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Changes between Initial Version and Version 1 of Ticket #16623

Timestamp:: Jan 15, 2025, 11:51:30 AM (10 months ago)
Author:: Eric Pettersen
Comment:

Legend:

: Unmodified
: Added
: Removed
: Modified

Ticket #16623
- Property Component Unassigned → Input/Output
- Property Owner set to Greg Couch
- Property Platform → all
- Property Project → ChimeraX
- Property Status new → assigned
- Property Summary ChimeraX bug report submission → MemoryError opening mmCIF file

Ticket #16623 – Description

-              initial
+              v1
 atoms, 3 bonds, 1 residue, 1 model selected
+> select #8/A:135
+atoms, 6 bonds, 1 residue, 1 model selected
+> select clear
+> select #2/I:147
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #8/A:133
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #8/A:133
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> hide #!8 models
+> select #8/D
+atoms, 1346 bonds, 171 residues, 1 model selected
+> show #2 cartoons
+> hide #2 cartoons
+> hide #2 models
+> show #2 models
+> select #2/I
+atoms, 1169 bonds, 149 residues, 1 model selected
+> show sel cartoons
+> select #8/D
+atoms, 1346 bonds, 171 residues, 1 model selected
+> show #2 cartoons
+> hide #2 cartoons
+> select #2/I
+atoms, 1169 bonds, 149 residues, 1 model selected
+> show sel cartoons
+> select clear
+> select #8/G
+atoms, 1346 bonds, 171 residues, 1 model selected
+> show #2 cartoons
+> hide #2 cartoons
+> select #2/I
+atoms, 1169 bonds, 149 residues, 1 model selected
+> show sel cartoons
+> select clear
+> show #!8 models
+Drag select of 9 residues
+Drag select of 5 residues
+> ui mousemode right select
+> ui mousemode right rotate
+> ui mousemode right translate
+> ui mousemode right select
+> select #8/A:133
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel blue
+> ui mousemode right rotate
+> ui mousemode right select
+> select #8/A:151
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:165
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #8/A:151
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #8/A:151
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right select
+> select #8/A:226
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right rotate
+> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/CHIKV 3j2w
+> vs Getah 7vga vs Sindbis 1kxf vs VEEV 7sfu vs Mayaro 7ko8 vs EEEV 7ko8 vs
+> Aura 4agk vs SFV 1vcp vs Barmah Forrest 2yew.cxs"
+> save /Users/mauriciocomas/Desktop/image14.png supersample 3
+> ui mousemode right select
+> select #8/A:112
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #8/A:133
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #8/A:112
+atoms, 7 bonds, 1 residue, 1 model selected
+> select clear
+> select #8/A:133
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #8/A:151
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #8/A:226
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #8/A:133
+atoms, 8 bonds, 1 residue, 1 model selected
+> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/CHIKV 3j2w
+> vs Getah 7vga vs Sindbis 1kxf vs VEEV 7sfu vs Mayaro 7ko8 vs EEEV 7ko8 vs
+> Aura 4agk vs SFV 1vcp vs Barmah Forrest 2yew.cxs"
+——— End of log from Fri Mar 10 16:26:58 2023 ———
+opened ChimeraX session
+> open /Users/mauriciocomas/Downloads/7ko8.pdb
+ko8.pdb title:
+Cryo-em structure of the mature and infective mayaro virus [more info...]
+Chain information for 7ko8.pdb #9
+---
+Chain | Description
+A D G J | capsid protein
+B E H L | E1 glycoprotein
+C F I M | E2 glycoprotein
+Non-standard residues in 7ko8.pdb #9
+---
+BMA — β-D-mannopyranose (β-D-mannose; D-mannose; mannose)
+MAN — α-D-mannopyranose (α-D-mannose; D-mannose; mannose)
+NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
+-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
+-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
+> hide #!8 models
+> select #9/A
+atoms, 1200 bonds, 152 residues, 1 model selected
+> hide sel atoms
+> select #9/D
+atoms, 1199 bonds, 152 residues, 1 model selected
+> hide sel atoms
+> select #9/G
+atoms, 1199 bonds, 152 residues, 1 model selected
+> hide sel atoms
+> select #9/G
+atoms, 1199 bonds, 152 residues, 1 model selected
+> hide sel atoms
+> select #9/J
+atoms, 1199 bonds, 152 residues, 1 model selected
+> hide sel atoms
+> select #9/B#9/E#9/H#9/L
+atoms, 13517 bonds, 1732 residues, 1 model selected
+> hide sel atoms
+> select #9/C#9/F#9/I#9/M
+atoms, 13269 bonds, 1664 residues, 1 model selected
+> hide sel atoms
+> select #9/A
+atoms, 1200 bonds, 152 residues, 1 model selected
+> show sel cartoons
+> ui tool show Matchmaker
+> ui mousemode right translate
+> ui mousemode right select
+> matchmaker #9/A to #2/I pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 3j2w.pdb, chain I (#2) with 7ko8.pdb, chain A (#9), sequence
+alignment score = 566.3
+RMSD between 131 pruned atom pairs is 1.142 angstroms; (across all 149 pairs:
+.442)
+> ui mousemode right zoom
+> select ligand
+atoms, 581 bonds, 43 residues, 2 models selected
+> hide sel & #9 atoms
+> ui mousemode right translate
+> save /Users/mauriciocomas/Desktop/mayaro format fasta alignment 8/A
+> ui mousemode right select
+> select #9/A:117
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #8/A:108
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #8/A:108-253
+atoms, 1139 bonds, 146 residues, 1 model selected
+> ui tool show "Show Sequence Viewer"
+> sequence chain #9/A
+Alignment identifier is 9/A
+> select clear
+> select #9/A:117
+atoms, 8 bonds, 1 residue, 1 model selected
+> save /Users/mauriciocomas/Desktop/mayaro format fasta alignment 9/A
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel red
+> hide #9 models
+> show #9 models
+> select #9/A:117
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #9/A:117-118
+atoms, 12 bonds, 2 residues, 1 model selected
+> select #9/A:117
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #9/A:117
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #9/A:117
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #9/A:117
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel red
+> select #9/A:138
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> style sel stick
+Changed 7 atom styles
+> style sel stick
+Changed 7 atom styles
+> show sel atoms
+> color sel dim gray
+> select #9/A:138
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #9/A:138
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #9/A:156
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel blue
+> select #9/A:156
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #9/A:156
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #9/A:231
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #9/A:231
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #9/A:231
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel red
+> select #9/A:231
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #9/A:231
+atoms, 8 bonds, 1 residue, 1 model selected
+> save
+> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
+> show #!8 models
+> hide #9 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #8/A
+Alignment identifier is 8/A
+> save /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/BFV format
+> fasta alignment 8/A
+> save /Users/mauriciocomas/Desktop/BFV format fasta alignment 8/A
+> select clear
+> select #8/A:112
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #8/A:112
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #8/A:133
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #8/A:151
+atoms, 8 bonds, 1 residue, 1 model selected
+> select clear
+> select clear
+> select #8/A:226
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #8/A:112
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #8/A:133@CA
+atom, 1 residue, 1 model selected
+> select #8/A:151
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #8/A:226
+atoms, 8 bonds, 1 residue, 1 model selected
+> hide #!8 models
+> show #3 models
+> hide #3 models
+> show #!7 models
+> select #7/A:248
+atoms, 6 bonds, 1 residue, 1 model selected
+> ui tool show "Show Sequence Viewer"
+> sequence chain #7/A
+Alignment identifier is 7/A
+> select #7/A:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> save /Users/mauriciocomas/Desktop/SINV format fasta alignment 7/A
+> select #7/A:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #7/A:126-127
+atoms, 12 bonds, 2 residues, 1 model selected
+> select #7/A:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #7/A:126-127
+atoms, 12 bonds, 2 residues, 1 model selected
+> select #7/A:147
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #7/A:165
+atoms, 8 bonds, 1 residue, 1 model selected
+> show #3 models
+> hide #!7 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #3/A
+Alignment identifier is 3/A
+> save /Users/mauriciocomas/Desktop/SINV format fasta alignment 3/A
+> select #3/A:121
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:147
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #3/A:143
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:147
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #3/A:143
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel blue
+> save
+> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
+> select #3/A:161
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #3/A:236
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #3/A:236
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #3/A:236
+atoms, 8 bonds, 1 residue, 1 model selected
+> show #6 models
+> hide #3 models
+Drag select of 4 residues
+> ui mousemode right rotate
+> ui tool show "Show Sequence Viewer"
+> sequence chain #6/A
+Alignment identifier is 6/A
+> save /Users/mauriciocomas/Desktop/Aura format fasta alignment 6/A
+> ui mousemode right select
+> select #6/A:125
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #6/A:146
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #6/A:164
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #6/A:164
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #6/A:239
+atoms, 8 bonds, 1 residue, 1 model selected
+> show #4 models
+> hide #6 models
+> select #2/I:195
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #4/L:254
+atoms, 5 bonds, 1 residue, 1 model selected
+> ui tool show "Show Sequence Viewer"
+> sequence chain #6/A
+Alignment identifier is 6/A
+> save /Users/mauriciocomas/Desktop/VEEV format fasta alignment 6/A
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> ui tool show "Show Sequence Viewer"
+> sequence chain #4/L
+Alignment identifier is 4/L
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select clear
+> select #4/L:133
+atoms, 8 bonds, 1 residue, 1 model selected
+> save /Users/mauriciocomas/Desktop/VEEV format fasta alignment 4/L
+> select #4/L:154
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel red
+> select #4/L:172
+atoms, 8 bonds, 1 residue, 1 model selected
+> select clear
+> select #4/L:247@CA
+atom, 1 residue, 1 model selected
+> select clear
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select clear
+> select #4/L:247
+atoms, 8 bonds, 1 residue, 1 model selected
+> save
+> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
+——— End of log from Tue Mar 14 17:14:03 2023 ———
+opened ChimeraX session
+> hide #4 models
+> ui mousemode right rotate
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel blue
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel red
+> show #!7 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #7/A
+Alignment identifier is 7/A
+> select #7/A:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #7/A:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel red
+> select #7/A:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #7/A:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right translate
+> select clear
+> save /Users/mauriciocomas/Desktop/image31.png supersample 3
+> select #7/A:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #7/A:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #7/A:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #7/A:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:182
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #2/I:182-183
+atoms, 14 bonds, 2 residues, 1 model selected
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:190-191
+atoms, 12 bonds, 2 residues, 1 model selected
+> select #2/I:165
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:165
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:183-184
+atoms, 20 bonds, 2 residues, 1 model selected
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:166
+atoms, 12 bonds, 1 residue, 1 model selected
+> select #2/I:166-181
+atoms, 127 bonds, 16 residues, 1 model selected
+> select #2/I:169
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:169
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:165
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:165
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:183-184
+atoms, 20 bonds, 2 residues, 1 model selected
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:122
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:122
+atoms, 8 bonds, 1 residue, 1 model selected
+> ui mousemode right select
+> select #7/A:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:147
+atoms, 8 bonds, 1 residue, 1 model selected
+Drag select of 4 residues
+> ui mousemode right rotate
+> select #7/A:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #7/A:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #7/A:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #7/A:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #7/A:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #7/A:183-184
+atoms, 21 bonds, 2 residues, 1 model selected
+> save
+> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
+> hide #!7 models
+> show #1 models
+> hide #1 models
+> show #9 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #9/A
+Alignment identifier is 9/A
+> select #9/A:174
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #9/A:174
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel blue
+> select #9/A:181
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #9/A:181
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel red
+> select clear
+> save /Users/mauriciocomas/Desktop/image32.png supersample 3
+> ui mousemode right select
+> select #9/A:156
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #9/A:181
+atoms, 8 bonds, 1 residue, 1 model selected
+> hide #9 models
+> show #1 models
+> select #9/A:174
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #9/A:174
+atoms, 8 bonds, 1 residue, 1 model selected
+> ui tool show "Show Sequence Viewer"
+> sequence chain #1/C
+Alignment identifier is 1/C
+> select #1/C:184
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #1/C:184
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel blue
+> save /Users/mauriciocomas/Desktop/image33.png supersample 3
+> select #1/C:191
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #1/C:191
+atoms, 8 bonds, 1 residue, 1 model selected
+> show sel atoms
+> show sel atoms
+> style sel stick
+Changed 9 atom styles
+> color sel red
+> select #1/C:148
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel blue
+> select clear
+> save /Users/mauriciocomas/Desktop/image34.png supersample 3
+> save
+> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
+> hide #2 models
+> show #!8 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #8/A
+Alignment identifier is 8/A
+> select #8/A:169
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #8/A:169
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel blue
+> select #8/A:176
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #8/A:176
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel red
+> select clear
+> save /Users/mauriciocomas/Desktop/image35.png supersample 3
+> select #8/A:133@CB
+atom, 1 residue, 1 model selected
+> show #2 models
+> hide #1 models
+> hide sel atoms
+> undo
+> select #8/A:176
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #8/A:176
+atoms, 8 bonds, 1 residue, 1 model selected
+> save /Users/mauriciocomas/Desktop/image36.png supersample 3
+> select #8/A:151
+atoms, 8 bonds, 1 residue, 1 model selected
+> hide #!8 models
+> show #3 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #3/A
+Alignment identifier is 3/A
+> select #3/A:162
+atoms, 12 bonds, 1 residue, 1 model selected
+> select #3/A:162
+atoms, 12 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 12 atom styles
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel dark gray
+> select #3/A:168
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #3/A:168
