Mutation Scores / Interfaces: self._node_artist is None

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-15.3.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5-AF2_green_purple_muts_4.cxs" format session

Log from Mon Mar 17 13:59:51 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/cameroncriswell15/King
> Lab/Manuscript/Structures/AF_TLR2_unrelaxed_rank_1_model_3.pdb"

Chain information for AF_TLR2_unrelaxed_rank_1_model_3.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> open "/Users/cameroncriswell15/King
> Lab/Manuscript/Structures/2S5_unrelaxed_rank_1_model_3.pdb"

Chain information for 2S5_unrelaxed_rank_1_model_3.pdb #2  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> mmaker #1 to #2

Computing secondary structure  
[Repeated 1 time(s)]  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 2S5_unrelaxed_rank_1_model_3.pdb, chain A (#2) with
AF_TLR2_unrelaxed_rank_1_model_3.pdb, chain A (#1), sequence alignment score =
2366.4  
RMSD between 520 pruned atom pairs is 1.033 angstroms; (across all 562 pairs:
1.239)  
  

> mmaker #1 to #2 showAlignment 1

Computing secondary structure  
[Repeated 1 time(s)]  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 2S5_unrelaxed_rank_1_model_3.pdb, chain A (#2) with
AF_TLR2_unrelaxed_rank_1_model_3.pdb, chain A (#1), sequence alignment score =
2366.4  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1:
AF_TLR2_unrelaxed_rank_1_model_3.pdb #1/A, 2S5_unrelaxed_rank_1_model_3.pdb
#2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 520 pruned atom pairs is 1.033 angstroms; (across all 562 pairs:
1.239)  
  

> select :249

15 atoms, 13 bonds, 2 residues, 2 models selected  

> show sel

> select
> #2/A:1-2,9-22,24,30-46,52-147,150-213,215-216,219,221-269,276-294,299-487,492-493,495-553,557-561
> #1/A:1-2,9-22,24,30-46,52-147,150-213,215-216,219,221-269,276-294,299-487,492-493,495-553,557-561

8273 atoms, 8392 bonds, 1040 residues, 2 models selected  

> select
> #2/A:1-2,9-22,24,30-46,52-147,150-213,215-216,219,221-269,276-294,299-487,492-493,495-553,557-561
> #1/A:1-2,9-22,24,30-46,52-147,150-213,215-216,219,221-269,276-294,299-487,492-493,495-553,557-561

8273 atoms, 8392 bonds, 1040 residues, 2 models selected  

> select :73-262

3067 atoms, 3122 bonds, 380 residues, 2 models selected  

> select :73-240

2713 atoms, 2763 bonds, 336 residues, 2 models selected  

> select :106-240

2177 atoms, 2212 bonds, 270 residues, 2 models selected  

> select :172-228

922 atoms, 936 bonds, 114 residues, 2 models selected  

> select #2/A:1

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

> select #2/A:1-160

1262 atoms, 1281 bonds, 160 residues, 1 model selected  

> select #1/A:131 #2/A:131

8 atoms, 6 bonds, 2 residues, 2 models selected  

> select :228,206,249,250,244,243,203

117 atoms, 110 bonds, 14 residues, 2 models selected  

> show sel atoms

> select :228,206,249,250,244,243,203,200

133 atoms, 125 bonds, 16 residues, 2 models selected  

> select :228,206,249,250,244,243,203,200,149,78,159,74

194 atoms, 180 bonds, 24 residues, 2 models selected  

> select :228,206,249,250,244,243,203,200,149,78,159,74,261

205 atoms, 189 bonds, 26 residues, 2 models selected  

> select :228,206,249,250,244,243,203,200,149,78,159,74,261,379,392

236 atoms, 216 bonds, 30 residues, 2 models selected  

> show sel atoms

> color ribbon #D1CBC7

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color #1,#2 #D1CBC7

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color #1,#2 #D1CBC7 ribbon

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color byribbon #D1CBC7 ribbon

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color byribbon #D1CBC7

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color #1 #D1CBC7

> color #2 #D1CBC7

> select #1:228,206,249,250,244,243,203,200,149,78,159,74,261,379,392

118 atoms, 108 bonds, 15 residues, 1 model selected  

> color sel #516E53

> color sel #86AC83

> color sel byhetero target a

> select up

859 atoms, 862 bonds, 110 residues, 1 model selected  

> select down

118 atoms, 108 bonds, 15 residues, 1 model selected  

> select #2:228,206,249,250,244,243,203,200,149,78,159,74,261,379,392

118 atoms, 108 bonds, 15 residues, 1 model selected  

> color sel #918597

> color sel byhetero target a

> set bgColor white

> lighting simple

> lighting soft

> lighting shadows true intensity 0.5

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows false

> lighting shadows true

> select #1:228,206,249,250,244,243,203,200,149,78,159,74,261,379,392

118 atoms, 108 bonds, 15 residues, 1 model selected  

> color sel #86AC83

> color sel #67885E

> color sel byhetero target a

> select #1:228,206,250,203

34 atoms, 31 bonds, 4 residues, 1 model selected  

> color sel #516E53

> color sel #182525

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> color sel byhetero target a

> select #1:228,206,249,250,244,243,203,200,149,78,159,74,261,379,392

118 atoms, 108 bonds, 15 residues, 1 model selected  

> color sel #918597

> color sel byhetero target a

> select #2:228,206,249,250,244,243,203,200,149,78,159,74,261,379,392

118 atoms, 108 bonds, 15 residues, 1 model selected  

> color sel #516E53

> color sel byhetero target a

> select #2:228,206,250,203

34 atoms, 31 bonds, 4 residues, 1 model selected  

> color sel #182525

> color sel byhetero target a

> select clear

> hide #2 models

> show #2 models

> align #1:200-300 toAtoms #2:200-300 matchNumbering true

Pairing dropped 11 atoms and 12 reference atoms  
RMSD between 816 atom pairs is 1.802 angstroms  

> align #1:200-250 toAtoms #2:200-300 matchNumbering true

Pairing dropped 10 atoms and 419 reference atoms  
RMSD between 409 atom pairs is 2.045 angstroms  

> set transparency 50 ribbons

Expected a keyword  

> transparency 50 ribbons

> transparency 0 ribbons

> select clear

> transparency 50 ribbons

> transparency 80 ribbons

> hide #1 ribbons

> show #1 ribbons

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #1 models

> select #2/A:257

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

> select #2/A:257

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

> select #2/A:257

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

> select #2/A:256

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

> select #2/A:286

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

> select add #2/A:256

16 atoms, 14 bonds, 2 residues, 1 model selected  

> select subtract #2/A:286

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

> show sel atoms

> transparency 80 sel atoms

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

> transparency sel 80 atoms

> select clear

> show #1 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> hide #2 models

> ui mousemode right clip

> show #2 models

> hide #1 models

> select #2/A:253

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

> select #2/A:283

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

> select add #2/A:253

15 atoms, 13 bonds, 2 residues, 1 model selected  

> select add #2/A:191

23 atoms, 20 bonds, 3 residues, 1 model selected  

> show sel atoms

> transparency sel 80 atoms

> show #1 models

> select clear

> hide #2 models

> show #2 models

> hide #2 models

> select add #1/A:191

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

> select subtract #1/A:191

Nothing selected  

> select add #1/A:191

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

> select add #1/A:187

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

> select add #1/A:257

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

> select subtract #1/A:257

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

> select add #1/A:256

27 atoms, 25 bonds, 3 residues, 1 model selected  

> select add #1/A:253

35 atoms, 32 bonds, 4 residues, 1 model selected  

> select add #1/A:286

43 atoms, 39 bonds, 5 residues, 1 model selected  

> show sel atoms

> transparency sel 80 atoms

> show #2 models

> select add #2/A:188

51 atoms, 46 bonds, 6 residues, 2 models selected  

> select subtract #2/A:188

43 atoms, 39 bonds, 5 residues, 1 model selected  

> select add #2/A:187

51 atoms, 46 bonds, 6 residues, 2 models selected  

> select add #2/A:191

59 atoms, 53 bonds, 7 residues, 2 models selected  

> select add #2/A:286

67 atoms, 60 bonds, 8 residues, 2 models selected  

> select add #1/A:283

74 atoms, 66 bonds, 9 residues, 2 models selected  

> show sel atoms

> transparency sel 80 atoms

> select clear

> select add #1/A:191

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

> color sel #918597 atoms

> select add #2/A:191

19 atoms, 18 bonds, 2 residues, 2 models selected  

> select #1/A:191

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

> select subtract #1/A:191

Nothing selected  

> select add #2/A:192

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

> select subtract #2/A:192

Nothing selected  

> select add #2/A:191

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

> color sel #67885E atoms

[Repeated 1 time(s)]

> select add #1/A:191

19 atoms, 18 bonds, 2 residues, 2 models selected  

> transparency sel 0 atoms

> select clear

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> select #1/A:149

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

> hide sel atoms

> select clear

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #1 models

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_Nbend_side_1.png" width 2000 height 1597
> supersample 3 transparentBackground true

> show #1 models

> hide #2 models

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/AF2_Nbend_side_1.png" width 2000 height 1597
> supersample 3 transparentBackground true

> show #2 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> select clear

> hide #1 models

> hide #2 models

> show #1 models

> select add #1/A:149

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

> show sel atoms

> show #2 models

> select clear

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #1 models

> hide #2 models

> show #1 models

> show #2 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_191_228_250_closeup.png" width 2000 height 1597
> supersample 3 transparentBackground true

> show #1 models

> hide #2 models

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/AF2_191_228_250_closeup.png" width 2000 height 1597
> supersample 3 transparentBackground true

> undo

[Repeated 2 time(s)]

> ui mousemode right "clip rotate"

> ui mousemode right translate

> ui mousemode right clip

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> hide #1 models

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_203_206_closeup.png" width 2000 height 1597
> supersample 3 transparentBackground true

> show #1 models

> hide #2 models

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/AF2_203_206_closeup.png" width 2000 height 1597
> supersample 3 transparentBackground true

> show #2 models

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/Both_203_206_closeup.png" width 2000 height 1597
> supersample 3 transparentBackground true

> hide #1 models

> show #1 models

> hide #1 models

> ui mousemode right "clip rotate"

> ui mousemode right clip

> ui mousemode right translate

> ui mousemode right "clip rotate"

> ui mousemode right translate

> show #1 models

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> hide #2 models

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/AF2_Nbend_purple.png" width 2000 height 1597
> supersample 3 transparentBackground true

> show #2 models

> hide #1 models

> save "/Users/cameroncriswell15/King Lab/Manuscript/Figures/2S5_Nbend.png"
> width 2000 height 1597 supersample 3 transparentBackground true

> show #1 models

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #1 models

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_Nbend_topdown.png" width 2000 height 1597
> supersample 3 transparentBackground true

> show #1 models

> hide #2 models

> show #2 models

> hide #2 models

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/AF2_Nbend_topdown.png" width 2000 height 1597
> supersample 3 transparentBackground true

> show #2 models

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/Both_Nbend_topdown.png" width 2000 height 1597
> supersample 3 transparentBackground true

> hide #1 models

> save "/Users/cameroncriswell15/King Lab/Manuscript/Figures/2S5_Nbend_1.png"
> width 2000 height 1597 supersample 3 transparentBackground true

> show #1 models

> hide #2 models

> show #2 models

> hide #2 models

> select add #1/A:311

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

> select add #1/A:310

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

> select add #1/A:312

27 atoms, 24 bonds, 3 residues, 1 model selected  

> hide sel ribbons

> show #2 models

> hide #1 models

> select add #2/A:312

34 atoms, 30 bonds, 4 residues, 2 models selected  

> select add #2/A:311

45 atoms, 40 bonds, 5 residues, 2 models selected  

> hide sel ribbons

> save "/Users/cameroncriswell15/King Lab/Manuscript/Figures/2S5_Nbend_2.png"
> width 2000 height 1597 supersample 3 transparentBackground true

