp_膜内表示用.mrc

Opened cryosparc_P16_J82_004_volume_map_sharp_膜内表示用.mrc as #5, grid size
320,320,320, pixel 0.88, shown at level 0.255, step 2, values float32  

> hide #2 models

> hide #!1 models

> volume #4 step 1

> volume #5 step 1

> volume #5 level 0.4291

> volume #4 level 0.2812

> volume #4 level 0.3298

> select add #4

2 models selected  

> select subtract #4

Nothing selected  

> select add #5

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #5,-0.41702,0.16127,-0.89448,304.78,0.36846,0.92964,-0.0041719,-42.013,0.83086,-0.33132,-0.4471,131.38

> view matrix models
> #5,0.53079,0.25045,-0.80965,145.2,0.44869,-0.89351,0.01777,200.54,-0.71898,-0.37272,-0.58664,377.72

> view matrix models
> #5,0.51404,-0.27213,0.81345,-6.5241,0.28308,-0.84138,-0.46037,283.9,0.80971,0.46692,-0.35547,8.9809

> view matrix models
> #5,-0.96425,-0.10541,-0.24315,328.97,0.14139,-0.98062,-0.13561,278.15,-0.22414,-0.16514,0.96046,60.783

> view matrix models
> #5,-0.9461,-0.25742,-0.19654,341.28,0.2685,-0.96276,-0.031528,242.91,-0.1811,-0.082599,0.97999,40.269

> volume #4 level 0.3703

> volume #5 level 0.6032

> ui tool show "Fit in Map"

> fitmap #4 inMap #5

Fit map cryosparc_P19_J70_008_volume_map_sharp.mrc in map
cryosparc_P16_J82_004_volume_map_sharp_膜内表示用.mrc using 128896 points  
correlation = 0.7459, correlation about mean = 0.5621, overlap = 1.13e+05  
steps = 184, shift = 4.15, angle = 20.1 degrees  
  
Position of cryosparc_P19_J70_008_volume_map_sharp.mrc (#4) relative to
cryosparc_P16_J82_004_volume_map_sharp_膜内表示用.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.99973568 -0.02291850 -0.00182360 285.03774143  
0.02293937 -0.99966006 -0.01239152 279.82193386  
-0.00153898 -0.01243007 0.99992156 2.12217460  
Axis -0.00084074 -0.00620640 0.99998039  
Axis point 140.91547919 141.55173509 0.00000000  
Rotation angle (degrees) 178.68612795  
Shift along axis 0.14580107  
  

> fitmap #4 inMap #5

Fit map cryosparc_P19_J70_008_volume_map_sharp.mrc in map
cryosparc_P16_J82_004_volume_map_sharp_膜内表示用.mrc using 128896 points  
correlation = 0.7459, correlation about mean = 0.5621, overlap = 1.13e+05  
steps = 44, shift = 0.014, angle = 0.0158 degrees  
  
Position of cryosparc_P19_J70_008_volume_map_sharp.mrc (#4) relative to
cryosparc_P16_J82_004_volume_map_sharp_膜内表示用.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.99973925 -0.02275026 -0.00196457 285.02340377  
0.02277318 -0.99966176 -0.01255980 279.86154585  
-0.00167816 -0.01260127 0.99991920 2.17001966  
Axis -0.00091079 -0.00629128 0.99997979  
Axis point 140.91988141 141.55978147 0.00000000  
Rotation angle (degrees) 178.69571042  
Shift along axis 0.14969224  
  

> view matrix models
> #5,-0.93558,-0.28116,-0.21365,345.49,0.29114,-0.95655,-0.016115,236.66,-0.19983,-0.077278,0.97678,42.636

> volume #4 level 0.4568

> volume #5 level 0.7895

> view matrix models
> #5,-0.94391,-0.23945,-0.22737,342.9,0.2498,-0.96814,-0.017472,244.28,-0.21594,-0.07329,0.97365,44.807

> ui tool show "Fit in Map"

