Matchmaker chain-chooser: 'Sequence' object has no attribute 'structure'

[lp212@…]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> set bgColor #ffffff00

Log from Mon Apr 29 17:00:00 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/luca/Dropbox (Cambridge University)/Zhan Yin/Pol alpha
> inhibitors/ST1926/st1926.cxs"

Log from Mon Jan 15 10:05:20 2024UCSF ChimeraX version: 1.7.dev202306060017
(2023-06-06)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/luca/Dropbox (Cambridge University)/Zhan's Data/2. Work/7.
> Manuscripts/CD437_inhibitors/Maps&Models/ST1926/Luca's
> model/cryosparc_P38_J102_007_volume_map_sharp_real_space_refined_020-coot-17_real_space_refined_029.pdb"

Chain information for
cryosparc_P38_J102_007_volume_map_sharp_real_space_refined_020-coot-17_real_space_refined_029.pdb
#1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> select ::name="ST1"

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

> view sel

> select sel :< 5

192 atoms, 186 bonds, 22 residues, 1 model selected  

> show sel atoms

> select clear

> select /A:764@CG

1 atom, 1 residue, 1 model selected  

> select up

8 atoms, 7 bonds, 1 residue, 1 model selected  

> color sel yellow

> select /A:768@CB

1 atom, 1 residue, 1 model selected  

> select up

8 atoms, 7 bonds, 1 residue, 1 model selected  

> color sel yellow

> select /A:762

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel target ab

> color sel yellow

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> select /A:700

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:700

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

[Repeated 1 time(s)]

> color sel yellow

> select /A:691

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /A:691

6 atoms, 5 bonds, 1 residue, 1 model selected  

> color sel yellow

> show sel atoms

> select /A:772

5 atoms, 4 bonds, 1 residue, 1 model selected  

> color sel yellow

> show sel atoms

> open 7opl

7opl title:  
CryoEM structure of DNA Polymerase α - primase bound to SARS CoV nsp1 [more
info...]  
  
Chain information for 7opl #2  
---  
Chain | Description | UniProt  
A | DNA polymerase alpha catalytic subunit | DPOLA_HUMAN 334-1462  
B | DNA polymerase alpha subunit B | DPOA2_HUMAN 149-598  
C | DNA primase small subunit | PRI1_HUMAN 1-420  
D | DNA primase large subunit | PRI2_HUMAN 1-509  
E | Non-structural protein 1 | R1A_SARS 13-127  
  
Non-standard residues in 7opl #2  
---  
SF4 — iron/sulfur cluster  
ZN — zinc ion  
  

> ui tool show Matchmaker

> matchmaker #!2 to #1

Parameters  
---  
Chain pairing | bb  
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
cryosparc_P38_J102_007_volume_map_sharp_real_space_refined_020-coot-17_real_space_refined_029.pdb,
chain A (#1) with 7opl, chain A (#2), sequence alignment score = 5226.7  
RMSD between 1026 pruned atom pairs is 0.889 angstroms; (across all 1064
pairs: 1.026)  
  

> show sel cartoons

> hide sel atoms

> show sel cartoons

> hide sel atoms

> ui tool show "Model Panel"

> hide sel atoms

> show sel cartoons

> select add #2

19748 atoms, 20187 bonds, 22 pseudobonds, 2447 residues, 4 models selected  

> hide sel atoms

> show sel cartoons

> select clear

> select #1/A:772

5 atoms, 4 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide #!2 models

> select clear

> select #1/A:1503@C11

1 atom, 1 residue, 1 model selected  

> select up

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

> ui tool show "Color Actions"

> color sel white target a

> color sel byhetero target a

> color sel cornflower blue target a

> color sel light sea green target a

> color sel light blue target a

> color sel byhetero target a

> select clear

> save "/Users/luca/Dropbox (Cambridge University)/Zhan Yin/Pol alpha
> inhibitors/ST1926/st1926.cxs"

——— End of log from Mon Jan 15 10:05:20 2024 ———

opened ChimeraX session  

> ui tool show "Model Panel"

> open "/Users/luca/Dropbox (Cambridge University)/Zhan's Data/2. Work/7.
> Manuscripts/CD437_inhibitors/Maps&Models/ST1926/cryosparc_P38_J102_007_volume_map.mrc"

Opened cryosparc_P38_J102_007_volume_map.mrc as #3, grid size 360,360,360,
pixel 1.07, shown at level 0.0545, step 2, values float32  

