Opened 7 months ago

Closed 7 months ago

#17306 closed defect (duplicate)

Render By Attribute: switching attributes does not preserve marker radius

Reported by: jessica.d.tolbert.gr@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Analysis Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

The following bug report has been submitted:
Platform:        macOS-15.3.2-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/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-ch/rmsd-y139e.cxs format
> session

Log from Thu Apr 3 22:05:55 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-
> ch/PDBs/WTRns-R75A-RnsY139E-crystallographic-dimer.cxs format session

Log from Tue Apr 1 10:44:55 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-
> ch/PDBs/RnsY139E-crystallographic-dimer.cxs

Log from Mon Mar 31 12:55:41 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/jessicatolbert/OneDrive - Dartmouth College/Lab-
> Report/figures/dimerization-ch/WT-Y139E-overlay-seperateWTPDB.cxs" format
> session

Opened 20240927-jdt8-6-process1_refine_071_2mFo-DFc_no_fill_no_fill.ccp4 as
#2, grid size 216,216,216, pixel 0.494,0.494,0.511, shown at level 3.64, step
1, values float32  
Opened 20240927-jdt8-6-process1_refine_071_2mFo-DFc.ccp4 as #3, grid size
216,216,216, pixel 0.494,0.494,0.511, shown at level 3.67, step 1, values
float32  
Opened 20240927-jdt8-6-process1_refine_071_mFo-DFc.ccp4 as #4, grid size
216,216,216, pixel 0.494,0.494,0.511, shown at level 2.38, step 1, values
float32  
Log from Mon Mar 31 11:54:25 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-ch/wt-y139e-dimerization-
> interface-coloredbyexpression.cxs format session

Opened 20240927-jdt8-6-process1_refine_071_2mFo-DFc_no_fill_no_fill.ccp4 as
#2, grid size 216,216,216, pixel 0.494,0.494,0.511, shown at level 3.64, step
1, values float32  
Opened 20240927-jdt8-6-process1_refine_071_2mFo-DFc.ccp4 as #3, grid size
216,216,216, pixel 0.494,0.494,0.511, shown at level 3.67, step 1, values
float32  
Opened 20240927-jdt8-6-process1_refine_071_mFo-DFc.ccp4 as #4, grid size
216,216,216, pixel 0.494,0.494,0.511, shown at level 2.38, step 1, values
float32  
Log from Sun Mar 30 18:40:30 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-ch/figure-wtrns-
> dimerization-interface.cxs

Opened 20240927-jdt8-6-process1_refine_071_2mFo-DFc_no_fill_no_fill.ccp4 as
#2, grid size 216,216,216, pixel 0.494,0.494,0.511, shown at level 3.64, step
1, values float32  
Opened 20240927-jdt8-6-process1_refine_071_2mFo-DFc.ccp4 as #3, grid size
216,216,216, pixel 0.494,0.494,0.511, shown at level 3.67, step 1, values
float32  
Opened 20240927-jdt8-6-process1_refine_071_mFo-DFc.ccp4 as #4, grid size
216,216,216, pixel 0.494,0.494,0.511, shown at level 2.38, step 1, values
float32  
Log from Sun Mar 30 16:59:12 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/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-
> ch/20240927-jdt8-6-process1_refine_071.pdb

Chain information for 20240927-jdt8-6-process1_refine_071.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> open /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-
> ch/FFT_74/20240927-jdt8-6-process1_refine_071_2mFo-DFc_no_fill_no_fill.ccp4

Opened 20240927-jdt8-6-process1_refine_071_2mFo-DFc_no_fill_no_fill.ccp4 as
#2, grid size 216,216,216, pixel 0.494,0.494,0.511, shown at level 3.64, step
1, values float32  

> open /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-
> ch/FFT_74/20240927-jdt8-6-process1_refine_071_2mFo-DFc.ccp4

Opened 20240927-jdt8-6-process1_refine_071_2mFo-DFc.ccp4 as #3, grid size
216,216,216, pixel 0.494,0.494,0.511, shown at level 3.67, step 1, values
float32  

> open /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-
> ch/FFT_74/20240927-jdt8-6-process1_refine_071_mFo-DFc.ccp4

Opened 20240927-jdt8-6-process1_refine_071_mFo-DFc.ccp4 as #4, grid size
216,216,216, pixel 0.494,0.494,0.511, shown at level 2.38, step 1, values
float32  

> ui tool show "Fit in Map"

> ui mousemode right select

Drag select of 100 atoms, 255 residues, 1 pseudobonds, 86 bonds  

> fitmap sel inMap #2

Fit molecule 20240927-jdt8-6-process1_refine_071.pdb (#1) to map
20240927-jdt8-6-process1_refine_071_2mFo-DFc_no_fill_no_fill.ccp4 (#2) using
2096 atoms  
average map value = 0, steps = 24  
shifted from previous position = 0  
rotated from previous position = 0 degrees  
atoms outside contour = 2096, contour level = 3.6425  
  
Position of 20240927-jdt8-6-process1_refine_071.pdb (#1) relative to
20240927-jdt8-6-process1_refine_071_2mFo-DFc_no_fill_no_fill.ccp4 (#2)
coordinates:  
Matrix rotation and translation  
1.00000000 0.00000000 0.00000000 0.00000000  
0.00000000 1.00000000 0.00000000 0.00000000  
0.00000000 0.00000000 1.00000000 0.00000000  
Axis 0.00000000 0.00000000 1.00000000  
Axis point 0.00000000 0.00000000 0.00000000  
Rotation angle (degrees) 0.00000000  
Shift along axis 0.00000000  
  

> select clear

> opwn 6xiu

Unknown command: opwn 6xiu  

> open 6xiu

6xiu title:  
ETEC Rns bound to a potential inhibitor, decanoic acid [more info...]  
  
Chain information for 6xiu #5  
---  
Chain | Description | UniProt  
A B | Regulatory protein Rns | RNS_ECOLX 1-265  
  
Non-standard residues in 6xiu #5  
---  
DKA — decanoic acid  
  
6xiu mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> windowsize

window size 584 682  

> windowsize

window size 584 682  

> windowsize 1000 1000

> windowsize 800 1000

> windowsize 800 800

> windowsize 900 800

> ui tool show Matchmaker

> matchmaker #!5 to #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 20240927-jdt8-6-process1_refine_071.pdb, chain A (#1) with 6xiu,
chain B (#5), sequence alignment score = 1240.7  
RMSD between 206 pruned atom pairs is 0.838 angstroms; (across all 248 pairs:
1.673)  
  

> select #1/A:210

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

> select add #5/B:221

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

> select up

291 atoms, 291 bonds, 36 residues, 2 models selected  

> matchmaker #!5 to #1/A pairing bs

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 20240927-jdt8-6-process1_refine_071.pdb, chain A (#1) with 6xiu,
chain B (#5), sequence alignment score = 1240.7  
RMSD between 206 pruned atom pairs is 0.838 angstroms; (across all 248 pairs:
1.673)  
  

> matchmaker #!5 to #1/A pairing bs

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 20240927-jdt8-6-process1_refine_071.pdb, chain A (#1) with 6xiu,
chain B (#5), sequence alignment score = 1240.7  
RMSD between 206 pruned atom pairs is 0.838 angstroms; (across all 248 pairs:
1.673)  
  

> matchmaker #!5 & sel to #1/A & sel pairing bs

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 20240927-jdt8-6-process1_refine_071.pdb, chain A (#1) with 6xiu,
chain B (#5), sequence alignment score = 80.6  
RMSD between 16 pruned atom pairs is 0.328 angstroms; (across all 16 pairs:
0.328)  
  

> matchmaker #!5 & sel to #1/A & sel pairing bs

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 20240927-jdt8-6-process1_refine_071.pdb, chain A (#1) with 6xiu,
chain B (#5), sequence alignment score = 80.6  
RMSD between 16 pruned atom pairs is 0.328 angstroms; (across all 16 pairs:
0.328)  
  

> hide #!4 models

> hide #!3 models

> hide #!2 models

> select #5/A:233

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

> select up

74 atoms, 73 bonds, 10 residues, 1 model selected  

> select up

1314 atoms, 1334 bonds, 161 residues, 1 model selected  

> select up

1318 atoms, 1337 bonds, 162 residues, 1 model selected  

> select up

2015 atoms, 2045 bonds, 246 residues, 1 model selected  

> select up

2027 atoms, 2056 bonds, 247 residues, 1 model selected  

> select up

4068 atoms, 4126 bonds, 496 residues, 1 model selected  

> select up

6318 atoms, 6246 bonds, 910 residues, 8 models selected  

> select down

4068 atoms, 4126 bonds, 496 residues, 1 model selected  

> select down

2027 atoms, 2056 bonds, 247 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select #1/A:117

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

> select clear

> color #1 #d741c9ff

> color #1 #61a9d7ff

> color #1 #5388d7ff

> color #1 #35cbd7ff

> color #1 #13cbd7ff

> color #1 #d7b483ff

> color #1 #d7c27fff

> color #1 #d73a52ff

> color #1 #d74856ff

> color #5 #4989d9ff

> select :DKA

36 atoms, 33 bonds, 3 residues, 2 models selected  

> color sel byhetero

> select #5 :DKA

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

> color sel magenta

> color sel byhetero

> select up

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

> select up

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

> color sel black

> color sel byhetero

> select clear

> color byhetero

> select :14,17

49 atoms, 42 bonds, 7 residues, 2 models selected  

> show sel atoms

> select clear

[Repeated 1 time(s)]Drag select of 15 atoms, 13 bonds  

> select up

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

> hide sel atoms

> ui tool show "Crystal Contacts"

> crystalcontacts #1

4 pairs of asymmetric units of 20240927-jdt8-6-process1_refine_071.pdb contact
at distance 3.0 A

    
    
      Atoms  MTRIX  SMTRY   Unit cell  MTRIXref  Copies
        12     0      9     -1 -1  0      0         1
        11     0      5      0  0 -1      0         1
        11     0      4      0  0  0      0         1
         6     0     10      0  0  0      0         1
    

  

> crystalcontacts #5

8 pairs of asymmetric units of 6xiu contact at distance 3.0 A

    
    
      Atoms  MTRIX  SMTRY   Unit cell  MTRIXref  Copies
         6     0      0      1  0  0      0         1
         5     0      1     -1  0  0      0         1
         5     0      1     -1  0 -1      0         1
         5     0      0     -1  0  0      0         1
         4     0      2     -1  0  0      0         1
         4     0      2     -1 -1  0      0         1
         4     0      2     -2 -1  0      0         1
         2     0      2     -2  0  0      0         1
    

  

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!7 models

> hide #!6 models

> show #!7 models

> show sel cartoons

[Repeated 5 time(s)]

> hide #!5 models

> show #!5 models

> select add #5

4068 atoms, 4126 bonds, 2 pseudobonds, 496 residues, 3 models selected  

> show sel cartoons

> select subtract #5

Nothing selected  

> crystalcontacts delete #5

> crystalcontacts #5

8 pairs of asymmetric units of 6xiu contact at distance 3.0 A

    
    
      Atoms  MTRIX  SMTRY   Unit cell  MTRIXref  Copies
         6     0      0      1  0  0      0         1
         5     0      1     -1  0  0      0         1
         5     0      1     -1  0 -1      0         1
         5     0      0     -1  0  0      0         1
         4     0      2     -1  0  0      0         1
         4     0      2     -1 -1  0      0         1
         4     0      2     -2 -1  0      0         1
         2     0      2     -2  0  0      0         1
    

  

> show #!6 models

> hide #!7 models

> select #5/A:61

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

> select up

66 atoms, 65 bonds, 8 residues, 1 model selected  

> select up

701 atoms, 711 bonds, 85 residues, 1 model selected  

> select up

752 atoms, 761 bonds, 91 residues, 1 model selected  

> select up

2015 atoms, 2045 bonds, 246 residues, 1 model selected  

> select up

2027 atoms, 2056 bonds, 247 residues, 1 model selected  

> select up

4068 atoms, 4126 bonds, 496 residues, 1 model selected  

> select down

2027 atoms, 2056 bonds, 247 residues, 1 model selected  

> hide sel cartoons

Drag select of 5 residues  

> select clear

[Repeated 1 time(s)]

> select :139

261 atoms, 256 bonds, 23 residues, 14 models selected  

> show sel & #!1,5#!6.1-4 atoms

> color sel & #!1,5#!6.1-4 byhetero

> show #!7 models

> select :139

261 atoms, 256 bonds, 23 residues, 14 models selected  

> show sel atoms

> color sel byhetero

> ui mousemode right "clip rotate"

> ui mousemode right clip

> ui mousemode right select

> select #5/B:139

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

> select add #1/A:140

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

> select up

192 atoms, 193 bonds, 25 residues, 2 models selected  

> save /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-ch/wtrns-y139e-alignment-
> against-long-DBD-helix.cxs

> ui tool show Matchmaker

> matchmaker #!5#!6.1-4#!7.1-8 & sel to #1/A & sel pairing bs

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 20240927-jdt8-6-process1_refine_071.pdb, chain A (#1) with 6xiu,
chain B (#5), sequence alignment score = 43.2  
RMSD between 10 pruned atom pairs is 0.242 angstroms; (across all 10 pairs:
0.242)  
  

> crystalcontacts delete #5

> crystalcontacts delete #1

> crystalcontacts #1

4 pairs of asymmetric units of 20240927-jdt8-6-process1_refine_071.pdb contact
at distance 3.0 A

    
    
      Atoms  MTRIX  SMTRY   Unit cell  MTRIXref  Copies
        12     0      9     -1 -1  0      0         1
        11     0      5      0  0 -1      0         1
        11     0      4      0  0  0      0         1
         6     0     10      0  0  0      0         1
    

  

> crystalcontacts #5

8 pairs of asymmetric units of 6xiu contact at distance 3.0 A

    
    
      Atoms  MTRIX  SMTRY   Unit cell  MTRIXref  Copies
         6     0      0      1  0  0      0         1
         5     0      1     -1  0  0      0         1
         5     0      1     -1  0 -1      0         1
         5     0      0     -1  0  0      0         1
         4     0      2     -1  0  0      0         1
         4     0      2     -1 -1  0      0         1
         4     0      2     -2 -1  0      0         1
         2     0      2     -2  0  0      0         1
    

  

> crystalcontacts #5

8 pairs of asymmetric units of 6xiu contact at distance 3.0 A

    
    
      Atoms  MTRIX  SMTRY   Unit cell  MTRIXref  Copies
         6     0      0      1  0  0      0         1
         5     0      1     -1  0  0      0         1
         5     0      1     -1  0 -1      0         1
         5     0      0     -1  0  0      0         1
         4     0      2     -1  0  0      0         1
         4     0      2     -1 -1  0      0         1
         4     0      2     -2 -1  0      0         1
         2     0      2     -2  0  0      0         1
    

  

> crystalcontacts #5

8 pairs of asymmetric units of 6xiu contact at distance 3.0 A

    
    
      Atoms  MTRIX  SMTRY   Unit cell  MTRIXref  Copies
         6     0      0      1  0  0      0         1
         5     0      1     -1  0  0      0         1
         5     0      1     -1  0 -1      0         1
         5     0      0     -1  0  0      0         1
         4     0      2     -1  0  0      0         1
         4     0      2     -1 -1  0      0         1
         4     0      2     -2 -1  0      0         1
         2     0      2     -2  0  0      0         1
    

  

> crystalcontacts #5

8 pairs of asymmetric units of 6xiu contact at distance 3.0 A

    
    
      Atoms  MTRIX  SMTRY   Unit cell  MTRIXref  Copies
         6     0      0      1  0  0      0         1
         5     0      1     -1  0  0      0         1
         5     0      1     -1  0 -1      0         1
         5     0      0     -1  0  0      0         1
         4     0      2     -1  0  0      0         1
         4     0      2     -1 -1  0      0         1
         4     0      2     -2 -1  0      0         1
         2     0      2     -2  0  0      0         1
    

