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 | |
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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