> view #3 clip false

> ui tool show "Volume Viewer"

> volume #3 step 1

> volume #3 level 0.675

> hide #!3 models

> select #2/B

3451 atoms, 3529 bonds, 444 residues, 1 model selected  

> select #1/B

3451 atoms, 3529 bonds, 444 residues, 1 model selected  

> select #1/B

3451 atoms, 3529 bonds, 444 residues, 1 model selected  

> select #1/A

8662 atoms, 8848 bonds, 10 pseudobonds, 1074 residues, 3 models selected  

> color (#!1 & sel) orange

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

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

> color sel cyan

> set bgColor white

> select clear

> graphics silhouettes true

> select clear

> select #1/B:593

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

60 atoms, 59 bonds, 8 residues, 1 model selected  

> select up

3451 atoms, 3529 bonds, 444 residues, 1 model selected  

> select up

18945 atoms, 19366 bonds, 2343 residues, 1 model selected  

> select down

3451 atoms, 3529 bonds, 444 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel light blue target c

> select clear

> select #1/C

3262 atoms, 3343 bonds, 6 pseudobonds, 390 residues, 3 models selected  

> ui tool show "Color Actions"

> color sel yellow green target c

> color sel green yellow target c

> color sel medium aquamarine target c

> select #1/C

3262 atoms, 3343 bonds, 6 pseudobonds, 390 residues, 3 models selected  

> select #1/D

3570 atoms, 3646 bonds, 22 pseudobonds, 435 residues, 2 models selected  

> color sel medium sea green target c

> color sel cornflower blue target c

> color sel dark olive green target c

> color sel light green target c

> color sel pale green target c

> select clear

> select #1/C:64

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select up

92 atoms, 91 bonds, 11 residues, 1 model selected  

> select up

2385 atoms, 2444 bonds, 283 residues, 1 model selected  

> select up

2410 atoms, 2471 bonds, 286 residues, 1 model selected  

> select up

2971 atoms, 3048 bonds, 355 residues, 1 model selected  

> select up

3059 atoms, 3136 bonds, 365 residues, 1 model selected  

> select up

3261 atoms, 3343 bonds, 389 residues, 1 model selected  

> select up

3262 atoms, 3343 bonds, 390 residues, 1 model selected  

> select up

18945 atoms, 19366 bonds, 2343 residues, 1 model selected  

> select up

38688 atoms, 39549 bonds, 4789 residues, 4 models selected  

> select down

18945 atoms, 19366 bonds, 2343 residues, 1 model selected  

> select down

3262 atoms, 3343 bonds, 390 residues, 1 model selected  

> select down

3261 atoms, 3343 bonds, 389 residues, 1 model selected  

> select up

3262 atoms, 3343 bonds, 390 residues, 1 model selected  

> color sel light pink target c

> select clear

> select #1/A:1503@C27

1 atom, 1 residue, 1 model selected  

> select up

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

> style sel sphere

Changed 28 atom styles  

> color sel byhetero

> color sel white

> color sel byhetero

> select clear

> select #1/A:1503@C21

1 atom, 1 residue, 1 model selected  

> select up

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

> style sel ball

Changed 28 atom styles  

> ui tool show "Color Actions"

> color sel khaki target c

> color sel khaki target a

[Repeated 2 time(s)]

> color sel wheat target a

[Repeated 1 time(s)]

> color sel khaki target a

> color sel byhetero

> select clear

> volume #3 level 0.5392

> select add #1

18945 atoms, 19366 bonds, 38 pseudobonds, 2343 residues, 3 models selected  

> ui tool show "Color Actions"

> color sel wheat target c

> color sel khaki target c

[Repeated 1 time(s)]

> color sel pale goldenrod target c

[Repeated 1 time(s)]

> color sel burly wood target c

> color sel tan target c

[Repeated 3 time(s)]

> select ::name="ST1"

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

> color sel khaki target a

[Repeated 1 time(s)]

> select clear

> select #1/A:1503@C26

1 atom, 1 residue, 1 model selected  

> select up

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

> color sel byhetero

> select clear

> ui tool show "Side View"

> select #1/A

8662 atoms, 8848 bonds, 10 pseudobonds, 1074 residues, 3 models selected  

> hide sel atoms

> select clear

> select ::name="ST1"