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> hide sel atoms
+> select #3/A:161-162
+atoms, 17 bonds, 2 residues, 1 model selected
+> select #3/A:161-162
+atoms, 17 bonds, 2 residues, 1 model selected
+> select #3/A:162
+atoms, 12 bonds, 1 residue, 1 model selected
+> select #3/A:162-163
+atoms, 20 bonds, 2 residues, 1 model selected
+> select #3/A:162
+atoms, 12 bonds, 1 residue, 1 model selected
+> select #3/A:162
+atoms, 12 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #3/A:179
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #3/A:178
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #3/A:178
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #3/A:179
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #3/A:179-180
+atoms, 19 bonds, 2 residues, 1 model selected
+> select #3/A:179
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #3/A:179
+atoms, 6 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 7 atom styles
+> show sel atoms
+> color sel dim gray
+> select #3/A:186
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #3/A:186
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel red
+> select clear
+> select #3/A:186
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #3/A:186
+atoms, 8 bonds, 1 residue, 1 model selected
+> save /Users/mauriciocomas/Desktop/image37.png supersample 3
+> select #3/A:121
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel red
+> select clear
+> save /Users/mauriciocomas/Desktop/image38.png supersample 3
+> save
+> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
+> hide #3 models
+> show #6 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #6/A
+Alignment identifier is 6/A
+> select #6/A:181
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #6/A:181
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #6/A:182
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #6/A:182
+atoms, 3 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 4 atom styles
+> show sel atoms
+> show sel atoms
+> show sel cartoons
+> select #6/A:131
+atoms, 12 bonds, 1 residue, 1 model selected
+> select #6/A:131-267
+atoms, 1064 bonds, 137 residues, 1 model selected
+> select #6/A:182
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #6/A:182
+atoms, 3 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 4 atom styles
+> style sel sphere
+Changed 4 atom styles
+> style sel stick
+Changed 4 atom styles
+> show sel atoms
+> style sel sphere
+Changed 4 atom styles
+> color sel dim gray
+> select #6/A:182
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #6/A:182
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #6/A:189
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #6/A:189
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel red
+> select clear
+> save /Users/mauriciocomas/Desktop/image39.png supersample 3
+> save
+> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
+> hide #6 models
+> show #4 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #4/L
+Alignment identifier is 4/L
+> select #4/L:133
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel red
+> select clear
+> select #4/L:154
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #4/L:203
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #4/L:172
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #4/L:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel blue
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #4/L:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #4/L:197
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #4/L:197
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #4/L:198
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #4/L:198
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #4/L:197
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #4/L:197
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel red
+> select #4/L:133
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #4/L:133
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #4/L:196-197
+atoms, 16 bonds, 2 residues, 1 model selected
+> select #4/L:196-197
+atoms, 16 bonds, 2 residues, 1 model selected
+> select #4/L:197
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #4/L:197
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #4/L:198
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #4/L:198
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #4/L:197
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #4/L:197
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel dim gray
+> select clear
+> save /Users/mauriciocomas/Desktop/image40.png supersample 3
+> save
+> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
+> show #!5 models
+> hide #!5 models
+> hide #4 models
+> show #!5 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #5/C
+Alignment identifier is 5/C
+> select #5/C:176
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #5/C:175
+atoms, 7 bonds, 1 residue, 1 model selected
+> color sel dark gray
+> style sel stick
+Changed 8 atom styles
+> show sel atoms
+> color sel dim gray
+> ui mousemode right select
+> select #5/C:183
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #5/C:183
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #5/C:183-184
+atoms, 11 bonds, 2 residues, 1 model selected
+> select #5/C:184
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #5/C:184
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #5/C:183
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #5/C:183
+atoms, 7 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 7 atom styles
+> show sel atoms
+> color sel dim gray
+> select clear
+> save /Users/mauriciocomas/Desktop/image41.png supersample 3
+> save
+> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
+> hide #!5 models
+> select clear
+> save /Users/mauriciocomas/Desktop/image42.png supersample 3
+> save
+> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
+——— End of log from Wed Mar 15 16:42:48 2023 ———
+opened ChimeraX session
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:126-127
+atoms, 12 bonds, 2 residues, 1 model selected
+> select #2/I:126-184
+atoms, 455 bonds, 59 residues, 1 model selected
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel red
+> ui tool show "Show Sequence Viewer"
+> sequence chain #2/I
+Alignment identifier is 2/I
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:126-133
+atoms, 58 bonds, 8 residues, 1 model selected
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:126-127
+atoms, 12 bonds, 2 residues, 1 model selected
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel blue
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> color sel red
+> style sel stick
+Changed 8 atom styles
+> show sel atoms
+> save /Users/mauriciocomas/Desktop/image9.png supersample 3
+> show #3 models
+> hide #3 models
+> show #!7 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #7/A
+Alignment identifier is 7/A
+> select #7/A:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #7/A:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel blue
+> select #7/A:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #7/A:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 8 atom styles
+> show sel atoms
+> color sel red
+> save /Users/mauriciocomas/Desktop/image10.png supersample 3
+> hide #!7 models
+> show #9 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #9/A
+Alignment identifier is 9/A
+> select #9/A:119
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #9/A:119
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel blue
+> select #9/A:145
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #9/A:145
+atoms, 7 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 8 atom styles
+> show sel atoms
+> color sel red
+> select clear
+> save /Users/mauriciocomas/Desktop/image11.png supersample 3
+> save
+> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
+> ui mousemode right select
+> select #2/I:154@CG
+atom, 1 residue, 1 model selected
+> hide #9 models
+> show #1 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #1/C
+Alignment identifier is 1/C
+> select #1/C:123
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #1/C:123
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #1/C:123
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #1/C:123-128
+atoms, 44 bonds, 6 residues, 1 model selected
+> select #1/C:123
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #1/C:123
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #1/C:127
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #1/C:127
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #1/C:129
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #1/C:129
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel blue
+> select #1/C:155
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #1/C:155
+atoms, 7 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 8 atom styles
+> show sel atoms
+> color sel red
+> save /Users/mauriciocomas/Desktop/image12.png supersample 3
+> hide #1 models
+> show #!8 models
+> hide #!8 models
+> ui mousemode right rotate
+> ui mousemode right translate
+> ui mousemode right rotate
+> ui mousemode right zoom
+> ui mousemode right translate
+> show #!8 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #8/A
+Alignment identifier is 8/A
+> select #8/A:112
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #8/A:112-113
+atoms, 11 bonds, 2 residues, 1 model selected
+> select #8/A:112
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #8/A:112
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #8/A:114
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #8/A:114
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel blue
+> select #8/A:153
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #8/A:153
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #8/A:155
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #8/A:155
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #8/A:153
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #8/A:153
+atoms, 7 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 8 atom styles
+> show sel atoms
+> hide sel cartoons
+> hide sel cartoons
+> show sel cartoons
+> style sel stick
+Changed 8 atom styles
+> style sel stick
+Changed 8 atom styles
+> select #8/A:153
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #8/A:153
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> ui mousemode right select
+> select #8/A:140
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #8/A:140
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #8/A:140
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel red
+> select clear
+> save /Users/mauriciocomas/Desktop/image13.png supersample 3
+> hide #!8 models
+> show #!7 models
+> hide #!7 models
+> show #6 models
+> hide #6 models
+> show #3 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #6/A
+Alignment identifier is 6/A
+> select #6/A:136
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #6/A:136
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #6/A:137
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #6/A:137-186
+atoms, 399 bonds, 50 residues, 1 model selected
+> show #6 models
+> hide #6 models
+> select #6
+atoms, 1181 bonds, 279 residues, 1 model selected
+> ~select #6
+Nothing selected
+> select #6
+atoms, 1181 bonds, 279 residues, 1 model selected
+> ~select #6
+Nothing selected
+> select #3
+atoms, 1252 bonds, 175 residues, 1 model selected
+> ~select #3
+Nothing selected
+> ui tool show "Show Sequence Viewer"
+> sequence chain #3/A
+Alignment identifier is 3/A
+> select #3/A:135
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #3/A:135
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> hide sel atoms
+> select #3/A:121
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #3/A:123
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #3/A:123
+atoms, 3 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 4 atom styles
+> show sel atoms
+> show sel atoms
+> style sel stick
+Changed 4 atom styles
+> show sel atoms
+> hide sel atoms
+> select #3/A:123
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #3/A:123
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #3/A:123
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #3/A:123-129
+atoms, 46 bonds, 7 residues, 1 model selected
+> select #3/A:123
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #3/A:123
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #3/A:123-124
+atoms, 11 bonds, 2 residues, 1 model selected
+> select #3/A:123-124
+atoms, 11 bonds, 2 residues, 1 model selected
+> select #3/A:124-125
+atoms, 14 bonds, 2 residues, 1 model selected
+> select #3/A:124-125
+atoms, 14 bonds, 2 residues, 1 model selected
+> select #3/A:124
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #3/A:124
+atoms, 7 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 8 atom styles
+> show sel atoms
+> color sel red
+> select #3/A:163
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #3/A:163
+atoms, 7 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 8 atom styles
+> show sel atoms
+> hide sel atoms
+> select #3/A:150
+atoms, 6 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 7 atom styles
+> show sel atoms
+> color sel gray
+> select clear
+> save /Users/mauriciocomas/Desktop/image14.png supersample 3
+> hide #3 models
+> show #9 models
+> hide #9 models
+> show #6 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #6/A
+Alignment identifier is 6/A
+> select #6/A:138
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #6/A:138
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> hide sel atoms
+> select #6/A:125
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #6/A:125
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #6/A:127
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #6/A:127
+atoms, 8 bonds, 1 residue, 1 model selected
+> show sel cartoons
+> show sel atoms
+> color sel blue
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #6/A:157
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #6/A:156
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #6/A:156
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel blue
+> save /Users/mauriciocomas/Desktop/image15.png supersample 3
+> hide #6 models
+> show #!5 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #5/C
+Alignment identifier is 5/C
+> select clear
+> select #5/C:121
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #5/C:120
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #5/C:120
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #5/C:121
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #5/C:121
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #5/C:118
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #5/C:118
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #5/C:119
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #5/C:119
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #5/C:121
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #5/C:121
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel red
+> color sel dim gray
+> select #5/C:150
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #5/C:119-120
+atoms, 11 bonds, 2 residues, 1 model selected
+> select #5/C:119-120
+atoms, 11 bonds, 2 residues, 1 model selected
+> select #5/C:120
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #5/C:120
+atoms, 3 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 4 atom styles
+> show sel atoms
+> hide sel atoms
+> select #5/C:117
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #5/C:117-123
+atoms, 51 bonds, 7 residues, 1 model selected
+> select #5/C:115
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #5/C:115-118
+atoms, 31 bonds, 4 residues, 1 model selected
+> select #5/C:150
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #5/C:148
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #5/C:148-149
+atoms, 12 bonds, 2 residues, 1 model selected
+> select #5/C:147
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #5/C:147
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #5/C:145
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #5/C:145-146
+atoms, 16 bonds, 2 residues, 1 model selected
+> select #5/C:146
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #5/C:146
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> hide sel atoms
+> select #5/C:146-147
+atoms, 17 bonds, 2 residues, 1 model selected
+> select #5/C:146-147
+atoms, 17 bonds, 2 residues, 1 model selected
+> select #5/C:147-148
+atoms, 16 bonds, 2 residues, 1 model selected
+> select #5/C:147-148
+atoms, 16 bonds, 2 residues, 1 model selected
+> select #5/C:147