  

> select clear

[Repeated 1 time(s)]

> ui mousemode right zone

> ui mousemode right "clip rotate"

> crystalcontacts delete #5

> ui mousemode right select

> select #5/B:185

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

> select up

64 atoms, 64 bonds, 9 residues, 1 model selected  

> select up

1314 atoms, 1334 bonds, 161 residues, 1 model selected  

> select up

1332 atoms, 1351 bonds, 164 residues, 1 model selected  

> select up

2029 atoms, 2059 bonds, 248 residues, 1 model selected  

> select up

2041 atoms, 2070 bonds, 249 residues, 1 model selected  

> select up

4068 atoms, 4126 bonds, 496 residues, 1 model selected  

> select down

2041 atoms, 2070 bonds, 249 residues, 1 model selected  

> show sel cartoons

[Repeated 1 time(s)]

> select up

4068 atoms, 4126 bonds, 496 residues, 1 model selected  

> select up

6318 atoms, 6246 bonds, 910 residues, 9 models selected  

> select up

6318 atoms, 6246 bonds, 910 residues, 9 models selected  

> select up

6318 atoms, 6246 bonds, 910 residues, 9 models selected  

> select up

6318 atoms, 6246 bonds, 910 residues, 9 models selected  

> select up

6318 atoms, 6246 bonds, 910 residues, 9 models selected  

> show sel cartoons

> crystalcontacts delete #5

> crystalcontacts #5

8 pairs of asymmetric units of 6xiu contact at distance 3.0 A

    
    
      Atoms  MTRIX  SMTRY   Unit cell  MTRIXref  Copies
         6     0      0      1  0  0      0         1
         5     0      1     -1  0  0      0         1
         5     0      1     -1  0 -1      0         1
         5     0      0     -1  0  0      0         1
         4     0      2     -1  0  0      0         1
         4     0      2     -1 -1  0      0         1
         4     0      2     -2 -1  0      0         1
         2     0      2     -2  0  0      0         1
    

  

> ui mousemode right "clip rotate"

> ui mousemode right clip

> select :139

261 atoms, 256 bonds, 23 residues, 14 models selected  

> color sel byhetero

> ui mousemode right select

> select add #5/B:140

269 atoms, 263 bonds, 24 residues, 14 models selected  

> select add #1/A:136

275 atoms, 268 bonds, 25 residues, 14 models selected  

> select up

2481 atoms, 2499 bonds, 320 residues, 14 models selected  

> select up

30257 atoms, 30712 bonds, 3713 residues, 14 models selected  

> select down

2481 atoms, 2499 bonds, 320 residues, 14 models selected  

> show sel atoms

> color sel byhetero

> select #6.4/A:143

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

> select up

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

> select up

1321 atoms, 1340 bonds, 163 residues, 1 model selected  

> select down

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

> select up

1321 atoms, 1340 bonds, 163 residues, 1 model selected  

> hide #!1 models

> hide #!6 models

> hide #!7 models

> show #!1 models

> select #5/B:241

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

> select up

121 atoms, 125 bonds, 14 residues, 1 model selected  

> select up

1314 atoms, 1334 bonds, 161 residues, 1 model selected  

> select up

1332 atoms, 1351 bonds, 164 residues, 1 model selected  

> select up

2029 atoms, 2059 bonds, 248 residues, 1 model selected  

> select up

2041 atoms, 2070 bonds, 249 residues, 1 model selected  

> select up

4068 atoms, 4126 bonds, 496 residues, 1 model selected  

> select down

2041 atoms, 2070 bonds, 249 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select #5/A:215

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

> select add #1/A:210

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

> select up

291 atoms, 291 bonds, 36 residues, 2 models selected  

> ui tool show Matchmaker

> matchmaker #!5 & sel to #1/A & sel pairing bs

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 20240927-jdt8-6-process1_refine_071.pdb, chain A (#1) with 6xiu,
chain A (#5), sequence alignment score = 80.6  
RMSD between 16 pruned atom pairs is 0.248 angstroms; (across all 16 pairs:
0.248)  
  

> matchmaker #!5 & sel to #1/A & sel pairing bs

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 20240927-jdt8-6-process1_refine_071.pdb, chain A (#1) with 6xiu,
chain A (#5), sequence alignment score = 80.6  
RMSD between 16 pruned atom pairs is 0.248 angstroms; (across all 16 pairs:
0.248)  
  

> hide #!1 models

> select clear

Drag select of 72 atoms, 49 residues, 59 bonds  

> hide sel atoms

> select clear

> show #!7 models

> hide #!5 models

> show #!5 models

> select #7.1/A:75

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

> select add #7.5/B:154

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

> select add #7.3/B:218

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

> select add #7.4/A:121

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

> select add #7.3/B:249

42 atoms, 37 bonds, 5 residues, 4 models selected  

> select add #7.7/B:107

53 atoms, 47 bonds, 6 residues, 5 models selected  

> select add #7.6/A:247

64 atoms, 58 bonds, 7 residues, 6 models selected  

> select up

650 atoms, 656 bonds, 78 residues, 6 models selected  

> select down

64 atoms, 58 bonds, 7 residues, 6 models selected  

> select up

650 atoms, 656 bonds, 78 residues, 6 models selected  

> select up

7271 atoms, 7381 bonds, 890 residues, 6 models selected  

> select up

7384 atoms, 7488 bonds, 907 residues, 6 models selected  

> select up

12132 atoms, 12312 bonds, 1482 residues, 6 models selected  

> select up

12204 atoms, 12378 bonds, 1488 residues, 6 models selected  

> select up

24408 atoms, 24756 bonds, 2976 residues, 6 models selected  

> select up

32544 atoms, 33008 bonds, 3968 residues, 8 models selected  

> select up

32544 atoms, 33008 bonds, 3968 residues, 9 models selected  

> select down

32544 atoms, 33008 bonds, 3968 residues, 8 models selected  

> select down

24408 atoms, 24756 bonds, 2976 residues, 6 models selected  

> hide sel cartoons

> hide sel atoms

> select #7.2/B:121

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

> select up

82 atoms, 81 bonds, 10 residues, 1 model selected  

> select up

1314 atoms, 1334 bonds, 161 residues, 1 model selected  

> select up

1332 atoms, 1351 bonds, 164 residues, 1 model selected  

> select up

2029 atoms, 2059 bonds, 248 residues, 1 model selected  

> select up

2041 atoms, 2070 bonds, 249 residues, 1 model selected  

> select up

4068 atoms, 4126 bonds, 496 residues, 1 model selected  

> select down

2041 atoms, 2070 bonds, 249 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

Drag select of 452 residues, 2 pseudobonds, 72 atoms, 59 bonds  
Drag select of 492 residues, 2 pseudobonds, 72 atoms, 59 bonds  

> color (#!5#!7.2 & sel) cornflower blue

> color sel byhetero

> select clear

[Repeated 1 time(s)]

> ~label #5,7 atoms

> ~label #5,7 residues

> ui mousemode right label

> label delete residues

[Repeated 5 time(s)]

> ui mousemode right label

> ui mousemode right select

> label missing 3

> label missing 2

> label missing 1

> label missing 0

> select #5/A:140

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

> select up

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

> select up

1314 atoms, 1334 bonds, 161 residues, 1 model selected  

> select down

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

> show sel atoms

> select clear

> set bgColor white

> set bgColor #ffffff00

> lighting simple

> view

[Repeated 2 time(s)]

> ui tool show "Side View"

> show #!1 models

> select #1/A:140

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

> select up

75 atoms, 75 bonds, 10 residues, 1 model selected  

> select up

1321 atoms, 1340 bonds, 163 residues, 1 model selected  

> select down

75 atoms, 75 bonds, 10 residues, 1 model selected  

> style sel stick

Changed 75 atom styles  

> style sel stick

Changed 75 atom styles  

> show sel atoms

> color sel byhetero

> select clear

> select #1/A:143

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

> select up

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

> select up

1321 atoms, 1340 bonds, 163 residues, 1 model selected  

> select down

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

> show sel atoms

> show #!6 models

> select #6.2/A:79

8 atoms, 7 bonds, 1 residue, 1 model selected  
Drag select of 78 atoms, 68 bonds, 124 residues  
Drag select of 149 atoms, 125 bonds, 187 residues, 1 pseudobonds  

> select up

2591 atoms, 2586 bonds, 1 pseudobond, 322 residues, 3 models selected  

> select up

2599 atoms, 2595 bonds, 1 pseudobond, 322 residues, 3 models selected  

> select up

3498 atoms, 3535 bonds, 1 pseudobond, 435 residues, 3 models selected  

> select up

4186 atoms, 4235 bonds, 1 pseudobond, 519 residues, 3 models selected  

> select up

4500 atoms, 4240 bonds, 1 pseudobond, 828 residues, 3 models selected  

> select up

4500 atoms, 4240 bonds, 1 pseudobond, 828 residues, 3 models selected  

> select up

9000 atoms, 8480 bonds, 1 pseudobond, 1656 residues, 5 models selected  

> select down

4500 atoms, 4240 bonds, 1 pseudobond, 828 residues, 3 models selected  

> hide sel atoms

> hide sel cartoons

> select clear

Drag select of 2 residues  

> select up

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

> select up

1321 atoms, 1340 bonds, 163 residues, 1 model selected  

> select up

1369 atoms, 1387 bonds, 170 residues, 1 model selected  

> select up

2075 atoms, 2104 bonds, 255 residues, 1 model selected  

> select up

2250 atoms, 2120 bonds, 414 residues, 1 model selected  

> select up

9000 atoms, 8480 bonds, 1656 residues, 4 models selected  

> select down

2250 atoms, 2120 bonds, 414 residues, 1 model selected  

> hide sel atoms

[Repeated 1 time(s)]

> hide sel cartoons

> select #7.2/A:81

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

> select clear

[Repeated 1 time(s)]

> hide #!5 models

> show #!5 models

> hide #!5 models

> hide #!7 models

> hide #!6 models

> show #!6 models

> select #6.4/A:113

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

> select up

39 atoms, 38 bonds, 5 residues, 1 model selected  

> select up

1321 atoms, 1340 bonds, 163 residues, 1 model selected  

> select up

1369 atoms, 1387 bonds, 170 residues, 1 model selected  

> select up

2075 atoms, 2104 bonds, 255 residues, 1 model selected  

> select up

2250 atoms, 2120 bonds, 414 residues, 1 model selected  

> select up

9000 atoms, 8480 bonds, 1656 residues, 4 models selected  

> select up

9000 atoms, 8480 bonds, 1656 residues, 5 models selected  

> select up

15318 atoms, 14726 bonds, 2566 residues, 14 models selected  

> select down

9000 atoms, 8480 bonds, 1656 residues, 5 models selected  

> color sel #ec89a0ff

> color sel #ffa6b1ff

> color sel #ffa7b2ff

[Repeated 1 time(s)]

> color sel #f39faaff

> color sel #e696a0ff

> color sel #d68c95ff

> color sel #d58b94ff

[Repeated 1 time(s)]

> color sel #d48b94ff

> color sel #d28992ff

> color sel #cf8891ff

> color sel #cc858eff

> color sel #c8838cff

> color sel #c37f88ff

> color sel #bc7b83ff

> color sel #bb7a82ff

> color sel #b87880ff

> color sel #b6777fff

> color sel #b5767eff

> color sel #ae727aff

> color sel #ac7078ff

> color sel #a36a72ff

> color sel #9b666cff

> color sel #9b656cff

> color sel #99646bff

[Repeated 1 time(s)]

> color sel #99646aff

> color sel #956268ff

[Repeated 1 time(s)]

> color sel #966269ff

> color sel #98636aff

> color sel #99646bff

> color sel #9c666dff

[Repeated 2 time(s)]

> color sel #9d676eff

[Repeated 1 time(s)]

> color sel #9e676eff

> color sel #a46b73ff

> color sel #aa6f76ff

> color sel #b5767eff

> color sel #b97981ff

> color sel #c17e87ff

> color sel #c6828aff

> color sel #cf8790ff

> color sel #d18992ff

> color sel #d58b95ff

> color sel #e0929cff

> color sel #e595a0ff

> color sel #ee9ca6ff

> color sel #f9a3aeff

> color sel #ffa7b2ff

> color sel #df929bff

> color sel #d58b95ff

> select clear

> select #6.4/A:139

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

> select up

75 atoms, 75 bonds, 10 residues, 1 model selected  

> select up

1321 atoms, 1340 bonds, 163 residues, 1 model selected  

> select down

75 atoms, 75 bonds, 10 residues, 1 model selected  

> select add #6.4/A:141

83 atoms, 82 bonds, 11 residues, 1 model selected  

> select up

98 atoms, 98 bonds, 13 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> show #!5 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!7 models

> hide #!1 models

> show #!1 models

> show #!6 models

> hide #!5 models

> hide #!7 models

> show #!5 models

> show #!7 models

> select clear

> select #5 :90

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

> select clear

> select #5 :140

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

> select #5 :141

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

> hide #!1 models

> hide #!6 models

> select clear

> select #5/6

Nothing selected  

> select #5-6 :90

48 atoms, 42 bonds, 6 residues, 5 models selected  

> select #5-6 :87,90,121,139,143

254 atoms, 218 bonds, 38 residues, 5 models selected  

> ui tool show "Color Actions"

> color sel bynucleotide

> color sel byelement

> color sel byhetero

> show sel & #!5 atoms

> color (#!5 & sel) medium blue

> color dark blue #5-6 :87,90,121,139,143

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

> color blue #5-6,a :87,90,121,139,143

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

> color blue #5-6,atoms :87,90,121,139,143

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

> color blue #5-6 atoms :87,90,121,139,143

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

> color #5-6 :87,90,121,139,143 blue

> color #5-6 :87,90,121,139,143 blue target a

> color (#!5 & sel) cornflower blue

> color sel & #!5 byhetero

> color #5-6 :87,90,121,139,143 blue target atom

Invalid "target" argument: Character 't' is not an allowed target, must be one
of acrsbmpfl  

> color #5-6 :87,90,121,139,143 blue target a

> color sel & #!5 byhetero

> color #5-7 :87,90,121,139,143 blue target a

> color sel & #!5 byhetero

> color #5-7 :87,90,121,139,143 light blue target a

> color #5-7 :87,90,121,139,143 lightblue orange target a

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

> color #5-7 :87,90,121,139,143 orange target a

> color sel & #!5 byhetero

[Repeated 1 time(s)]

> select #7.2/A:139

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

> color sel byhetero

> select #7.2/A:143

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

> color sel byhetero

> select clear

Drag select of 2 atoms, 2 residues  

> select clear

> select #7.2/A:92

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

> select #5-7 :87,90,121,139,143

942 atoms, 842 bonds, 118 residues, 13 models selected  

> show sel & #!5#!7.1-8 atoms

> select #7.2/A:121

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

> color sel byhetero

> select clear

> select #5/A:132

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

> select clear

> ui mousemode right "clip rotate"

> ui mousemode right clip

> ui mousemode right select

Drag select of 1 atoms, 33 residues  

> select clear

Drag select of 19 residues  
Drag select of 7 residues  
Drag select of 31 residues  
Drag select of 2 atoms, 21 residues, 1 pseudobonds  

> select subtract #7.2/A:151

532 atoms, 1 pseudobond, 63 residues, 3 models selected  

> select #7.2/A:81

8 atoms, 7 bonds, 1 residue, 1 model selected  
Drag select of 26 residues  

> select clear

Drag select of 26 residues  
Drag select of 23 residues  

> select up

730 atoms, 732 bonds, 88 residues, 2 models selected  

> select up

4030 atoms, 4090 bonds, 492 residues, 2 models selected  

> select down

730 atoms, 732 bonds, 88 residues, 2 models selected  

> select down

421 atoms, 49 residues, 2 models selected  

> select up

730 atoms, 732 bonds, 88 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel light sky blue