> fitmap #1 inMap #3

Fit molecule P19_J70_model.pdb (#1) to map
cryosparc_P20_J217_flex_map_Fdown.mrc (#3) using 14842 atoms  
average map value = 0.001622, steps = 172  
shifted from previous position = 8.26  
rotated from previous position = 14 degrees  
atoms outside contour = 10708, contour level = 0.0025383  
  
Position of P19_J70_model.pdb (#1) relative to
cryosparc_P20_J217_flex_map_Fdown.mrc (#3) coordinates:  
Matrix rotation and translation  
0.99636165 0.03835104 -0.07610959 3.44746178  
-0.02006997 0.97350090 0.22780077 -24.43599244  
0.08282915 -0.22544444 0.97072866 16.74662262  
Axis -0.93675750 -0.32849117 -0.12074328  
Axis point 0.00000000 61.43336699 110.41307633  
Rotation angle (degrees) 14.00002875  
Shift along axis 2.77552980  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> fitmap #4 inMap #5

Fit map cryosparc_P19_J70_008_volume_map_sharp.mrc in map
cryosparc_P16_J82_004_volume_map_sharp_膜内表示用.mrc using 97593 points  
correlation = 0.7694, correlation about mean = 0.5175, overlap = 1.095e+05  
steps = 60, shift = 0.156, angle = 2.29 degrees  
  
Position of cryosparc_P19_J70_008_volume_map_sharp.mrc (#4) relative to
cryosparc_P16_J82_004_volume_map_sharp_膜内表示用.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.99973953 -0.02273930 -0.00195001 285.01871138  
0.02276196 -0.99966262 -0.01251134 279.87256706  
-0.00166485 -0.01255247 0.99991983 2.16384216  
Axis -0.00090382 -0.00626696 0.99997995  
Axis point 140.91823889 141.56442853 0.00000000  
Rotation angle (degrees) 178.69634624  
Shift along axis 0.15224277  
  

> view matrix models
> #5,-0.86815,-0.38328,-0.3153,364.36,0.4143,-0.90946,-0.035197,215.53,-0.27326,-0.16118,0.94834,68.525

> volume #5 level 1.295

> view matrix models
> #5,-0.94028,-0.22539,-0.25511,344.65,0.24477,-0.96846,-0.046555,249.15,-0.23657,-0.10622,0.96579,53.407

> fitmap #4 inMap #5

Fit map cryosparc_P19_J70_008_volume_map_sharp.mrc in map
cryosparc_P16_J82_004_volume_map_sharp_膜内表示用.mrc using 97593 points  
correlation = 0.7694, correlation about mean = 0.5175, overlap = 1.095e+05  
steps = 80, shift = 0.239, angle = 2.37 degrees  
  
Position of cryosparc_P19_J70_008_volume_map_sharp.mrc (#4) relative to
cryosparc_P16_J82_004_volume_map_sharp_膜内表示用.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.99973911 -0.02276000 -0.00192368 285.01984789  
0.02278230 -0.99966235 -0.01249591 279.86333900  
-0.00163862 -0.01253648 0.99992008 2.15859012  
Axis -0.00089068 -0.00625910 0.99998001  
Axis point 140.91740679 141.56125875 0.00000000  
Rotation angle (degrees) 178.69517017  
Shift along axis 0.15299172  
  

> volume #4 level 0.6816

> volume #4 level 0.6397

> view matrix models
> #5,-0.87015,-0.38466,-0.30802,363.81,0.41282,-0.91034,-0.029352,215.04,-0.26911,-0.1527,0.95093,66.42

> undo

> select subtract #5

Nothing selected  

> volume #4 level 0.7286

> volume #5 level 1.708

> 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

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> close #5

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type AtomicStructureListWidget has been
deleted  
  
Error processing trigger "remove models":  
RuntimeError: wrapped C/C++ object of type AtomicStructureListWidget has been
deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> volume #4 level 0.4972

> volume #4 level 0.569

> open /Users/ishikawamoe/Desktop/analysis/reference/ours_NQR/7xk3_cryoNQR.pdb

7xk3_cryoNQR.pdb title:  
Cryo-em structure of Na+-pumping nadh-ubiquinone oxidoreductase from vibrio
cholerae, state 1 [more info...]  
  