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #5/C:147
+atoms, 8 bonds, 1 residue, 1 model selected
+> show sel cartoons
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel dim gray
+> save /Users/mauriciocomas/Desktop/image16.png supersample 3
+> hide #!5 models
+> show #4 models
+> select clear
+> ui mousemode right zoom
+> ui mousemode right translate
+> ui mousemode right select
+> ui tool show "Show Sequence Viewer"
+> sequence chain #4/L
+Alignment identifier is 4/L
+> select #4/L:135
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #4/L:135-136
+atoms, 16 bonds, 2 residues, 1 model selected
+> select #4/L:135
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #4/L:135
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel blue
+> select #4/L:164
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #4/L:165
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #4/L:165-166
+atoms, 16 bonds, 2 residues, 1 model selected
+> select #4/L:162
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #4/L:162
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #4/L:161
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #4/L:161
+atoms, 6 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 7 atom styles
+> show sel atoms
+> color sel dim gray
+> save
+> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
+——— End of log from Fri Mar 17 10:55:50 2023 ———
+opened ChimeraX session
+> show #1 models
+> hide #4 models
+> ui mousemode right select
+> select #1/C:127
+atoms, 7 bonds, 1 residue, 1 model selected
+> color sel red
+> select clear
+> select clear
+> save /Users/mauriciocomas/Desktop/image1.png supersample 3
+> save
+> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
+——— End of log from Thu Mar 23 12:13:26 2023 ———
+opened ChimeraX session
+> hide #1 models
+> ui mousemode right select
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:120
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #2/I:120
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> save "/Users/mauriciocomas/Desktop/3j2w monomer" format fasta alignment 2/I
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> ui mousemode right "move label"
+> ui mousemode right label
+> label #2/I:128
+> ui mousemode right "move label"
+> ui mousemode right label
+> label delete residues
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:126-127
+atoms, 12 bonds, 2 residues, 1 model selected
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #2/I:147
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:147
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:147
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:147
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #2/I:147
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:147
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:122
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:122
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right select
+> select #2/I:147
+atoms, 8 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> ui tool show "Color Actions"
+> color sel bychain
+> color sel cyan
+> select clear
+> select #2/I:180
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #2/I:180
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:139
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:139
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel blue
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select clear
+> select #2/I:165
+atoms, 8 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> color sel cyan
+> select #2/I:190@CB
+atom, 1 residue, 1 model selected
+> select clear
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select clear
+> save /Users/mauriciocomas/Desktop/image2.png supersample 3
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select clear
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> show #!7 models
+> select #7/A:147
+atoms, 8 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> color sel hot pink
+> ui tool show "Color Actions"
+> select #7/A:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel red
+> select #7/A:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #7/A:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #7/A:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #7/A:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select clear
+> select #7/A:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> ui mousemode right label
+> label #7/A:128
+> ui mousemode right "move label"
+> ui mousemode right label
+> label delete residues
+> color sel blue
+> ui tool show "Show Sequence Viewer"
+> sequence chain #7/A
+Alignment identifier is 7/A
+> ui mousemode right select
+> select #7/A:154@CB
+atom, 1 residue, 1 model selected
+> select #7/A:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #7/A:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> color sel red
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #7/A:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #7/A:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel blue
+> select #7/A:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #7/A:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #7/A:178
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #7/A:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #7/A:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #7/A:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #7/A:154@CB
+atom, 1 residue, 1 model selected
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #7/A:178
+atoms, 10 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 11 atom styles
+> show sel atoms
+> color sel blue
+> select #7/A:183@CB
+atom, 1 residue, 1 model selected
+> color sel blue
+> select #7/A:190@CB
+atom, 1 residue, 1 model selected
+> color sel red
+> select #7/A:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel red
+> select clear
+> save /Users/mauriciocomas/Desktop/image2.png supersample 3
+> select clear
+> select #7/A:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel red
+> select clear
+> save /Users/mauriciocomas/Desktop/image2.png supersample 3
+> select #7/A:183@CA
+atom, 1 residue, 1 model selected
+> select #7/A:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel blue
+> select clear
+> save /Users/mauriciocomas/Desktop/image2.png supersample 3
+> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
+> structures correct.cxs"
+> hide #!7 models
+> hide #2 models
+> show #2 models
+> show #9 models
+> select #9/A:138
+atoms, 7 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 7 atom styles
+> style sel stick
+Changed 7 atom styles
+> hide sel atoms
+> select #9/A:117
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel red
+> select #9/A:119
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel blue
+> select #9/A:145@CB
+atom, 1 residue, 1 model selected
+> select #9/A:148
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #9/A:145
+atoms, 7 bonds, 1 residue, 1 model selected
+> color sel red
+> ui tool show "Show Sequence Viewer"
+> sequence chain #9/A
+Alignment identifier is 9/A
+> select #9/A:148
+atoms, 10 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 11 atom styles
+> show sel atoms
+> color sel blue
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:179
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #9/A:170
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #9/A:169
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #9/A:169
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #9/A:169
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel blue
+> select #9/A:174@CD
+atom, 1 residue, 1 model selected
+> select #9/A:174
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #9/A:174
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel blue
+> select #9/A:169
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #9/A:169
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #9/A:181
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel red
+> select #9/A:231@CA
+atom, 1 residue, 1 model selected
+> select #9/A:231
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #9/A:231
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel red
+> select clear
+> save /Users/mauriciocomas/Desktop/image2.png supersample 3
+> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
+> structures correct.cxs"
+> hide #9 models
+> show #1 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #1/C
+Alignment identifier is 1/C
+> hide #1-2 atoms
+> undo
+> select #1/C:148
+atoms, 8 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #1/C:127
+atoms, 7 bonds, 1 residue, 1 model selected
+> color sel red
+> select #1/C:129
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel blue
+> select #1/C:129
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #1/C:129
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #1/C:155
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #1/C:157-158
+atoms, 13 bonds, 2 residues, 1 model selected
+> select #1/C:157-158
+atoms, 13 bonds, 2 residues, 1 model selected
+> select #1/C:158
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #1/C:158
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right select
+> select #1/C:155
+atoms, 7 bonds, 1 residue, 1 model selected
+> color sel red
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #1/C:179
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #1/C:179
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel blue
+> select #1/C:179
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #1/C:179
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #1/C:184
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel blue
+> select #1/C:191
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel red
+> select #1/C:241
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #1/C:241
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel red
+> select #1/C:191
+atoms, 8 bonds, 1 residue, 1 model selected
+> select clear
+> save /Users/mauriciocomas/Desktop/image2.png supersample 3
+> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
+> structures correct.cxs"
+> hide #1 models
+> show #!8 models
+> select #8/A:133
+atoms, 8 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> select #8/A:112
+atoms, 7 bonds, 1 residue, 1 model selected
+> ui tool show "Show Sequence Viewer"
+> sequence chain #8/A
+Alignment identifier is 8/A
+> color sel red
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #8/A:114
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel blue
+> select #8/A:133@N
+atom, 1 residue, 1 model selected
+> select #8/A:133@CA
+atom, 1 residue, 1 model selected
+> select #8/A:133
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #8/A:133
+atoms, 8 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #8/A:143
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #8/A:143
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #8/A:143
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #8/A:143
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel blue
+> select #8/A:140
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #8/A:140
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel red
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #8/A:164
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #8/A:164
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel blue
+> select #8/A:164
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #8/A:164
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #8/A:169
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #8/A:169
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel blue
+> select clear
+> select #8/A:242
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:178-179
+atoms, 14 bonds, 2 residues, 1 model selected
+> select #8/A:176
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #8/A:176
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel red
+> select #8/A:226
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #8/A:226
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel red
+> select clear
+> save /Users/mauriciocomas/Desktop/image2.png supersample 3
+> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
+> structures correct.cxs"
+> show #3 models
+> hide #!8 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #3/A
+Alignment identifier is 3/A
+> select #3/A:143
+atoms, 8 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #3/A:161
+atoms, 4 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #3/A:121
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel red
+> select #3/A:124
+atoms, 7 bonds, 1 residue, 1 model selected
+> color sel red
+> select #3/A:150@CB
+atom, 1 residue, 1 model selected
+> select #3/A:150@CB
+atom, 1 residue, 1 model selected
+> select #3/A:150
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #3/A:150
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #3/A:150
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #3/A:150
+atoms, 6 bonds, 1 residue, 1 model selected
+> color sel dim gray
+> select #2/I:154@CB
+atom, 1 residue, 1 model selected
+> select #3/A:153
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #3/A:153-154
+atoms, 16 bonds, 2 residues, 1 model selected
+> select #3/A:153
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #3/A:153
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel blue
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #3/A:174
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #3/A:174
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #3/A:174
+atoms, 10 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 11 atom styles
+> style sel stick
+Changed 11 atom styles
+> show sel atoms
+> color sel blue
+> select #3/A:174
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #3/A:174
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #3/A:174
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #3/A:174
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #3/A:176
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #3/A:176-177
+atoms, 13 bonds, 2 residues, 1 model selected
+> select #3/A:174
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #3/A:174
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #3/A:179@CA
+atom, 1 residue, 1 model selected
+> select #3/A:179
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #3/A:179
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #3/A:179
+atoms, 6 bonds, 1 residue, 1 model selected
+> color sel dim gray
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #3/A:174
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #3/A:174
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #3/A:180
+atoms, 12 bonds, 1 residue, 1 model selected
+> select #3/A:180
+atoms, 12 bonds, 1 residue, 1 model selected
+> select #3/A:186
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel red
+> select #3/A:236
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel red
+> select clear
+> save /Users/mauriciocomas/Desktop/image2.png supersample 3
+> select #3/A:186
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #3/A:236
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #3/A:236
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:240@OE2
+atom, 1 residue, 1 model selected
+> select #2/I:240@CB
+atom, 1 residue, 1 model selected
+> select #3/A:236
+atoms, 8 bonds, 1 residue, 1 model selected
+> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
+> structures correct.cxs"
+> show #6 models
+> hide #3 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #6/A
+Alignment identifier is 6/A
+> select #6/A:146@CA
+atom, 1 residue, 1 model selected
+> select #6/A:146
+atoms, 8 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #6/A:164
+atoms, 5 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #6/A:125
+atoms, 7 bonds, 1 residue, 1 model selected
+> color sel red
+> select #6/A:127
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel red
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #6/A:156@CA
+atom, 1 residue, 1 model selected
+> select #6/A:156
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #6/A:156
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #6/A:156
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #6/A:127
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel blue
+> select #2/I:153
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #6/A:156
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel blue
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #6/A:168
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #6/A:168
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #6/A:153