> color sel light blue

> color sel #6597f0ff

> color sel #6597f0fe

> color sel #6597f0fa

> color sel #6597f0ea

> color sel #6597f0e6

> color sel #6597f0c9

> color sel #6597f0b2

> color sel #6597f09b

> color sel #6597f08d

> color sel #6597f088

[Repeated 2 time(s)]

> color sel #6597f087

> color sel #6597f084

> color sel #6597f083

> color sel #6597f082

[Repeated 1 time(s)]

> color sel #6597f080

> color sel #6597f075

> color sel #6597f073

> color sel #6597f072

> color sel #6597f071

[Repeated 1 time(s)]

> color sel #6597f070

[Repeated 2 time(s)]

> color sel #6597f06c

> color sel #6597f063

> color sel #6597f060

> color sel #6597f05c

> color sel #6597f058

> color sel #6597f057

> color sel #6597f056

[Repeated 3 time(s)]

> color sel #6597f054

> color sel #6597f052

> color sel #6597f051

> color sel #6597f04f

> color sel #6597f04e

> color sel #6597f04d

[Repeated 1 time(s)]

> color sel #6597f04c

[Repeated 1 time(s)]

> color sel #6597f04b

[Repeated 1 time(s)]

> color sel #6597f04a

> color sel #6597f049

[Repeated 1 time(s)]

> color sel #6597f047

> color sel #6597f046

> color sel #6597f045

> color sel #6597f043

> color sel #6597f042

> color sel #6597f03c

> color sel #6597f03b

> color sel #6597f038

> color sel #6597f034

> color sel #6597f031

> color sel #6597f02f

> color sel #6597f02e

> color sel #6597f02d

> color sel #6597f02a

> color sel #6597f029

> color sel #6597f026

[Repeated 1 time(s)]

> color sel #6597f025

[Repeated 5 time(s)]

> color sel #6597f024

[Repeated 1 time(s)]

> color sel #6597f023

> color sel #6597f020

> color sel #6597f01e

> color sel #6597f01c

[Repeated 1 time(s)]

> color sel #6597f01b

> color sel #6597f01a

[Repeated 3 time(s)]

> color sel #6597f019

[Repeated 4 time(s)]

> color sel #6597f018

[Repeated 1 time(s)]

> color sel #6597f016

> color sel #6597f015

[Repeated 2 time(s)]

> color sel #6497f015

> color sel #6496ef15

> color sel #6395ed15

> color sel #6394ec15

> color sel #6090e515

> color sel #5e8ee115

> color sel #5986d515

> color sel #5783d015

> color sel #547fca15

> color sel #547ec915

> color sel #537dc615

> color sel #5078bf15

[Repeated 1 time(s)]

> color sel #4f76bc15

> color sel #4e76bc15

> color sel #4e76bb15

[Repeated 1 time(s)]

> color sel #537cc615

> color sel #5b88d915

> color sel #5e8de015

> color sel #6294eb15

> color sel #6ba0ff15

> select clear

> select #7.2/A:27

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

> select clear

> select #7.2/A:28

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

> select add #7.2/A:27

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

> save /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-ch/figure-wtrns-
> dimerization-interface.cxs

——— End of log from Sun Mar 30 16:59:12 2025 ———

opened ChimeraX session  

> select #5/A:157

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

> select up

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

> select up

1314 atoms, 1334 bonds, 161 residues, 1 model selected  

> select down

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

> color sel #4989d9ff

> color sel #4989d99e

[Repeated 1 time(s)]

> color sel #4989d997

[Repeated 1 time(s)]

> color sel #4989d994

> color sel #4989d993

> color sel #4989d992

> color sel #4989d98b

> color sel #4989d986

> color sel #4989d981

> color sel #4989d975

> color sel #4989d969

> color sel #4989d964

> color sel #4989d95f

> color sel #4989d95b

> color sel #4989d95a

> color sel #4989d953

> color sel #4989d94e

> color sel #4989d949

> color sel #4989d947

> color sel #4989d944

> color sel #4989d943

> color sel #4989d942

[Repeated 1 time(s)]

> color sel #4989d940

> color sel #4989d93e

> color sel #4989d93d

> color sel #4989d93c

[Repeated 2 time(s)]

> color sel #4989d93b

> color sel #4989d939

> color sel #4989d937

> color sel #4989d934

> color sel #4989d932

> color sel #4989d929

> color sel #4989d927

> color sel #4989d926

[Repeated 3 time(s)]

> color sel #4989d925

> color sel #4989d923

> color sel #4989d921

> color sel #4989d91f

> color sel #4989d91d

> color sel #4989d91b

[Repeated 1 time(s)]

> color sel #4989d91a

[Repeated 3 time(s)]

> color sel #4989d919

[Repeated 1 time(s)]

> select #5/A:158

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

> select add #5/A:159

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

> color sel #4989d935

> color sel #4989d93e

> color sel #4989d957

> color sel #4989d956

[Repeated 1 time(s)]

> select #7.2/A:114

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

> color sel #4989d957

[Repeated 3 time(s)]

> color sel #4989d959

> color sel #4989d95e

> color sel #4989d962

> color sel #4989d963

[Repeated 1 time(s)]

> color sel #4989d967

> color sel #4989d969

> color sel #4989d96a

> color sel #4989d972

> color sel #4989d97b

[Repeated 1 time(s)]

> color sel #4989d97d

> color sel #4989d97f

> color sel #4989d980

[Repeated 1 time(s)]

> color sel #4989d982

> color sel #4989d983

> color sel #4989d985

[Repeated 3 time(s)]

> color sel #4989d984

> color sel #4989d983

> color sel #4989d981

> color sel #4989d97f

[Repeated 1 time(s)]

> color sel #4989d97e

> color sel #4989d97b

> color sel #4989d977

> color sel #4989d976

> color sel #4989d975

> color sel #4989d974

> color sel #4989d973

> color sel #4989d972

[Repeated 1 time(s)]

> select #7.2/A:27

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

> select add #7.2/A:71

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

> select up

89 atoms, 89 bonds, 11 residues, 1 model selected  

> color sel #4989d99d

> color sel #4989d99e

> color sel #4989d9b4

[Repeated 1 time(s)]

> color sel #4989d9c4

[Repeated 3 time(s)]

> color sel #4989d9c3

> color sel #4989d9bf

> color sel #4989d9bc

> color sel #4989d9bb

[Repeated 2 time(s)]

> color sel #4989d9ba

[Repeated 1 time(s)]

> color sel #4989d9bb

> color sel #4989d9be

> color sel #4989d9bf

> color sel #4989d9c0

> color sel #4989d9c2

> color sel #4989d9c6

> color sel #4989d9cc

> color sel #4989d9d2

> color sel #4989d9d5

[Repeated 1 time(s)]

> color sel #4989d9d7

> color sel #4989d9da

> color sel #4989d9e7

> color sel #4989d9eb

[Repeated 2 time(s)]

> color sel #4989d9ec

[Repeated 2 time(s)]

> color sel #4989d9f6

> color sel #4989d9fc

> color sel #4989d9ff

> color sel #4989d9f3

> color sel #4989d9c8

> color sel #4989d9bc

> color sel #4989d99a

> color sel #4989d974

> color sel #4989d96f

> color sel #4989d967

> color sel #4989d95d

> color sel #4989d958

> color sel #4989d953

> color sel #4989d94a

> color sel #4989d946

> color sel #4989d940

> color sel #4989d936

> color sel #4989d931

> color sel #4989d92f

[Repeated 2 time(s)]

> color sel #4989d92e

[Repeated 1 time(s)]

> color sel #4989d92d

[Repeated 3 time(s)]

> color sel #4989d92c

[Repeated 4 time(s)]

> color sel #4989d92b

[Repeated 3 time(s)]

> color sel #4989d92a

[Repeated 1 time(s)]

> color sel #4989d929

> color sel #4989d928

> color sel #4989d926

[Repeated 1 time(s)]

> color sel #4989d925

[Repeated 3 time(s)]

> color sel #4989d924

[Repeated 2 time(s)]

> color sel #4989d923

> color sel #4989d922

[Repeated 3 time(s)]

> select #7.2/A:161

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

> color sel #4989d922

> color sel #4989d921

> color sel #4989d91e

[Repeated 1 time(s)]

> color sel #4989d91d

[Repeated 1 time(s)]

> color sel #4989d91b

[Repeated 2 time(s)]

> color sel #4989d91a

[Repeated 1 time(s)]

> color sel #4989d919

[Repeated 3 time(s)]

> color sel #4989d917

[Repeated 1 time(s)]

> color sel #4989d916

[Repeated 2 time(s)]

> color sel #4989d915

> select clear

> save /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-ch/full-dimerization-
> interface.png width 884 height 662 supersample 3

> select #5-7 :87,90,121,143

690 atoms, 594 bonds, 96 residues, 13 models selected  

> color #5-7 :87,90,121,143 dark orange target a

> ui tool show "Color Actions"

> color #5-7 :87,90,121,143 orange red target a

> color sel & #!5#!7.1-8 byhetero

> select clear

> save /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-ch/full-dimerization-
> interface-coloredbyexpression.png width 884 height 662 supersample 3

> save /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-ch/full-dimerization-
> interface-coloredbyexpression.pdb displayedOnly true

> save /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-ch/full-dimerization-
> interface-coloredbyexpression.cxs

> save /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-ch/full-dimerization-
> interface-coloredbyexpression.glb

Drag select of 140 atoms, 84 residues, 1 pseudobonds, 111 bonds  

> select up

688 atoms, 686 bonds, 1 pseudobond, 85 residues, 3 models selected  

> select up

693 atoms, 692 bonds, 1 pseudobond, 85 residues, 3 models selected  

> select up

986 atoms, 991 bonds, 1 pseudobond, 122 residues, 3 models selected  

> select up

4030 atoms, 4090 bonds, 1 pseudobond, 492 residues, 3 models selected  

> select down

986 atoms, 991 bonds, 1 pseudobond, 122 residues, 3 models selected  

> select down

693 atoms, 692 bonds, 1 pseudobond, 85 residues, 3 models selected  

> preset cartoons/nucleotides cylinders/stubs

Using preset: Cartoons/Nucleotides / Cylinders/Stubs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> select #7.1/B:104

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

> select up

31 atoms, 30 bonds, 4 residues, 1 model selected  

> select up

1314 atoms, 1334 bonds, 161 residues, 1 model selected  

> select up

1332 atoms, 1351 bonds, 164 residues, 1 model selected  

> select up

2029 atoms, 2059 bonds, 248 residues, 1 model selected  

> select up

2041 atoms, 2070 bonds, 249 residues, 1 model selected  

> select up

4068 atoms, 4126 bonds, 496 residues, 1 model selected  

> select up

32544 atoms, 33008 bonds, 3968 residues, 8 models selected  

> select down

4068 atoms, 4126 bonds, 496 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select #7.6/A:186

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

> select up

64 atoms, 64 bonds, 9 residues, 1 model selected  

> select up

1314 atoms, 1334 bonds, 161 residues, 1 model selected  

> select up

1318 atoms, 1337 bonds, 162 residues, 1 model selected  

> select up

2015 atoms, 2045 bonds, 246 residues, 1 model selected  

> hide sel cartoons

> select #7.5/A:9

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

> select add #7.4/A:229

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

> select up

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

> select up

2015 atoms, 2045 bonds, 246 residues, 2 models selected  

> select up

2070 atoms, 2098 bonds, 253 residues, 2 models selected  

> select up

4030 atoms, 4090 bonds, 492 residues, 2 models selected  

> select up

4054 atoms, 4112 bonds, 494 residues, 2 models selected  

> select up

8136 atoms, 8252 bonds, 992 residues, 2 models selected  

> select up

32544 atoms, 33008 bonds, 3968 residues, 8 models selected  

> select up

32544 atoms, 33008 bonds, 3968 residues, 9 models selected  

> select up

38862 atoms, 39254 bonds, 4878 residues, 18 models selected  

> select up

38862 atoms, 39254 bonds, 4878 residues, 18 models selected  

> select up

38862 atoms, 39254 bonds, 4878 residues, 18 models selected  

> select up

38862 atoms, 39254 bonds, 4878 residues, 18 models selected  

> select up

38862 atoms, 39254 bonds, 4878 residues, 18 models selected  

> select up

38862 atoms, 39254 bonds, 4878 residues, 18 models selected  

> select up

38862 atoms, 39254 bonds, 4878 residues, 18 models selected  

> select up

38862 atoms, 39254 bonds, 4878 residues, 18 models selected  

> select up

38862 atoms, 39254 bonds, 4878 residues, 18 models selected  

> select down

32544 atoms, 33008 bonds, 3968 residues, 9 models selected  

> select down

32544 atoms, 33008 bonds, 3968 residues, 8 models selected  

> select down

8136 atoms, 8252 bonds, 992 residues, 2 models selected  

> select down

4054 atoms, 4112 bonds, 494 residues, 2 models selected  

> select down

4030 atoms, 4090 bonds, 492 residues, 2 models selected  

> select down

2070 atoms, 2098 bonds, 253 residues, 2 models selected  

> select down

2015 atoms, 2045 bonds, 246 residues, 2 models selected  

> select down

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

> select down

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

> select up

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

> select up

2015 atoms, 2045 bonds, 246 residues, 2 models selected  

> hide sel cartoons

> select #7.8/B:190

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

> select up

101 atoms, 100 bonds, 12 residues, 1 model selected  

> select up

1314 atoms, 1334 bonds, 161 residues, 1 model selected  

> select up

1332 atoms, 1351 bonds, 164 residues, 1 model selected  

> select up

2029 atoms, 2059 bonds, 248 residues, 1 model selected  

> select up

2041 atoms, 2070 bonds, 249 residues, 1 model selected  

> select up

4068 atoms, 4126 bonds, 496 residues, 1 model selected  

> select up

32544 atoms, 33008 bonds, 3968 residues, 8 models selected  

> select up

32544 atoms, 33008 bonds, 3968 residues, 9 models selected  

> select down

32544 atoms, 33008 bonds, 3968 residues, 8 models selected  

> select down

4068 atoms, 4126 bonds, 496 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select #5,7 :139

216 atoms, 216 bonds, 18 residues, 9 models selected  

> show sel atoms

> select clear

> select #5-7 :87,90,121,139,143

942 atoms, 842 bonds, 118 residues, 13 models selected  

> show sel & #!5#!7.1-8 atoms

> select clear

> select #7.2/A:92

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

> select add #5/A:134

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

> select add #7.2/A:115

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

> select add #7.2/A:139

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

> select add #5/A:140

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

> select add #5/A:120

56 atoms, 52 bonds, 6 residues, 2 models selected  

> select add #7.2/A:90

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

> select up

529 atoms, 530 bonds, 66 residues, 2 models selected  

> select up

3329 atoms, 3379 bonds, 407 residues, 2 models selected  

> select down

529 atoms, 530 bonds, 66 residues, 2 models selected  

> color sel #4079c115

> color sel #3e75ba15

> color sel #3e76ba15

> color sel #3f78be15

> color sel #3f78bf15

> color sel #3f79c015

> color sel #4079c015

> color sel #407ac115

> color sel #407bc215

> color sel #417bc415

> color sel #427ec815

[Repeated 1 time(s)]

> color sel #437fca15

> color sel #4380cc15

> color sel #4481cd15

> color sel #4482ce15

> color sel #4583cf15

> undo

> select clear

> color #5,7 #4583cf4f

> color #5,7 #4583cf2a

[Repeated 1 time(s)]

> color #5,7 #4583cf34

> color #5,7 #4583cf3b

[Repeated 1 time(s)]

> color #5,7 #4583cf48

> color #5,7 #4583cf4d

> color #5,7 #4583cf52

> color #5,7 #4583cf59

[Repeated 1 time(s)]

