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Opened 7 months ago
Closed 7 months ago
#17306 closed defect (duplicate)
Render By Attribute: switching attributes does not preserve marker radius
| Reported by: | 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 , 7 months ago
| Component: | Unassigned → Structure Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Render By Attribute: switching attributes does not preserve marker radius |
comment:2 by , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Hi Jess,
--Eric