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #6/A:156
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #6/A:156
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #2/I:152
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #2/I:152-156
+atoms, 33 bonds, 5 residues, 1 model selected
+> select #6/A:160
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #6/A:160-162
+atoms, 21 bonds, 3 residues, 1 model selected
+> select #6/A:148
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #6/A:148-157
+atoms, 76 bonds, 10 residues, 1 model selected
+> select #6/A:156
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #6/A:156
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #6/A:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #6/A:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #6/A:153
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #6/A:153
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #6/A:152
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #6/A:152
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #6/A:153
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #6/A:153
+atoms, 4 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> show sel atoms
+> color sel dim gray
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #6/A:177
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #6/A:153
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #6/A:153
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #6/A:156-157
+atoms, 16 bonds, 2 residues, 1 model selected
+> select #6/A:156-157
+atoms, 16 bonds, 2 residues, 1 model selected
+> select #6/A:177
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #6/A:177
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #6/A:177
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel atoms
+> color sel blue
+> select #6/A:182
+atoms, 3 bonds, 1 residue, 1 model selected
+> select clear
+> select #6/A:183
+atoms, 12 bonds, 1 residue, 1 model selected
+> select clear
+> select #6/A:182
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #6/A:183
+atoms, 12 bonds, 1 residue, 1 model selected
+> select #6/A:183
+atoms, 12 bonds, 1 residue, 1 model selected
+> select #6/A:182
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #6/A:182
+atoms, 3 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 4 atom styles
+> show sel atoms
+> color sel dim gray
+> select clear
+> select #6/A:189
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel red
+> select #6/A:239
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel red
+> select clear
+> save /Users/mauriciocomas/Desktop/image2.png supersample 3
+> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
+> structures correct.cxs"
+> hide #6 models
+> show #!5 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #5/C
+Alignment identifier is 5/C
+> select #5/C:119
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #5/C:119
+atoms, 7 bonds, 1 residue, 1 model selected
+> color sel dim gray
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #5/C:121@CA
+atom, 1 residue, 1 model selected
+> select #5/C:121
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #5/C:121
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel dim gray
+> select #5/C:140
+atoms, 8 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #5/C:147
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #5/C:147
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel dim gray
+> select #5/C:150
+atoms, 4 bonds, 1 residue, 1 model selected
+> select clear
+> select #2/I:157@CB
+atom, 1 residue, 1 model selected
+> select #5/C:150
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #5/C:150
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #5/C:152
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #5/C:152
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #5/C:150
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #5/C:150-151
+atoms, 12 bonds, 2 residues, 1 model selected
+> select #5/C:150
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #5/C:150
+atoms, 4 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 5 atom styles
+> show sel atoms
+> select #5/C:147
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #5/C:147
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #5/C:150
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #5/C:150
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #5/C:155-156
+atoms, 13 bonds, 2 residues, 1 model selected
+> select #5/C:154-156
+atoms, 22 bonds, 3 residues, 1 model selected
+> select #5/C:152
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #5/C:152-153
+atoms, 16 bonds, 2 residues, 1 model selected
+> select #5/C:152
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #5/C:152
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:161
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:161
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #5/C:154
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #5/C:154
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #5/C:153
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #5/C:153
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #2/I:159-160
+atoms, 16 bonds, 2 residues, 1 model selected
+> select #2/I:159-160
+atoms, 16 bonds, 2 residues, 1 model selected
+> select #2/I:160
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #2/I:160
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #5/C:152
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #5/C:152
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:159
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #2/I:159
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #5/C:152
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #5/C:152
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #5/C:149
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #5/C:149
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #5/C:150
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #5/C:150
+atoms, 4 bonds, 1 residue, 1 model selected
+> color sel dim gray
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #5/C:171
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #5/C:171
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #5/C:171
+atoms, 8 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 9 atom styles
+> show sel cartoons
+> show sel atoms
+> color sel blue
+> select #5/C:171
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #5/C:171
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #5/C:158
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #5/C:158
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #5/C:175
+atoms, 7 bonds, 1 residue, 1 model selected
+> color sel dim gray
+> select #2/I:190@CG
+atom, 1 residue, 1 model selected
+> select #5/C:183
+atoms, 7 bonds, 1 residue, 1 model selected
+> color sel dim gray
+> select #5/C:233-234
+atoms, 12 bonds, 2 residues, 1 model selected
+> select #5/C:233-234
+atoms, 12 bonds, 2 residues, 1 model selected
+> select #5/C:233
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #5/C:233
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel dim gray
+> select clear
+> save /Users/mauriciocomas/Desktop/image2.png supersample 3
+> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
+> structures correct.cxs"
+> hide #!5 models
+> show #4 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #4/L
+Alignment identifier is 4/L
+> select #4/L:154
+atoms, 8 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #4/L:172
+atoms, 8 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #4/L:133
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel red
+> select #4/L:135
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel blue
+> select #4/L:161
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #4/L:161
+atoms, 6 bonds, 1 residue, 1 model selected
+> color sel dim gray
+> select #4/L:164
+atoms, 4 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 5 atom styles
+> show sel atoms
+> color sel dim gray
+> select #4/L:185
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #4/L:164
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select clear
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #4/L:185
+atoms, 10 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 11 atom styles
+> show sel atoms
+> color sel blue
+> select clear
+> select #4/L:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel blue
+> select #4/L:197
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel dim gray
+> select #4/L:247
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel red
+> select clear
+> save /Users/mauriciocomas/Desktop/image2.png supersample 3
+> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
+> structures correct.cxs"
+> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
+> structures correct.cxs"
+——— End of log from Wed Mar 29 11:43:44 2023 ———
+opened ChimeraX session
+> hide #4 models
+> open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/AlphFold
+> Colaboratory Ross River.pdb"
+Chain information for AlphFold Colaboratory Ross River.pdb #10
+---
+Chain | Description
+A | No description available
+> ui tool show Matchmaker
+> matchmaker #10 to #2
+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 3j2w.pdb, chain I (#2) with AlphFold Colaboratory Ross River.pdb,
+chain A (#10), sequence alignment score = 670.2
+RMSD between 146 pruned atom pairs is 0.751 angstroms; (across all 149 pairs:
+.841)
+> ui tool show "Show Sequence Viewer"
+> sequence chain #10/A
+Alignment identifier is 10/A
+> ui mousemode right select
+> select #10/A:129
+atoms, 11 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 12 atom styles
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> select #10/A:131
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> select #10/A:160
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> select #10/A:157
+atoms, 11 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel blue
+> select #10/A:181
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> select #10/A:186
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> select #10/A:193
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> select #10/A:243
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> select clear
+> save /Users/mauriciocomas/Desktop/image3.png supersample 3
+> select #10/A:157
+atoms, 11 bonds, 1 residue, 1 model selected
+> color sel red
+> select clear
+> save /Users/mauriciocomas/Desktop/image4.png supersample 3
+> save
+> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
+> open "/Users/mauriciocomas/Downloads/YP_009020571.1 and 20 other
+> sequences.aln"
+Traceback (most recent call last):
+File
+"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
+packages/chimerax/seqalign/parse.py", line 31, in open_file
+seqs, file_attrs, file_markups = ns['read'](session, stream)
+File
+"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
+packages/chimerax/seqalign/io/readALN.py", line 33, in read
+raise FormatSyntaxError("First non-blank line does not start with 'CLUSTAL'")
+chimerax.seqalign.parse.FormatSyntaxError: First non-blank line does not start
+with 'CLUSTAL'
+During handling of the above exception, another exception occurred:
+Traceback (most recent call last):
+File
+"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
+packages/chimerax/ui/gui.py", line 261, in event
+_open_dropped_file(self.session, event.file())
+File
+"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
+packages/chimerax/ui/gui.py", line 1812, in _open_dropped_file
+run(session, 'open %s' % FileNameArg.unparse(path))
+File
+"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
+packages/chimerax/core/commands/run.py", line 36, in run
+results = command.run(text, log=log, return_json=return_json)
+File
+"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
+packages/chimerax/core/commands/cli.py", line 2852, in run
+result = ci.function(session, **kw_args)
+File
+"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
+packages/chimerax/open_command/cmd.py", line 118, in cmd_open
+models = Command(session, registry=registry).run(provider_cmd_text,
+log=log)[0]
+File
+"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
+packages/chimerax/core/commands/cli.py", line 2852, in run
+result = ci.function(session, **kw_args)
+File
+"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
+packages/chimerax/open_command/cmd.py", line 179, in provider_open
+models, status = collated_open(session, None, [data], data_format,
+_add_models,
+File
+"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
+packages/chimerax/open_command/cmd.py", line 421, in collated_open
+return func(*func_args, **func_kw)
+File
+"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
+packages/chimerax/seqalign/__init__.py", line 61, in open
+return open_file(session, data, file_name,
+File
+"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
+packages/chimerax/seqalign/parse.py", line 33, in open_file
+raise IOError("Syntax error in %s file '%s': %s" % (format_name, fname, err))
+OSError: Syntax error in ALN file 'YP_009020571.1 and 20 other sequences.aln':
+First non-blank line does not start with 'CLUSTAL'
+OSError: Syntax error in ALN file 'YP_009020571.1 and 20 other sequences.aln':
+First non-blank line does not start with 'CLUSTAL'
+File
+"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
+packages/chimerax/seqalign/parse.py", line 33, in open_file
+raise IOError("Syntax error in %s file '%s': %s" % (format_name, fname, err))
+See log for complete Python traceback.
+> open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/Alphavirus
+> sequences/Madaragia YP_009020571.1 and 20 other sequences.aln"
+Traceback (most recent call last):
+File
+"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
+packages/chimerax/seqalign/parse.py", line 31, in open_file
+seqs, file_attrs, file_markups = ns['read'](session, stream)
+File
+"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
+packages/chimerax/seqalign/io/readALN.py", line 33, in read
+raise FormatSyntaxError("First non-blank line does not start with 'CLUSTAL'")
+chimerax.seqalign.parse.FormatSyntaxError: First non-blank line does not start
+with 'CLUSTAL'
+During handling of the above exception, another exception occurred:
+Traceback (most recent call last):
+File
+"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
+packages/chimerax/ui/gui.py", line 261, in event
+_open_dropped_file(self.session, event.file())
+File
+"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
+packages/chimerax/ui/gui.py", line 1812, in _open_dropped_file
+run(session, 'open %s' % FileNameArg.unparse(path))
+File
+"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
+packages/chimerax/core/commands/run.py", line 36, in run
+results = command.run(text, log=log, return_json=return_json)
+File
+"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
+packages/chimerax/core/commands/cli.py", line 2852, in run
+result = ci.function(session, **kw_args)
+File
+"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
+packages/chimerax/open_command/cmd.py", line 118, in cmd_open
+models = Command(session, registry=registry).run(provider_cmd_text,
+log=log)[0]
+File
+"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
+packages/chimerax/core/commands/cli.py", line 2852, in run
+result = ci.function(session, **kw_args)
+File
+"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
+packages/chimerax/open_command/cmd.py", line 179, in provider_open
+models, status = collated_open(session, None, [data], data_format,
+_add_models,
+File
+"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
+packages/chimerax/open_command/cmd.py", line 421, in collated_open
+return func(*func_args, **func_kw)
+File
+"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
+packages/chimerax/seqalign/__init__.py", line 61, in open
+return open_file(session, data, file_name,
+File
+"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
+packages/chimerax/seqalign/parse.py", line 33, in open_file
+raise IOError("Syntax error in %s file '%s': %s" % (format_name, fname, err))
+OSError: Syntax error in ALN file 'Madaragia YP_009020571.1 and 20 other
+sequences.aln': First non-blank line does not start with 'CLUSTAL'
+OSError: Syntax error in ALN file 'Madaragia YP_009020571.1 and 20 other
+sequences.aln': First non-blank line does not start with 'CLUSTAL'
+File
+"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
+packages/chimerax/seqalign/parse.py", line 33, in open_file
+raise IOError("Syntax error in %s file '%s': %s" % (format_name, fname, err))
+See log for complete Python traceback.