Chain information for 7xk3_cryoNQR.pdb #5  
---  
Chain | Description | UniProt  
A | Na(+)-translocating nadh-quinone reductase subunit A | NQRA_VIBC3 1-446  
B | Na(+)-translocating nadh-quinone reductase subunit B | NQRB_VIBC3 1-415  
C | Na(+)-translocating nadh-quinone reductase subunit C | NQRC_VIBC3 1-257  
D | Na(+)-translocating nadh-quinone reductase subunit D | NQRD_VIBC3 1-210  
E | Na(+)-translocating nadh-quinone reductase subunit E | NQRE_VIBC3 1-198  
F | Na(+)-translocating nadh-quinone reductase subunit F | NQRF_VIBC3 1-408  
  
Non-standard residues in 7xk3_cryoNQR.pdb #5  
---  
CA — calcium ion  
FAD — flavin-adenine dinucleotide  
FES — FE2/S2 (inorganic) cluster  
FMN — flavin mononucleotide (riboflavin monophosphate)  
LMT — dodecyl-β-D-maltoside  
PEE — 1,2-dioleoyl-Sn-glycero-3-phosphoethanolamine (DOPE)  
RBF — riboflavin (riboflavine; vitamin B2)  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type AtomicStructureListWidget has been
deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type AtomicStructureListWidget has been
deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> view

[Repeated 1 time(s)]

> select add #5

14841 atoms, 15181 bonds, 1905 residues, 1 model selected  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> show sel cartoons

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> show sel atoms

> hide sel atoms

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

[deleted to fit within ticket limits]

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> view matrix models
> #5,-0.95163,-0.22604,-0.20808,337.88,0.25897,-0.95456,-0.14745,257.39,-0.1653,-0.19421,0.96693,54.409

> ui tool show "Fit in Map"

> fitmap #5 inMap #4

Fit molecule 7xk3_cryoNQR.pdb (#5) to map
cryosparc_P19_J70_008_volume_map_sharp.mrc (#4) using 14841 atoms  
average map value = 0.646, steps = 100  
shifted from previous position = 3.11  
rotated from previous position = 6.59 degrees  
atoms outside contour = 7209, contour level = 0.56903  
  
Position of 7xk3_cryoNQR.pdb (#5) relative to
cryosparc_P19_J70_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.99981644 0.01835044 -0.00550835 279.49611152  
-0.01827801 -0.99974942 -0.01292336 285.63003619  
-0.00574411 -0.01282031 0.99990132 2.33363336  
Axis 0.00281344 0.00643659 -0.99997533  
Axis point 141.05927742 141.54267321 0.00000000  
Rotation angle (degrees) 178.95058765  
Shift along axis 0.29125122  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> select subtract #5

Nothing selected  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> select #5/F

3222 atoms, 3305 bonds, 410 residues, 1 model selected  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> hide sel cartoons

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> volume #4 level 0.4134

> volume #4 level 0.3319

> volume #4 level 0.3689

> volume #4 level 0.4801

> volume #4 level 0.5987

> volume #4 level 0.4356

> volume #4 level 0.3986

> show #!3 models

> close #5

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type AtomicStructureListWidget has been
deleted  
  
Error processing trigger "remove models":  
RuntimeError: wrapped C/C++ object of type AtomicStructureListWidget has been
deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> show #2 models

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> select add #4

2 models selected  

> view matrix models
> #4,-0.18205,-0.13503,0.97397,48.147,-0.43877,0.8976,0.042432,69.902,-0.87997,-0.41962,-0.22266,355.54

> view matrix models
> #4,-0.84061,0.50492,0.19603,159.02,-0.54074,-0.76151,-0.35736,376.87,-0.031156,-0.4064,0.91316,74.504

> view matrix models
> #4,-0.97907,-0.15383,0.13328,280.8,0.16017,-0.98635,0.038158,255.53,0.12559,0.058707,0.99034,-24.321