> color #5,7 #4583cf63

> color #5,7 #4583cf66

[Repeated 1 time(s)]

> color #5,7 #4583cf63

[Repeated 1 time(s)]

> color #5,7 #4583cf62

> color #5,7 #4583cf5f

> color #5,7 #4583cf5a

> color #5,7 #4583cf59

> select clear

> select #5/A:132

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

> select #7.2/A:90

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

> select add #7.2/A:142

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

> select add #7.2/A:115

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

> select add #5/A:122

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

> select add #5/A:135

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

> select add #5/A:155

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

> select add #7.2/A:84

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

> select up

620 atoms, 621 bonds, 77 residues, 2 models selected  

> color sel #4583cf5a

> color sel #4583cf60

> color sel #4583cf63

> color sel #4583cf64

> color sel #4583cf67

> color sel #4583cf68

> color sel #4583cf69

> color sel #4583cf6d

> color sel #4583cf71

> color sel #4583cf73

> color sel #4583cf74

[Repeated 2 time(s)]

> color sel #4583cf75

[Repeated 1 time(s)]

> color sel #4583cf76

> color sel #4583cf77

> color sel #4583cf78

> color sel #4583cf79

> color sel #4583cf7d

> color sel #4583cf80

> color sel #4583cf84

> color sel #4583cf85

> color sel #4583cf88

> color sel #4583cf89

> color sel #4583cf8b

> color sel #4583cf8c

[Repeated 3 time(s)]

> color sel #4583cf8b

> color sel #4583cf85

> color sel #4583cf81

> color sel #4583cf7f

> color sel #4583cf7e

> color sel #4583cf7c

> color sel #4583cf79

> color sel #4583cf73

> color sel #4583cf69

> color sel #4583cf68

> color sel #4583cf67

> color sel #4583cf66

[Repeated 1 time(s)]

> color sel #4583cf63

> color sel #4583cf61

> color sel #4583cf5e

> color sel #4583cf5b

> color sel #4583cf59

[Repeated 1 time(s)]

> color sel #4583cf58

> color sel #4583cf4d

> color sel #4583cf48

> color sel #4583cf42

> color sel #4583cf41

> color sel #4583cf3f

> color sel #4583cf3b

> color sel #4583cf3a

> color sel #4583cf37

> color sel #4583cf35

> color sel #4583cf32

> color sel #4583cf30

> color sel #4583cf2e

> color sel #4583cf2c

> color sel #4583cf29

> color sel #4583cf27

[Repeated 1 time(s)]

> color sel #4583cf26

> color sel #4583cf25

> color sel #4583cf20

[Repeated 1 time(s)]

> color sel #4583cf1f

[Repeated 1 time(s)]

> color sel #4583cf1e

> color sel #4583cf1d

> color sel #4583cf1c

> color sel #4583cf1b

> color sel #4583cf1a

> color sel #4583cf18

> color sel #4583cf17

[Repeated 1 time(s)]

> color sel #4583cf15

> color sel #4583cf12

> color sel #4583cf11

> color sel #4583cf0f

[Repeated 1 time(s)]

> color sel #4583cf0d

[Repeated 1 time(s)]

> color sel #4583cf0c

> color sel #4583cf0b

> color sel #4583cf09

[Repeated 1 time(s)]

> color sel #4583cf08

> color sel #4583cf07

> color sel #4583cf06

[Repeated 2 time(s)]

> color sel #4583cf0c

> color sel #4583cf13

> color sel #4583cf14

> color sel #4583cf18

[Repeated 2 time(s)]

> color sel #4583cf19

> select add #5/A:82

631 atoms, 631 bonds, 78 residues, 2 models selected  

> select up

751 atoms, 753 bonds, 93 residues, 2 models selected  

> color sel #4583cf19

> color sel #427ec819

> color sel #3f77bd19

[Repeated 1 time(s)]

> color sel #3e76bb19

> color sel #3d75b919

> color sel #3a6fb119

> color sel #396cab19

[Repeated 1 time(s)]

> color sel #396cac19

> color sel #3a6eaf19

> color sel #3d75b919

> color sel #3f79c019

> color sel #417cc519

> color sel #4380ca19

> color sel #4481cd19

> color sel #4889d919

> color sel #488adb19

> color sel #4b90e419

> color sel #4c91e519

> color sel #4f96ee19

> color sel #529cf719

[Repeated 2 time(s)]

> color sel #5098f119

> color sel #498adb19

> color sel #4788d719

> color sel #427dc619

> color sel #407bc219

> color sel #3f78bf19

[Repeated 1 time(s)]

> color sel #3f78bf2e

> color sel #3f78bf49

> color sel #3f78bf56

> color sel #3f78bf51

[Repeated 1 time(s)]

> color sel #3f78bf50

> color sel #3f78bf4f

> color sel #3f78bf4d

[Repeated 1 time(s)]

> color sel #3f78bf4c

[Repeated 1 time(s)]

> color sel #3f78bf4b

> color sel #3f78bf4a

> color sel #3f78bf47

> color sel #3f78bf46

> color sel #3f78bf45

> color sel #3f78bf44

[Repeated 1 time(s)]

> color sel #3f78bf42

> color sel #3f78bf40

> color sel #3f78bf3d

> color sel #3f78bf3b

> color sel #3f78bf38

> color sel #3f78bf33

> color sel #3f78bf31

> color sel #3f78bf30

> color sel #3f78bf2f

> color sel #3f78bf2e

> color sel #3f78bf2b

> color sel #3f78bf29

> color sel #3f78bf28

> color sel #3f78bf27

[Repeated 1 time(s)]

> color sel #3f78bf26

[Repeated 1 time(s)]

> color sel #3f78bf25

[Repeated 3 time(s)]

> color sel #3f78bf26

[Repeated 1 time(s)]

> color sel #3f78bf27

[Repeated 1 time(s)]

> color sel #3f78bf28

[Repeated 2 time(s)]

> color sel #3f78bf29

[Repeated 1 time(s)]

> color sel #3f78bf2a

[Repeated 2 time(s)]

> color sel #3f78bf2b

> color sel #3f78bf2d

[Repeated 1 time(s)]

> color sel byhetero

> select #5-7 :87,90,121,139,143

942 atoms, 842 bonds, 118 residues, 13 models selected  

> color (#!5#!7.1-8 & sel) orange

> select #5-7 :87,90,121,139,143 orange target a

Expected a keyword  

> color #5-7 :87,90,121,139,143 orange target a

> color sel & #!5#!7.1-8 byhetero

> color (#!5#!7.1-8 & sel) #3f78bf49

[Repeated 1 time(s)]

> color (#!5#!7.1-8 & sel) #3f78bf58

> color (#!5#!7.1-8 & sel) #3f78bf72

> color (#!5#!7.1-8 & sel) #3f78bf78

> undo

[Repeated 4 time(s)]

> ui tool show "Color Actions"

> color sel orange

> undo

> color #5-7 :139 orange orange target a

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

> color #5-7 :139 orange target a

> color #5-7 :139 orange red target a

> color sel & #!5#!7.1-8 byhetero

> select clear

> color #5-7 :87,90,121,139,143 transparency 0 orange target a

Expected a keyword  

> transparency 0 target a

> color #5-7 :139 orange target a

> color #!5#!7.1-8 byhetero

> color #5-7 :87,90,121,143 orange red target a

> color #!5#!7.1-8 byhetero

> select clear

> save /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-ch/full-dimerization-
> interface-coloredbyexpression-cylinders.png width 884 height 662 supersample
> 3

> save /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-ch/full-dimerization-
> interface-coloredbyexpression-cylinders.cxs

> lighting simple

[Repeated 1 time(s)]

> lighting soft

> lighting simple

> lighting shadows true

> lighting shadows false

> lighting shadows true

> graphics silhouettes true

> graphics silhouettes false

> lighting flat

[Repeated 1 time(s)]

> lighting full

> lighting soft

[Repeated 2 time(s)]

> lighting full

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> save /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-ch/full-dimerization-
> interface-coloredbyexpression-cylinders2.png width 884 height 662
> supersample 3

> select #5-7 :87,90,121,143

690 atoms, 594 bonds, 96 residues, 13 models selected  

> label (#!5#!7.1-8 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> ~label (#!5#!7.1-8 & sel) residues

> select clear

> save /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-ch/full-dimerization-
> interface-coloredbyexpression-cylinders3.png width 884 height 662
> supersample 3

> save /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-ch/full-dimerization-
> interface-coloredbyexpression-cylinders3closeup.png width 884 height 662
> supersample 3

[Repeated 1 time(s)]

> lighting shadows false

> graphics silhouettes false

> graphics silhouettes true

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> graphics silhouettes true

> lighting full

[Repeated 1 time(s)]

> graphics silhouettes false

> graphics silhouettes true

> windowsize 1000 1000

> windowsize 3000

> windowsize 500

> windowsize 200

> windowsize 2000

> windowsize 800

> show #!1 models

> show #!6 models

> select #5-7 :87,90,121,139,143

942 atoms, 842 bonds, 118 residues, 13 models selected  

> select #5,7 :87,90,121,139,143

774 atoms, 702 bonds, 90 residues, 9 models selected  

> select #5,6,7 :87,90,121,139,143

942 atoms, 842 bonds, 118 residues, 13 models selected  

> color sel #ffabb8ff

> undo

> select #6 :87,90,121,139,143

168 atoms, 140 bonds, 28 residues, 4 models selected  

> select #6 :87,90,121,139,143

168 atoms, 140 bonds, 28 residues, 4 models selected  

> color sel #ffabb8ff

> color sel #d98d98ff

> select clear

> select #5,6,7 :87,90,121,139,143

942 atoms, 842 bonds, 118 residues, 13 models selected  

> show sel atoms

> select #1/A:222

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

> select add #1/A:217

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

> select up

154 atoms, 154 bonds, 19 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #!7.2 & sel to #1/A & sel pairing bs

No molecules/chains to match specified  

> select add #5/A:223

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

> select up

316 atoms, 316 bonds, 39 residues, 2 models selected  

> matchmaker #!7.2 & sel to #1/A & sel pairing bs

No molecules/chains to match specified  

> select #1/A:220

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

> select add #5/A:222

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

> select add #5/A:220

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

> select up

291 atoms, 291 bonds, 36 residues, 2 models selected  

> matchmaker #!7.2 & sel to #1/A & sel pairing bs

No molecules/chains to match specified  
Drag select of 22 residues  

> select up

300 atoms, 299 bonds, 37 residues, 2 models selected  

> select up

347 atoms, 348 bonds, 42 residues, 2 models selected  

> select up

2635 atoms, 2674 bonds, 324 residues, 2 models selected  

> select down

347 atoms, 348 bonds, 42 residues, 2 models selected  

> select down

300 atoms, 299 bonds, 37 residues, 2 models selected  

> select subtract #5/A:177

291 atoms, 291 bonds, 36 residues, 2 models selected  

> select #1/A:218

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

> select add #1/A:221

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

> select add #5/A:222

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

> select add #5/A:217

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

> select add #5/A:216

35 atoms, 30 bonds, 5 residues, 2 models selected  

> select up

316 atoms, 316 bonds, 39 residues, 2 models selected  

> select up

2635 atoms, 2674 bonds, 324 residues, 2 models selected  

> select down

316 atoms, 316 bonds, 39 residues, 2 models selected  

> ui tool show Matchmaker

> matchmaker #!5 & sel to #1 & sel

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 20240927-jdt8-6-process1_refine_071.pdb, chain A (#1) with 6xiu,
chain A (#5), sequence alignment score = 95.1  
RMSD between 19 pruned atom pairs is 0.308 angstroms; (across all 19 pairs:
0.308)  
  

> dssp

[Repeated 1 time(s)]

> select #1/A:173

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

> dssp

[Repeated 3 time(s)]

> select #6.1/A:234

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

> select add #7.6/B:109

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

> select up

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

> select up

2635 atoms, 2674 bonds, 324 residues, 2 models selected  

> select up

2713 atoms, 2751 bonds, 335 residues, 2 models selected  

> select up

4104 atoms, 4163 bonds, 503 residues, 2 models selected  

> select up

4116 atoms, 4174 bonds, 504 residues, 2 models selected  

> select up

6318 atoms, 6246 bonds, 910 residues, 2 models selected  

> select up

13068 atoms, 12606 bonds, 2152 residues, 5 models selected  

> select down

6318 atoms, 6246 bonds, 910 residues, 2 models selected  

> hide sel atoms

> hide sel cartoons

Drag select of 38 atoms, 148 residues, 1 pseudobonds, 30 bonds  

> select up

7448 atoms, 7359 bonds, 1 pseudobond, 1051 residues, 7 models selected  

> select up

7468 atoms, 7383 bonds, 1 pseudobond, 1051 residues, 7 models selected  

> select up

7991 atoms, 7927 bonds, 1 pseudobond, 1119 residues, 7 models selected  

> select up

13052 atoms, 13077 bonds, 1 pseudobond, 1737 residues, 7 models selected  

> select up

13112 atoms, 13137 bonds, 1 pseudobond, 1745 residues, 7 models selected  

> select up

14482 atoms, 14527 bonds, 1 pseudobond, 1911 residues, 7 models selected  

> select up

14673 atoms, 14560 bonds, 1 pseudobond, 2069 residues, 7 models selected  

> select up

20772 atoms, 20744 bonds, 1 pseudobond, 2812 residues, 7 models selected  

> select up

20772 atoms, 20744 bonds, 1 pseudobond, 2812 residues, 7 models selected  

> select up

25272 atoms, 24984 bonds, 1 pseudobond, 3640 residues, 9 models selected  

> select down

18522 atoms, 18624 bonds, 1 pseudobond, 2398 residues, 6 models selected  

> hide sel atoms

> hide sel cartoons

Drag select of 37 atoms, 255 residues, 1 pseudobonds, 29 bonds  

> select up

1828 atoms, 149 bonds, 1 pseudobond, 227 residues, 3 models selected  

> select up

1833 atoms, 154 bonds, 1 pseudobond, 227 residues, 3 models selected  

> select up

2268 atoms, 2290 bonds, 1 pseudobond, 282 residues, 3 models selected  

> select up

4106 atoms, 4163 bonds, 1 pseudobond, 505 residues, 3 models selected  

> select up

4273 atoms, 4174 bonds, 1 pseudobond, 661 residues, 3 models selected  

> select up

6318 atoms, 6246 bonds, 1 pseudobond, 910 residues, 3 models selected  

> select up

6318 atoms, 6246 bonds, 1 pseudobond, 910 residues, 3 models selected  

> select up

13068 atoms, 12606 bonds, 1 pseudobond, 2152 residues, 6 models selected  

> select down

6318 atoms, 6246 bonds, 1 pseudobond, 910 residues, 3 models selected  

> hide sel cartoons

> hide sel atoms

> select #1,6 :87,90,121,139,143

210 atoms, 175 bonds, 35 residues, 5 models selected  

> select #1,6 :87,90,121,139,143 target a

Expected a keyword  

> color #1,6 :87,90,121,139,143 white target a

> color sel byhetero

> show sel atoms

> select clear

> color #1,6 :139 white target a

> color #1,6 :87,90,121,139,143 grey target a

> color byhetero

Drag select of 4 atoms, 5 bonds  

> select up

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

> hide sel cartoons

> hide sel atoms

> select up

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

> select down

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

> select down

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

> select up

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

> select up

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

> select up

2250 atoms, 2120 bonds, 414 residues, 1 model selected  

> select clear

> color #1,6 :139 white target a

> color byhetero

> lighting shadows false

> lighting shadows true

> lighting shadows false

> save /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-ch/wt-y139e-dimerization-
> interface-coloredbyexpression.png width 800 height 682 supersample 3

> save /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-ch/wt-y139e-dimerization-
> interface-coloredbyexpression.cxs