+> hide #10 models
+> open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/AlphaFold
+> 2/AlphaFold Colaboratory Middelburg virus.pdb"
+Chain information for AlphaFold Colaboratory Middelburg virus.pdb #11
+---
+Chain | Description
+A | No description available
+> ui tool show Matchmaker
+> matchmaker #11 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 7vga.pdb, chain C (#1) with AlphaFold Colaboratory Middelburg
+virus.pdb, chain A (#11), sequence alignment score = 810.9
+RMSD between 151 pruned atom pairs is 0.862 angstroms; (across all 158 pairs:
+.359)
+> show #10 models
+> hide #10 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #11/A
+Alignment identifier is 11/A
+> select #11/A:130
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> select #11/A:132
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right select
+> select #11/A:158
+atoms, 11 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> select #11/A:161
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> select #11/A:182
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> select #11/A:187
+atoms, 16 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 17 atom styles
+> show sel atoms
+> color sel dim gray
+> select #11/A:184
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #11/A:184
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #11/A:184
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #11/A:184-185
+atoms, 21 bonds, 2 residues, 1 model selected
+> select #11/A:184
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #11/A:184
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #11/A:194
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> select #11/A:244
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> select clear
+> save /Users/mauriciocomas/Desktop/image1.png supersample 3
+> show #10 models
+> hide #10 models
+> show #10 models
+> hide #10 models
+> show #10 models
+> hide #10 models
+> show #10 models
+> hide #10 models
+> show #10 models
+> hide #10 models
+> show #10 models
+> hide #10 models
+> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/Chimera X
+> sessions/structures.cxs"
+——— End of log from Wed May 24 12:56:46 2023 ———
+opened ChimeraX session
+> hide #11 models
+> open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/AlphaFold
+> 2/AlphaFold Colaboratory Everglades virus.pdb"
+Chain information for AlphaFold Colaboratory Everglades virus.pdb #12
+---
+Chain | Description
+A | No description available
+> ui tool show Matchmaker
+> matchmaker #12 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 7vga.pdb, chain C (#1) with AlphaFold Colaboratory Everglades
+virus.pdb, chain A (#12), sequence alignment score = 512.4
+RMSD between 151 pruned atom pairs is 0.937 angstroms; (across all 158 pairs:
+.296)
+> ui tool show "Show Sequence Viewer"
+> sequence chain #12/A
+Alignment identifier is 12/A
+> ui mousemode right select
+> select #12/A:132
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> select #12/A:134
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> select #12/A:163
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #12/A:159
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #12/A:160
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #12/A:163
+atoms, 9 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 10 atom styles
+> show sel atoms
+> color sel dim gray
+> select #12/A:160
+atoms, 15 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 16 atom styles
+> style sel stick
+Changed 16 atom styles
+> show sel atoms
+> color sel dim gray
+> select #12/A:159-160
+atoms, 27 bonds, 2 residues, 1 model selected
+> select #12/A:159-160
+atoms, 27 bonds, 2 residues, 1 model selected
+> style sel stick
+Changed 28 atom styles
+> show sel atoms
+> select #12/A:160
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #12/A:160
+atoms, 15 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> ui tool show "Color Actions"
+> color sel bychain
+> select #12/A:159
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #12/A:159
+atoms, 11 bonds, 1 residue, 1 model selected
+> show sel atoms
+> color sel red
+> select #2/I:152
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #12/A:163
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #12/A:165
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #12/A:165
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #12/A:184
+atoms, 23 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 24 atom styles
+> show sel atoms
+> color sel blue
+> select #12/A:189
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel medium blue
+> select #12/A:196
+atoms, 16 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 17 atom styles
+> show sel atoms
+> color sel dim gray
+> select #12/A:247
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #12/A:246
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #12/A:246
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> select clear
+> save /Users/mauriciocomas/Desktop/image2.png supersample 3
+> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/Chimera X
+> sessions/structures.cxs"
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #12/A:163
+atoms, 9 bonds, 1 residue, 1 model selected
+> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/Chimera X
+> sessions/overlap of CP structures.cxs"
+——— End of log from Thu May 25 12:52:10 2023 ———
+opened ChimeraX session
+> hide #12 models
+> open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/AlphaFold
+> 2/Alpha Fold Collaboratory Salmon Pancrease Disease.pdb"
+Chain information for Alpha Fold Collaboratory Salmon Pancrease Disease.pdb
+#13
+---
+Chain | Description
+A | No description available
+> ui tool show Matchmaker
+> matchmaker #13 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 7vga.pdb, chain C (#1) with Alpha Fold Collaboratory Salmon
+Pancrease Disease.pdb, chain A (#13), sequence alignment score = 305.8
+RMSD between 123 pruned atom pairs is 1.087 angstroms; (across all 157 pairs:
+.548)
+> ui mousemode right rotate
+> ui tool show "Show Sequence Viewer"
+> sequence chain #13/A
+Alignment identifier is 13/A
+> ui mousemode right select
+> select #13/A:141
+atoms, 11 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> select #13/A:143
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #13/A:144
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #13/A:143
+atoms, 9 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 10 atom styles
+> show sel atoms
+> color sel dim gray
+> select #13/A:142
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #13/A:142
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #13/A:143
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #13/A:143
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #13/A:172
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #13/A:169
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #13/A:172
+atoms, 11 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> select #13/A:174
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #13/A:174-175
+atoms, 42 bonds, 2 residues, 1 model selected
+> select #13/A:174
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #13/A:174
+atoms, 21 bonds, 1 residue, 1 model selected
+Drag select of 5 residues
+> select #13/A:174
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #13/A:174
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #13/A:169
+atoms, 14 bonds, 1 residue, 1 model selected
+> color sel red
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> select #13/A:192
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #13/A:193
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #13/A:193
+atoms, 23 bonds, 1 residue, 1 model selected
+> color sel blue
+> style sel stick
+Changed 24 atom styles
+> show sel atoms
+> select #13/A:129
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #13/A:198
+atoms, 14 bonds, 1 residue, 1 model selected
+> color sel red
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> select #13/A:204
+atoms, 11 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> select #13/A:254
+atoms, 11 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> select clear
+> select clear
+> ui mousemode right rotate
+> save /Users/mauriciocomas/Desktop/image9.png supersample 3
+> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/Chimera X
+> sessions/overlap of CP structures.cxs"
+——— End of log from Thu May 25 17:54:54 2023 ———
+opened ChimeraX session
+> hide #13 models
+> open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/AlphaFold
+> 2/Alpha Fold Collaboratory Fort Morgan virus.pdb"
+Chain information for Alpha Fold Collaboratory Fort Morgan virus.pdb #14
+---
+Chain | Description
+A | No description available
+> ui tool show Matchmaker
+> matchmaker #14 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 7vga.pdb, chain C (#1) with Alpha Fold Collaboratory Fort Morgan
+virus.pdb, chain A (#14), sequence alignment score = 506.1
+RMSD between 152 pruned atom pairs is 0.926 angstroms; (across all 158 pairs:
+.271)
+> ui tool show "Show Sequence Viewer"
+> sequence chain #14/A
+Alignment identifier is 14/A
+> ui mousemode right select
+> select #14/A:119
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #14/A:120
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #14/A:120
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #14/A:121
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #14/A:121
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #14/A:118
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #14/A:118
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #14/A:119
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #14/A:119
+atoms, 13 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 14 atom styles
+> show sel atoms
+> color sel dim gray
+> select #14/A:121
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #14/A:121
+atoms, 16 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 17 atom styles
+> show sel atoms
+> color sel dim gray
+> select #14/A:150
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #14/A:147
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #14/A:146
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #14/A:146
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> select #14/A:150
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #14/A:151-152
+atoms, 37 bonds, 2 residues, 1 model selected
+> select #14/A:151-152
+atoms, 37 bonds, 2 residues, 1 model selected
+> select #14/A:152
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #14/A:152
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #14/A:150
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #14/A:150
+atoms, 9 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 10 atom styles
+> show sel atoms
+> color sel dim gray
+> select #14/A:171
+atoms, 21 bonds, 1 residue, 1 model selected
+> color sel medium blue
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> select #14/A:176
+atoms, 16 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 17 atom styles
+> show sel atoms
+> color sel dim gray
+> select #14/A:183
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #14/A:184
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #14/A:184
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #14/A:183
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #14/A:183
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 14 atom styles
+> show sel atoms
+> color sel dim gray
+> select #14/A:234
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #14/A:233
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #14/A:233
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> select clear
+> save /Users/mauriciocomas/Desktop/image11.png supersample 3
+> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/Chimera X
+> sessions/overlap of CP structures.cxs"
+——— End of log from Fri May 26 15:30:48 2023 ———
+opened ChimeraX session
+> hide #14 models
+> open "C:/Users/Carolina/Downloads/Ndumu virus Alphafold.pdb"
+Chain information for Ndumu virus Alphafold.pdb #15
+---
+Chain | Description
+A | No description available
+> ui tool show Matchmaker
+> matchmaker #15 to #2
+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 3j2w.pdb, chain I (#2) with Ndumu virus Alphafold.pdb, chain A
+(#15), sequence alignment score = 653.9
+RMSD between 144 pruned atom pairs is 0.776 angstroms; (across all 149 pairs:
+.015)
+> matchmaker #15 to #2
+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 3j2w.pdb, chain I (#2) with Ndumu virus Alphafold.pdb, chain A
+(#15), sequence alignment score = 653.9
+RMSD between 144 pruned atom pairs is 0.776 angstroms; (across all 149 pairs:
+.015)
+> save "C:/Users/Carolina/Downloads/overlap of CP structures.cxs"
+> ui mousemode right translate
+> show #10 models
+> hide #10 models
+> color #15 #ff5500ff
+> color #15 #ffaa00ff
+> color #15 #ffaa7fff
+> color #15 #ffa470ff
+> color #15 #ff9c6bff
+> color #15 #ff9a67ff
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
+——— End of log from Tue Jun 6 14:16:52 2023 ———
+opened ChimeraX session
+> ui tool show "Show Sequence Viewer"
+> sequence chain #15/A
+Alignment identifier is 15/A
+> ui mousemode right select
+> ui mousemode right translate
+> ui mousemode right select
+> select #15/A:128
+atoms, 11 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> select #15/A:130
+atoms, 14 bonds, 1 residue, 1 model selected
+> select clear
+[Repeated 2 time(s)]
+> select #15/A:130
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right translate
+> show sel atoms
+> style sel stick
+Changed 15 atom styles
+> style sel stick
+Changed 15 atom styles
+> show sel cartoons
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> hide sel atoms
+> show sel atoms
+> color sel red
+> ui mousemode right select
+> select #15/A:242
+atoms, 14 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+[Repeated 1 time(s)]
+> ui mousemode right rotate
+> ui mousemode right translate
+> ui mousemode right select
+> select #15/A:159
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #15/A:156
+atoms, 14 bonds, 1 residue, 1 model selected
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
+——— End of log from Tue Jun 6 14:34:43 2023 ———
+opened ChimeraX session
+> ui mousemode right select
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #15/A:130
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #15/A:130
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #15/A:127
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #15/A:128
+atoms, 11 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #15/A:242
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right translate
+[Repeated 1 time(s)]
+> ui mousemode right select
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #15/A:192
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #15/A:193
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #15/A:192
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
+Drag select of 1 residues
+> ui mousemode right select
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select clear
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #15/A:185
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right select
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #15/A:180
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #15/A:180
+atoms, 23 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> style sel stick
+Changed 24 atom styles
+> show sel atoms
+> color sel blue
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
+> ui mousemode right select
+> select #2/I:153
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #15/A:156
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #15/A:159
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
+——— End of log from Wed Jun 7 14:34:33 2023 ———
+opened ChimeraX session
+> show target m
+> hide target m
+> show #15 models
+> show #2 models
+> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/Alpha fold/Everglades virus Alphafold.pdb"
+Chain information for Everglades virus Alphafold.pdb #16
+---
+Chain | Description
+A | No description available
+> ui tool show Matchmaker
+> matchmaker #2-4,6,9-15#!5,7-8 to #16
+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 Everglades virus Alphafold.pdb, chain A (#16) with 3j2w.pdb, chain
+I (#2), sequence alignment score = 536
+RMSD between 147 pruned atom pairs is 0.728 angstroms; (across all 149 pairs:
+.822)
+Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with 1kxf.pdb, chain
+A (#3), sequence alignment score = 570.4
+RMSD between 149 pruned atom pairs is 0.682 angstroms; (across all 158 pairs:
+.151)
+Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with 7sfu.pdb, chain
+F (#4), sequence alignment score = 808
+RMSD between 147 pruned atom pairs is 0.721 angstroms; (across all 162 pairs:
+.067)
+Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with 4agk.pdb, chain
+A (#6), sequence alignment score = 550.5
+RMSD between 149 pruned atom pairs is 0.715 angstroms; (across all 151 pairs:
+.781)
+Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with 7ko8.pdb, chain
+G (#9), sequence alignment score = 563
+RMSD between 134 pruned atom pairs is 1.120 angstroms; (across all 152 pairs:
+.600)
+Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with AlphFold
+Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 797
+RMSD between 150 pruned atom pairs is 0.554 angstroms; (across all 260 pairs:
+.148)
+Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with AlphaFold
+Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
+.3
+RMSD between 152 pruned atom pairs is 0.630 angstroms; (across all 262 pairs:
+.549)
+Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with AlphaFold
+Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
+.7
+RMSD between 274 pruned atom pairs is 0.060 angstroms; (across all 274 pairs:
+.060)
+Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with Alpha Fold
+Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
+score = 549.1
+RMSD between 134 pruned atom pairs is 0.953 angstroms; (across all 266 pairs:
+.039)
+Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with Alpha Fold
+Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
+.7
+RMSD between 162 pruned atom pairs is 0.329 angstroms; (across all 254 pairs:
+.074)
+Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with Ndumu virus
+Alphafold.pdb, chain A (#15), sequence alignment score = 814.3
+RMSD between 142 pruned atom pairs is 0.555 angstroms; (across all 266 pairs:
+.306)
+Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with 6xo4.pdb, chain
+C (#5), sequence alignment score = 677.5
+RMSD between 106 pruned atom pairs is 1.220 angstroms; (across all 151 pairs:
+.045)
+Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with 1vcp.pdb, chain
+C (#7), sequence alignment score = 569.9
+RMSD between 147 pruned atom pairs is 0.619 angstroms; (across all 149 pairs:
+.761)
+Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with 2yew.pdb, chain
+G (#8), sequence alignment score = 512.3
+RMSD between 55 pruned atom pairs is 1.276 angstroms; (across all 171 pairs:
+.421)
+> hide #15 models
+> color #16 #0055ffff
+> color #16 #ff55ffff
+> color #16 magenta
+> hide #16 models
+> show #16 models
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
+——— End of log from Wed Jun 7 16:42:56 2023 ———
+opened ChimeraX session
+> ui mousemode right select
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #16/A:132
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #16/A:134
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right rotate
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #16/A:246
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right translate
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
+> ui mousemode right select
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #16/A:196
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #16/A:196
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #16/A:197
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #16/A:196
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #16/A:196
+atoms, 16 bonds, 1 residue, 1 model selected
+> view clip false
+[Repeated 1 time(s)]Drag select of 4 atoms, 9 residues, 2 bonds
+> ui mousemode right translate
+> ui mousemode right select
+> select #16/A:196
+atoms, 16 bonds, 1 residue, 1 model selected
+> select clear
+[Repeated 1 time(s)]
+> ui mousemode right translate
+> ui mousemode right select
+> select #16/A:196
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #16/A:197
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #16/A:196
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #16/A:195
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #16/A:196
+atoms, 16 bonds, 1 residue, 1 model selected
+Alignment identifier is 16/A
+Drag select of 3 residues
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #16/A:189
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #16/A:184
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #16/A:183
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #16/A:184
+atoms, 23 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 24 atom styles
+> show sel atoms
+> color sel blue
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #16/A:160
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #16/A:160
+atoms, 15 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 16 atom styles
+> show sel atoms
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #16/A:163
+atoms, 9 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 10 atom styles
+> show sel atoms
+> select clear
+> ui mousemode right translate
+> ui mousemode right select
+Drag select of 1 residues
+> select #16/A:197
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #16/A:196
+atoms, 16 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 17 atom styles
+> show sel atoms
+> select clear
+> ui mousemode right translate
+> ui mousemode right select
+> select #16/A:163
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #16/A:160
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #16/A:163
+atoms, 9 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
+——— End of log from Thu Jun 8 09:54:20 2023 ———
+opened ChimeraX session
+> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/Alpha fold/Bebaru virus Alphafold.pdb"
+Chain information for Bebaru virus Alphafold.pdb #17
+---
+Chain | Description
+A | No description available
+> color #17 #00aa7fff
+> ui tool show Matchmaker
+> matchmaker #2-4,6,9-16#!5,7-8 to #17
+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 Bebaru virus Alphafold.pdb, chain A (#17) with 3j2w.pdb, chain I
+(#2), sequence alignment score = 675.4
+RMSD between 148 pruned atom pairs is 0.764 angstroms; (across all 149 pairs:
+.786)
+Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with 1kxf.pdb, chain A
+(#3), sequence alignment score = 566.3
+RMSD between 148 pruned atom pairs is 0.837 angstroms; (across all 157 pairs:
+.897)
+Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with 7sfu.pdb, chain I
+(#4), sequence alignment score = 593
+RMSD between 143 pruned atom pairs is 0.808 angstroms; (across all 161 pairs:
+.693)
+Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with 4agk.pdb, chain A
+(#6), sequence alignment score = 561
+RMSD between 148 pruned atom pairs is 0.729 angstroms; (across all 150 pairs:
+.808)
+Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with 7ko8.pdb, chain D
+(#9), sequence alignment score = 805.5
+RMSD between 138 pruned atom pairs is 1.056 angstroms; (across all 152 pairs:
+.688)
+Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with AlphFold
+Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 1142
+RMSD between 163 pruned atom pairs is 0.340 angstroms; (across all 262 pairs:
+.400)
+Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with AlphaFold
+Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
+.9
+RMSD between 166 pruned atom pairs is 0.337 angstroms; (across all 260 pairs:
+.918)
+Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with AlphaFold
+Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
+.6
+RMSD between 147 pruned atom pairs is 0.553 angstroms; (across all 256 pairs:
+.037)
+Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with Alpha Fold
+Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
+score = 509.8
+RMSD between 129 pruned atom pairs is 0.766 angstroms; (across all 258 pairs:
+.546)
+Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with Alpha Fold
+Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
+.1
+RMSD between 148 pruned atom pairs is 0.467 angstroms; (across all 255 pairs:
+.095)
+Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with Ndumu virus
+Alphafold.pdb, chain A (#15), sequence alignment score = 946.6
+RMSD between 150 pruned atom pairs is 0.331 angstroms; (across all 257 pairs:
+.554)
+Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with Everglades virus
+Alphafold.pdb, chain A (#16), sequence alignment score = 814.6
+RMSD between 147 pruned atom pairs is 0.553 angstroms; (across all 256 pairs:
+.039)
+Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with 6xo4.pdb, chain C
+(#5), sequence alignment score = 520.4
+RMSD between 100 pruned atom pairs is 1.207 angstroms; (across all 150 pairs:
+.057)
+Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with 1vcp.pdb, chain C
+(#7), sequence alignment score = 729.6
+RMSD between 149 pruned atom pairs is 0.572 angstroms; (across all 149 pairs:
+.572)
+Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with 2yew.pdb, chain G
+(#8), sequence alignment score = 724.2
+RMSD between 49 pruned atom pairs is 1.194 angstroms; (across all 171 pairs:
+.614)
+> hide #16 models
+> color #17 #007d5cff
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
+> ui mousemode right select
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #17/A:122
+atoms, 11 bonds, 1 residue, 1 model selected
+Alignment identifier is 17/A
+> select #17/A:122
+atoms, 11 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 12 atom styles
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #17/A:124
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right select
+Drag select of 1 atoms, 1 bonds
+Drag select of 4 residues
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right rotate
+> ui mousemode right select
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #17/A:236
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #17/A:186
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #17/A:187
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #17/A:186
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> select clear
+> ui mousemode right translate
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
+> ui mousemode right select
+> select #17/A:124
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #17/A:122
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #17/A:124
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #17/A:236
+atoms, 14 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #17/A:186
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #17/A:179
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #17/A:179
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #17/A:174
+atoms, 23 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 24 atom styles
+> show sel atoms
+> color sel blue
+> select clear
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #17/A:174
+atoms, 23 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #17/A:153
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #17/A:150
+atoms, 11 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
+> select clear
+> ui mousemode right translate
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
+——— End of log from Thu Jun 8 12:29:59 2023 ———
+opened ChimeraX session
+> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/Alpha fold/Caaingua virus AlphaFold.pdb"
+Chain information for Caaingua virus AlphaFold.pdb #18
+---
+Chain | Description
+A | No description available
+> ui tool show Matchmaker
+> matchmaker #2-4,6,9-17#!5,7-8 to #18
+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 Caaingua virus AlphaFold.pdb, chain A (#18) with 3j2w.pdb, chain I
+(#2), sequence alignment score = 458.4
+RMSD between 130 pruned atom pairs is 0.780 angstroms; (across all 149 pairs:
+.000)
+Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with 1kxf.pdb, chain A
+(#3), sequence alignment score = 475.4
+RMSD between 137 pruned atom pairs is 0.844 angstroms; (across all 158 pairs:
+.636)
+Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with 7sfu.pdb, chain I
+(#4), sequence alignment score = 487.6
+RMSD between 132 pruned atom pairs is 0.852 angstroms; (across all 162 pairs:
+.515)
+Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with 4agk.pdb, chain A
+(#6), sequence alignment score = 508.1
+RMSD between 138 pruned atom pairs is 0.816 angstroms; (across all 151 pairs:
+.682)
+Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with 7ko8.pdb, chain D
+(#9), sequence alignment score = 485.3
+RMSD between 124 pruned atom pairs is 1.036 angstroms; (across all 152 pairs:
+.096)
+Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with AlphFold
+Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 707.3
+RMSD between 138 pruned atom pairs is 0.591 angstroms; (across all 252 pairs:
+.368)
+Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with AlphaFold
+Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
+RMSD between 133 pruned atom pairs is 0.547 angstroms; (across all 249 pairs:
+.925)
+Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with AlphaFold
+Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
+.8
+RMSD between 151 pruned atom pairs is 0.608 angstroms; (across all 265 pairs:
+.650)
+Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with Alpha Fold
+Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
+score = 529
+RMSD between 121 pruned atom pairs is 0.853 angstroms; (across all 258 pairs:
+.133)
+Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with Alpha Fold
+Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
+.6
+RMSD between 139 pruned atom pairs is 0.598 angstroms; (across all 247 pairs:
+.105)
+Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with Ndumu virus
+Alphafold.pdb, chain A (#15), sequence alignment score = 669.2
+RMSD between 135 pruned atom pairs is 0.619 angstroms; (across all 259 pairs:
+.678)
+Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with Everglades virus
+Alphafold.pdb, chain A (#16), sequence alignment score = 681.8
+RMSD between 151 pruned atom pairs is 0.608 angstroms; (across all 265 pairs:
+.649)
+Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with Bebaru virus
+Alphafold.pdb, chain A (#17), sequence alignment score = 705
+RMSD between 117 pruned atom pairs is 0.563 angstroms; (across all 250 pairs:
+.618)
+Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with 6xo4.pdb, chain C
+(#5), sequence alignment score = 413.1
+RMSD between 95 pruned atom pairs is 1.212 angstroms; (across all 151 pairs:
+.833)
+Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with 1vcp.pdb, chain C
+(#7), sequence alignment score = 489.6
+RMSD between 136 pruned atom pairs is 0.711 angstroms; (across all 149 pairs:
+.711)
+Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with 2yew.pdb, chain G
+(#8), sequence alignment score = 446.9
+RMSD between 52 pruned atom pairs is 1.300 angstroms; (across all 171 pairs:
+.079)
+> hide #17 models
+> color #18 #ff5500ff
+> color #18 #c54200ff
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
+——— End of log from Thu Jun 8 14:55:45 2023 ———
+opened ChimeraX session
+> ui mousemode right select
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #18/A:123
+atoms, 11 bonds, 1 residue, 1 model selected
+Alignment identifier is 18/A
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> select #18/A:125
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #18/A:125
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right translate
+[Repeated 1 time(s)]
+> ui mousemode right select
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #18/A:242
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #18/A:242
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #18/A:241
+atoms, 14 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> color #18 #f35100ff
+> color #18 #eb4e00ff
+> color sel red
+> color #18 #ffaa00ff
+> color #18 #ff9b0eff
+> color #18 #ff790cff
+> color #18 #ff850aff
+> show #15 models
+> hide #15 models
+> color #18 #ee7c09ff
+> color sel red
+> ui mousemode right select
+Drag select of 2 residues
+> ui mousemode right translate
+> ui mousemode right select
+> select #18/A:123
+atoms, 11 bonds, 1 residue, 1 model selected
+> color sel red
+> select #18/A:125
+atoms, 21 bonds, 1 residue, 1 model selected
+> color sel blue
+> select clear
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:240@CA
+atom, 1 residue, 1 model selected
+> select #18/A:241
+atoms, 14 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #18/A:189
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #18/A:190