> show #1 models

> hide #2 models

> save "/Users/cameroncriswell15/King Lab/Manuscript/Figures/AF2_Nbend_2.png"
> width 2000 height 1597 supersample 3 transparentBackground true

> ui mousemode right clip

> ui mousemode right translate

> select :373,379,392,398,412

77 atoms, 67 bonds, 10 residues, 2 models selected  

> select :330,360,373,379,392,398,412

113 atoms, 102 bonds, 14 residues, 2 models selected  

> show sel atoms

> select up

834 atoms, 847 bonds, 105 residues, 2 models selected  

> select down

113 atoms, 102 bonds, 14 residues, 2 models selected  

> select #1:330,360,373,379,392,398,412

57 atoms, 52 bonds, 7 residues, 1 model selected  

> color sel #918597

[Repeated 1 time(s)]

> color byhetero target a

> select #2:330,360,373,379,392,398,412

56 atoms, 50 bonds, 7 residues, 1 model selected  

> show #2 models

> color sel #67885E

> color byhetero target a

> align #1:320-450 toAtoms #2:320-450 matchNumbering true

Pairing dropped 18 atoms and 6 reference atoms  
RMSD between 1026 atom pairs is 0.833 angstroms  

> select clear

> select #2/A:397

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

> select clear

> hide #2 models

> show #2 models

> select add #2/A:330

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

> select add #2/A:360

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

> color sel #162521

> select add #1/A:367

24 atoms, 22 bonds, 3 residues, 2 models selected  

> show sel atoms

> hide sel atoms

> select clear

> select #1/A:367

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

> hide sel atoms

> select #1/A:366

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

> show sel atoms

> transparency sel 80 atoms

> select #1/A:339

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

> show sel atoms

> transparency sel 80 atoms

> select add #1/A:354

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

> select add #1/A:355

19 atoms, 16 bonds, 3 residues, 1 model selected  

> select #2/A:354

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

> select add #1/A:355

11 atoms, 9 bonds, 2 residues, 2 models selected  

> select subtract #2/A:354

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

> select add #2/A:348

14 atoms, 12 bonds, 2 residues, 2 models selected  

> select subtract #2/A:348

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

> select add #2/A:355

10 atoms, 8 bonds, 2 residues, 2 models selected  

> select #2/A:355

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

> select add #1/A:356

11 atoms, 9 bonds, 2 residues, 2 models selected  

> select subtract #1/A:356

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

> select add #1/A:356

11 atoms, 9 bonds, 2 residues, 2 models selected  

> select subtract #1/A:356

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

> select add #1/A:356

11 atoms, 9 bonds, 2 residues, 2 models selected  

> select subtract #1/A:356

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

> select add #1/A:355

10 atoms, 8 bonds, 2 residues, 2 models selected  

> show sel atoms

> transparency sel 80 atoms

> select clear

[Repeated 1 time(s)]

> select #2/A:354

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

> select add #2/A:355

11 atoms, 9 bonds, 2 residues, 1 model selected  

> select add #1/A:355

16 atoms, 13 bonds, 3 residues, 2 models selected  

> select subtract #1/A:355

11 atoms, 9 bonds, 2 residues, 1 model selected  

> select subtract #2/A:355

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

> show sel atoms

> select add #2/A:325

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

> select add #1/A:325

20 atoms, 17 bonds, 3 residues, 2 models selected  

> show sel atoms

> transparency sel 80 atoms

> select add #1/A:354

26 atoms, 22 bonds, 4 residues, 2 models selected  

> show sel atoms

> transparency sel 80 atoms

> select clear

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #2 models

> select add #1/A:360

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

> select add #1/A:330

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

> select clear

> hide #1 models

> show #2 models

> select add #2/A:360

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

> select add #2/A:330

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

> select up

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

> select down

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

> color sel #67885E

> color byhetero target a

> color sel #67885E

> color byhetero target a

> select clear

> ui mousemode right clip

> ui mousemode right "clip rotate"

> ui mousemode right clip

> ui mousemode right "clip rotate"

> ui mousemode right clip

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5-AF2_green_purple_muts.cxs"

> select :360,379,398

54 atoms, 51 bonds, 6 residues, 2 models selected  

> select clear

> select :360,379,398

54 atoms, 51 bonds, 6 residues, 2 models selected  
Drag select of 1 residues  

> select :360,379,398

54 atoms, 51 bonds, 6 residues, 2 models selected  

> select #2/A:392

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

> show #1 models

> select :360,379,392,398

70 atoms, 65 bonds, 8 residues, 2 models selected  

> select :360,379,392,398,412

86 atoms, 79 bonds, 10 residues, 2 models selected  

> select #1/:360,379,392,398,412

Expected an objects specifier or a keyword  

> select #1:360,379,392,398,412

43 atoms, 40 bonds, 5 residues, 1 model selected  

> color sel #182525

> color sel byhetero target a

> select up

304 atoms, 310 bonds, 38 residues, 1 model selected  

> select down

43 atoms, 40 bonds, 5 residues, 1 model selected  

> select #2:360,379,392,398,412

43 atoms, 39 bonds, 5 residues, 1 model selected  

> color sel #182525

> color sel byhetero target a

> select clear

> select #2:360,379,392,398,412

43 atoms, 39 bonds, 5 residues, 1 model selected  

> select clear

[Repeated 1 time(s)]

> select #2/A:398

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

> select add #2/A:360

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

> color sel #67885E

> color sel byhetero target a

> select clear

> select #2/A:383

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

> select add #1/A:408

22 atoms, 22 bonds, 2 residues, 2 models selected  

> show sel atoms

> transparency sel 80 atoms

> select add #1/A:394

30 atoms, 29 bonds, 3 residues, 2 models selected  

> select add #2/A:415

38 atoms, 36 bonds, 4 residues, 2 models selected  

> select add #2/A:417

46 atoms, 43 bonds, 5 residues, 2 models selected  

> select add #1/A:417

54 atoms, 50 bonds, 6 residues, 2 models selected  

> select subtract #1/A:417

46 atoms, 43 bonds, 5 residues, 2 models selected  

> select subtract #2/A:417

38 atoms, 36 bonds, 4 residues, 2 models selected  

> show sel atoms

> transparency sel 80 atoms

> select add #2/A:408

52 atoms, 51 bonds, 5 residues, 2 models selected  

> select add #1/A:383

60 atoms, 58 bonds, 6 residues, 2 models selected  

> select add #2/A:394

67 atoms, 64 bonds, 7 residues, 2 models selected  

> select add #1/A:415

75 atoms, 71 bonds, 8 residues, 2 models selected  

> show sel atoms

> transparency sel 80 atoms

> hide #2 models

> show #2 models

> hide #1 models

> select :373,379,392,394,396,398,412,420,421,422,425

166 atoms, 148 bonds, 22 residues, 2 models selected  

> select #1:373,379,392,394,396,398,412,420,421,422,425

87 atoms, 78 bonds, 11 residues, 1 model selected  

> transparency sel 0 atoms

> color sel #918597 atoms

> show #1 models

> select #1:373,379,392,394,396,398,412,420,421,422,425

87 atoms, 78 bonds, 11 residues, 1 model selected  

> show sel atoms

> color sel byhetero target a

> hide #2 models

> show #2 models

> hide #1 models

> select #2:373,379,392,394,396,398,412,420,421,422,425

79 atoms, 70 bonds, 11 residues, 1 model selected  

> select subtract #2/A:392

71 atoms, 63 bonds, 10 residues, 1 model selected  

> select subtract #2/A:379

63 atoms, 56 bonds, 9 residues, 1 model selected  

> select subtract #2/A:412

55 atoms, 49 bonds, 8 residues, 1 model selected  

> show sel atoms

> color sel #67885E

> show sel atoms

> color sel byhetero target a

> select up

355 atoms, 361 bonds, 46 residues, 1 model selected  

> select down

55 atoms, 49 bonds, 8 residues, 1 model selected  

> transparency sel 0 atoms

> show #1 models

> hide #2 models

> show #2 models

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5-AF2_green_purple_muts_2.cxs"

> hide #1 models

> show #1 models

> select clear

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #2 models

> select add #1/A:408

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

> clip -10 near pos sel

Expected a keyword  

> clip near -10 position sel

> clip near 10 position sel

> clip near 9 position sel

> clip near 6 position sel

> clip near 2 position sel

> clip near -1 position sel

> clip front-1 pos sel

Expected a keyword  

> clip front -1 position sel

> clip front -10 position sel

> clip front -15 position sel

> clip back-15 pos sel

Expected a keyword  

> clip back -10 position sel

> clip back 10 position sel

> clip back 11 position sel

> clip back 8 position sel

> clip back 9 position sel

> clip back 10 position sel

> clip back 11 position sel

> clip back 12 position sel

> show #2 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> select #2/A:429

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

> select add #2/A:428

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

> select add #1/A:428

19 atoms, 16 bonds, 3 residues, 2 models selected  

> select add #1/A:429

27 atoms, 23 bonds, 4 residues, 2 models selected  

> hide sel ribbons

> hide #2 models

> show #2 models

> hide #1 models

> select add #2/A:422@CD1

28 atoms, 23 bonds, 5 residues, 2 models selected  

> hide sel atoms

> select clear

> show #1 models

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> hide #1 models

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_379_392_412_closeup.png" width 2000 height 1597
> supersample 3 transparentBackground true

> show #1 models

> hide #2 models

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/AF2_379_392_412_closeup.png" width 2000 height 1597
> supersample 3 transparentBackground true

> select add #1/A:396

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

> color sel byhetero target a

> show sel atoms

> show #2 models

> hide #1 models

> select add #2/A:422

17 atoms, 15 bonds, 2 residues, 2 models selected  

> show sel atoms

> select #2/A:427

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select add #2/A:430

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

> select up

128 atoms, 129 bonds, 18 residues, 1 model selected  

> show sel ribbons

> select clear

> show #1 models

> select add #2/A:427

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select up

128 atoms, 129 bonds, 18 residues, 1 model selected  

> show sel ribbons

> select clear

> hide #2 models

> select add #1/A:427

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select up

134 atoms, 135 bonds, 18 residues, 1 model selected  

> show sel ribbons

> select clear

> select add #1/A:396

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

> color sel byhetero target a

> select clear

> show #2 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> hide #2 models

> hide #1 models

> show #1 models

> show #2 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> hide #1 models

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_Cbend_topdown.png" width 894 height 714
> supersample 3

> show #1 models

> hide #2 models

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_Cbend_topdown.png" width 2000 height 1597
> supersample 3 transparentBackground true

> show #2 models

> hide #1 models

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_Cbend_topdown.png" width 2000 height 1597
> supersample 3 transparentBackground true

> show #1 models

> hide #2 models

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/AF2_Cbend_topdown.png" width 2000 height 1597
> supersample 3 transparentBackground true