——— End of log from Sun Mar 30 18:40:30 2025 ———

opened ChimeraX session  

> ui mousemode right select

> select #6.4/A:214

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

> select add #7.2/A:216

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

> select add #7.2/A:223

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

> select add #6.4/A:223

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

> select up

308 atoms, 308 bonds, 38 residues, 2 models selected  

> select up

2635 atoms, 2674 bonds, 324 residues, 2 models selected  

> select down

308 atoms, 308 bonds, 38 residues, 2 models selected  

> ui tool show Matchmaker

> matchmaker #!5#!6.1-4#!7.1-8 & sel to #1 & sel

No 'to' model specified  

> select clear

> select up

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

> select up

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

> select up

66 atoms, 65 bonds, 8 residues, 1 model selected  

> select down

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

> hide sel atoms

> hide #!5 models

> hide #!7 models

Drag select of 40 atoms, 35 bonds  

> select clear

Drag select of 30 atoms, 26 bonds  
Drag select of 40 atoms, 35 bonds  

> hide sel atoms

Drag select of 25 atoms, 22 bonds  

> hide sel atoms

> select clear

Drag select of 33 atoms, 27 bonds  

> hide sel atoms

> show #!5 models

> select #5/B:217

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

> select add #6.4/A:208

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

> select up

283 atoms, 283 bonds, 35 residues, 2 models selected  

> select up

2635 atoms, 2674 bonds, 324 residues, 2 models selected  

> select down

283 atoms, 283 bonds, 35 residues, 2 models selected  

> select add #6.4/A:223

292 atoms, 291 bonds, 36 residues, 2 models selected  

> select up

308 atoms, 308 bonds, 38 residues, 2 models selected  

> select up

2635 atoms, 2674 bonds, 324 residues, 2 models selected  

> select down

308 atoms, 308 bonds, 38 residues, 2 models selected  

> ui tool show Matchmaker

> matchmaker #!5 & sel to #1 & sel

No 'to' model specified  

> matchmaker #5/B & sel to #6.1/A & sel pairing ss

No 'to' chains specified  

> matchmaker #5/B & sel to #6.1/A & sel pairing ss

No 'to' chains specified  

> matchmaker #5/B & sel to #6.1/A & sel pairing ss

No 'to' chains specified  

> matchmaker #!5 & sel to #6.1/A & sel pairing bs

No 'to' chains specified  

> matchmaker #5/B to #6.1/A & sel pairing ss

No 'to' chains specified  

> help help:user/tools/matchmaker.html

> matchmaker #5/B & sel to #6.1/A & sel pairing ss

No 'to' chains specified  

> select #6.4/A:201

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

> select #6.4/A:206

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

> select add #5/B:218

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

> select up

283 atoms, 283 bonds, 35 residues, 2 models selected  

> matchmaker #5/B & sel to #6.1/A & sel pairing ss

No 'to' chains specified  

> matchmaker #!5 & sel to #6.1 & sel

No 'to' model specified  

> matchmaker #!5 to #6.1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 20240927-jdt8-6-process1_refine_071.pdb -1 -1 0 sym 9, chain A
(#6.1) with 6xiu, chain B (#5), sequence alignment score = 1240.7  
RMSD between 206 pruned atom pairs is 0.838 angstroms; (across all 248 pairs:
1.673)  
  

> matchmaker #!5 to #6.4

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 20240927-jdt8-6-process1_refine_071.pdb 0 0 0 sym 10, chain A
(#6.4) with 6xiu, chain B (#5), sequence alignment score = 1240.7  
RMSD between 206 pruned atom pairs is 0.838 angstroms; (across all 248 pairs:
1.673)  
  

> open 6xiu

6xiu title:  
ETEC Rns bound to a potential inhibitor, decanoic acid [more info...]  
  
Chain information for 6xiu #8  
---  
Chain | Description | UniProt  
A B | Regulatory protein Rns | RNS_ECOLX 1-265  
  
Non-standard residues in 6xiu #8  
---  
DKA — decanoic acid  
  
6xiu mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> ui mousemode right "clip rotate"

> hide #!2 models

> ui mousemode right select

> select #8/A:218

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

> select add #1/A:216

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

> select up

291 atoms, 291 bonds, 36 residues, 2 models selected  

> select up

2635 atoms, 2674 bonds, 324 residues, 2 models selected  

> select down

291 atoms, 291 bonds, 36 residues, 2 models selected  

> matchmaker #!5 to #6.4

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 20240927-jdt8-6-process1_refine_071.pdb 0 0 0 sym 10, chain A
(#6.4) with 6xiu, chain B (#5), sequence alignment score = 1240.7  
RMSD between 206 pruned atom pairs is 0.838 angstroms; (across all 248 pairs:
1.673)  
  

> matchmaker #!5 to #6.4

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 20240927-jdt8-6-process1_refine_071.pdb 0 0 0 sym 10, chain A
(#6.4) with 6xiu, chain B (#5), sequence alignment score = 1240.7  
RMSD between 206 pruned atom pairs is 0.838 angstroms; (across all 248 pairs:
1.673)  
  

> matchmaker #!8 to #1

Computing secondary structure  
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 20240927-jdt8-6-process1_refine_071.pdb, chain A (#1) with 6xiu,
chain B (#8), sequence alignment score = 1240.7  
RMSD between 206 pruned atom pairs is 0.838 angstroms; (across all 248 pairs:
1.673)  
  

> select #8/A:112

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

> select up

39 atoms, 38 bonds, 5 residues, 1 model selected  

> select up

1314 atoms, 1334 bonds, 161 residues, 1 model selected  

> select up

1318 atoms, 1337 bonds, 162 residues, 1 model selected  

> select up

2015 atoms, 2045 bonds, 246 residues, 1 model selected  

> select up

2027 atoms, 2056 bonds, 247 residues, 1 model selected  

> select up

4068 atoms, 4126 bonds, 496 residues, 1 model selected  

> select up

10386 atoms, 10372 bonds, 1406 residues, 11 models selected  

> select down

4068 atoms, 4126 bonds, 496 residues, 1 model selected  

> select down

2027 atoms, 2056 bonds, 247 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

Drag select of 28 atoms, 99 residues, 24 bonds  

> select up

925 atoms, 934 bonds, 113 residues, 1 model selected  

> select up

2015 atoms, 2045 bonds, 246 residues, 1 model selected  

> select up

2027 atoms, 2056 bonds, 247 residues, 1 model selected  

> select up

4068 atoms, 4126 bonds, 496 residues, 1 model selected  

> select down

2027 atoms, 2056 bonds, 247 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

Drag select of 15 atoms, 12 bonds  

> select up

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

> select up

141 atoms, 140 bonds, 18 residues, 1 model selected  

> hide sel atoms

> select #8/B:117

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

> select up

82 atoms, 81 bonds, 10 residues, 1 model selected  

> select up

1314 atoms, 1334 bonds, 161 residues, 1 model selected  

> select up

1332 atoms, 1351 bonds, 164 residues, 1 model selected  

> select up

2029 atoms, 2059 bonds, 248 residues, 1 model selected  

> select up

2041 atoms, 2070 bonds, 249 residues, 1 model selected  

> select up

4068 atoms, 4126 bonds, 496 residues, 1 model selected  

> select up

10386 atoms, 10372 bonds, 1406 residues, 11 models selected  

> select down

4068 atoms, 4126 bonds, 496 residues, 1 model selected  

> color #8 #4583cf59

> select clear

> preset cartoons/nucleotides cylinders/stubs

Using preset: Cartoons/Nucleotides / Cylinders/Stubs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> undo

> select #1,8 :14,17,20,75

114 atoms, 102 bonds, 15 residues, 2 models selected  

> show sel atoms

> select #1,8b :14,17,20,75

Expected an objects specifier or a keyword  

> select #1,8/b :14,17,20,75

37 atoms, 34 bonds, 4 residues, 1 model selected  
Drag select of 35 atoms, 33 bonds  

> select up

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

> select up

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

> hide sel atoms

> save "/Users/jessicatolbert/OneDrive - Dartmouth College/Lab-
> Report/figures/dimerization-ch/WT-Y139E-overlay-seperateWTPDB.cxs"

> select #1/A:71

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

> select up

75 atoms, 76 bonds, 9 residues, 1 model selected  

> select up

754 atoms, 764 bonds, 92 residues, 1 model selected  

> select down

75 atoms, 76 bonds, 9 residues, 1 model selected  

> hide sel atoms

[Repeated 1 time(s)]

> select #8/B:73

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

> select up

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

> select up

715 atoms, 725 bonds, 87 residues, 1 model selected  

> select down

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

> select up

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

> select up

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

> hide sel atoms

> show sel atoms

[Repeated 1 time(s)]

> color sel byhetero

> select #1/a,8/b :14,17,20,71,75

2075 atoms, 2104 bonds, 1 pseudobond, 255 residues, 2 models selected  

> select #1/a :14,17,20,71,75

49 atoms, 46 bonds, 5 residues, 1 model selected  

> show sel atoms

> select clear

> select up

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

> select up

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

> select up

2041 atoms, 2070 bonds, 249 residues, 1 model selected  

> select up

4068 atoms, 4126 bonds, 496 residues, 1 model selected  

> select down

2041 atoms, 2070 bonds, 249 residues, 1 model selected  

> select down

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

> color sel byhetero

> select clear

> select #1/A:169

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

> select #8/B:168

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

> select #8/B:83

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

> select up

131 atoms, 132 bonds, 16 residues, 1 model selected  

> select up

715 atoms, 725 bonds, 87 residues, 1 model selected  

> select up

726 atoms, 735 bonds, 88 residues, 1 model selected  

> select up

2029 atoms, 2059 bonds, 248 residues, 1 model selected  

> select up

2041 atoms, 2070 bonds, 249 residues, 1 model selected  

> select up

4068 atoms, 4126 bonds, 496 residues, 1 model selected  

> select up

10386 atoms, 10372 bonds, 1406 residues, 11 models selected  

> select down

4068 atoms, 4126 bonds, 496 residues, 1 model selected  

> preset cartoons/nucleotides cylinders/stubs

Using preset: Cartoons/Nucleotides / Cylinders/Stubs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> undo

> nucleotides sel tube/slab shape box

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> cartoon style sel modeHelix tube sides 20

> select clear

> select #1/L:303@C03

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

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

> select down

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

> hide sel atoms

> save "/Users/jessicatolbert/OneDrive - Dartmouth College/Lab-
> Report/figures/dimerization-ch/WT-Y139E-overlay-seperateWTPDB.cxs"

——— End of log from Mon Mar 31 11:54:25 2025 ———

opened ChimeraX session  

> hide #!8 models

> show #!8 models

> ui tool show "Crystal Contacts"

> crystalcontacts delete #1

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> close #5

> crystalcontacts #1

4 pairs of asymmetric units of 20240927-jdt8-6-process1_refine_071.pdb contact
at distance 3.0 A

    
    
      Atoms  MTRIX  SMTRY   Unit cell  MTRIXref  Copies
        12     0      9     -1 -1  0      0         1
        11     0      5      0  0 -1      0         1
        11     0      4      0  0  0      0         1
         6     0     10      0  0  0      0         1
    

  

> crystalcontacts #8

8 pairs of asymmetric units of 6xiu contact at distance 3.0 A

    
    
      Atoms  MTRIX  SMTRY   Unit cell  MTRIXref  Copies
         6     0      0      1  0  0      0         1
         5     0      1     -1  0  0      0         1
         5     0      1     -1  0 -1      0         1
         5     0      0     -1  0  0      0         1
         4     0      2     -1  0  0      0         1
         4     0      2     -1 -1  0      0         1
         4     0      2     -2 -1  0      0         1
         2     0      2     -2  0  0      0         1
    

  

> hide #!6 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!6 models

> hide #!6 models

> hide #!8 models

> show #!8 models

> show #!6 models

> hide #!6 models

> show #!4 models

> hide #!4 models

> close #2-4

> hide #!8 models

> show #!8 models

> ui mousemode right select

> select #8/B:219

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

> select add #1/A:213

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

> select up

291 atoms, 291 bonds, 36 residues, 2 models selected  

> ui tool show Matchmaker

> matchmaker #!8#!5.1-4#!6.1-8 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 20240927-jdt8-6-process1_refine_071.pdb, chain A (#1) with 6xiu,
chain B (#8), sequence alignment score = 1240.7  
RMSD between 206 pruned atom pairs is 0.838 angstroms; (across all 248 pairs:
1.673)  
  
Matchmaker 20240927-jdt8-6-process1_refine_071.pdb, chain A (#1) with
20240927-jdt8-6-process1_refine_071.pdb -1 -1 0 sym 9, chain A (#5.1),
sequence alignment score = 1295  
RMSD between 255 pruned atom pairs is 0.000 angstroms; (across all 255 pairs:
0.000)  
  
Matchmaker 20240927-jdt8-6-process1_refine_071.pdb, chain A (#1) with
20240927-jdt8-6-process1_refine_071.pdb 0 0 -1 sym 5, chain A (#5.2), sequence
alignment score = 1295  
RMSD between 255 pruned atom pairs is 0.000 angstroms; (across all 255 pairs:
0.000)  
  
Matchmaker 20240927-jdt8-6-process1_refine_071.pdb, chain A (#1) with
20240927-jdt8-6-process1_refine_071.pdb 0 0 0 sym 4, chain A (#5.3), sequence
alignment score = 1295  
RMSD between 255 pruned atom pairs is 0.000 angstroms; (across all 255 pairs:
0.000)  
  
Matchmaker 20240927-jdt8-6-process1_refine_071.pdb, chain A (#1) with
20240927-jdt8-6-process1_refine_071.pdb 0 0 0 sym 10, chain A (#5.4), sequence
alignment score = 1295  
RMSD between 255 pruned atom pairs is 0.000 angstroms; (across all 255 pairs:
0.000)  
  
Matchmaker 20240927-jdt8-6-process1_refine_071.pdb, chain A (#1) with 6xiu 1 0
0 sym 0, chain B (#6.1), sequence alignment score = 1240.7  
RMSD between 206 pruned atom pairs is 0.838 angstroms; (across all 248 pairs:
1.673)  
  
Matchmaker 20240927-jdt8-6-process1_refine_071.pdb, chain A (#1) with 6xiu -1
0 0 sym 1, chain B (#6.2), sequence alignment score = 1240.7  
RMSD between 206 pruned atom pairs is 0.838 angstroms; (across all 248 pairs:
1.673)  
  
Matchmaker 20240927-jdt8-6-process1_refine_071.pdb, chain A (#1) with 6xiu -1
0 -1 sym 1, chain B (#6.3), sequence alignment score = 1240.7  
RMSD between 206 pruned atom pairs is 0.838 angstroms; (across all 248 pairs:
1.673)  
  
Matchmaker 20240927-jdt8-6-process1_refine_071.pdb, chain A (#1) with 6xiu -1
0 0 sym 0, chain B (#6.4), sequence alignment score = 1240.7  
RMSD between 206 pruned atom pairs is 0.838 angstroms; (across all 248 pairs:
1.673)  
  
Matchmaker 20240927-jdt8-6-process1_refine_071.pdb, chain A (#1) with 6xiu -1
0 0 sym 2, chain B (#6.5), sequence alignment score = 1240.7  
RMSD between 206 pruned atom pairs is 0.838 angstroms; (across all 248 pairs:
1.673)  
  
Matchmaker 20240927-jdt8-6-process1_refine_071.pdb, chain A (#1) with 6xiu -1
-1 0 sym 2, chain B (#6.6), sequence alignment score = 1240.7  
RMSD between 206 pruned atom pairs is 0.838 angstroms; (across all 248 pairs:
1.673)  
  