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #18/A:189
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #18/A:189
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #18/A:189
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #18/A:190
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #18/A:189
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #18/A:190
+atoms, 16 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 17 atom styles
+> show sel atoms
+> color sel gray
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #18/A:190
+atoms, 16 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #18/A:182
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #18/A:181
+atoms, 17 bonds, 1 residue, 1 model selected
+> select #18/A:182
+atoms, 13 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 14 atom styles
+> show sel atoms
+> color sel orange
+> ui mousemode right translate
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
+> ui mousemode right select
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #18/A:175
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #18/A:174
+atoms, 20 bonds, 1 residue, 1 model selected
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #18/A:175
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #18/A:175
+atoms, 18 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 19 atom styles
+> show sel atoms
+> color sel gray
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #18/A:175
+atoms, 18 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #18/A:151
+atoms, 14 bonds, 1 residue, 1 model selected
+> show sel atoms
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+Drag select of 3 residues
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #18/A:154
+atoms, 13 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 14 atom styles
+> show sel atoms
+> color sel orange
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
+> ui mousemode right translate
+> ui mousemode right select
+> select #18/A:182
+atoms, 13 bonds, 1 residue, 1 model selected
+Drag select of 11 residues
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> hide #18 models
+> show #16 models
+> ui mousemode right rotate
+> ui mousemode right select
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #16/A:196@CA
+atom, 1 residue, 1 model selected
+Alignment identifier is 16/A
+> color sel orange
+> style sel stick
+Changed 1 atom style
+> show sel atoms
+> select #16/A:196
+atoms, 16 bonds, 1 residue, 1 model selected
+> ui mousemode right select
+> select #16/A:196
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #16/A:196
+atoms, 16 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 17 atom styles
+> show sel atoms
+> hide sel atoms
+> show sel atoms
+> color sel red
+> color sel orange
+> ui mousemode right translate
+> ui mousemode right rotate
+> ui mousemode right select
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #16/A:163
+atoms, 9 bonds, 1 residue, 1 model selected
+> color sel gray
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #16/A:160
+atoms, 15 bonds, 1 residue, 1 model selected
+> color sel gray
+> ui mousemode right translate
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
+——— End of log from Thu Jun 8 16:20:57 2023 ———
+opened ChimeraX session
+> hide #16 models
+> show #18 models
+> ui mousemode right select
+Drag select of 1 residues
+> select clear
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #18/A:154
+atoms, 13 bonds, 1 residue, 1 model selected
+> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/Alpha fold/Cabassou virus Alphafold.pdb"
+Chain information for Cabassou virus Alphafold.pdb #19
+---
+Chain | Description
+A | No description available
+> hide #18 models
+> select add #18
+atoms, 4396 bonds, 269 residues, 1 model selected
+> select subtract #18
+Nothing selected
+> ui tool show Matchmaker
+> matchmaker #2-4,6,9-18#!5,7-8 to #19
+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 Cabassou virus Alphafold.pdb, chain A (#19) with 3j2w.pdb, chain I
+(#2), sequence alignment score = 523.2
+RMSD between 146 pruned atom pairs is 0.713 angstroms; (across all 149 pairs:
+.884)
+Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with 1kxf.pdb, chain A
+(#3), sequence alignment score = 557.2
+RMSD between 150 pruned atom pairs is 0.659 angstroms; (across all 158 pairs:
+.145)
+Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with 7sfu.pdb, chain F
+(#4), sequence alignment score = 796.5
+RMSD between 148 pruned atom pairs is 0.761 angstroms; (across all 162 pairs:
+.057)
+Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with 4agk.pdb, chain A
+(#6), sequence alignment score = 555.1
+RMSD between 150 pruned atom pairs is 0.694 angstroms; (across all 151 pairs:
+.721)
+Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with 7ko8.pdb, chain G
+(#9), sequence alignment score = 565
+RMSD between 133 pruned atom pairs is 1.092 angstroms; (across all 152 pairs:
+.625)
+Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with AlphFold
+Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 820.3
+RMSD between 151 pruned atom pairs is 0.605 angstroms; (across all 258 pairs:
+.418)
+Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with AlphaFold
+Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
+.7
+RMSD between 8 pruned atom pairs is 1.343 angstroms; (across all 261 pairs:
+.012)
+Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with AlphaFold
+Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
+.2
+RMSD between 165 pruned atom pairs is 0.252 angstroms; (across all 273 pairs:
+.940)
+Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with Alpha Fold
+Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
+score = 567.2
+RMSD between 5 pruned atom pairs is 1.242 angstroms; (across all 269 pairs:
+.754)
+Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with Alpha Fold
+Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
+.6
+RMSD between 162 pruned atom pairs is 0.383 angstroms; (across all 255 pairs:
+.412)
+Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with Ndumu virus
+Alphafold.pdb, chain A (#15), sequence alignment score = 812.5
+RMSD between 147 pruned atom pairs is 0.649 angstroms; (across all 265 pairs:
+.998)
+Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with Everglades virus
+Alphafold.pdb, chain A (#16), sequence alignment score = 1238.2
+RMSD between 165 pruned atom pairs is 0.252 angstroms; (across all 273 pairs:
+.940)
+Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with Bebaru virus
+Alphafold.pdb, chain A (#17), sequence alignment score = 803.3
+RMSD between 13 pruned atom pairs is 1.246 angstroms; (across all 257 pairs:
+.843)
+Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with Caaingua virus
+AlphaFold.pdb, chain A (#18), sequence alignment score = 703.7
+RMSD between 149 pruned atom pairs is 0.682 angstroms; (across all 261 pairs:
+.890)
+Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with 6xo4.pdb, chain C
+(#5), sequence alignment score = 693.4
+RMSD between 104 pruned atom pairs is 1.218 angstroms; (across all 151 pairs:
+.050)
+Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with 1vcp.pdb, chain C
+(#7), sequence alignment score = 557.1
+RMSD between 147 pruned atom pairs is 0.589 angstroms; (across all 149 pairs:
+.717)
+Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with 2yew.pdb, chain G
+(#8), sequence alignment score = 512.3
+RMSD between 54 pruned atom pairs is 1.264 angstroms; (across all 171 pairs:
+.925)
+> show #18 models
+> hide #18 models
+> color #19 #aaff7fff
+> color #19 #92d96cff
+> color #19 #90d56aff
+> color #19 #88ca65ff
+> color #19 #8fd46aff
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
+——— End of log from Fri Jun 9 12:21:12 2023 ———
+opened ChimeraX session
+> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/Alpha fold/Eilat virus Alphafold.pdb"
+Chain information for Eilat virus Alphafold.pdb #20
+---
+Chain | Description
+A | No description available
+> ui tool show Matchmaker
+> matchmaker #2-4,6,9-19#!5,7-8 to #20
+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 Eilat virus Alphafold.pdb, chain A (#20) with 3j2w.pdb, chain I
+(#2), sequence alignment score = 459.1
+RMSD between 145 pruned atom pairs is 0.743 angstroms; (across all 149 pairs:
+.843)
+Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with 1kxf.pdb, chain A
+(#3), sequence alignment score = 618.2
+RMSD between 148 pruned atom pairs is 0.717 angstroms; (across all 159 pairs:
+.840)
+Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with 7sfu.pdb, chain I
+(#4), sequence alignment score = 520.6
+RMSD between 138 pruned atom pairs is 0.873 angstroms; (across all 162 pairs:
+.526)
+Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with 4agk.pdb, chain A
+(#6), sequence alignment score = 660.7
+RMSD between 150 pruned atom pairs is 0.630 angstroms; (across all 152 pairs:
+.685)
+Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with 7ko8.pdb, chain G
+(#9), sequence alignment score = 491.3
+RMSD between 125 pruned atom pairs is 1.096 angstroms; (across all 152 pairs:
+.726)
+Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with AlphFold Colaboratory
+Ross River.pdb, chain A (#10), sequence alignment score = 688.4
+RMSD between 151 pruned atom pairs is 0.721 angstroms; (across all 251 pairs:
+.337)
+Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with AlphaFold
+Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
+.8
+RMSD between 7 pruned atom pairs is 1.275 angstroms; (across all 248 pairs:
+.093)
+Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with AlphaFold
+Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
+.4
+RMSD between 10 pruned atom pairs is 1.510 angstroms; (across all 254 pairs:
+.648)
+Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with Alpha Fold
+Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
+score = 512.7
+RMSD between 5 pruned atom pairs is 1.118 angstroms; (across all 251 pairs:
+.761)
+Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with Alpha Fold
+Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
+.5
+RMSD between 151 pruned atom pairs is 0.659 angstroms; (across all 245 pairs:
+.518)
+Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with Ndumu virus
+Alphafold.pdb, chain A (#15), sequence alignment score = 640.6
+RMSD between 149 pruned atom pairs is 0.662 angstroms; (across all 252 pairs:
+.525)
+Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with Everglades virus
+Alphafold.pdb, chain A (#16), sequence alignment score = 706.4
+RMSD between 10 pruned atom pairs is 1.511 angstroms; (across all 254 pairs:
+.647)
+Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with Bebaru virus
+Alphafold.pdb, chain A (#17), sequence alignment score = 702.4
+RMSD between 127 pruned atom pairs is 0.613 angstroms; (across all 251 pairs:
+.013)
+Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with Caaingua virus
+AlphaFold.pdb, chain A (#18), sequence alignment score = 647.9
+RMSD between 142 pruned atom pairs is 0.759 angstroms; (across all 242 pairs:
+.358)
+Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with Cabassou virus
+Alphafold.pdb, chain A (#19), sequence alignment score = 707.1
+RMSD between 148 pruned atom pairs is 0.716 angstroms; (across all 253 pairs:
+.904)
+Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with 6xo4.pdb, chain C
+(#5), sequence alignment score = 441.5
+RMSD between 91 pruned atom pairs is 1.178 angstroms; (across all 150 pairs:
+.235)
+Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with 1vcp.pdb, chain C
+(#7), sequence alignment score = 506.2
+RMSD between 144 pruned atom pairs is 0.683 angstroms; (across all 149 pairs:
+.855)
+Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with 2yew.pdb, chain G
+(#8), sequence alignment score = 461.4
+RMSD between 55 pruned atom pairs is 1.242 angstroms; (across all 171 pairs:
+.961)
+> color #20 #55aa00ff
+> color #20 #00aa7fff
+> color #20 #00b182ff
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
+> hide #20 models
+> show #20 models
+> hide #20 models
+> ui mousemode right select
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #19/A:133
+atoms, 11 bonds, 1 residue, 1 model selected
+Alignment identifier is 19/A
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #19/A:135
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> select clear
+> ui mousemode right translate
+> ui mousemode right select
+> select clear
+Drag select of 2 residues
+> ui mousemode right translate
+> ui mousemode right select
+> select #19/A:45
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+[Repeated 1 time(s)]
+> ui mousemode right rotate
+> ui mousemode right select
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #19/A:133
+atoms, 11 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #19/A:247
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> select clear
+> ui mousemode right translate
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
+> ui mousemode right select
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #19/A:197
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #19/A:197
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #19/A:198
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #19/A:197
+atoms, 16 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 17 atom styles
+> show sel atoms
+> ui mousemode right select
+> select #19/A:198
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #19/A:197
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #19/A:197
+atoms, 16 bonds, 1 residue, 1 model selected
+> color sel orange
+> ui mousemode right translate
+[Repeated 1 time(s)]
+> ui mousemode right rotate
+> ui mousemode right select
+> select clear
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #19/A:190
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #19/A:189
+atoms, 20 bonds, 1 residue, 1 model selected
+> select #2/I:184
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #19/A:191
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #19/A:190
+atoms, 23 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 24 atom styles
+> show sel atoms
+> color sel blue
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> ui mousemode right rotate
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+Drag select of 2 residues
+> select #19/A:185
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #19/A:185
+atoms, 23 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 24 atom styles
+> show sel atoms
+> color sel blue
+> select #19/A:184
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #19/A:185
+atoms, 23 bonds, 1 residue, 1 model selected
+> select clear
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #19/A:164
+atoms, 9 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 10 atom styles
+> show sel atoms
+> color sel gray
+Drag select of 2 residues
+> select #19/A:164
+atoms, 9 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #19/A:161
+atoms, 13 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 14 atom styles
+> show sel atoms
+> color sel orange
+> ui mousemode right translate
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
+> show #18 models
+> hide #18 models
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #19/A:135
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #19/A:135
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #19/A:135
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #19/A:133
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #19/A:247
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #19/A:197
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #19/A:190
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #19/A:185
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #19/A:164
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #19/A:161
+atoms, 13 bonds, 1 residue, 1 model selected
+> hide #19 models
+> show #20 models
+Drag select of 1 atoms, 5 residues
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #20/A:113
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #20/A:112
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #20/A:113
+atoms, 21 bonds, 1 residue, 1 model selected
+Alignment identifier is 20/A
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+Drag select of 1 bonds
+> ui mousemode right translate
+> ui mousemode right select
+> select #20/A:113
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #20/A:113
+atoms, 21 bonds, 1 residue, 1 model selected
+> color sel blue
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #20/A:113