> show #2 models

> hide #2 models

> show #2 models

> hide #1 models

> select clear

> select add #2/A:430

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

> select add #2/A:429

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select add #2/A:428

20 atoms, 18 bonds, 3 residues, 1 model selected  

> select clear

> show #1 models

> hide #2 models

> select clear

> select #1/A:415

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

> clip back 10 position sel

> clip back 12 position sel

> clip back 8 position sel

> clip back 5 position sel

> clip back 4 position sel

> clip back 2 position sel

> clip back 3 position sel

> select clear

> select add #1/A:415

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

> clip near 3 position sel

> clip near 5 position sel

> clip near 2 position sel

> clip near 5 position sel

> clip near -5 position sel

> clip near -6 position sel

> clip near -8 position sel

> clip near -9 position sel

> clip near -15 position sel

> select clear

> select add #1/A:293

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

> select add #1/A:292

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

> select up

55 atoms, 56 bonds, 6 residues, 1 model selected  

> select up

4464 atoms, 4539 bonds, 562 residues, 1 model selected  

> select down

55 atoms, 56 bonds, 6 residues, 1 model selected  

> select add #1/A:297

67 atoms, 68 bonds, 7 residues, 1 model selected  

> select up

86 atoms, 89 bonds, 9 residues, 1 model selected  

> select add #1/A:300

98 atoms, 101 bonds, 10 residues, 1 model selected  

> select up

125 atoms, 130 bonds, 13 residues, 1 model selected  

> select add #1/A:272

131 atoms, 135 bonds, 14 residues, 1 model selected  

> select up

275 atoms, 281 bonds, 33 residues, 1 model selected  

> select add #1/A:237

283 atoms, 288 bonds, 34 residues, 1 model selected  

> select add #1/A:264

291 atoms, 295 bonds, 35 residues, 1 model selected  

> select up

381 atoms, 387 bonds, 46 residues, 1 model selected  

> select add #1/A:305

389 atoms, 394 bonds, 47 residues, 1 model selected  

> select up

435 atoms, 442 bonds, 53 residues, 1 model selected  

> hide sel ribbons

> select add #1/A:349

444 atoms, 450 bonds, 54 residues, 1 model selected  

> select up

496 atoms, 503 bonds, 60 residues, 1 model selected  

> select up

4464 atoms, 4539 bonds, 562 residues, 1 model selected  

> select down

496 atoms, 503 bonds, 60 residues, 1 model selected  

> select add #1/A:356

502 atoms, 508 bonds, 61 residues, 1 model selected  

> select add #1/A:327

508 atoms, 513 bonds, 62 residues, 1 model selected  

> select up

620 atoms, 630 bonds, 76 residues, 1 model selected  

> hide sel

> hide sel ribbons

> select add #1/A:322

627 atoms, 636 bonds, 77 residues, 1 model selected  

> select up

683 atoms, 695 bonds, 84 residues, 1 model selected  

> select add #1/A:333

691 atoms, 702 bonds, 85 residues, 1 model selected  

> select add #1/A:334

700 atoms, 710 bonds, 86 residues, 1 model selected  

> select up

723 atoms, 735 bonds, 89 residues, 1 model selected  

> select down

700 atoms, 710 bonds, 86 residues, 1 model selected  

> hide sel ribbons

> hide sel atoms

> show #2 models

> hide #2 models

> hide #1 models

> show #2 models

> show #1 models

> select add #2/A:348

709 atoms, 718 bonds, 87 residues, 2 models selected  

> select up

784 atoms, 796 bonds, 96 residues, 2 models selected  

> select add #2/A:359

789 atoms, 800 bonds, 97 residues, 2 models selected  

> select up

858 atoms, 872 bonds, 106 residues, 2 models selected  

> select add #2/A:329

866 atoms, 879 bonds, 107 residues, 2 models selected  

> select up

904 atoms, 918 bonds, 112 residues, 2 models selected  

> select add #2/A:326

911 atoms, 925 bonds, 113 residues, 2 models selected  

> select up

967 atoms, 983 bonds, 120 residues, 2 models selected  

> select add #2/A:304

974 atoms, 989 bonds, 121 residues, 2 models selected  

> select up

1030 atoms, 1046 bonds, 128 residues, 2 models selected  

> select add #2/A:300

1042 atoms, 1058 bonds, 129 residues, 2 models selected  

> select add #2/A:297

1054 atoms, 1070 bonds, 130 residues, 2 models selected  

> select add #2/A:265

1058 atoms, 1073 bonds, 131 residues, 2 models selected  

> select add #2/A:267

1062 atoms, 1076 bonds, 132 residues, 2 models selected  

> select add #2/A:270

1073 atoms, 1086 bonds, 133 residues, 2 models selected  

> select add #2/A:275

1081 atoms, 1093 bonds, 134 residues, 2 models selected  

> select up

1286 atoms, 1307 bonds, 160 residues, 2 models selected  

> select add #2/A:293

1294 atoms, 1314 bonds, 161 residues, 2 models selected  

> select up

1341 atoms, 1364 bonds, 166 residues, 2 models selected  

> hide sel atoms

> hide sel ribbons

> select add #2/A:333

1349 atoms, 1371 bonds, 167 residues, 2 models selected  

> select up

1381 atoms, 1404 bonds, 171 residues, 2 models selected  

> hide sel ribbons

> select clear

> hide #2 models

> clip near -9 position sel

Invalid "position" argument: Center argument no objects specified  

> select add #1/A:425

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

> clip near -9 position sel

> show #2 models

> select add #2/A:425

15 atoms, 13 bonds, 2 residues, 2 models selected  

> clip near -9 position sel

> undo

> clip near -9 position sel

> select add #2/A:425

15 atoms, 13 bonds, 2 residues, 2 models selected  

> clip near -9 position sel

> select clear

> select add #2/A:446

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

> select add #1/A:446

22 atoms, 22 bonds, 2 residues, 2 models selected  

> select up

270 atoms, 272 bonds, 34 residues, 2 models selected  

> hide sel ribbons

> select clear

> select add #1/A:396

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

> hide sel atoms

> select clear

> show sel atoms

> select add #1/A:396

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

> show sel atoms

> select clear

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #1 models

> select add #2/A:346

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

> select up

54 atoms, 53 bonds, 7 residues, 1 model selected  

> hide sel ribbons

> show #1 models

> select add #1/A:347

61 atoms, 59 bonds, 8 residues, 2 models selected  

> select up

108 atoms, 106 bonds, 14 residues, 2 models selected  

> hide sel ribbons

> select clear

> hide #1 models

> save "/Users/cameroncriswell15/King Lab/Manuscript/Figures/2S5_all_muts.png"
> width 2000 height 1597 supersample 3 transparentBackground true

> show #1 models

> hide #2 models

> save "/Users/cameroncriswell15/King Lab/Manuscript/Figures/AF2_all_muts.png"
> width 2000 height 1597 supersample 3 transparentBackground true

> show #2 models

> show #1 ribbons

> show #2 ribbons

> ui mousemode right clip

> clip

> clip off

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5-AF2_green_purple_muts_2.cxs"

> hide #2 models

> select clear

> show #2 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #1 models

> ui mousemode right translate

> show #1 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> hide #1 models

> show #1 surfaces

> show #!1 models

> hide #2 models

> show #2 models

> hide #1 surfaces

> hide #2 models

> show #2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> select add #2/A:428

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

> select add #2/A:429

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

> select add #2/A:430

20 atoms, 18 bonds, 3 residues, 1 model selected  

> select add #2/A:431

29 atoms, 26 bonds, 4 residues, 1 model selected  

> show #!1 models

> select add #1/A:429

37 atoms, 33 bonds, 5 residues, 2 models selected  

> select add #1/A:430

44 atoms, 40 bonds, 6 residues, 3 models selected  

> select add #1/A:431

53 atoms, 48 bonds, 7 residues, 3 models selected  

> select add #2/A:379

61 atoms, 55 bonds, 8 residues, 3 models selected  

> select subtract #2/A:379

53 atoms, 48 bonds, 7 residues, 3 models selected  

> select add #1/A:428

59 atoms, 53 bonds, 8 residues, 3 models selected  

> hide sel ribbons

> hide #2 models

> select add #1/A:237

67 atoms, 60 bonds, 9 residues, 3 models selected  

> select up

345 atoms, 347 bonds, 46 residues, 3 models selected  

> select up

8928 atoms, 9081 bonds, 1124 residues, 3 models selected  

> select down

345 atoms, 347 bonds, 46 residues, 3 models selected  
Drag select of 1 atoms, 8 residues  

> select up

417 atoms, 417 bonds, 55 residues, 3 models selected  

> select down

410 atoms, 347 bonds, 55 residues, 3 models selected  

> select clear

> select #1/A:304

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

> select up

54 atoms, 54 bonds, 7 residues, 2 models selected  

> select add #1/A:269

65 atoms, 65 bonds, 8 residues, 2 models selected  

> select up

204 atoms, 205 bonds, 27 residues, 2 models selected  

> select add #1/A:333

212 atoms, 212 bonds, 28 residues, 2 models selected  

> select up

244 atoms, 244 bonds, 32 residues, 2 models selected  

> select add #1/A:240

252 atoms, 251 bonds, 33 residues, 2 models selected  

> select up

327 atoms, 327 bonds, 42 residues, 2 models selected  

> select add #1/A:236

334 atoms, 333 bonds, 43 residues, 2 models selected  

> select up

351 atoms, 351 bonds, 45 residues, 2 models selected  

> select add #1/A:368

359 atoms, 358 bonds, 46 residues, 2 models selected  

> select up

416 atoms, 416 bonds, 53 residues, 2 models selected  

> select add #1/A:367

424 atoms, 423 bonds, 54 residues, 2 models selected  

> select up

439 atoms, 439 bonds, 56 residues, 2 models selected  

> select down

424 atoms, 423 bonds, 54 residues, 2 models selected  

> select clear

> select add #1/A:392

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

> clip back -10 position sel

> clip off

> clip far -10 position sel

> clip far 10 position sel

> select clear

> clip far 11 position sel

Invalid "position" argument: Center argument no objects specified  

> select add #1/A:392

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

> clip far 11 position sel

> clip far 15 position sel

> select clear

> show #2 models

> hide #!1 models

> show #!1 models

> hide #2 models

> show #2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> clip far 5 position sel

Invalid "position" argument: Center argument no objects specified  

> select #2/A:392

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

> clip far 5 position sel

> clip far 15 position sel

> clip far 25 position sel

> clip far 20 position sel

> clip far 18 position sel

> clip far 17 position sel

> show #!1 models

> hide #!1 models

> show #!1 models

> clip far 17 position sel

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> select clear

> ui mousemode right rotate

> ui mousemode right translate

> select add #2/A:444

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

> select add #2/A:445

16 atoms, 14 bonds, 2 residues, 1 model selected  

> select add #2/A:446

27 atoms, 25 bonds, 3 residues, 1 model selected  

> select add #2/A:443

35 atoms, 32 bonds, 4 residues, 1 model selected  

> select add #2/A:424

41 atoms, 37 bonds, 5 residues, 1 model selected  

> select add #2/A:425

49 atoms, 44 bonds, 6 residues, 1 model selected  

> hide sel ribbons

> hide sel ra

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

> hide sel atoms

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> select add #1/A:425

56 atoms, 50 bonds, 7 residues, 2 models selected  

> select add #1/A:445

64 atoms, 57 bonds, 8 residues, 3 models selected  

> select add #1/A:446

75 atoms, 68 bonds, 9 residues, 3 models selected  

> select add #1/A:444

83 atoms, 75 bonds, 10 residues, 3 models selected  

> hide sel atoms

> hide sel ribbons

> hide #2 models

> select #1/A:392

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

> clip far 18 position sel

> clip far 25 position sel

> clip far 15 position sel

> clip far 17 position sel

> clip far 25 position sel

> clip far 20 position sel

> select clear

> show #2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #2 models

> show #2 models

> hide #2 models

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/AF2_379_392_412_closeup_2.png" width 2000 height 1597
> supersample 3 transparentBackground true

> show #2 models

> hide #!1 models

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_379_392_412_closeup_2.png" width 2000 height 1597
> supersample 3 transparentBackground true

> hide #2 models

> show #2 models

> show #!1 models

> hide #2 models

> show #2 models

> hide #!1 models

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_whole_topview.png" width 2000 height 1597
> supersample 3 transparentBackground true