Matchmaker 20240927-jdt8-6-process1_refine_071.pdb, chain A (#1) with 6xiu -2
-1 0 sym 2, chain B (#6.7), sequence alignment score = 1240.7  
RMSD between 206 pruned atom pairs is 0.838 angstroms; (across all 248 pairs:
1.673)  
  
Matchmaker 20240927-jdt8-6-process1_refine_071.pdb, chain A (#1) with 6xiu -2
0 0 sym 2, chain B (#6.8), sequence alignment score = 1240.7  
RMSD between 206 pruned atom pairs is 0.838 angstroms; (across all 248 pairs:
1.673)  
  

> matchmaker #!8#!5.1-4#!6.1-8 & sel to #1 & sel

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 20240927-jdt8-6-process1_refine_071.pdb, chain A (#1) with 6xiu,
chain B (#8), sequence alignment score = 80.6  
RMSD between 16 pruned atom pairs is 0.328 angstroms; (across all 16 pairs:
0.328)  
  

> matchmaker #!8#!5.1-4#!6.1-8 & sel to #1 & sel

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 20240927-jdt8-6-process1_refine_071.pdb, chain A (#1) with 6xiu,
chain B (#8), sequence alignment score = 80.6  
RMSD between 16 pruned atom pairs is 0.328 angstroms; (across all 16 pairs:
0.328)  
  

> matchmaker #!8#!5.1-4#!6.1-8 & sel to #1 & sel

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 20240927-jdt8-6-process1_refine_071.pdb, chain A (#1) with 6xiu,
chain B (#8), sequence alignment score = 80.6  
RMSD between 16 pruned atom pairs is 0.328 angstroms; (across all 16 pairs:
0.328)  
  

> select clear

> hide #!1 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!5 models

> hide #!5 models

> show #!6 models

> hide #!6 models

> show #!1 models

> show #!6 models

> hide #!6 models

> crystalcontacts delete #8

> crystalcontacts delete #1

> crystalcontacts #1

4 pairs of asymmetric units of 20240927-jdt8-6-process1_refine_071.pdb contact
at distance 3.0 A

    
    
      Atoms  MTRIX  SMTRY   Unit cell  MTRIXref  Copies
        12     0      9     -1 -1  0      0         1
        11     0      5      0  0 -1      0         1
        11     0      4      0  0  0      0         1
         6     0     10      0  0  0      0         1
    

  

> crystalcontacts #8

8 pairs of asymmetric units of 6xiu contact at distance 3.0 A

    
    
      Atoms  MTRIX  SMTRY   Unit cell  MTRIXref  Copies
         6     0      0      1  0  0      0         1
         5     0      1     -1  0  0      0         1
         5     0      1     -1  0 -1      0         1
         5     0      0     -1  0  0      0         1
         4     0      2     -1  0  0      0         1
         4     0      2     -1 -1  0      0         1
         4     0      2     -2 -1  0      0         1
         2     0      2     -2  0  0      0         1
    

  

> hide #!3 models

> hide #!8 models

Drag select of 49 atoms, 42 bonds, 140 residues  
Drag select of 14 residues  
Drag select of 31 atoms, 25 bonds, 152 residues  

> select up

2236 atoms, 1146 bonds, 277 residues, 3 models selected  

> select up

2244 atoms, 1154 bonds, 277 residues, 3 models selected  

> select up

2916 atoms, 2943 bonds, 360 residues, 3 models selected  

> select up

5499 atoms, 5570 bonds, 679 residues, 3 models selected  

> select up

5547 atoms, 5617 bonds, 686 residues, 3 models selected  

> select up

6253 atoms, 6334 bonds, 771 residues, 3 models selected  

> select up

6575 atoms, 6344 bonds, 1083 residues, 3 models selected  

> select up

6750 atoms, 6360 bonds, 1242 residues, 3 models selected  

> select up

9000 atoms, 8480 bonds, 1656 residues, 4 models selected  

> select up

9000 atoms, 8480 bonds, 1656 residues, 5 models selected  

> select down

9000 atoms, 8480 bonds, 1656 residues, 4 models selected  

> select down

6750 atoms, 6360 bonds, 1242 residues, 3 models selected  

> delete sel

Drag select of 152 atoms, 578 residues, 2 pseudobonds, 124 bonds  

> select clear

Drag select of 152 atoms, 578 residues, 2 pseudobonds, 124 bonds  

> select clear

Drag select of 152 atoms, 578 residues, 2 pseudobonds, 124 bonds  

> save "/Users/jessicatolbert/OneDrive - Dartmouth College/Lab-
> Report/figures/dimerization-ch/PDBs/RnsY139E-crystallographic-dimer.cxs"

——— End of log from Mon Mar 31 12:55:41 2025 ———

opened ChimeraX session  

> hide #!2 models

> show #!2 models

> hide #!2.4 models

> show #!2.4 models

> hide #!2.4 models

> show #!2.4 models

> show #!3 models

> show #!8 models

> hide #!2.4 models

> show #!2.4 models

> open /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-ch/PDBs/WTRns-
> crystallographic-dimer.pdb

Summary of feedback from opening
/Users/jessicatolbert/Library/CloudStorage/OneDrive-DartmouthCollege/Lab-
Report/figures/dimerization-ch/PDBs/WTRns-crystallographic-dimer.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 78 TYR A 92 1 15  
Start residue of secondary structure not found: HELIX 2 2 MET A 105 ARG A 107
1 3  
Start residue of secondary structure not found: HELIX 3 3 LYS A 116 LYS A 123
1 8  
Start residue of secondary structure not found: HELIX 4 4 SER A 131 LEU A 140
1 10  
Start residue of secondary structure not found: HELIX 5 5 ILE A 141 LYS A 143
1 3  
20 messages similar to the above omitted  
  
Chain information for WTRns-crystallographic-dimer.pdb  
---  
Chain | Description  
4.1/A | No description available  
4.2/B | No description available  
  
Computing secondary structure  
[Repeated 1 time(s)]

> close #4#4.1-2

> hide #!1 models

> hide #!2 models

> hide #!2.4 models

> hide #!3 models

> ui mousemode right select

Drag select of 49 atoms, 138 residues, 45 bonds  

> select up

1091 atoms, 1102 bonds, 131 residues, 1 model selected  

> select up

1097 atoms, 1108 bonds, 131 residues, 1 model selected  

> select up

1273 atoms, 1291 bonds, 152 residues, 1 model selected  

> select up

2041 atoms, 2070 bonds, 249 residues, 1 model selected  

> select up

4068 atoms, 4126 bonds, 496 residues, 1 model selected  

> select up

6318 atoms, 6246 bonds, 910 residues, 4 models selected  

> select up

6318 atoms, 6246 bonds, 910 residues, 4 models selected  

> select up

6318 atoms, 6246 bonds, 910 residues, 4 models selected  

> select up

6318 atoms, 6246 bonds, 910 residues, 4 models selected  

> show sel & #!8 cartoons

> select clear

> select #8/A:222

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

> select up

162 atoms, 162 bonds, 20 residues, 1 model selected  

> select up

1314 atoms, 1334 bonds, 161 residues, 1 model selected  

> select down

162 atoms, 162 bonds, 20 residues, 1 model selected  

> show #!1 models

> select add #1/A:222

170 atoms, 169 bonds, 21 residues, 2 models selected  

> select up

187 atoms, 186 bonds, 23 residues, 2 models selected  

> select up

2635 atoms, 2674 bonds, 324 residues, 2 models selected  

> select down

187 atoms, 186 bonds, 23 residues, 2 models selected  

> select add #1/A:214

195 atoms, 193 bonds, 24 residues, 2 models selected  

> select up

316 atoms, 316 bonds, 39 residues, 2 models selected  

> ui tool show Matchmaker

> matchmaker #!8#!2.4#!3.1-8 & sel to #1 & sel

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 20240927-jdt8-6-process1_refine_071.pdb, chain A (#1) with 6xiu,
chain A (#8), sequence alignment score = 95.1  
RMSD between 19 pruned atom pairs is 0.308 angstroms; (across all 19 pairs:
0.308)  
  

> select clear

> ui tool show "Crystal Contacts"

> crystalcontacts #1

4 pairs of asymmetric units of 20240927-jdt8-6-process1_refine_071.pdb contact
at distance 3.0 A

    
    
      Atoms  MTRIX  SMTRY   Unit cell  MTRIXref  Copies
        12     0      9     -1 -1  0      0         1
        11     0      5      0  0 -1      0         1
        11     0      4      0  0  0      0         1
         6     0     10      0  0  0      0         1
    

  

> crystalcontacts #8

8 pairs of asymmetric units of 6xiu contact at distance 3.0 A

    
    
      Atoms  MTRIX  SMTRY   Unit cell  MTRIXref  Copies
         6     0      0      1  0  0      0         1
         5     0      1     -1  0  0      0         1
         5     0      1     -1  0 -1      0         1
         5     0      0     -1  0  0      0         1
         4     0      2     -1  0  0      0         1
         4     0      2     -1 -1  0      0         1
         4     0      2     -2 -1  0      0         1
         2     0      2     -2  0  0      0         1
    

  

> hide #!3 models

> hide #!2 models

Drag select of 23 atoms, 72 residues, 21 bonds  

> select up

572 atoms, 573 bonds, 70 residues, 1 model selected  

> select up

579 atoms, 580 bonds, 70 residues, 1 model selected  

> select up

770 atoms, 777 bonds, 93 residues, 1 model selected  

> select up

2041 atoms, 2070 bonds, 249 residues, 1 model selected  

> select up

4068 atoms, 4126 bonds, 496 residues, 1 model selected  

> select down

2041 atoms, 2070 bonds, 249 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> show #!2 models

Drag select of 32 atoms, 28 bonds, 41 residues  

> select up

357 atoms, 352 bonds, 43 residues, 1 model selected  

> select up

656 atoms, 658 bonds, 79 residues, 1 model selected  

> select up

2087 atoms, 2115 bonds, 256 residues, 1 model selected  

> select up

2093 atoms, 2120 bonds, 257 residues, 1 model selected  

> select up

2250 atoms, 2120 bonds, 414 residues, 1 model selected  

> select up

9000 atoms, 8480 bonds, 1656 residues, 4 models selected  

> select down

2250 atoms, 2120 bonds, 414 residues, 1 model selected  

> hide sel cartoons

> show sel cartoons

> hide sel cartoons

> hide sel atoms

Drag select of 33 atoms, 30 bonds, 126 residues  
Drag select of 23 atoms, 20 bonds, 40 residues  

> select up

1269 atoms, 1263 bonds, 156 residues, 2 models selected  

> select up

1280 atoms, 1275 bonds, 156 residues, 2 models selected  

> select up

1895 atoms, 1907 bonds, 230 residues, 2 models selected  

> select up

4176 atoms, 4230 bonds, 514 residues, 2 models selected  

> select up

4500 atoms, 4240 bonds, 828 residues, 2 models selected  

> select up

9000 atoms, 8480 bonds, 1656 residues, 4 models selected  

> select up

9000 atoms, 8480 bonds, 1656 residues, 5 models selected  

> select down

9000 atoms, 8480 bonds, 1656 residues, 4 models selected  

> select down

4500 atoms, 4240 bonds, 828 residues, 2 models selected  

> hide sel atoms

> hide sel cartoons

> hide #!1 models

> hide #!2 models

> show #!3 models

Drag select of 12 residues  
Drag select of 75 atoms, 67 bonds, 912 residues, 2 pseudobonds  
Drag select of 26 residues  
Drag select of 10 atoms, 6 bonds, 364 residues, 1 pseudobonds  

> select up

8603 atoms, 7624 bonds, 3 pseudobonds, 1048 residues, 10 models selected  

> select up

8620 atoms, 7644 bonds, 3 pseudobonds, 1048 residues, 10 models selected  

> select up

10913 atoms, 11059 bonds, 3 pseudobonds, 1324 residues, 10 models selected  

> select up

21544 atoms, 21862 bonds, 3 pseudobonds, 2631 residues, 10 models selected  

> select up

21548 atoms, 21865 bonds, 3 pseudobonds, 2632 residues, 10 models selected  

> select up

22245 atoms, 22573 bonds, 3 pseudobonds, 2716 residues, 10 models selected  

> select up

22353 atoms, 22672 bonds, 3 pseudobonds, 2725 residues, 10 models selected  

> select up

28476 atoms, 28882 bonds, 6 pseudobonds, 3472 residues, 10 models selected  

> select down

22353 atoms, 22672 bonds, 3 pseudobonds, 2725 residues, 10 models selected  

> hide sel cartoons

> hide sel atoms

Drag select of 50 atoms, 44 bonds, 120 residues  
Drag select of 56 residues  
Drag select of 158 residues  
Drag select of 17 residues  

> select up

25099 atoms, 23647 bonds, 3 pseudobonds, 3059 residues, 11 models selected  

> select up

26436 atoms, 26800 bonds, 3 pseudobonds, 3221 residues, 11 models selected  

> select up

30467 atoms, 30905 bonds, 3 pseudobonds, 3716 residues, 11 models selected  

> select up

30503 atoms, 30938 bonds, 3 pseudobonds, 3719 residues, 11 models selected  

> select up

32544 atoms, 33008 bonds, 6 pseudobonds, 3968 residues, 11 models selected  

> select down

30503 atoms, 30938 bonds, 3 pseudobonds, 3719 residues, 11 models selected  

> hide sel atoms

> hide sel cartoons

> show #!2 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> hide #!8 models

> save /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-
> ch/PDBs/RnsY139E-crystallographic-dimer.pdb displayedOnly true

> open /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-
> ch/PDBs/RnsY139E-crystallographic-dimer.pdb

Summary of feedback from opening
/Users/jessicatolbert/Library/CloudStorage/OneDrive-DartmouthCollege/Lab-
Report/figures/dimerization-ch/PDBs/RnsY139E-crystallographic-dimer.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 78 TYR A 92 1 15  
Start residue of secondary structure not found: HELIX 2 2 MET A 105 ARG A 107
1 3  
Start residue of secondary structure not found: HELIX 3 3 LYS A 116 LYS A 123
1 8  
Start residue of secondary structure not found: HELIX 4 4 SER A 131 LEU A 140
1 10  
Start residue of secondary structure not found: HELIX 5 5 ILE A 141 LYS A 143
1 3  
70 messages similar to the above omitted  
  
Chain information for RnsY139E-crystallographic-dimer.pdb  
---  
Chain | Description  
4.1/A 4.2/A | No description available  
4.3/B | No description available  
  

> hide #!2 models

> hide #!1 models

> show #!1 models

> show #!2 models

> hide #!4.1 models

> show #!4.1 models

> hide #!4.2 models

> show #!4.2 models

> hide #!4.3 models

> show #!4.3 models

> hide #!4.3 models

> show #!4.3 models

> close #4#4.1-3

Drag select of 152 atoms, 578 residues, 2 pseudobonds, 124 bonds  

> save /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-
> ch/PDBs/RnsY139E-crystallographic-dimer.pdb models #1 displayedOnly true
> selectedOnly true

> open /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-
> ch/PDBs/RnsY139E-crystallographic-dimer.pdb format pdb

Summary of feedback from opening
/Users/jessicatolbert/Library/CloudStorage/OneDrive-DartmouthCollege/Lab-
Report/figures/dimerization-ch/PDBs/RnsY139E-crystallographic-dimer.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 78 TYR A 92 1 15  
Start residue of secondary structure not found: HELIX 2 2 MET A 105 ARG A 107
1 3  
Start residue of secondary structure not found: HELIX 3 3 LYS A 116 LYS A 123
1 8  
Start residue of secondary structure not found: HELIX 4 4 SER A 131 LEU A 140
1 10  
Start residue of secondary structure not found: HELIX 5 5 ILE A 141 LYS A 143
1 3  
20 messages similar to the above omitted  
  
Chain information for RnsY139E-crystallographic-dimer.pdb #4  
---  
Chain | Description  
A | No description available  
  