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

> show sel atoms

> style sel sphere

Changed 28 atom styles  

> select clear

> save /Users/luca/Desktop/image4.png supersample 3

> save /Users/luca/Desktop/image5.png supersample 3

> open "/Users/luca/Dropbox (Cambridge University)/Zhan's Data/2. Work/7.
> Manuscripts/CD437_inhibitors/Maps&Models/ST1926/Sharpened
> maps/Autosharpen_19_sharpened_map.ccp4"

Opened Autosharpen_19_sharpened_map.ccp4 as #4, grid size 360,360,360, pixel
1.07, shown at level 1.89, step 2, values float32  

> volume #4 step 1

> volume #4 level 6.401

> open "/Users/luca/Dropbox (Cambridge University)/Zhan's Data/2. Work/7.
> Manuscripts/CD437_inhibitors/Maps&Models/ST1926/Sharpened
> maps/ResolveCryoEM_11_denmod_map.ccp4"

Opened ResolveCryoEM_11_denmod_map.ccp4 as #5, grid size 97,109,129, pixel
1.07, shown at level 1.21, step 1, values float32  

> select ::name="ST1"

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

> view sel

> select ::name="ST1"

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

> style sel stick

Changed 28 atom styles  

> transparency #3.1 50

> select sel :< 5

382 atoms, 366 bonds, 47 residues, 2 models selected  

> select sel :< 5

1348 atoms, 1343 bonds, 167 residues, 2 models selected  

> show (#!1 & sel) target ab

> hide sel & #!1 atoms

> select ::name="ST1"

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

> select clear

> select ::name="ST1"

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

> show sel atoms

> select sel :< 3 & ~sel

92 atoms, 88 bonds, 10 residues, 2 models selected  

> show (#!1 & sel) target ab

> select #1/A:1503@O14

1 atom, 1 residue, 1 model selected  

> select up

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

> select sel :< 4 & ~sel

273 atoms, 254 bonds, 34 residues, 2 models selected  

> show (#!1 & sel) target ab

> color sel & #!1 byhetero

> ui tool show "Color Actions"

> color sel seashell target a

> color sel tan target a

> color sel byhetero target a

> select clear

> select #1/A:699@OE2

1 atom, 1 residue, 1 model selected  

> select up

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

> hide sel atoms

> select #1/A:786@OE2

1 atom, 1 residue, 1 model selected  

> select up

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

> select add #1/A:789@OE1

10 atoms, 8 bonds, 2 residues, 1 model selected  

> select up

18 atoms, 16 bonds, 2 residues, 1 model selected  

> hide sel atoms

> hide #!3 models

> select #1/A:780

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #1/A:695

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #1/A:696

6 atoms, 5 bonds, 1 residue, 1 model selected  

> show sel atoms

[Repeated 1 time(s)]

> select #1/A:695@CG2

1 atom, 1 residue, 1 model selected  

> select up

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #1/A:790@CB

1 atom, 1 residue, 1 model selected  

> select up

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

> select add #1/A:788@CB

12 atoms, 11 bonds, 2 residues, 1 model selected  

> select up

19 atoms, 18 bonds, 2 residues, 1 model selected  

> hide sel atoms

> select #1/A:1503@C11

1 atom, 1 residue, 1 model selected  

> select up

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

> color sel cornflower blue

> color sel byhetero

> select clear

> transparency #4.1 50

> volume #4 level 13.51

> select #1/A:784

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

> show sel atoms

> hide sel atoms

> volume #4 level 7.348

> volume #4 level 10.67

> volume #5 level 0.6144

> transparency #5.1 50

> volume #5 level 0.4684

> volume zone #4 nearAtoms #1/A:1503

> ui tool show "Side View"

> volume #4 color #bfbfbf

> transparency #4.1 50

> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"

38638 atoms, 39505 bonds, 10 pseudobonds, 4780 residues, 4 models selected  

> ui tool show "Color Actions"

> color sel tan target a

[Repeated 1 time(s)]