> show #!1 models

> hide #2 models

> color #2 #D1CBC7 ribbons

> show #2 models

> hide #!1 models

> show #2 surfaces

> transparency #2 0 ribbons

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5-AF2_green_purple_muts_2.cxs"

> transparency #2 80 surfaces

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_whole_topview_2.png" width 2000 height 1597
> supersample 3 transparentBackground true

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_whole_sideview.png" width 2000 height 1597
> supersample 3 transparentBackground true

[Repeated 3 time(s)]

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_whole_topview_2.png" width 2000 height 1597
> supersample 3 transparentBackground true

> hide surfacew

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

> hide surfacee

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

> hide surfaces

> show ribbons

> undo

> show #1:330,360

> show #1:330,360 atoms

> show #2:330,360 atoms

> select add #2/A:244

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

> select add #2/A:243

19 atoms, 18 bonds, 2 residues, 2 models selected  

> color sel #67885E

> color sel #67885E target a

> select add #2/A:201

27 atoms, 25 bonds, 3 residues, 2 models selected  

> select subtract #2/A:201

19 atoms, 18 bonds, 2 residues, 2 models selected  

> select add #2/A:200

29 atoms, 28 bonds, 3 residues, 2 models selected  

> select add #2/A:74

36 atoms, 34 bonds, 4 residues, 2 models selected  

> select add #2/A:78

43 atoms, 40 bonds, 5 residues, 2 models selected  

> select add #2/A:150

51 atoms, 47 bonds, 6 residues, 2 models selected  

> select subtract #2/A:150

43 atoms, 40 bonds, 5 residues, 2 models selected  

> select add #2/A:149

49 atoms, 45 bonds, 6 residues, 2 models selected  
Drag select of 1 residues  

> select subtract #2/A:150

49 atoms, 45 bonds, 6 residues, 2 models selected  
Drag select of 1 residues  

> select subtract #2/A:157

49 atoms, 45 bonds, 6 residues, 2 models selected  

> select add #2/A:159

57 atoms, 52 bonds, 7 residues, 2 models selected  

> color sel #67885E target a

> color byhetero target a

> select add #2/A:249

63 atoms, 57 bonds, 8 residues, 2 models selected  

> color sel #67885E target a

> color byhetero target a

> select clear

> show surfaces

> show ribbons

Drag select of 2S5_unrelaxed_rank_1_model_3.pdb_A SES surface, 83240 of 474396
triangles, 8 atoms, 102 residues, 6 bonds  

> hide sel ribbons

Drag select of 2S5_unrelaxed_rank_1_model_3.pdb_A SES surface, 99440 of 474396
triangles, 113 residues  

> hide sel ribbons

> select clear

[Repeated 1 time(s)]

> hide surfaces

> show surfaces

> hide ribbons

> show ribbons

> hide surfaces

> set transparency 50 ribbons

Expected a keyword  

> transparency 50 ribbons

> transparency 80 ribbons

> select clear

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_whole_topview_rib.png" width 2000 height 1597
> supersample 3 transparentBackground true

> show surfaces

> transparency 0 ribbons

> transparency 80 ribbons

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_whole_topview_surf.png" width 2000 height 1597
> supersample 3 transparentBackground true

> transparency 0 ribbons

Drag select of 2S5_unrelaxed_rank_1_model_3.pdb_A SES surface, 162360 of
474396 triangles, 8 atoms, 193 residues, 6 bonds  

> hide ribbons

> show ribbons

> hide sel ribbons

> select clear

> hide surfaces

> transparency 80 ribbons

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_whole_topview_rib.png" width 2000 height 1597
> supersample 3 transparentBackground true

> transparency 80 ribbons

> show surfaces

> show ribbons

> transparency 0 ribbons

> hide sel ribbons

Drag select of 2S5_unrelaxed_rank_1_model_3.pdb_A SES surface, 160876 of
474396 triangles, 4 atoms, 188 residues, 3 bonds  

> select clear

Drag select of 2S5_unrelaxed_rank_1_model_3.pdb_A SES surface, 157706 of
474396 triangles, 4 atoms, 180 residues, 3 bonds  
Drag select of 2S5_unrelaxed_rank_1_model_3.pdb_A SES surface, 32995 of 474396
triangles, 7 atoms, 56 residues, 5 bonds  
Drag select of 2S5_unrelaxed_rank_1_model_3.pdb_A SES surface, 101402 of
474396 triangles, 11 atoms, 130 residues, 8 bonds  

> select clear

Drag select of 2S5_unrelaxed_rank_1_model_3.pdb_A SES surface, 151577 of
474396 triangles, 4 atoms, 173 residues, 3 bonds  

> hide ribbons

> show ribbons

> hide sel ribbons

> select clear

> hide surfaces

> transparency 80 ribbons

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_whole_topview_rib.png" width 2000 height 1597
> supersample 3 transparentBackground true

> transparency 0 ribbons

> show surfaces

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_whole_topview_surf.png" width 2000 height 1597
> supersample 3 transparentBackground true

> show ribbons

> hides

Unknown command: hides  

> hide surfaces

> transparency 80 ribbons

> select #2/A:249

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

> hbonds sel reveal true

4 hydrogen bonds found  

> show #!1 models

> select clear

> select add #1/A:249

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

> hide #3 models

> show #3 models

> hide #3 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> select #2:249

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

> color sel #162521

> color sel byhetero target a

> show #3 models

> hide #3 models

> select clear

> hide #!1 models

> show #3 models

> hide #3 models

> select #2/A:221

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

> select up

174 atoms, 176 bonds, 22 residues, 2 models selected  

> show sel atoms

> show #!1 models

> show sel atoms

> hide #!2 models

> show #!2 models

> select add #1/A:215

183 atoms, 184 bonds, 23 residues, 3 models selected  

> select up

347 atoms, 351 bonds, 44 residues, 4 models selected  

> show sel atoms

> hide #!2 models

> hbonds sel & #!1 reveal true

46 hydrogen bonds found  

> show #3 models

> show #!2 models

> hide #3 models

> hide #!1 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> hbonds sel & #!2 reveal true