> open /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-
> ch/PDBs/RnsY139E-crystallographic-dimer.pdb

Summary of feedback from opening
/Users/jessicatolbert/Library/CloudStorage/OneDrive-DartmouthCollege/Lab-
Report/figures/dimerization-ch/PDBs/RnsY139E-crystallographic-dimer.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 78 TYR A 92 1 15  
Start residue of secondary structure not found: HELIX 2 2 MET A 105 ARG A 107
1 3  
Start residue of secondary structure not found: HELIX 3 3 LYS A 116 LYS A 123
1 8  
Start residue of secondary structure not found: HELIX 4 4 SER A 131 LEU A 140
1 10  
Start residue of secondary structure not found: HELIX 5 5 ILE A 141 LYS A 143
1 3  
20 messages similar to the above omitted  
  
Chain information for RnsY139E-crystallographic-dimer.pdb #5  
---  
Chain | Description  
A | No description available  
  

> hide #!4 models

> show #!4 models

> hide #!4 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> close #4-5

> save /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-
> ch/PDBs/RnsY139E-crystallographic-dimer.pdb selectedOnly true

> open /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-
> ch/PDBs/RnsY139E-crystallographic-dimer.pdb

Chain information for RnsY139E-crystallographic-dimer.pdb  
---  
Chain | Description  
4.1/A 4.2/A | No description available  
  

> open /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-ch/PDBs/WTRns-
> crystallographic-dimer.pdb

Summary of feedback from opening
/Users/jessicatolbert/Library/CloudStorage/OneDrive-DartmouthCollege/Lab-
Report/figures/dimerization-ch/PDBs/WTRns-crystallographic-dimer.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 78 TYR A 92 1 15  
Start residue of secondary structure not found: HELIX 2 2 MET A 105 ARG A 107
1 3  
Start residue of secondary structure not found: HELIX 3 3 LYS A 116 LYS A 123
1 8  
Start residue of secondary structure not found: HELIX 4 4 SER A 131 LEU A 140
1 10  
Start residue of secondary structure not found: HELIX 5 5 ILE A 141 LYS A 143
1 3  
20 messages similar to the above omitted  
  
Chain information for WTRns-crystallographic-dimer.pdb  
---  
Chain | Description  
5.1/A | No description available  
5.2/B | No description available  
  
Computing secondary structure  

> save /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-ch/PDBs/crystallographic-
> dimers.cxs

> select clear

> hide #!1 models

> hide #!2 models

> hide #!4 models

> show #!4 models

> hide #!5.2 models

> hide #!5.1 models

> show #!5.1 models

> show #!5.2 models

> hide #!4.2 models

> show #!4.2 models

> hide #!4.1 models

> show #!4.1 models

Drag select of 28 residues  

> select :139

303 atoms, 296 bonds, 27 residues, 18 models selected  

> show sel & #!4.1-2#!5.1-2 atoms

> open "/Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/2022 Rns Pocket Paper/2024_Rns-Pocket-Paper-
> Depositions/R75A/20210916_RnsR75A_jdt6_v4_refine_102.pdb"

Chain information for 20210916_RnsR75A_jdt6_v4_refine_102.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  
Drag select of 28 residues  

> select #6/B:211

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

> select up

154 atoms, 154 bonds, 19 residues, 1 model selected  

> select #6/A:216

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

> select add #5.1/A:207

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

> select up

283 atoms, 283 bonds, 35 residues, 2 models selected  

> select up

2636 atoms, 2676 bonds, 324 residues, 2 models selected  

> select down

283 atoms, 283 bonds, 35 residues, 2 models selected  

> ui tool show Matchmaker

> matchmaker #!6 & sel to #5.1 & sel

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 WTRns-crystallographic-dimer.pdb, chain A (#5.1) with
20210916_RnsR75A_jdt6_v4_refine_102.pdb, chain A (#6), sequence alignment
score = 80.6  
RMSD between 16 pruned atom pairs is 0.161 angstroms; (across all 16 pairs:
0.161)  
  

> hide #!4 models

> show #!4 models

> hide #!5 models

> show #!5 models

> hide #!6 models

> show #!6 models

Drag select of 25 residues  

> select :139

327 atoms, 320 bonds, 29 residues, 19 models selected  

> show sel & #!6#!4.1-2#!5.1-2 atoms

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> save /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-
> ch/PDBs/WTRns-R75A-RnsY139E-crystallographic-dimer.cxs

——— End of log from Tue Apr 1 10:44:55 2025 ———

opened ChimeraX session  

> close

> open /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-ch/PDBs/wtrns-cryst-dimer-
> combine.pdb /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-ch/PDBs/rnsy139e-cryst-
> dimer-combine.pdb

Summary of feedback from opening
/Users/jessicatolbert/Library/CloudStorage/OneDrive-DartmouthCollege/Lab-
Report/figures/dimerization-ch/PDBs/rnsy139e-cryst-dimer-combine.pdb  
---  
notes | Combining 2 symmetry atoms into HOH /S:87 O  
Combining 2 symmetry atoms into HOH /S:121 O  
Combining 2 symmetry atoms into HOH /S:14 O  
Combining 2 symmetry atoms into HOH /S:75 O  
Combining 2 symmetry atoms into HOH /T:20 O  
5 messages similar to the above omitted  
  
Chain information for wtrns-cryst-dimer-combine.pdb #1  
---  
Chain | Description  
A B | No description available  
  
Chain information for rnsy139e-cryst-dimer-combine.pdb #2  
---  
Chain | Description  
A B C D | No description available  
  

> matchmaker #1 to #2 showAlignment true

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 rnsy139e-cryst-dimer-combine.pdb, chain A (#2) with wtrns-cryst-
dimer-combine.pdb, chain A (#1), sequence alignment score = 1022  
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: wtrns-cryst-dimer-combine.pdb
#1/A, rnsy139e-cryst-dimer-combine.pdb #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 202 pruned atom pairs is 0.806 angstroms; (across all 246 pairs:
1.790)  
  

> ui tool show "Render/Select by Attribute"

> color byattribute r:seq_rmsd #!1-2 target sabc palette
> 0.3,blue:0.676478,white:1,red noValueColor #275631

12426 atoms, 1530 residues, atom seq_rmsd range 0.113 to 6.3  

> ui tool show "Render/Select by Attribute"

> color byattribute r:seq_rmsd #!1-2 target sabc palette
> 0.113059,blue:3.20778,white:6.3025,red

12426 atoms, 1530 residues, atom seq_rmsd range 0.113 to 6.3  

> 1

Unknown command: 1  

> color byattribute r:seq_rmsd #!1-2 target sabc palette
> 0,blue:0.5,white:1,red noValueColor #78697b

12426 atoms, 1530 residues, atom seq_rmsd range 0.113 to 6.3  

> ui tool show "Render/Select by Attribute"

> key blue-white-red :0.0 :0.5 :1.0 showTool true

> ui mousemode right "color key"

> key blue-white-red :0.0 :0.5 :1.0 white:

> key blue-white-red :0.0 :0.5 :1.0

> ui mousemode right translate

> color byattribute r:seq_rmsd #!1-2 target sabc palette
> 0,blue:0.5,white:1,red noValueColor #78697b

12426 atoms, 1530 residues, atom seq_rmsd range 0.113 to 6.3  

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> show #!2 models

> show #!1 models

> ui tool show "Render/Select by Attribute"

> color byattribute r:seq_rmsd #!2 target sabc palette
> 0.113059,blue:3.20778,white:6.3025,red

8358 atoms, 1034 residues, atom seq_rmsd range 0.113 to 6.3  

> color byattribute r:seq_rmsd #!2 target sabc palette
> 0.113059,blue:3.20778,white:6.3025,red

8358 atoms, 1034 residues, atom seq_rmsd range 0.113 to 6.3  

> matchmaker #2 to #1 showAlignment true

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 wtrns-cryst-dimer-combine.pdb, chain A (#1) with rnsy139e-cryst-
dimer-combine.pdb, chain A (#2), sequence alignment score = 1022  
Alignment identifier is 2  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2  
Hiding conservation header for alignment 2  
Chains used in RMSD evaluation for alignment 2: wtrns-cryst-dimer-combine.pdb
#1/A, rnsy139e-cryst-dimer-combine.pdb #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  
RMSD between 202 pruned atom pairs is 0.806 angstroms; (across all 246 pairs:
1.790)  
  

> ui tool show Toolbar

> ui tool show "Render/Select by Attribute"

> color byattribute r:seq_rmsd #!1-2 target sabc palette
> 0.113059,blue:3.20778,white:6.3025,red

12426 atoms, 1530 residues, atom seq_rmsd range 0.113 to 6.3  

> key blue-white-red :0.11 :3.21 :6.30 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> 6

Unknown command: 6  

> key blue-white-red :0 :3 :6 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> color byattribute r:seq_rmsd #!1-2 target sabc palette 0,blue:3,white:6,red

12426 atoms, 1530 residues, atom seq_rmsd range 0.113 to 6.3  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> ui tool show Matchmaker

> ui tool show "Render/Select by Attribute"

[Repeated 1 time(s)]

> key blue-white-red :0 :3 :6 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> color byattribute r:seq_rmsd #!2 target sabc palette 0,blue:3,white:6,red

8358 atoms, 1034 residues, atom seq_rmsd range 0.113 to 6.3  

> color byattribute r:seq_rmsd #!2 target sabc palette 0,blue:3,white:6,red

8358 atoms, 1034 residues, atom seq_rmsd range 0.113 to 6.3  

> select add #2

8358 atoms, 8460 bonds, 4 pseudobonds, 1034 residues, 2 models selected  

> cartoon byattribute r:seq_rmsd #!1 & sel 0.113059:0.25 6.3025:2
> noValueRadius 0.1

No structures with polymeric residues specified  

> cartoon byattribute r:seq_rmsd #!1 & sel 0.113059:0.25 6.3025:2
> noValueRadius 0.1

No structures with polymeric residues specified  

> cartoon byattribute r:seq_rmsd #!1 & sel 0.113059:0.25 6.3025:2
> noValueRadius 0.1

No structures with polymeric residues specified  

> select #!1::seq_rmsd>=0.0 & ::seq_rmsd<=6.0

2008 atoms, 2037 bonds, 1 pseudobond, 245 residues, 2 models selected  

> select #!1::seq_rmsd>=0.0 & ::seq_rmsd<=6.0

2008 atoms, 2037 bonds, 1 pseudobond, 245 residues, 2 models selected  

> ui mousemode right rotate

> ui mousemode right select

> select clear

> matchmaker #2 to #1 showAlignment true

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 wtrns-cryst-dimer-combine.pdb, chain A (#1) with rnsy139e-cryst-
dimer-combine.pdb, chain A (#2), sequence alignment score = 1022  
Alignment identifier is 3  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3  
Hiding conservation header for alignment 3  
Chains used in RMSD evaluation for alignment 3: wtrns-cryst-dimer-combine.pdb
#1/A, rnsy139e-cryst-dimer-combine.pdb #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3  
RMSD between 202 pruned atom pairs is 0.806 angstroms; (across all 246 pairs:
1.790)  
  

> matchmaker #1 to #2 showAlignment true

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 rnsy139e-cryst-dimer-combine.pdb, chain A (#2) with wtrns-cryst-
dimer-combine.pdb, chain A (#1), sequence alignment score = 1022  
Alignment identifier is 4  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 4  
Hiding conservation header for alignment 4  
Chains used in RMSD evaluation for alignment 4: wtrns-cryst-dimer-combine.pdb
#1/A, rnsy139e-cryst-dimer-combine.pdb #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 4  
RMSD between 202 pruned atom pairs is 0.806 angstroms; (across all 246 pairs:
1.790)  
  

> matchmaker #2 to #1 showAlignment true

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 wtrns-cryst-dimer-combine.pdb, chain A (#1) with rnsy139e-cryst-
dimer-combine.pdb, chain A (#2), sequence alignment score = 1022  
Alignment identifier is 5  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 5  
Hiding conservation header for alignment 5  
Chains used in RMSD evaluation for alignment 5: wtrns-cryst-dimer-combine.pdb
#1/A, rnsy139e-cryst-dimer-combine.pdb #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 5  
RMSD between 202 pruned atom pairs is 0.806 angstroms; (across all 246 pairs:
1.790)  
  

> select #2/A:123

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

> select up

66 atoms, 65 bonds, 8 residues, 1 model selected  

> select up

1321 atoms, 1340 bonds, 163 residues, 1 model selected  

> select up

1369 atoms, 1387 bonds, 170 residues, 1 model selected  

> select up

2075 atoms, 2104 bonds, 255 residues, 1 model selected  

> select up

8358 atoms, 8460 bonds, 1034 residues, 1 model selected  

> select up

12426 atoms, 12586 bonds, 1530 residues, 2 models selected  

> select down

8358 atoms, 8460 bonds, 1034 residues, 1 model selected  

> select up

12426 atoms, 12586 bonds, 1530 residues, 2 models selected  

> ui tool show "Similar Structures"

> ui tool show "Render/Select by Attribute"

> select #!1-2::seq_rmsd>=2.174143313970123 & ::seq_rmsd<=4.241417264107728

425 atoms, 418 bonds, 54 residues, 2 models selected  

> select #!1-2::seq_rmsd>=2.174143313970123 & ::seq_rmsd<=4.241417264107728

425 atoms, 418 bonds, 54 residues, 2 models selected  

> select clear

> select #2/A:117

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

> select up

66 atoms, 65 bonds, 8 residues, 1 model selected  

> select up

1321 atoms, 1340 bonds, 163 residues, 1 model selected  

> select up

1369 atoms, 1387 bonds, 170 residues, 1 model selected  

> select up

2075 atoms, 2104 bonds, 255 residues, 1 model selected  

> select up

8358 atoms, 8460 bonds, 1034 residues, 1 model selected  

> select down

2075 atoms, 2104 bonds, 255 residues, 1 model selected  

> key blue-white-red :0.11 :3.21 :6.30 showTool true

> ui mousemode right "color key"

> ui mousemode right select

> color byattribute r:seq_rmsd #!1-2 target sabc palette
> 0.113059,blue:3.20778,white:6.3025,red

12426 atoms, 1530 residues, atom seq_rmsd range 0.113 to 6.3  

> color byattribute r:seq_rmsd #!2 target sabc palette
> 0.113059,blue:3.20778,white:6.3025,red

8358 atoms, 1034 residues, atom seq_rmsd range 0.113 to 6.3  

> color byattribute r:seq_rmsd #!2 target sabc palette
> 0.113059,blue:3.20778,white:6.3025,red

8358 atoms, 1034 residues, atom seq_rmsd range 0.113 to 6.3  

> color byattribute r:seq_rmsd #!2 target sabc palette
> 0.113059,blue:3.20778,white:6.3025,red

8358 atoms, 1034 residues, atom seq_rmsd range 0.113 to 6.3  

> color byattribute r:seq_rmsd #!2 target sabc palette
> 0.113059,blue:3.20778,white:6.3025,red

8358 atoms, 1034 residues, atom seq_rmsd range 0.113 to 6.3  

> color byattribute r:seq_rmsd #!2 target sabc palette
> 0.113059,blue:3.20778,white:6.3025,red

8358 atoms, 1034 residues, atom seq_rmsd range 0.113 to 6.3  

> color byattribute r:seq_rmsd #!2 & sel target sabc palette
> 0.113059,blue:3.20778,white:6.3025,red

2075 atoms, 255 residues, atom seq_rmsd range 0.113 to 6.3  

> color byattribute r:seq_rmsd #!2 & sel target sabc palette
> 0.113059,blue:3.20778,white:6.3025,red

2075 atoms, 255 residues, atom seq_rmsd range 0.113 to 6.3  

> color byattribute r:seq_rmsd #!2 & sel target sabc palette
> 0.113059,blue:3.20778,white:6.3025,red