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.97907,-0.15383,0.13328,280.12,0.16017,-0.98635,0.038158,244.23,0.12559,0.058707,0.99034,-32.919

> volume #3 level 0.003205

> volume #3 level 0.00459

> view matrix models
> #4,-0.97907,-0.15383,0.13328,275.28,0.16017,-0.98635,0.038158,244.55,0.12559,0.058707,0.99034,-35.821

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.86468,-0.5018,-0.02281,331.15,0.50082,-0.86472,0.037836,180.15,-0.03871,0.021292,0.99902,-8.9942

> view matrix models
> #4,-0.95575,-0.2656,0.12645,288.92,0.26146,-0.96399,-0.04862,239.7,0.13481,-0.013407,0.99078,-26.904

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.95575,-0.2656,0.12645,289.97,0.26146,-0.96399,-0.04862,241.19,0.13481,-0.013407,0.99078,-26.311

> hide #2 models

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> fitmap #4 inMap #3

Fit map cryosparc_P19_J70_008_volume_map_sharp.mrc in map
cryosparc_P20_J217_flex_map_Fdown.mrc using 116653 points  
correlation = 0.9185, correlation about mean = 0.6015, overlap = 574.5  
steps = 176, shift = 5.36, angle = 21.2 degrees  
  
Position of cryosparc_P19_J70_008_volume_map_sharp.mrc (#4) relative to
cryosparc_P20_J217_flex_map_Fdown.mrc (#3) coordinates:  
Matrix rotation and translation  
-0.99747875 0.06604579 -0.02596328 265.69114177  
-0.06528909 -0.99744529 -0.02898653 286.04250047  
-0.02781139 -0.02721833 0.99924255 -0.82595486  
Axis 0.01346076 0.01406907 -0.99981042  
Axis point 137.54083963 138.64911922 0.00000000  
Rotation angle (degrees) 176.23410856  
Shift along axis 8.42655542  
  

> fitmap #4 inMap #3

Fit map cryosparc_P19_J70_008_volume_map_sharp.mrc in map
cryosparc_P20_J217_flex_map_Fdown.mrc using 116653 points  
correlation = 0.9185, correlation about mean = 0.6015, overlap = 574.5  
steps = 44, shift = 0.0141, angle = 0.0117 degrees  
  
Position of cryosparc_P19_J70_008_volume_map_sharp.mrc (#4) relative to
cryosparc_P20_J217_flex_map_Fdown.mrc (#3) coordinates:  
Matrix rotation and translation  
-0.99748292 0.06596037 -0.02602010 265.72059766  
-0.06519728 -0.99744623 -0.02916026 286.05506261  
-0.02787707 -0.02739042 0.99923602 -0.77901367  
Axis 0.01349141 0.01415562 -0.99980878  
Axis point 137.54972715 138.66110505 0.00000000  
Rotation angle (degrees) 176.23919160  
Shift along axis 8.41309591  
  

> volume #4 level 0.4885

> select subtract #4

Nothing selected  

> volume #4 level 0.562

> volume #3 level 0.00691

> volume #4 level 0.4558

> volume #3 level 0.004025

> ui tool show "Side View"

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type AtomicStructureListWidget has been
deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type AtomicStructureListWidget has been
deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type AtomicStructureListWidget has been
deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type AtomicStructureListWidget has been
deleted  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir10,1
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 7429.81.3
      OS Loader Version: 7429.81.3

Software:

    System Software Overview:

      System Version: macOS 12.2.1 (21D62)
      Kernel Version: Darwin 21.3.0
      Time since boot: 6:56

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 7
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        Sidecar Display:
          Resolution: 2204 x 1484
          UI Looks like: 1102 x 742 @ 60.00Hz
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Mirror: Off
          Connection Type: AirPlay
          Virtual Device: Yes


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

[Eric Pettersen]

Does destroying MatchMaker actually eventually call delete() on the various list widgets?

[Eric Pettersen]

Fix: ​https://github.com/RBVI/ChimeraX/commit/e36231f73ff3bd7c2cb46159831b5bbf16a721d0