> color sel byhetero target a

> select clear

> volume zone #4 nearAtoms #1/A:1503 radius 2

Expected a keyword  

> volume zone #4 nearAtoms #1/A:1503

> volume zone #4 nearAtoms #1/A:1503 range 2

> volume zone #4 nearAtoms #1/A:1503 range 2.5

> volume zone #4 nearAtoms #1/A:1503 range 3

> volume zone #4 nearAtoms #1/A:1503 range 3.5

> volume zone #4 nearAtoms #1/A:1503

> volume zone #4 nearAtoms #1/A:1503 range 2

> volume #4 level 9.244

> volume #4 level 10.9

> select #1/A:791@CB

1 atom, 1 residue, 1 model selected  

> select up

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel atoms

> ui tool show H-Bonds

> select #1/A:1503@O1

1 atom, 1 residue, 1 model selected  

> select up

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

> select add #1/A:790

39 atoms, 43 bonds, 2 residues, 1 model selected  

> select up

119 atoms, 126 bonds, 11 residues, 1 model selected  

> hbonds sel color #52fbff restrict both distSlop 0.1 angleSlop 30.0 intraRes
> false

6 hydrogen bonds found  

> select clear

> save /Users/luca/Desktop/image5.png supersample 3

> save "/Users/luca/Dropbox (Cambridge University)/Zhan Yin/Pol alpha
> inhibitors/ST1926/st1926.cxs" includeMaps true

——— End of log from Mon Apr 29 17:00:00 2024 ———

opened ChimeraX session  

> select #1/A:789

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

> hide #!4 models

> select #1/A:788

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #1/A:789

17 atoms, 15 bonds, 2 residues, 1 model selected  

> select add #1/A:790

28 atoms, 26 bonds, 3 residues, 1 model selected  

> select add #1/A:791

36 atoms, 33 bonds, 4 residues, 1 model selected  

> show sel atoms

> select #1/A:786

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

> show sel atoms

> show #!4 models

> show #!5 models

> ui tool show "Volume Viewer"

> volume #5 level 0.7426

> ui tool show "Side View"

> graphics silhouettes false

> select #1/A:1503@C4

1 atom, 1 residue, 1 model selected  

> select up

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

> view sel

> hide #!5 models

> show #!5 models

> hide #!4 models

> volume #5 level 0.5712

> select clear

> volume #5 level 0.469

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> select #1/A:787

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

> select up

121 atoms, 120 bonds, 16 residues, 1 model selected  

> show sel atoms

> hide sel cartoons

> select clear

> open "/Users/luca/Cambridge University Dropbox/Dr Luca
> Pellegrini/RAD51/STRUCTURES/RAD51
> synapsis/AlphaFold3/fold_2024_05_14_09_53/fold_2024_05_14_09_53_model_0.cif"

Chain information for fold_2024_05_14_09_53_model_0.cif #6  
---  
Chain | Description  
A B C D E F G H I | .  
S | .  
T | .  
U | .  
  

> open "/Users/luca/Cambridge University Dropbox/Dr Luca
> Pellegrini/RAD51/STRUCTURES/RAD51
> synapsis/AlphaFold3/fold_2024_05_14_09_53/fold_2024_05_14_09_53_model_1.cif"

Chain information for fold_2024_05_14_09_53_model_1.cif #7  
---  
Chain | Description  
A B C D E F G H I | .  
S | .  
T | .  
U | .  
  

> open "/Users/luca/Cambridge University Dropbox/Dr Luca
> Pellegrini/RAD51/STRUCTURES/RAD51
> synapsis/AlphaFold3/fold_2024_05_14_09_53/fold_2024_05_14_09_53_model_2.cif"

Chain information for fold_2024_05_14_09_53_model_2.cif #8  
---  
Chain | Description  
A B C D E F G H I | .  
S | .  
T | .  
U | .  
  

> open "/Users/luca/Cambridge University Dropbox/Dr Luca
> Pellegrini/RAD51/STRUCTURES/RAD51
> synapsis/AlphaFold3/fold_2024_05_14_09_53/fold_2024_05_14_09_53_model_3.cif"

Chain information for fold_2024_05_14_09_53_model_3.cif #9  
---  
Chain | Description  
A B C D E F G H I | .  
S | .  
T | .  
U | .  
  

> open "/Users/luca/Cambridge University Dropbox/Dr Luca
> Pellegrini/RAD51/STRUCTURES/RAD51
> synapsis/AlphaFold3/fold_2024_05_14_09_53/fold_2024_05_14_09_53_model_4.cif"

Chain information for fold_2024_05_14_09_53_model_4.cif #10  
---  
Chain | Description  
A B C D E F G H I | .  
S | .  
T | .  
U | .  
  