2075 atoms, 255 residues, atom seq_rmsd range 0.113 to 6.3  

> color byattribute r:seq_rmsd #!2 & sel target sabc palette
> 0.113059,blue:3.20778,white:6.3025,red

2075 atoms, 255 residues, atom seq_rmsd range 0.113 to 6.3  

> color byattribute r:seq_rmsd #!2 & sel target sabc palette
> 0.113059,blue:3.20778,white:6.3025,red

2075 atoms, 255 residues, atom seq_rmsd range 0.113 to 6.3  

> close

> open /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-ch/PDBs/rnsy139e-cryst-
> dimer-combine.pdb

Summary of feedback from opening
/Users/jessicatolbert/Library/CloudStorage/OneDrive-DartmouthCollege/Lab-
Report/figures/dimerization-ch/PDBs/rnsy139e-cryst-dimer-combine.pdb  
---  
notes | Combining 2 symmetry atoms into HOH /S:87 O  
Combining 2 symmetry atoms into HOH /S:121 O  
Combining 2 symmetry atoms into HOH /S:14 O  
Combining 2 symmetry atoms into HOH /S:75 O  
Combining 2 symmetry atoms into HOH /T:20 O  
5 messages similar to the above omitted  
  
Chain information for rnsy139e-cryst-dimer-combine.pdb #1  
---  
Chain | Description  
A B C D | No description available  
  
Associated rnsy139e-cryst-dimer-combine.pdb chain A to rnsy139e-cryst-dimer-
combine.pdb, chain A with 0 mismatches  
Associated rnsy139e-cryst-dimer-combine.pdb chain B to rnsy139e-cryst-dimer-
combine.pdb, chain A with 0 mismatches  
Associated rnsy139e-cryst-dimer-combine.pdb chain C to rnsy139e-cryst-dimer-
combine.pdb, chain A with 0 mismatches  
Associated rnsy139e-cryst-dimer-combine.pdb chain D to rnsy139e-cryst-dimer-
combine.pdb, chain A with 0 mismatches  
Associated rnsy139e-cryst-dimer-combine.pdb chain A to rnsy139e-cryst-dimer-
combine.pdb, chain A with 0 mismatches  
Associated rnsy139e-cryst-dimer-combine.pdb chain B to rnsy139e-cryst-dimer-
combine.pdb, chain A with 0 mismatches  
Associated rnsy139e-cryst-dimer-combine.pdb chain C to rnsy139e-cryst-dimer-
combine.pdb, chain A with 0 mismatches  
Associated rnsy139e-cryst-dimer-combine.pdb chain D to rnsy139e-cryst-dimer-
combine.pdb, chain A with 0 mismatches  
Associated rnsy139e-cryst-dimer-combine.pdb chain A to rnsy139e-cryst-dimer-
combine.pdb, chain A with 0 mismatches  
Associated rnsy139e-cryst-dimer-combine.pdb chain B to rnsy139e-cryst-dimer-
combine.pdb, chain A with 0 mismatches  
Associated rnsy139e-cryst-dimer-combine.pdb chain C to rnsy139e-cryst-dimer-
combine.pdb, chain A with 0 mismatches  
Associated rnsy139e-cryst-dimer-combine.pdb chain D to rnsy139e-cryst-dimer-
combine.pdb, chain A with 0 mismatches  
Associated rnsy139e-cryst-dimer-combine.pdb chain A to rnsy139e-cryst-dimer-
combine.pdb, chain A with 0 mismatches  
Associated rnsy139e-cryst-dimer-combine.pdb chain B to rnsy139e-cryst-dimer-
combine.pdb, chain A with 0 mismatches  
Associated rnsy139e-cryst-dimer-combine.pdb chain C to rnsy139e-cryst-dimer-
combine.pdb, chain A with 0 mismatches  
Associated rnsy139e-cryst-dimer-combine.pdb chain D to rnsy139e-cryst-dimer-
combine.pdb, chain A with 0 mismatches  
Associated rnsy139e-cryst-dimer-combine.pdb chain A to rnsy139e-cryst-dimer-
combine.pdb, chain A with 0 mismatches  
Associated rnsy139e-cryst-dimer-combine.pdb chain B to rnsy139e-cryst-dimer-
combine.pdb, chain A with 0 mismatches  
Associated rnsy139e-cryst-dimer-combine.pdb chain C to rnsy139e-cryst-dimer-
combine.pdb, chain A with 0 mismatches  
Associated rnsy139e-cryst-dimer-combine.pdb chain D to rnsy139e-cryst-dimer-
combine.pdb, chain A with 0 mismatches  

> open /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-ch/PDBs/wtrns-cryst-dimer-
> combine.pdb

Chain information for wtrns-cryst-dimer-combine.pdb #2  
---  
Chain | Description  
A B | No description available  
  
Associated wtrns-cryst-dimer-combine.pdb chain A to wtrns-cryst-dimer-
combine.pdb, chain A with 0 mismatches  
Associated wtrns-cryst-dimer-combine.pdb chain B to wtrns-cryst-dimer-
combine.pdb, chain A with 0 mismatches  
Chains used in RMSD evaluation for alignment 1: rnsy139e-cryst-dimer-
combine.pdb #1/A, wtrns-cryst-dimer-combine.pdb #2/A  
Associated wtrns-cryst-dimer-combine.pdb chain A to wtrns-cryst-dimer-
combine.pdb, chain A with 0 mismatches  
Associated wtrns-cryst-dimer-combine.pdb chain B to wtrns-cryst-dimer-
combine.pdb, chain A with 0 mismatches  
Chains used in RMSD evaluation for alignment 2: rnsy139e-cryst-dimer-
combine.pdb #1/A, wtrns-cryst-dimer-combine.pdb #2/A  
Associated wtrns-cryst-dimer-combine.pdb chain A to wtrns-cryst-dimer-
combine.pdb, chain A with 0 mismatches  
Associated wtrns-cryst-dimer-combine.pdb chain B to wtrns-cryst-dimer-
combine.pdb, chain A with 0 mismatches  
Chains used in RMSD evaluation for alignment 3: rnsy139e-cryst-dimer-
combine.pdb #1/A, wtrns-cryst-dimer-combine.pdb #2/A  
Associated wtrns-cryst-dimer-combine.pdb chain A to wtrns-cryst-dimer-
combine.pdb, chain A with 0 mismatches  
Associated wtrns-cryst-dimer-combine.pdb chain B to wtrns-cryst-dimer-
combine.pdb, chain A with 0 mismatches  
Chains used in RMSD evaluation for alignment 4: rnsy139e-cryst-dimer-
combine.pdb #1/A, wtrns-cryst-dimer-combine.pdb #2/A  
Associated wtrns-cryst-dimer-combine.pdb chain A to wtrns-cryst-dimer-
combine.pdb, chain A with 0 mismatches  
Associated wtrns-cryst-dimer-combine.pdb chain B to wtrns-cryst-dimer-
combine.pdb, chain A with 0 mismatches  
Chains used in RMSD evaluation for alignment 5: rnsy139e-cryst-dimer-
combine.pdb #1/A, wtrns-cryst-dimer-combine.pdb #2/A  

> matchmaker #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 wtrns-cryst-dimer-combine.pdb, chain A (#2) with rnsy139e-cryst-
dimer-combine.pdb, chain A (#1), sequence alignment score = 1022  
RMSD between 202 pruned atom pairs is 0.806 angstroms; (across all 246 pairs:
1.790)  
  

> matchmaker #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 wtrns-cryst-dimer-combine.pdb, chain A (#2) with rnsy139e-cryst-
dimer-combine.pdb, chain A (#1), sequence alignment score = 1022  
RMSD between 202 pruned atom pairs is 0.806 angstroms; (across all 246 pairs:
1.790)  
  

> 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/ui/widgets/histogram.py", line 775, in _set_value_cb  
v = eval(self._value_entry.text())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "<string>", line 1  
09  
^  
SyntaxError: leading zeros in decimal integer literals are not permitted; use
an 0o prefix for octal integers  
  
During handling of the above exception, another exception occurred:  
  
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/ui/widgets/histogram.py", line 777, in _set_value_cb  
raise ValueError("Invalid histogram value")  
ValueError: Invalid histogram value  
  
ValueError: Invalid histogram value  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 777, in _set_value_cb  
raise ValueError("Invalid histogram value")  
  
See log for complete Python traceback.  
  

> ui tool show "Render/Select by Attribute"

> key blue-white-red :0 :3 :6 showTool true

> ui mousemode right "color key"

> key delete

> ui mousemode right select

> key blue-white-red :0 :3 :6 showTool true

> ui mousemode right "color key"

> ui mousemode right select

> color byattribute r:seq_rmsd #!1-2 target sabc palette 0,blue:3,white:6,red

12426 atoms, 1530 residues, atom seq_rmsd range 0.113 to 6.3  

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> select #1/D:33

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

> select up

2075 atoms, 2104 bonds, 255 residues, 1 model selected  

> select up

8358 atoms, 8460 bonds, 1034 residues, 1 model selected  

> select down

2075 atoms, 2104 bonds, 255 residues, 1 model selected  

> hide sel cartoons

> select clear

> hide #4 models

> show #4 models

> save /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-ch/rmsd-y139e.cxs

——— End of log from Thu Apr 3 22:05:55 2025 ———

opened ChimeraX session  

> close #2

> color bfactor

8358 atoms, 1034 residues, atom bfactor range 16.7 to 106  

> ui tool show "Render/Select by Attribute"

> cartoon byattribute a:bfactor #!1 17.4496:0.25 106.38:2

1020 residues, residue bfactor range 19.8 to 99.2  

> cartoon byattribute a:bfactor #!1 17.4496:0.25 106.38:2

1020 residues, residue bfactor range 19.8 to 99.2  

> cartoon byattribute a:bfactor #!1 17.4496:0.25 106.38:2

1020 residues, residue bfactor range 19.8 to 99.2  

> cartoon byattribute a:bfactor #!1 17.4496:0.25 106.38:2

1020 residues, residue bfactor range 19.8 to 99.2  

> cartoon byattribute a:bfactor #!1 17.4496:0.25 106.38:2

1020 residues, residue bfactor range 19.8 to 99.2  

> rainbow

> hide atoms

> open /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-ch/wtrns-dimerization-
> interfacce.pdb

Summary of feedback from opening
/Users/jessicatolbert/Library/CloudStorage/OneDrive-DartmouthCollege/Lab-
Report/figures/dimerization-ch/wtrns-dimerization-interfacce.pdb  
---  
warnings | End residue of secondary structure not found: HELIX 1 1 GLY A 78 TYR A 92 1 15  
Start residue of secondary structure not found: HELIX 2 2 MET A 105 ARG A 107
1 3  
Start residue of secondary structure not found: HELIX 3 3 LYS A 116 LYS A 123
1 8  
Start residue of secondary structure not found: HELIX 6 6 GLU A 148 SER A 158
1 11  
Start residue of secondary structure not found: HELIX 7 7 PHE A 162 LEU A 169
1 8  
Start residue of secondary structure not found: HELIX 8 8 ILE A 170 ASP A 173
1 4  
40 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 1 1 GLY A 78 TYR A 92 1 15  
Start residue of secondary structure not found: HELIX 2 2 MET A 105 ARG A 107
1 3  
Start residue of secondary structure not found: HELIX 3 3 LYS A 116 LYS A 123
1 8  
Start residue of secondary structure not found: HELIX 6 6 GLU A 148 SER A 158
1 11  
Start residue of secondary structure not found: HELIX 7 7 PHE A 162 LEU A 169
1 8  
Start residue of secondary structure not found: HELIX 8 8 ILE A 170 ASP A 173
1 4  
213 messages similar to the above omitted  
  
Chain information for wtrns-dimerization-interfacce.pdb  
---  
Chain | Description  
2.1/A 2.3/A | No description available  
2.2/A 2.5/A 2.11/A | No description available  
2.4/A 2.6/A 2.7/A 2.8/A 2.9/A 2.10/A 2.2/B 2.4/B 2.5/B 2.6/B 2.7/B 2.8/B 2.9/B 2.10/B | No description available  
2.11/B | No description available  
  

> hide #!2 models

> show #!2 models

> show cartoons

[Repeated 1 time(s)]

> hide cartoons

> show cartoons

> hide cartoons

> show cartoons

> select add #2

1733 atoms, 1636 bonds, 98 pseudobonds, 218 residues, 23 models selected  

> show sel cartoons

[Repeated 1 time(s)]

> open /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-ch/PDBs/bfac-
> wtrns-y139e.png format images

Opened multi-channel map bfac-wtrns-y139e.png as #3, 3 channels, grid size
819,681,1, pixel 1, shown at step 1, values uint8  

> open /Users/jessicatolbert/Library/CloudStorage/OneDrive-
> DartmouthCollege/Lab-Report/figures/dimerization-ch/PDBs/wtrns-cryst-dimer-
> combine.pdb format pdb

Chain information for wtrns-cryst-dimer-combine.pdb #5  
---  
Chain | Description  
A B | No description available  
  

> hide #!2 models

> hide #!3 models

> hide #!3.1 models

> hide #!3.2 models

> hide #4 models

> hide #!3.3 models

> hide #!1 models

> show #!1 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!1 models

> select add #5

5801 atoms, 5762 bonds, 100 pseudobonds, 714 residues, 25 models selected  

> select subtract #2

4068 atoms, 4126 bonds, 2 pseudobonds, 496 residues, 2 models selected  

> close #4#2-3#3.1-3

> color bfactor sel

4068 atoms, 496 residues, atom bfactor range 45.8 to 170  

> 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/ui/widgets/histogram.py", line 181, in <lambda>  
if event.modifiers() & mod_key_info("shift")[0] else
self._select_marker_cb(event)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 740, in _select_marker_cb  
self._set_sel_marker(marker, drag_start=event)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 760, in _set_sel_marker  
self._select_callback(self._prev_markers, self._prev_marker,
self._active_markers, marker)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 728, in _render_sel_marker_cb  
value_entry.setText("%g" % cur_marker.radius)  
^^^^^^^^^^^^^^^^^  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 728, in _render_sel_marker_cb  
value_entry.setText("%g" % cur_marker.radius)  
^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> 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/render_by_attr/tool.py", line 348, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda: self._dispatch(apply=True))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 586, in _dispatch  
self.render(apply=apply)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> 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/render_by_attr/tool.py", line 348, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda: self._dispatch(apply=True))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 586, in _dispatch  
self.render(apply=apply)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> 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/render_by_attr/tool.py", line 348, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda: self._dispatch(apply=True))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 586, in _dispatch  
self.render(apply=apply)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> show #!1 models

> hide #!5 models

> show #!5 models

> hide #!1 models

> ui tool show "Render/Select by Attribute"

> select #!5@@bfactor>=45.779998779296875 & @@bfactor<=156.86641720239191

4067 atoms, 4124 bonds, 2 pseudobonds, 496 residues, 2 models selected  
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/render_by_attr/tool.py", line 348, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda: self._dispatch(apply=True))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 586, in _dispatch  
self.render(apply=apply)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
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: Z160000B1LL/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.81.4
      OS Loader Version: 11881.81.4

Software:

    System Software Overview:

      System Version: macOS 15.3.2 (24D81)
      Kernel Version: Darwin 24.3.0
      Time since boot: 5 days, 2 hours, 21 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      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

Change History (2)

comment:1 by Eric Pettersen, 7 months ago

Component: UnassignedStructure Analysis
Owner: set to Eric Pettersen
Platform: all
Project: ChimeraX
Status: newaccepted
Summary: ChimeraX bug report submissionRender By Attribute: switching attributes does not preserve marker radius

comment:2 by Eric Pettersen, 7 months ago

Resolution: duplicate
Status: acceptedclosed

Hi Jess,

Thanks for reporting this problem. It has been fixed in the daily build, so if you use that then you won't run into it anymore.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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