36 hydrogen bonds found  

> show #3 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> show #!2 models

> hide #3 models

> hide sel atoms

> select clear

> show #!1 models

> hide #!2 models

> select add #1/A:216

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

> select add #1/A:217

14 atoms, 12 bonds, 2 residues, 2 models selected  

> select #1/A:218

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

> select add #1/A:217

13 atoms, 11 bonds, 2 residues, 2 models selected  

> show sel atoms

> show #!2 models

> hide #!1 models

> select add #2/A:218

20 atoms, 17 bonds, 3 residues, 3 models selected  

> select add #2/A:222

28 atoms, 24 bonds, 4 residues, 4 models selected  

> select add #2/A:221

35 atoms, 30 bonds, 5 residues, 4 models selected  

> show sel atoms

> show #!1 models

> select clear

> hide #!2 models

> select add #1/A:223

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

> select clear

> show #!2 models

> hide #!2 models

> select #1/A:220

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

> show sel atoms

> show #!2 models

> hide #!1 models

> select add #2/A:218

16 atoms, 14 bonds, 2 residues, 3 models selected  

> select add #2/A:221

23 atoms, 20 bonds, 3 residues, 4 models selected  

> hide sel atoms

> select clear

Drag select of 1 residues  

> select clear

> select add #2/A:242

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

> hide sel atoms

> select #2/A:183

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

> select #2/A:183

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

> select #2/A:182

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

> select #2/A:183

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

> select add #2/A:184

19 atoms, 18 bonds, 2 residues, 2 models selected  

> hide sel atoms

> show #!1 models

> hide #!2 models

> select add #1/A:195

26 atoms, 24 bonds, 3 residues, 3 models selected  

> select add #1/A:251

32 atoms, 29 bonds, 4 residues, 4 models selected  

> select add #1/A:218

39 atoms, 35 bonds, 5 residues, 4 models selected  

> hide sel atoms

> show #!2 models

> select add #2/A:241

50 atoms, 45 bonds, 6 residues, 4 models selected  

> select subtract #2/A:241

39 atoms, 35 bonds, 5 residues, 4 models selected  

> select add #1/A:242

48 atoms, 43 bonds, 6 residues, 4 models selected  

> select add #2/A:242

54 atoms, 48 bonds, 7 residues, 4 models selected  

> select subtract #1/A:242

45 atoms, 40 bonds, 6 residues, 4 models selected  

> show sel atoms

> hide sel atoms

> select clear

> select add #2/A:242

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

> show sel atoms

> color sel #67885E

> color sel byhetero target a

> select add #1/A:242

15 atoms, 13 bonds, 2 residues, 3 models selected  

> select subtract #2/A:242

9 atoms, 8 bonds, 1 residue, 3 models selected  

> color sel #918597

> color sel byhetero target a

> select clear

> select add #1/A:239

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

> select add #1/A:235

14 atoms, 12 bonds, 2 residues, 2 models selected  

> select subtract #1/A:235

6 atoms, 5 bonds, 1 residue, 2 models selected  

> select add #1/A:236

13 atoms, 11 bonds, 2 residues, 2 models selected  
Drag select of 1 residues  

> select subtract #1/A:235

13 atoms, 11 bonds, 2 residues, 2 models selected  

> select add #2/A:236

20 atoms, 17 bonds, 3 residues, 3 models selected  

> select add #1/A:264

28 atoms, 24 bonds, 4 residues, 4 models selected  

> select add #1/A:263

36 atoms, 31 bonds, 5 residues, 4 models selected  

> select add #2/A:264

44 atoms, 38 bonds, 6 residues, 4 models selected  

> hide sel atoms

> hide #!2 models

> select add #1/A:180

54 atoms, 48 bonds, 7 residues, 4 models selected  

> select add #1/A:184

64 atoms, 58 bonds, 8 residues, 4 models selected  

> select add #1/A:232

72 atoms, 65 bonds, 9 residues, 4 models selected  

> select ~sel & ##selected

8856 atoms, 9015 bonds, 36 pseudobonds, 1115 residues, 3 models selected  

> select ~sel & ##selected

72 atoms, 66 bonds, 9 residues, 2 models selected  

> hide sel atoms

> show #!2 models

> hide #!2 models

> select add #1/A:217

78 atoms, 71 bonds, 10 residues, 4 models selected  

> hide sel atoms

> select add #1/A:246

86 atoms, 78 bonds, 11 residues, 4 models selected  

> select #1/A:246

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

> select subtract #1/A:246

1 model selected  

> select add #1/A:245

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

> show sel atoms

> show #!2 models

> hide #!1 models

> select #2/A:245

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

> show sel atoms

> show #!1 models

> hide #!1 models

> hide #!2 models

> show #!1 models

> select add #1/A:242

18 atoms, 16 bonds, 2 residues, 3 models selected  

> select add #1/A:245

27 atoms, 24 bonds, 3 residues, 4 models selected  

> select add #1/A:249

36 atoms, 32 bonds, 4 residues, 4 models selected  

> select add #1/A:213

47 atoms, 43 bonds, 5 residues, 4 models selected  

> select add #1/A:214

53 atoms, 48 bonds, 6 residues, 4 models selected  

> select add #1/A:216

61 atoms, 55 bonds, 7 residues, 4 models selected  

> select add #1/A:215

70 atoms, 63 bonds, 8 residues, 4 models selected  

> select add #1/A:217

76 atoms, 68 bonds, 9 residues, 4 models selected  

> select add #1/A:218

83 atoms, 74 bonds, 10 residues, 4 models selected  

> select add #1/A:222

91 atoms, 81 bonds, 11 residues, 4 models selected  

> select add #1/A:221

98 atoms, 87 bonds, 12 residues, 4 models selected  

> select add #1/A:220

107 atoms, 95 bonds, 13 residues, 4 models selected  

> select add #1/A:219

111 atoms, 98 bonds, 14 residues, 4 models selected  

> select add #1/A:212

121 atoms, 108 bonds, 15 residues, 4 models selected  

> hbonds sel & #!1 reveal true

16 hydrogen bonds found  

> show #3 models

> show #!2 models

> hide #3 models

> hide #!1 models

> select add #2/A:210

128 atoms, 114 bonds, 16 residues, 4 models selected  

> select add #2/A:211

139 atoms, 125 bonds, 17 residues, 4 models selected  

> select add #2/A:212

149 atoms, 135 bonds, 18 residues, 4 models selected  

> select add #2/A:213

160 atoms, 146 bonds, 19 residues, 4 models selected  

> select add #2/A:214

166 atoms, 151 bonds, 20 residues, 4 models selected  

> select add #2/A:215

175 atoms, 159 bonds, 21 residues, 4 models selected  

> select add #2/A:216

183 atoms, 166 bonds, 22 residues, 4 models selected  

> select add #2/A:217

189 atoms, 171 bonds, 23 residues, 4 models selected  

> select add #2/A:218

196 atoms, 177 bonds, 24 residues, 4 models selected  

> select add #2/A:219

200 atoms, 180 bonds, 25 residues, 4 models selected  

> select add #2/A:220

209 atoms, 188 bonds, 26 residues, 4 models selected  

> select clear

> select add #2/A:221

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

> select add #2/A:251

13 atoms, 11 bonds, 2 residues, 2 models selected  

> select add #2/A:222

21 atoms, 18 bonds, 3 residues, 2 models selected  

> hide sel atoms

> select clear

> show #!1 models

> select add #1/A:195

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

> show sel atoms

> color sel #918597

> color sel byhetero target a

> select clear

> select add #2/A:195

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

> color sel #67885E

> color sel byhetero target a

> select clear

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> hide #!2 models

> show #!1 models

> select add #1/A:251

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

> hide sel atoms

> select clear

> select add #1/A:245

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

> transparency 80 ribbons

> transparency 80 sel atoms

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

> transparency sel 80 atoms

> select clear

> show #!2 models

> hide #!1 models

> select add #2/A:212

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

> select add #2/A:213

21 atoms, 21 bonds, 2 residues, 2 models selected  

> select subtract #2/A:212

11 atoms, 11 bonds, 1 residue, 2 models selected  

> show sel atoms

> show #!1 models

> select add #1/A:213

22 atoms, 22 bonds, 2 residues, 3 models selected  

> show sel atoms

> transparency sel 80 atoms

> select clear

> hide #!2 models

> hide #!1 models

> show #!2 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> select add #2/A:214

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

> select add #2/A:215

15 atoms, 13 bonds, 2 residues, 2 models selected  

> select up

174 atoms, 176 bonds, 22 residues, 2 models selected  

> select down

15 atoms, 13 bonds, 2 residues, 2 models selected  

> select up

174 atoms, 176 bonds, 22 residues, 2 models selected  

> select down

15 atoms, 13 bonds, 2 residues, 2 models selected  

> select add #2/A:222

23 atoms, 20 bonds, 3 residues, 2 models selected  

> select subtract #2/A:222

15 atoms, 13 bonds, 2 residues, 2 models selected  

> select add #2/A:216

23 atoms, 20 bonds, 3 residues, 2 models selected  

> select add #2/A:217

29 atoms, 25 bonds, 4 residues, 2 models selected  

> hide sel ribbons

> select clear

> show #!1 models

> hide #!2 models

> align #1:250 toAtoms #2:250 matchNumbering true

Pairing dropped 0 atoms and 3 reference atoms  
RMSD between 8 atom pairs is 2.145 angstroms  

> show #!2 models

> align #1:250-300 toAtoms #2:250-300 matchNumbering true

Pairing dropped 1 atoms and 3 reference atoms  
RMSD between 415 atom pairs is 1.479 angstroms  

> align #1:250-275 toAtoms #2:250-275 matchNumbering true

Pairing dropped 1 atoms and 3 reference atoms  
RMSD between 195 atom pairs is 1.675 angstroms  

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_249_250_closeup.png" width 1138 height 1263
> supersample 3

> ui mousemode right clip

> clip off

> ui mousemode right translate

> select add #2/A:204

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

> hide sel atoms

> select add #2/A:180

21 atoms, 20 bonds, 2 residues, 2 models selected  

> hide sel atoms

> select clear

Drag select of 13 atoms, 145 residues, 10 bonds  

> select clear

> ui mousemode right clip

> ui mousemode right translate

> select #2/A:206

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

> show sel atoms

> select #2/A:233

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

> show sel atoms

> hide sel atoms

> select #2/A:261

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

> show sel atoms

> color sel #67885E

> select clear

> select add #2/A:232

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

> select up

39 atoms, 38 bonds, 5 residues, 2 models selected  

> select down

8 atoms, 7 bonds, 1 residue, 2 models selected  

> hide sel atoms

> select clear

> select add #2/A:244

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

> select subtract #2/A:244

1 model selected  

> select add #2/A:245

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

> transparency sel 80 atoms

> select clear

> ui mousemode right clip

> ui mousemode right translate

> ui mousemode right clip

> ui mousemode right translate

> save "/Users/cameroncriswell15/King Lab/Manuscript/Figures/2S5_Nbend_3.png"
> width 1138 height 1263 supersample 3

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> select add #1/A:256

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

> hide sel atoms

> show #!2 models

> hide #!1 models

> select add #2/A:256

16 atoms, 14 bonds, 2 residues, 3 models selected  

> hide sel atoms

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_228_250_closeup.png" width 2000 height 2220
> supersample 3 transparentBackground true

> show #!1 models

> hide #!2 models

> select #1/A:256

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

> select subtract #1/A:256

1 model selected  

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/AF2_228_250_closeup.png" width 2000 height 2220
> supersample 3 transparentBackground true

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> select add #1/A:181

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

> select subtract #1/A:181

1 model selected  

> select add #1/A:206

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

> show sel atoms

> select clear

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_203_206_closeup_2.png" width 1138 height 1263
> supersample 3

> show #!1 models

> hide #!2 models

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_203_206_closeup_2.png" width 2000 height 2220
> supersample 3 transparentBackground true

> show #!2 models

> hide #!1 models

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_203_206_closeup_2.png" width 2000 height 2220
> supersample 3 transparentBackground true

> show #!1 models

> hide #!2 models

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/AF2_203_206_closeup_2.png" width 2000 height 2220
> supersample 3 transparentBackground true

> clip off

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> select add #2/A:211

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

> select add #2/A:212

21 atoms, 21 bonds, 2 residues, 2 models selected  

> select subtract #2/A:212

11 atoms, 11 bonds, 1 residue, 2 models selected  

> select subtract #2/A:211

1 model selected  

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_249_250_closeup_2png.png" width 1138 height 1263
> supersample 3

> select #2:74,78,200

24 atoms, 22 bonds, 3 residues, 1 model selected  

> select #2:74,78,167,200

29 atoms, 26 bonds, 4 residues, 1 model selected  

> color sel #162521

> color byhey target a

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color byhetero target a

> select clear

> select add #2/A:149

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

> color sel #162521

[Repeated 1 time(s)]

> color byhetero target a

> select add #2/A:54

15 atoms, 13 bonds, 2 residues, 2 models selected  

> select add #2/A:77

24 atoms, 21 bonds, 3 residues, 2 models selected  

> select add #2/A:103

32 atoms, 28 bonds, 4 residues, 2 models selected  

> select add #2/A:102

43 atoms, 39 bonds, 5 residues, 2 models selected  

> select add #2/A:79

51 atoms, 46 bonds, 6 residues, 2 models selected  

> select add #2/A:55

59 atoms, 53 bonds, 7 residues, 2 models selected  

> select add #2/A:56

66 atoms, 59 bonds, 8 residues, 2 models selected  

> select add #2/A:80

74 atoms, 66 bonds, 9 residues, 2 models selected  

> select subtract #2/A:79

66 atoms, 59 bonds, 8 residues, 2 models selected  

> select add #2/A:104

74 atoms, 66 bonds, 9 residues, 2 models selected  

> select clear

> select #2:54

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

> show sel atoms

> select #2:30,54,53,9,58,12-14

66 atoms, 61 bonds, 8 residues, 1 model selected  

> show sel atoms

> color sel #67885E

> color sel byhetero target a

> select up

526 atoms, 530 bonds, 69 residues, 2 models selected  

> select down

66 atoms, 61 bonds, 8 residues, 2 models selected  

> select #2:11

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

> select up

22 atoms, 21 bonds, 3 residues, 2 models selected  

> select down

7 atoms, 6 bonds, 1 residue, 2 models selected  

> select #2:10-11

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

> select #2/A:10

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

> select #2:11

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

> select #2:49

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

> select add #2/A:10

11 atoms, 9 bonds, 2 residues, 2 models selected  

> select subtract #2/A:10

5 atoms, 4 bonds, 1 residue, 2 models selected  

> select add #2/A:11

12 atoms, 10 bonds, 2 residues, 2 models selected  

> show sel atoms

> color sel #67885E

> color sel byhetero target a

> select clear

> select #2/A:102

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

> show atoms

> show sel atoms

> select #2/A:101

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

> show sel atoms

> color sel #67885E

> color sel byhetero target a

> select add #2/A:102

20 atoms, 19 bonds, 2 residues, 2 models selected  

> select subtract #2/A:101

11 atoms, 11 bonds, 1 residue, 2 models selected  

> transparency sel 80 atoms

> show #!1 models

> align #1:1-100 toAtoms #2:1-100 matchNumbering true

Pairing dropped 18 atoms and 34 reference atoms  
RMSD between 735 atom pairs is 1.258 angstroms  

> select clear

> select #1/A:74

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select clear

> select #1/A:124

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

> show sel atoms

> transparency sel 80 atoms

> hide #!1 models

> select #2/A:124

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

> show sel atoms

> transparency sel 80 atoms

> select clear

> select #2/A:80

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

> show #!1 models

> select add #1/A:80

16 atoms, 14 bonds, 2 residues, 3 models selected  

> hide #!2 models

> show #!2 models

> show sel atoms

> transparency sel 80 atoms

> hide #!2 models

> select clear

> show #!2 models

> hide #!1 models

> select add #2/A:77

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

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show sel atoms

> transparency sel 80 atoms

> select clear

> ui mousemode right clip

> ui mousemode right translate

> ui mousemode right clip

> ui mousemode right translate

> save "/Users/cameroncriswell15/King Lab/Manuscript/Figures/2S5_Nterm_1.png"
> width 2000 height 2220 supersample 3 transparentBackground true

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> select add #2/A:49

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

> hide sel atoms

> select add #2/A:74

12 atoms, 10 bonds, 2 residues, 2 models selected  

> hide sel atoms

> select clear

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_Nterm_1_upclose.png" width 2000 height 2220
> supersample 3 transparentBackground true

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_Nterm_2_upclose.png" width 2000 height 2220
> supersample 3 transparentBackground true