> ui tool show "Model Panel"

> view #6-10 clip false

> hide #!1 models

> hide #!5 models

> show #6-10 cartoons

> hide #6-10 atoms

> ui tool show Matchmaker

> matchmaker #7-10 to #6

Parameters  
---  
Chain pairing | bb  
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 fold_2024_05_14_09_53_model_0.cif, chain I (#6) with
fold_2024_05_14_09_53_model_1.cif, chain A (#7), sequence alignment score =
1727.7  
RMSD between 321 pruned atom pairs is 0.217 angstroms; (across all 339 pairs:
2.272)  
  
Matchmaker fold_2024_05_14_09_53_model_0.cif, chain H (#6) with
fold_2024_05_14_09_53_model_2.cif, chain D (#8), sequence alignment score =
1725.3  
RMSD between 296 pruned atom pairs is 0.826 angstroms; (across all 339 pairs:
3.728)  
  
Matchmaker fold_2024_05_14_09_53_model_0.cif, chain H (#6) with
fold_2024_05_14_09_53_model_3.cif, chain G (#9), sequence alignment score =
1722.3  
RMSD between 294 pruned atom pairs is 0.650 angstroms; (across all 339 pairs:
5.442)  
  
Matchmaker fold_2024_05_14_09_53_model_0.cif, chain H (#6) with
fold_2024_05_14_09_53_model_4.cif, chain B (#10), sequence alignment score =
1725.3  
RMSD between 294 pruned atom pairs is 0.618 angstroms; (across all 339 pairs:
3.723)  
  

> hide #6 models

> hide #7 models

> hide #8 models

> hide #9 models

> hide #10 models

> show #6 models

> show #7 models

> ui tool show Matchmaker

> matchmaker #7/E to #6/E pairing ss

Parameters  
---  
Chain pairing | ss  
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 fold_2024_05_14_09_53_model_0.cif, chain E (#6) with
fold_2024_05_14_09_53_model_1.cif, chain E (#7), sequence alignment score =
1721.1  
RMSD between 331 pruned atom pairs is 0.300 angstroms; (across all 339 pairs:
0.798)  
  

> matchmaker #8/E to #6/E pairing ss

Parameters  
---  
Chain pairing | ss  
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 fold_2024_05_14_09_53_model_0.cif, chain E (#6) with
fold_2024_05_14_09_53_model_2.cif, chain E (#8), sequence alignment score =
1715.1  
RMSD between 300 pruned atom pairs is 0.838 angstroms; (across all 339 pairs:
5.037)  
  

> matchmaker #9/E to #6/E pairing ss

Parameters  
---  
Chain pairing | ss  
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 fold_2024_05_14_09_53_model_0.cif, chain E (#6) with
fold_2024_05_14_09_53_model_3.cif, chain E (#9), sequence alignment score =
1721.1  
RMSD between 292 pruned atom pairs is 0.656 angstroms; (across all 339 pairs:
5.400)  
  

> matchmaker #10/E to #6/E pairing ss

Parameters  
---  
Chain pairing | ss  
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 fold_2024_05_14_09_53_model_0.cif, chain E (#6) with
fold_2024_05_14_09_53_model_4.cif, chain E (#10), sequence alignment score =
1713.9  
RMSD between 298 pruned atom pairs is 0.582 angstroms; (across all 339 pairs:
3.009)  
  

> matchmaker #10/E to #6/E pairing ss

Parameters  
---  
Chain pairing | ss  
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 fold_2024_05_14_09_53_model_0.cif, chain E (#6) with
fold_2024_05_14_09_53_model_4.cif, chain E (#10), sequence alignment score =
1713.9  
RMSD between 298 pruned atom pairs is 0.582 angstroms; (across all 339 pairs:
3.009)  
  

> show #8 models

> show #9 models

> show #10 models

> hide #10 models

> hide #9 models

> hide #8 models

> ui tool show Matchmaker

> matchmaker #7/S to #6/S pairing ss

Using Nucleic matrix instead of BLOSUM-62 to match
fold_2024_05_14_09_53_model_1.cif #7/S to fold_2024_05_14_09_53_model_0.cif
#6/S  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
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 fold_2024_05_14_09_53_model_0.cif, chain S (#6) with
fold_2024_05_14_09_53_model_1.cif, chain S (#7), sequence alignment score =
128  
RMSD between 9 pruned atom pairs is 0.903 angstroms; (across all 32 pairs:
4.797)  
  