> select add #2/A:74

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

> select up

162 atoms, 164 bonds, 21 residues, 2 models selected  

> select down

7 atoms, 6 bonds, 1 residue, 2 models selected  

> show sel atoms

> select add #2/A:49

12 atoms, 10 bonds, 2 residues, 2 models selected  

> show sel atoms

> select clear

> select add #2/A:97

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

> select add #2/A:98

14 atoms, 12 bonds, 2 residues, 2 models selected  

> select subtract #2/A:97

6 atoms, 5 bonds, 1 residue, 2 models selected  

> select add #2/A:50

13 atoms, 11 bonds, 2 residues, 2 models selected  

> show #!1 models

> select add #1/A:50

20 atoms, 17 bonds, 3 residues, 3 models selected  

> select subtract #1/A:50

13 atoms, 11 bonds, 2 residues, 3 models selected  

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> select clear

> hide #!1 models

> select add #2/A:50

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

> show sel atoms

> color sel #67885E

> color sel byhetero target a

> select add #2/A:98

13 atoms, 11 bonds, 2 residues, 2 models selected  

> show sel atoms

[Repeated 1 time(s)]

> transparency sel 80 atoms

> select clear

> select add #2/A:121

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

> select clear

> select add #2/A:50

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

> select up

166 atoms, 166 bonds, 21 residues, 2 models selected  

> select down

7 atoms, 6 bonds, 1 residue, 2 models selected  

> show sel atoms

> transparency sel 0 atoms

> select clear

> show #!1 models

> hide #!2 models

> select add #1/A:50

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

> show sel atoms

> color sel #918597

> color sel byhetero target a

> select add #1/A:97

15 atoms, 13 bonds, 2 residues, 2 models selected  

> select subtract #1/A:50

8 atoms, 7 bonds, 1 residue, 2 models selected  

> select subtract #1/A:97

1 model selected  

> select add #1/A:99

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

> select subtract #1/A:99

1 model selected  

> select add #1/A:98

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

> select up

62 atoms, 63 bonds, 8 residues, 2 models selected  

> select down

6 atoms, 5 bonds, 1 residue, 2 models selected  

> show sel atoms

> color sel #918597

> show sel atoms

> transparency sel 80 atoms

> select clear

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/AF2_50_74_upclose.png" width 1138 height 1263
> supersample 3

> show #!2 models

> hide #!1 models

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_50_74_upclose.png" width 1138 height 1263
> supersample 3

> show #!1 models

> hide #!1 models

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_Nterm_side.png" width 1138 height 1263
> supersample 3

> show #!1 models

> hide #!2 models

> select add #1/A:53

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

> select add #1/A:54

14 atoms, 12 bonds, 2 residues, 2 models selected  

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> select add #1/A:77

23 atoms, 20 bonds, 3 residues, 2 models selected  

> show #!2 models

> select add #1/A:30

29 atoms, 25 bonds, 4 residues, 2 models selected  

> select add #1/A:9

37 atoms, 32 bonds, 5 residues, 2 models selected  

> select add #1/A:49

43 atoms, 37 bonds, 6 residues, 2 models selected  

> select add #1/A:101

50 atoms, 43 bonds, 7 residues, 2 models selected  

> show sel atoms

> color sel #918597

> color sel byhetero target a

> select add #1/A:11

59 atoms, 51 bonds, 8 residues, 2 models selected  

> show sel atoms

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> select #1:11

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

> show sel atoms

[Repeated 1 time(s)]

> transparency sel 80 atoms

> select #1:11

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

> color sel #918597

> show sel atoms

> transparency sel 0 atoms

> color sel byhetero target a

> select #1:58

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

> hide #!2 models

> show sel atoms

> color sel #918597

> color sel byhetero target a

> show #!2 models

> hide #!1 models

> select clear

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_Nterm_side_1.png" width 2000 height 2220
> supersample 3

> show #!1 models

> hide #!2 models

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/AF2_Nterm_side_1.png" width 2000 height 2220
> supersample 3

[Repeated 1 time(s)]

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> select #2/A:74

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

> select #2/A:50

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

> select add #2/A:74

14 atoms, 12 bonds, 2 residues, 2 models selected  

> select add #2/A:53

23 atoms, 20 bonds, 3 residues, 2 models selected  

> select subtract #2/A:53

14 atoms, 12 bonds, 2 residues, 2 models selected  

> select add #2/A:98

20 atoms, 17 bonds, 3 residues, 2 models selected  

> hbonds sel reveal true

6 hydrogen bonds found  

> show #3 models

> show #!1 models

> hide #!2 models

> select add #1/A:74

24 atoms, 20 bonds, 4 residues, 3 models selected  

> select add #1/A:98

30 atoms, 25 bonds, 5 residues, 4 models selected  

> show #!2 models

> hide #!2 models

> select add #1/A:50

37 atoms, 31 bonds, 6 residues, 4 models selected  

> hbonds sel & #!1 reveal true

7 hydrogen bonds found  

> hide #3 models

> show #!2 models

> hide #!1 models

> show #3 models

> hide #3 models

> show #!1 models

> hide #!2 models

> select clear

> show #!2 models

> hide #!1 models

> select add #2/A:75

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

> select add #2/A:99

14 atoms, 12 bonds, 2 residues, 2 models selected  

> hide sel atoms

> select clear

> show #!1 models

> hide #!2 models

> select add #1/A:75

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

> hide sel atoms

> show #!2 models

> select clear

[Repeated 1 time(s)]

> hide #!2 models

> show #!2 models

> hide #!1 models

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_50_74_upclose_1.png" width 2000 height 2220
> supersample 3 transparentBackground true

> show #!1 models

> hide #!2 models

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/AF2_50_74_upclose_1.png" width 2000 height 2220
> supersample 3 transparentBackground true

> show #!2 models

> hide #!1 models

> clip off

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5-AF2_green_purple_muts_3.cxs"

> ui mousemode right clip

[Repeated 1 time(s)]

> ui mousemode right translate

> ui mousemode right clip

> select add #2/A:256

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

> show sel atoms

> select clear

> select add #2/A:309

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

> select add #2/A:308

15 atoms, 13 bonds, 2 residues, 2 models selected  

> hide sel ribbons

> select add #2/A:306

27 atoms, 25 bonds, 3 residues, 2 models selected  

> select add #2/A:305

35 atoms, 32 bonds, 4 residues, 2 models selected  

> select add #2/A:304

42 atoms, 38 bonds, 5 residues, 2 models selected  

> select add #2/A:279

50 atoms, 45 bonds, 6 residues, 2 models selected  

> select add #2/A:278

58 atoms, 52 bonds, 7 residues, 2 models selected  

> hide sel ribbons

> select add #2/A:280

65 atoms, 59 bonds, 8 residues, 2 models selected  

> select add #2/A:281

69 atoms, 62 bonds, 9 residues, 2 models selected  

> select add #2/A:218

76 atoms, 68 bonds, 10 residues, 2 models selected  

> select add #2/A:217

82 atoms, 73 bonds, 11 residues, 2 models selected  

> select add #2/A:216

90 atoms, 80 bonds, 12 residues, 2 models selected  

> select add #2/A:215

99 atoms, 88 bonds, 13 residues, 2 models selected  

> hide sel ribbons

[Repeated 1 time(s)]

> hide sel atoms

> select add #2/A:307

105 atoms, 93 bonds, 14 residues, 2 models selected  

> select subtract #2/A:307

99 atoms, 88 bonds, 13 residues, 2 models selected  

> select add #2/A:307

105 atoms, 93 bonds, 14 residues, 2 models selected  

> hide sel ribbons

> select add #2/A:219

109 atoms, 96 bonds, 15 residues, 2 models selected  

> hide sel ribbons

> show #2 ribbons

> select clear

> select add #2/A:308

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

> select add #2/A:280

15 atoms, 14 bonds, 2 residues, 2 models selected  

> select add #2/A:279

23 atoms, 21 bonds, 3 residues, 2 models selected  

> select add #2/A:306

35 atoms, 33 bonds, 4 residues, 2 models selected  

> select subtract #2/A:306

23 atoms, 21 bonds, 3 residues, 2 models selected  

> select add #2/A:281

27 atoms, 24 bonds, 4 residues, 2 models selected  

> hide sel ribbons

> select clear

> save "/Users/cameroncriswell15/King Lab/Manuscript/Figures/2S5_Nbend_4.png"
> width 2000 height 2220 supersample 3

> clip off

> select add #2/A:227

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

> select add #2/A:176

19 atoms, 18 bonds, 2 residues, 2 models selected  

> select add #2/A:202

28 atoms, 26 bonds, 3 residues, 2 models selected  

> select clear

> select add #2/A:153

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

> select add #2/A:176

18 atoms, 17 bonds, 2 residues, 2 models selected  

> select subtract #2/A:153

10 atoms, 10 bonds, 1 residue, 2 models selected  

> select add #2/A:227

19 atoms, 18 bonds, 2 residues, 2 models selected  

> show sel atoms

[Repeated 1 time(s)]

> transparency sel 80 atoms

> show #!1 models

> select clear

> hide #!2 models

> show #!2 models

> hide #!1 models

> select clear

> select add #2/A:200

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

> select add #2/A:176

20 atoms, 20 bonds, 2 residues, 2 models selected  

> select add #2/A:227

29 atoms, 28 bonds, 3 residues, 2 models selected  

> hbonds sel reveal true

17 hydrogen bonds found  

> show #3 models

> hide #3 models

> select add #2/A:202

38 atoms, 36 bonds, 4 residues, 2 models selected  

> select add #2/A:230

49 atoms, 47 bonds, 5 residues, 2 models selected  

> select add #2/A:257

58 atoms, 55 bonds, 6 residues, 2 models selected  

> show sel atoms

> transparency sel 80 atoms

> select clear

> select add #2/A:200

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

> show sel atoms

> transparency sel 0 atoms

> select clear

> select add #2/A:229

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

> show sel atoms

> transparency sel 0 atoms

> show sel atoms

> transparency sel 80 atoms

> select clear

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #3 models

> select add #2/A:176

10 atoms, 10 bonds, 2 pseudobonds, 1 residue, 2 models selected  

> select subtract #2/A:176

1 pseudobond, 2 models selected  

> select clear

> select add #2/A:200

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

> hbonds sel reveal true

8 hydrogen bonds found  

> select subtract #2/A:200

1 model selected  

> hide sel

> color sel #182525

[Repeated 1 time(s)]

> select clear

> select add #2/A:202

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

> select add #2/A:257

18 atoms, 16 bonds, 2 residues, 2 models selected  

> hide sel atoms

> select clear

> select add #2/A:200

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

> clip near 10 position sel

> clip near -10 position sel

> clip far -10 position sel

clip far plane is in front of near plane  

> clip far 10 position sel

> clip far 11 position sel

> clip far 1 position sel

> clip far 5 position sel

> clip far 8 position sel

> clip far 810 position sel

> clip far 9 position sel

> select clear

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_200_upclose.png" width 2000 height 2220
> supersample 3 transparentBackground true

> hide #3 models

> clip off

> select #2/A:397

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

> show sel atoms

> transparency sel 80 atoms

> select clear

> select add #2/A:371

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

> select up

65 atoms, 65 bonds, 8 residues, 2 models selected  

> select down

8 atoms, 7 bonds, 1 residue, 2 models selected  

> show sel atoms

> transparency sel 80 atoms

> select clear

> select add #2/A:420

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

> select clear

> select add #2/A:397

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

> select clear

> select add #2/A:441

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

> show sel atoms

> transparency sel 80 atoms

> select clear

> select add #2/A:417

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

> show sel atoms

> transparency sel 80 atoms

> select clear

> select add #2/A:373

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

> select add #2/A:398

16 atoms, 14 bonds, 2 residues, 2 models selected  

> color sel #67885E

> select clear

> select add #2/A:397

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

> clip far 15 position sel

> clip far 10 position sel

> select clear

> clip far 1 position sel

Invalid "position" argument: Center argument no objects specified  

> select add #2/A:420

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

> select add #2/A:397

16 atoms, 14 bonds, 2 residues, 2 models selected  

> clip far 1 position sel

> clip far 10 position sel

> clip far 20 position sel

> clip far 15 position sel

> select clear

> select add #2/A:425

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

> select add #2/A:426

15 atoms, 13 bonds, 2 residues, 2 models selected  

> hide sel ribbons

> select add #2/A:429

23 atoms, 20 bonds, 3 residues, 2 models selected  

> select add #2/A:428

28 atoms, 24 bonds, 4 residues, 2 models selected  

> hide sel ribbons

> select add #2/A:398

36 atoms, 31 bonds, 5 residues, 2 models selected  

> color sel byhetero target a

> select clear

> select add #2/A:397

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

> select up

162 atoms, 167 bonds, 20 residues, 2 models selected  

> select down

8 atoms, 7 bonds, 1 residue, 2 models selected  

> clip far 15 position sel

> clip far 25 position sel

> clip far 20 position sel

> select clear

> hide #!2 models

> show #!1 models

> select add #1/A:449

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

> select add #1/A:448

16 atoms, 14 bonds, 2 residues, 2 models selected  

> hide sel ribbons

> select add #1/A:370

25 atoms, 22 bonds, 3 residues, 2 models selected  

> select subtract #1/A:370

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select add #1/A:371

24 atoms, 21 bonds, 3 residues, 2 models selected  

> select add #1/A:344

32 atoms, 28 bonds, 4 residues, 2 models selected  

> select add #1/A:397

40 atoms, 35 bonds, 5 residues, 2 models selected  

> show sel atoms

> hide sel atoms

> select clear

> select add #1/A:397

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

> select add #1/A:371

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select add #1/A:344

24 atoms, 21 bonds, 3 residues, 2 models selected  

> show sel atoms

> select add #1/A:441

32 atoms, 28 bonds, 4 residues, 2 models selected  

> show sel atoms

> transparency sel 80 atoms

> select clear

> select add #1/A:344

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

> hide sel atoms

> select clear

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> align #1:350-450 toAtoms #2:350-450 matchNumbering true

Pairing dropped 17 atoms and 6 reference atoms  
RMSD between 785 atom pairs is 0.922 angstroms  

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> select add #2/A:417

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

> hide sel atoms

> select add #2/A:394

15 atoms, 13 bonds, 2 residues, 1 model selected  

> select subtract #2/A:417

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

> color sel #67885E

> select clear

> select add #2/A:420

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

> color sel #67885E

> color sel byhetero target a

> select clear

> select add #2/A:422

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

> select up

128 atoms, 129 bonds, 18 residues, 2 models selected  

> select down

8 atoms, 7 bonds, 1 residue, 2 models selected  

> color sel #67885E\

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color sel #67885E

> color sel byhetero target a

> select clear

> select add #2/A:422

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

> hide atoms

> select clear

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5-AF2_green_purple_muts_3.cxs"

> select add #2/A:422

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

> hide sel atoms

> select clear

> select add #2/A:397

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

> clip far 15 position sel

> clip far 20 position sel

> clip far 10 position sel

> clip far 15 position sel

Invalid "position" argument: Center argument no objects specified  

> undo

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_420_closeup.png" width 2000 height 2220
> supersample 3 transparentBackground true

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_420_closeup_1.png" width 2000 height 2220
> supersample 3

> clip off

> ui mousemode right translate

> show #3 models

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_200_upclose_1.png" width 2000 height 1662
> supersample 3

> select add #2/A:200

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

> clip far 20 position sel

> clip far 25 position sel

> clip far 15 position sel

> select clear

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_200_upclose_1.png" width 2000 height 1662
> supersample 3

> clip off

> hide #3 models

> select :516,519,522

47 atoms, 41 bonds, 6 residues, 2 models selected  

> show sel atoms

> show #!1 models

> align #1:500-562 toAtoms #2:500-562

Unequal number of atoms to pair, 494 and 495  

> align #1:500-562 toAtoms #2:500-562 matchNumbering true

Pairing dropped 31 atoms and 32 reference atoms  
RMSD between 463 atom pairs is 2.134 angstroms  

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> select :516,519,522,523

63 atoms, 58 bonds, 8 residues, 2 models selected  

> select :516,519,522,523,556

79 atoms, 72 bonds, 10 residues, 2 models selected  

> select :516,519,522,523,556,560

97 atoms, 89 bonds, 12 residues, 2 models selected  

> show sel atoms

> hide #!2 models

> show #!2 models

> hide #!1 models

> select add #2/A:544

109 atoms, 101 bonds, 13 residues, 4 models selected  

> select :516,519,522,523,556,560,544

116 atoms, 107 bonds, 14 residues, 2 models selected  

> show sel atoms

> show #!1 models

> select :516,519,522,523,556,560,544,548

133 atoms, 122 bonds, 16 residues, 2 models selected  

> show sel atoms

> select :516,519,522,523,556,560,544,548,542

146 atoms, 134 bonds, 18 residues, 2 models selected  

> show sel atoms

> select :516,519,522,523,556,560,544,548,542,543

165 atoms, 156 bonds, 20 residues, 2 models selected  

> show sel atoms

> select :516,519,522,523,556,560,548,542,543

146 atoms, 136 bonds, 18 residues, 2 models selected  

> show sel atoms

> hide :544

> hide #!1 models

> hbonds sel & #!2 reveal true

21 hydrogen bonds found  

> show #3 models

> select clear

> select add #2/A:557

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

> select subtract #2/A:557

1 model selected  

> hide sel

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> select :516,519,522,523,556,560,548,542,543

146 atoms, 136 bonds, 3 pseudobonds, 18 residues, 3 models selected  

> color sel #67885E

> show #!1 models

> hide #!1 models

> color sel byhetero target a

> hide #!2 models

> show #!1 models

> select #2:516,519,522,523,556,560,548,542,543

71 atoms, 66 bonds, 1 pseudobond, 9 residues, 2 models selected  

> select #1:516,519,522,523,556,560,548,542,543

75 atoms, 70 bonds, 9 residues, 1 model selected  

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> hide #3 target m

> show #!2 target m

> hide #!1 target m

> show #!1 models

> hide #!2 models

> color sel #918597

> color sel byhetero target a

> show #!2 models

> hide #!1 models

> show #!1 models

> select clear

> select add #1/A:559

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

> select subtract #1/A:559

1 model selected  

> select add #1/A:558

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

> select add #1/A:559

15 atoms, 13 bonds, 2 residues, 2 models selected  

> select subtract #1/A:559

9 atoms, 8 bonds, 1 residue, 2 models selected  

> select add #2/A:558

18 atoms, 16 bonds, 2 residues, 3 models selected  

> transparency sel 80 atoms

> hide #!2 models

> show #3 models

> hide #!1 models

> show #!2 models

> select clear

> color sel #162521

> show #!1 models

> select clear

> hide sel

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> show #!2 models

> select :519

14 atoms, 12 bonds, 2 residues, 2 models selected  

> color sel #20321B

> select :532

26 atoms, 27 bonds, 2 residues, 2 models selected  

> show sel

> hide sel

> select :523

16 atoms, 15 bonds, 2 residues, 2 models selected  

> color sel #20321B

> color byhetero target a

> select clear

> select add #2/A:518

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

> show sel atoms

> hide sel atoms

> show #!1 models

> hide #!1 models

> select clear

> select add #2/A:489

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

> select add #2/A:490

15 atoms, 13 bonds, 2 residues, 2 models selected  

> select add #2/A:491

24 atoms, 21 bonds, 3 residues, 2 models selected  

> select add #2/A:492

33 atoms, 29 bonds, 4 residues, 2 models selected  

> hide sel atoms

> hide sel ribbons

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_519_522_523_upclose_1.png" width 2000 height 1662
> supersample 3 transparentBackground true

> show sel ribbons

> save "/Users/cameroncriswell15/King Lab/Manuscript/Figures/2S5_Cterm.png"
> width 2000 height 1662 supersample 3 transparentBackground true

> select clear

> select add #2/A:544

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

> show sel atoms

> color sel #162521

> color sel #918597

> color sel #162521

> color sel #67885E

> color byhetero target a

> select clear

> select add #2/A:544

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

> hbonds sel reveal true

7 hydrogen bonds found  

> select clear

[Repeated 1 time(s)]

> hide sel

> color sel #162521

> select clear

> select add #2/A:544

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

> select add #2/A:543

21 atoms, 20 bonds, 2 residues, 2 models selected  

> hbonds sel reveal true

9 hydrogen bonds found  

> select clear

> hide sel

> select up

9 pseudobonds, 1 model selected  

> select up

8928 atoms, 9081 bonds, 9 pseudobonds, 1124 residues, 3 models selected  

> select down

9 pseudobonds, 3 models selected  

> select down

5 pseudobonds, 1 model selected  

> color sel #162521

> select clear

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_542-544_upclose.png" width 2000 height 1662
> supersample 3

> select
> #2:509,510,515-519,521-524,526-528,530,532,534-535,539542-545,547-551,556,557,560-562

236 atoms, 231 bonds, 28 residues, 1 model selected  

> select
> #2:509,510,515-519,521-524,526-528,530,532,534-535,539,542-545,547-551,556,557,560-562

278 atoms, 273 bonds, 1 pseudobond, 33 residues, 2 models selected  

> select subtract #2/A:519

271 atoms, 266 bonds, 1 pseudobond, 32 residues, 3 models selected  

> select subtract #2/A:523

264 atoms, 257 bonds, 1 pseudobond, 31 residues, 3 models selected  

> color sel #67885E

> color byhetero target a

> select clear

> select
> #2:509,510,515-519,521-524,526-528,530,532,534-535,539,542-545,547-551,556,557,560-562

278 atoms, 273 bonds, 1 pseudobond, 33 residues, 2 models selected  

> select subtract #2/A:543

269 atoms, 263 bonds, 1 pseudobond, 32 residues, 3 models selected  

> select subtract #2/A:542

262 atoms, 256 bonds, 1 pseudobond, 31 residues, 3 models selected  

> select subtract #2/A:544

250 atoms, 243 bonds, 30 residues, 2 models selected  

> select subtract #2/A:557

241 atoms, 234 bonds, 29 residues, 2 models selected  

> select add #2/A:557

250 atoms, 242 bonds, 30 residues, 2 models selected  

> select subtract #2/A:556

241 atoms, 234 bonds, 29 residues, 2 models selected  

> select subtract #2/A:560

233 atoms, 226 bonds, 28 residues, 2 models selected  

> select subtract #2/A:516

225 atoms, 217 bonds, 27 residues, 2 models selected  

> select subtract #2/A:548

217 atoms, 208 bonds, 26 residues, 2 models selected  

> select subtract #2/A:519

210 atoms, 201 bonds, 25 residues, 2 models selected  

> select subtract #2/A:523

203 atoms, 192 bonds, 24 residues, 2 models selected  

> select subtract #2/A:522

195 atoms, 184 bonds, 23 residues, 2 models selected  

> show sel atoms

> hide sel atoms

> select clear

[Repeated 1 time(s)]

> hide sel

> select add #2/A:559

6 atoms, 5 bonds, 3 pseudobonds, 1 residue, 2 models selected  

> select add #2/A:512

12 atoms, 10 bonds, 3 pseudobonds, 2 residues, 3 models selected  

> select subtract #2/A:512

6 atoms, 5 bonds, 3 pseudobonds, 1 residue, 3 models selected  

> select add #2/A:513

12 atoms, 10 bonds, 3 pseudobonds, 2 residues, 3 models selected  

> show sel

> hide sel

> select clear

> save "/Users/cameroncriswell15/King Lab/Manuscript/Figures/2S5_Cterm_1.png"
> width 2000 height 1662 supersample 3 transparentBackground true