> matchmaker #7/S to #6/S pairing ss matrix Nucleic

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
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 fold_2024_05_14_09_53_model_0.cif, chain S (#6) with
fold_2024_05_14_09_53_model_1.cif, chain S (#7), sequence alignment score =
128  
RMSD between 9 pruned atom pairs is 0.903 angstroms; (across all 32 pairs:
4.797)  
  

> matchmaker #7/S to #6/S pairing ss matrix Nucleic

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
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 fold_2024_05_14_09_53_model_0.cif, chain S (#6) with
fold_2024_05_14_09_53_model_1.cif, chain S (#7), sequence alignment score =
128  
RMSD between 9 pruned atom pairs is 0.903 angstroms; (across all 32 pairs:
4.797)  
  

> matchmaker #7/E to #6/E pairing ss matrix Nucleic

Reference chain (fold_2024_05_14_09_53_model_0.cif (#6) chain E) not
compatible with Nucleic similarity matrix  

> matchmaker #7/E to #6/E pairing ss

Parameters  
---  
Chain pairing | ss  
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 fold_2024_05_14_09_53_model_0.cif, chain E (#6) with
fold_2024_05_14_09_53_model_1.cif, chain E (#7), sequence alignment score =
1721.1  
RMSD between 331 pruned atom pairs is 0.300 angstroms; (across all 339 pairs:
0.798)  
  

> show #8 models

> matchmaker #8/E to #6/E pairing ss

Parameters  
---  
Chain pairing | ss  
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 fold_2024_05_14_09_53_model_0.cif, chain E (#6) with
fold_2024_05_14_09_53_model_2.cif, chain E (#8), sequence alignment score =
1715.1  
RMSD between 300 pruned atom pairs is 0.838 angstroms; (across all 339 pairs:
5.037)  
  

> hide #7 models

> hide #6 models

> hide #8 models

> show #9 models

> select ::name="ATP"

1395 atoms, 1485 bonds, 45 residues, 5 models selected  

> show sel & #9 atoms

> hide #9 models

> show #10 models

> hide #10 models

> ui tool show "Model Panel"

> show #6 models

> select #6/U:31

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

> select up

1031 atoms, 1156 bonds, 50 residues, 1 model selected  

> select add #6/T:22

1051 atoms, 1177 bonds, 51 residues, 1 model selected  

> select up

2048 atoms, 2296 bonds, 100 residues, 1 model selected  

> select add #6/S:20

2069 atoms, 2319 bonds, 101 residues, 1 model selected  

> select up

2696 atoms, 3012 bonds, 132 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 2696 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 2696 atom styles  

> hide #6 models

> show #7 models

> select #7/U:29

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

> select up

1031 atoms, 1156 bonds, 50 residues, 1 model selected  

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 1031 atom styles  

> hide #7 models

> show #8 models

> close #6-10

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 392, in _items_change  
item_names = self._item_names()  
^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 47, in _item_names  
values = [v for v in self.list_func() if self.filter_func(v)]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 47, in <listcomp>  
values = [v for v in self.list_func() if self.filter_func(v)]  
^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/tool.py", line 518, in <lambda>  
filter_func=lambda c, ref=chain: c.structure != ref.structure)  
^^^^^^^^^^^^^  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
Error processing trigger "changes":  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/tool.py", line 518, in  
filter_func=lambda c, ref=chain: c.structure != ref.structure)  
^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.10.23
OpenGL renderer: AMD Radeon Pro Vega 48 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac19,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 3.6 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      Boot ROM Version: 1731.100.125.0.0
      SMC Version (system): 2.46f13

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H1824)
      Kernel Version: Darwin 19.6.0
      Time since boot: 1 day 1:35

Graphics/Displays:

    Radeon Pro Vega 48:

      Chipset Model: Radeon Pro Vega 48
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x6869
      Revision ID: 0x0000
      ROM Revision: 113-D0650E-072
      VBIOS Version: 113-D05001A1XG-011
      Option ROM Version: 113-D05001A1XG-011
      EFI Driver Version: 01.01.072
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: 5120 x 2880 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    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: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    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: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    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: 1.1.3
    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: 1.2.2
    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-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    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: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    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: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
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    ipywidgets: 8.1.1
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    matplotlib-inline: 0.1.6
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    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
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    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
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    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    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: 2.5
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    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

[Eric Pettersen]

I don't think this can happen anymore because in 1.8 Chains are no longer demoted to Sequences.