> select add #2/A:549

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

> select subtract #2/A:549

Nothing selected  

> select add #2/A:509

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

> select add #2/A:510

20 atoms, 19 bonds, 2 residues, 2 models selected  

> show sel

> hide sel

> select clear

> select add #2/A:516

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

> clip far 10 position sel

> clip far 20 position sel

[Repeated 1 time(s)]

> clip far 25 position sel

> select subtract #2/A:516

1 model selected  

> select add #2/A:551

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

> clip far 25 position sel

> clip far 55 position sel

> select clear

> clip near -10 position sel

Invalid "position" argument: Center argument no objects specified  

> select add #2/A:515

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

> clip near -10 position sel

[Repeated 1 time(s)]

> clip near 10 position sel

> clip near -10 position sel

> clip front -10 position sel

> clip back -10 position sel

clip back plane is in front of front plane  

> clip front 10 position sel

clip back plane is in front of front plane  

> clip back 10 position sel

clip back plane is in front of front plane  

> clip off

> clip back 10 position sel

> clip back 9 position sel

> clip back -3 position sel

> clip back 10 position sel

> clip back 12 position sel

> clip back 15 position sel

> select clear

> save "/Users/cameroncriswell15/King Lab/Manuscript/Figures/2S5_Cterm_2.png"
> width 2000 height 1662 supersample 3 transparentBackground true

> select add #2/A:562

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

> select add #2/A:561

16 atoms, 15 bonds, 2 residues, 2 models selected  

> select add #2/A:557

25 atoms, 23 bonds, 3 residues, 2 models selected  

> select add #2/A:545

34 atoms, 31 bonds, 4 residues, 2 models selected  

> select add #2/A:547

43 atoms, 39 bonds, 5 residues, 2 models selected  

> select add #2/A:539

48 atoms, 43 bonds, 6 residues, 2 models selected  

> select add #2/A:549

56 atoms, 50 bonds, 7 residues, 2 models selected  

> select add #2/A:550

66 atoms, 60 bonds, 8 residues, 2 models selected  

> select add #2/A:551

75 atoms, 68 bonds, 9 residues, 2 models selected  

> select add #2/A:510

83 atoms, 75 bonds, 10 residues, 2 models selected  

> select add #2/A:509

95 atoms, 87 bonds, 11 residues, 2 models selected  

> select add #2/A:518

102 atoms, 93 bonds, 12 residues, 2 models selected  

> select add #2/A:517

110 atoms, 100 bonds, 13 residues, 2 models selected  

> select add #2/A:515

118 atoms, 107 bonds, 14 residues, 2 models selected  

> select add #2/A:521

124 atoms, 112 bonds, 15 residues, 2 models selected  

> select add #2/A:534

132 atoms, 119 bonds, 16 residues, 2 models selected  

> select add #2/A:535

141 atoms, 127 bonds, 17 residues, 2 models selected  

> select add #2/A:532

153 atoms, 139 bonds, 18 residues, 2 models selected  

> select add #2/A:524

162 atoms, 147 bonds, 19 residues, 2 models selected  

> select add #2/A:527

171 atoms, 155 bonds, 20 residues, 2 models selected  

> select add #2/A:526

180 atoms, 163 bonds, 21 residues, 2 models selected  

> select add #2/A:530

187 atoms, 169 bonds, 22 residues, 2 models selected  

> select add #2/A:528

195 atoms, 176 bonds, 23 residues, 2 models selected  

> show sel atoms

> transparency sel 80 atoms

> select clear

> select add #2/A:489

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

> select subtract #2/A:489

1 model selected  

> select add #2/A:488

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

> select add #2/A:487

18 atoms, 17 bonds, 2 residues, 2 models selected  

> select subtract #2/A:487

11 atoms, 11 bonds, 1 residue, 2 models selected  

> show sel atoms

> transparency sel 80 atoms

> select clear

> select add #2/A:525

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

> select up

42 atoms, 42 bonds, 5 residues, 2 models selected  

> select down

8 atoms, 7 bonds, 1 residue, 2 models selected  

> show sel atoms

> transparency sel 80 atoms

> select clear

> transparency sel 80 ribbons

> transparency #2 80 ribbons

[Repeated 1 time(s)]

> save "/Users/cameroncriswell15/King Lab/Manuscript/Figures/2S5_Cterm_3.png"
> width 2000 height 1662 supersample 3 transparentBackground true

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_Cterm_downLRR.png" width 2000 height 1662
> supersample 3 transparentBackground true

> show #!1 models

> select add #1/A:519@OG1

1 atom, 1 residue, 1 model selected  

> select subtract #1/A:519@OG1

Nothing selected  

> select add #1/A:519

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

> select add #2/A:523

14 atoms, 13 bonds, 2 residues, 3 models selected  

> select subtract #2/A:523

7 atoms, 6 bonds, 1 residue, 3 models selected  

> select add #2/A:523

14 atoms, 13 bonds, 2 residues, 3 models selected  

> select subtract #2/A:523

7 atoms, 6 bonds, 1 residue, 3 models selected  

> select add #2/A:523

14 atoms, 13 bonds, 2 residues, 3 models selected  

> select subtract #2/A:523

7 atoms, 6 bonds, 1 residue, 3 models selected  

> select add #1/A:523

16 atoms, 14 bonds, 2 residues, 2 models selected  

> color sel #918597 atoms

> color sel byhetero target a

> select clear

> hide #3 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #3 models

> hide #3 models

> select add #2/A:549

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

> select add #2/A:515

16 atoms, 14 bonds, 2 residues, 1 model selected  

> select add #2/A:509

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

> select add #2/A:532

40 atoms, 38 bonds, 4 residues, 2 models selected  

> transparency sel 0 atoms

> select clear

> select add #2/A:544

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

> select add #2/A:543

21 atoms, 20 bonds, 2 residues, 2 models selected  

> transparency sel 80 atoms

> select clear

> select add #2/A:503

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

> select add #2/A:502

17 atoms, 15 bonds, 2 residues, 2 models selected  

> select add #2/A:478

25 atoms, 22 bonds, 3 residues, 2 models selected  

> select add #2/A:479

34 atoms, 30 bonds, 4 residues, 2 models selected  

> select add #2/A:480

39 atoms, 34 bonds, 5 residues, 2 models selected  

> select add #2/A:481

45 atoms, 39 bonds, 6 residues, 2 models selected  

> select add #2/A:504

50 atoms, 43 bonds, 7 residues, 2 models selected  

> select add #2/A:505

54 atoms, 46 bonds, 8 residues, 2 models selected  

> hide sel ribbons

> select add #2/A:522

62 atoms, 53 bonds, 9 residues, 2 models selected  

> transparency sel 80 atoms

> select clear

> select add #2/A:549

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

> select add #2/A:519

15 atoms, 13 bonds, 2 residues, 1 model selected  

> select add #2/A:516

23 atoms, 20 bonds, 3 residues, 2 models selected  

> select add #2/A:515

31 atoms, 27 bonds, 4 residues, 2 models selected  

> select add #2/A:509

43 atoms, 39 bonds, 5 residues, 2 models selected  

> select add #2/A:532

55 atoms, 51 bonds, 6 residues, 2 models selected  

> select add #2/A:488

66 atoms, 62 bonds, 7 residues, 2 models selected  

> select add #2/A:525

74 atoms, 69 bonds, 8 residues, 2 models selected  

> hide atoms

> show sel atoms

> select clear

> select add #2/A:530

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

> show sel atoms

> select add #2/A:548

15 atoms, 13 bonds, 2 residues, 2 models selected  

> show sel atoms

> select add #2/A:550

25 atoms, 23 bonds, 3 residues, 2 models selected  

> show sel atoms

> select add #2/A:544

37 atoms, 35 bonds, 4 residues, 2 models selected  

> show sel atoms

> select clear

> select add #2/A:506

4 atoms, 3 bonds, 1 residue, 1 model selected  

> hide sel ribbons

> select clear

> select add #2/A:501

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

> hide sel ribbons

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5_Cterm_inner.png" width 2000 height 1662
> supersample 3 transparentBackground true

> save "/Users/cameroncriswell15/King
> Lab/Manuscript/Figures/2S5-AF2_green_purple_muts_4.cxs"

——— End of log from Mon Mar 17 13:59:51 2025 ———

opened ChimeraX session  

> select #2/A:519

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

> select #2/A:519

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

> select clear

> clip off

> select add #2/A:490

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

> select clear

> show ribbons

> select :27

11 atoms, 9 bonds, 2 residues, 2 models selected  

> show atoms

> show sel atoms

> color sel #67885E

> color sel byhetero target a

> select add #2/A:50

18 atoms, 15 bonds, 3 residues, 4 models selected  

> select add #2/A:74

25 atoms, 21 bonds, 4 residues, 4 models selected  

> show sel atoms

> select add #2/A:49

30 atoms, 25 bonds, 5 residues, 4 models selected  

> show sel atoms

> select clear

>

Incomplete command: mutationscores  

> mutationscores define

No mutation scores found  

> mutationscores scatterplot

Missing or invalid "xScoreName" argument: Expected a text string  

> mutationscores scatterplot #1 #2

No mutation scores found  

> mutationscores structure #1 #2

Missing or invalid "chain" argument: must specify exactly one chain  

> mutationscores structure #1

No mutation scores found  

> ui tool show "Render/Select by Attribute"

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/interfaces/graph.py", line 415, in _mouse_move  
self.mouse_hover(e)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_scatter_plot.py", line 299, in
mouse_hover  
item = self.clicked_item(event)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/interfaces/graph.py", line 475, in clicked_item  
c,d = self._node_artist.contains(e)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'contains'  
  
AttributeError: 'NoneType' object has no attribute 'contains'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/interfaces/graph.py", line 475, in clicked_item  
c,d = self._node_artist.contains(e)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> sequence header consensus show

Showing consensus header ("seq_consensus" residue attribute) for alignment 1  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/interfaces/graph.py", line 415, in _mouse_move  
self.mouse_hover(e)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_scatter_plot.py", line 299, in
mouse_hover  
item = self.clicked_item(event)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/interfaces/graph.py", line 475, in clicked_item  
c,d = self._node_artist.contains(e)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'contains'  
  
AttributeError: 'NoneType' object has no attribute 'contains'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/interfaces/graph.py", line 475, in clicked_item  
c,d = self._node_artist.contains(e)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/interfaces/graph.py", line 415, in _mouse_move  
self.mouse_hover(e)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_scatter_plot.py", line 299, in
mouse_hover  
item = self.clicked_item(event)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/interfaces/graph.py", line 475, in clicked_item  
c,d = self._node_artist.contains(e)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'contains'  
  
AttributeError: 'NoneType' object has no attribute 'contains'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/interfaces/graph.py", line 475, in clicked_item  
c,d = self._node_artist.contains(e)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/interfaces/graph.py", line 415, in _mouse_move  
self.mouse_hover(e)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_scatter_plot.py", line 299, in
mouse_hover  
item = self.clicked_item(event)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/interfaces/graph.py", line 475, in clicked_item  
c,d = self._node_artist.contains(e)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'contains'  
  
AttributeError: 'NoneType' object has no attribute 'contains'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/interfaces/graph.py", line 475, in clicked_item  
c,d = self._node_artist.contains(e)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: Mac14,2
      Model Number: MLY43LL/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 11881.81.4
      OS Loader Version: 11881.81.4

Software:

    System Software Overview:

      System Version: macOS 15.3.1 (24D70)
      Kernel Version: Darwin 24.3.0
      Time since boot: 19 days, 12 hours, 58 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2560 x 1664 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    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-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    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: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13

[Tom Goddard]

Fixed.

User created a mutation scatter plot with no mutation data that was not fully initialized (no points were plotted). This led to errors whenever the mouse was hovered over the plot. I made the mutationscores scatterplot command not create the plot if no data is available.