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #20/A:115
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #20/A:115
+atoms, 15 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 16 atom styles
+> show sel atoms
+> color sel gray
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
+> ui mousemode right translate
+> ui mousemode right select
+> select #20/A:227
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #20/A:227
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #20/A:177
+atoms, 11 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> select clear
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #20/A:170
+atoms, 9 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 10 atom styles
+> show sel atoms
+> color sel gray
+Drag select of 4 residues
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #20/A:165
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #20/A:164
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #20/A:165
+atoms, 23 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 24 atom styles
+> show sel atoms
+> color sel blue
+Drag select of 12 atoms, 40 residues, 8 bonds
+> ui mousemode right translate
+> ui mousemode right rotate
+> ui mousemode right select
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #20/A:144
+atoms, 10 bonds, 1 residue, 1 model selected
+> color sel orange
+> style sel stick
+Changed 11 atom styles
+> show sel atoms
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> ui mousemode right select
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #20/A:141
+atoms, 18 bonds, 1 residue, 1 model selected
+> color sel gray
+> style sel stick
+Changed 19 atom styles
+> show sel atoms
+> ui mousemode right translate
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
+——— End of log from Fri Jun 9 15:09:21 2023 ———
+opened ChimeraX session
+> hide #20 models
+> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/Alpha fold/Highlands J. virus Alphafold.pdb"
+Chain information for Highlands J. virus Alphafold.pdb #21
+---
+Chain | Description
+A | No description available
+> ui tool show Matchmaker
+> matchmaker #2-4,6,9-20#!5,7-8 to #21
+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 Highlands J. virus Alphafold.pdb, chain A (#21) with 3j2w.pdb,
+chain I (#2), sequence alignment score = 534.6
+RMSD between 147 pruned atom pairs is 0.672 angstroms; (across all 149 pairs:
+.755)
+Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with 1kxf.pdb,
+chain A (#3), sequence alignment score = 584.9
+RMSD between 150 pruned atom pairs is 0.630 angstroms; (across all 158 pairs:
+.143)
+Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with 7sfu.pdb,
+chain F (#4), sequence alignment score = 704.2
+RMSD between 148 pruned atom pairs is 0.808 angstroms; (across all 162 pairs:
+.057)
+Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with 4agk.pdb,
+chain A (#6), sequence alignment score = 563.1
+RMSD between 150 pruned atom pairs is 0.643 angstroms; (across all 151 pairs:
+.671)
+Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with 7ko8.pdb,
+chain G (#9), sequence alignment score = 593.5
+RMSD between 134 pruned atom pairs is 1.109 angstroms; (across all 152 pairs:
+.587)
+Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with AlphFold
+Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 804.8
+RMSD between 148 pruned atom pairs is 0.558 angstroms; (across all 257 pairs:
+.440)
+Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with AlphaFold
+Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
+.8
+RMSD between 151 pruned atom pairs is 0.625 angstroms; (across all 258 pairs:
+.384)
+Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with AlphaFold
+Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
+.4
+RMSD between 163 pruned atom pairs is 0.346 angstroms; (across all 254 pairs:
+.033)
+Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with Alpha Fold
+Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
+score = 539.8
+RMSD between 132 pruned atom pairs is 0.906 angstroms; (across all 256 pairs:
+.694)
+Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with Alpha Fold
+Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
+.6
+RMSD between 164 pruned atom pairs is 0.338 angstroms; (across all 259 pairs:
+.527)
+Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with Ndumu virus
+Alphafold.pdb, chain A (#15), sequence alignment score = 774.7
+RMSD between 147 pruned atom pairs is 0.592 angstroms; (across all 251 pairs:
+.099)
+Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with Everglades
+virus Alphafold.pdb, chain A (#16), sequence alignment score = 996.4
+RMSD between 163 pruned atom pairs is 0.346 angstroms; (across all 254 pairs:
+.031)
+Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with Bebaru virus
+Alphafold.pdb, chain A (#17), sequence alignment score = 830.6
+RMSD between 151 pruned atom pairs is 0.547 angstroms; (across all 256 pairs:
+.017)
+Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with Caaingua virus
+AlphaFold.pdb, chain A (#18), sequence alignment score = 698.7
+RMSD between 151 pruned atom pairs is 0.680 angstroms; (across all 248 pairs:
+.738)
+Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with Cabassou virus
+Alphafold.pdb, chain A (#19), sequence alignment score = 1000.3
+RMSD between 159 pruned atom pairs is 0.253 angstroms; (across all 255 pairs:
+.413)
+Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with Eilat virus
+Alphafold.pdb, chain A (#20), sequence alignment score = 734.7
+RMSD between 151 pruned atom pairs is 0.665 angstroms; (across all 244 pairs:
+.300)
+Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with 6xo4.pdb,
+chain C (#5), sequence alignment score = 922.1
+RMSD between 103 pruned atom pairs is 1.185 angstroms; (across all 151 pairs:
+.034)
+Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with 1vcp.pdb,
+chain C (#7), sequence alignment score = 566.4
+RMSD between 147 pruned atom pairs is 0.527 angstroms; (across all 149 pairs:
+.665)
+Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with 2yew.pdb,
+chain G (#8), sequence alignment score = 540.8
+RMSD between 53 pruned atom pairs is 1.232 angstroms; (across all 169 pairs:
+.986)
+> color #21 #00aaffff
+> color #21 #007cbaff
+> select add #20
+atoms, 4011 bonds, 255 residues, 1 model selected
+> select subtract #20
+Nothing selected
+> show #20 models
+> hide #20 models
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
+——— End of log from Mon Jun 12 10:47:51 2023 ———
+opened ChimeraX session
+> ui mousemode right select
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #21/A:117
+atoms, 13 bonds, 1 residue, 1 model selected
+> select clear
+> select #21/A:117
+atoms, 13 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 14 atom styles
+> show sel atoms
+> color sel red
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+Destroying pre-existing alignment with identifier 2/I
+Alignment identifier is 2/I
+> select #21/A:117
+atoms, 13 bonds, 1 residue, 1 model selected
+Alignment identifier is 21/A
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #21/A:117
+atoms, 13 bonds, 1 residue, 1 model selected
+> color sel orange
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #21/A:119
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select clear
+> select #21/A:119
+atoms, 16 bonds, 1 residue, 1 model selected
+> color sel orange
+> style sel stick
+Changed 17 atom styles
+> show sel atoms
+Drag select of 8 atoms, 6 bonds
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #21/A:231
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right translate
+> ui mousemode right rotate
+> ui mousemode right select
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #21/A:181
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #21/A:181
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 14 atom styles
+> show sel atoms
+> color sel magenta
+Drag select of 1 atoms, 9 residues
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #21/A:174
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #21/A:175
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #21/A:174
+atoms, 16 bonds, 1 residue, 1 model selected
+> select clear
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #21/A:174
+atoms, 16 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 17 atom styles
+> show sel atoms
+> color sel orange
+Drag select of 2 residues
+> select clear
+[Repeated 3 time(s)]
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #21/A:169
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #21/A:145
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #21/A:145
+atoms, 16 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 17 atom styles
+> show sel atoms
+> color sel orange
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+Drag select of 1 residues
+> select clear
+> select #21/A:148
+atoms, 9 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 10 atom styles
+> show sel atoms
+> color sel gray
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
+Drag select of 6 residues
+> ui mousemode right translate
+> ui mousemode right select
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #21/A:117
+atoms, 13 bonds, 1 residue, 1 model selected
+> select clear
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #21/A:119
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #21/A:231
+atoms, 14 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #21/A:181
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+Drag select of 1 residues
+> select clear
+> ui mousemode right translate
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
+——— End of log from Mon Jun 12 13:04:04 2023 ———
+opened ChimeraX session
+> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/prediction Madariaga virus.zip"
+Unrecognized file suffix '.zip'
+> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/Madariaga virus Alpha Fold.pdb"
+Chain information for Madariaga virus Alpha Fold.pdb #22
+---
+Chain | Description
+A | No description available
+> ui tool show Matchmaker
+> matchmaker #2-4,6,9-21#!5,7-8 to #22
+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 Madariaga virus Alpha Fold.pdb, chain A (#22) with 3j2w.pdb, chain
+I (#2), sequence alignment score = 522
+RMSD between 147 pruned atom pairs is 0.696 angstroms; (across all 149 pairs:
+.789)
+Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with 1kxf.pdb, chain
+A (#3), sequence alignment score = 569.7
+RMSD between 150 pruned atom pairs is 0.715 angstroms; (across all 158 pairs:
+.187)
+Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with 7sfu.pdb, chain
+F (#4), sequence alignment score = 693.9
+RMSD between 145 pruned atom pairs is 0.763 angstroms; (across all 162 pairs:
+.000)
+Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with 4agk.pdb, chain
+A (#6), sequence alignment score = 550.5
+RMSD between 150 pruned atom pairs is 0.691 angstroms; (across all 151 pairs:
+.721)
+Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with 7ko8.pdb, chain
+G (#9), sequence alignment score = 589.5
+RMSD between 133 pruned atom pairs is 1.135 angstroms; (across all 152 pairs:
+.607)
+Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with AlphFold
+Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 785.6
+RMSD between 150 pruned atom pairs is 0.551 angstroms; (across all 253 pairs:
+.619)
+Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with AlphaFold
+Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
+.8
+RMSD between 149 pruned atom pairs is 0.602 angstroms; (across all 253 pairs:
+.010)
+Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with AlphaFold
+Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
+.5
+RMSD between 147 pruned atom pairs is 0.277 angstroms; (across all 256 pairs:
+.174)
+Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Alpha Fold
+Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
+score = 557.2
+RMSD between 107 pruned atom pairs is 0.830 angstroms; (across all 260 pairs:
+.521)
+Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Alpha Fold
+Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
+.4
+RMSD between 171 pruned atom pairs is 0.328 angstroms; (across all 259 pairs:
+.288)
+Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Ndumu virus
+Alphafold.pdb, chain A (#15), sequence alignment score = 767.1
+RMSD between 148 pruned atom pairs is 0.604 angstroms; (across all 253 pairs:
+.396)
+Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Everglades virus
+Alphafold.pdb, chain A (#16), sequence alignment score = 991.5
+RMSD between 147 pruned atom pairs is 0.278 angstroms; (across all 256 pairs:
+.175)
+Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Bebaru virus
+Alphafold.pdb, chain A (#17), sequence alignment score = 810.1
+RMSD between 150 pruned atom pairs is 0.536 angstroms; (across all 249 pairs:
+.607)
+Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Caaingua virus
+AlphaFold.pdb, chain A (#18), sequence alignment score = 679.6
+RMSD between 84 pruned atom pairs is 0.443 angstroms; (across all 250 pairs:
+.023)
+Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Cabassou virus
+Alphafold.pdb, chain A (#19), sequence alignment score = 996.6
+RMSD between 158 pruned atom pairs is 0.330 angstroms; (across all 257 pairs:
+.933)
+Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Eilat virus
+Alphafold.pdb, chain A (#20), sequence alignment score = 719.3
+RMSD between 148 pruned atom pairs is 0.691 angstroms; (across all 243 pairs:
+.968)
+Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Highlands J.
+virus Alphafold.pdb, chain A (#21), sequence alignment score = 1253.2
+RMSD between 119 pruned atom pairs is 0.235 angstroms; (across all 259 pairs:
+.666)
+Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with 6xo4.pdb, chain
+C (#5), sequence alignment score = 1014.1
+RMSD between 100 pruned atom pairs is 1.163 angstroms; (across all 151 pairs:
+.109)
+Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with 1vcp.pdb, chain
+C (#7), sequence alignment score = 555.2
+RMSD between 147 pruned atom pairs is 0.560 angstroms; (across all 149 pairs:
+.708)
+Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with 2yew.pdb, chain
+G (#8), sequence alignment score = 534.1
+RMSD between 54 pruned atom pairs is 1.237 angstroms; (across all 171 pairs:
+.062)
+> hide #21 models
+> show #21 models
+> hide #22 models
+> show #22 models
+> hide #21 models
+> color #22 #ff5500ff
+> color #22 #eb4e00ff
+> ui mousemode right select
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #22/A:118
+atoms, 18 bonds, 1 residue, 1 model selected
+Alignment identifier is 22/A
+> select #22/A:119
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #22/A:119
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #22/A:119
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #22/A:119
+atoms, 13 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 14 atom styles
+> show sel atoms
+> color sel orange
+> ui mousemode right translate
+> ui mousemode right select
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+> select #22/A:121
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #22/A:121
+atoms, 16 bonds, 1 residue, 1 model selected
+> color sel orange
+> style sel stick
+Changed 17 atom styles
+> show sel atoms
+> hide sel atoms
+> style sel stick
+Changed 17 atom styles
+> show sel atoms
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #22/A:233
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #22/A:233
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #22/A:233
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #22/A:233
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> hide sel atoms
+> show sel atoms
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #22/A:183
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 14 atom styles
+> show sel atoms
+> color sel magenta
+> ui mousemode right translate
+> color #22 #ffaa7fff
+> color #22 #ee9e77ff
+> color #22 #ffaa00ff
+> color #22 #cc8800ff
+> color #22 #b37700ff
+> color #22 #b57900ff
+> color #22 #ce8900ff
+> color #22 #ff5500ff
+> ui mousemode right select
+> select #22/A:119
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #22/A:121
+atoms, 16 bonds, 1 residue, 1 model selected
+> color sel orange
+> select #22/A:119
+atoms, 13 bonds, 1 residue, 1 model selected
+> color sel orange
+> select clear
+[Repeated 1 time(s)]
+> ui mousemode right translate
+> ui mousemode right select
+> select #22/A:233
+atoms, 14 bonds, 1 residue, 1 model selected
+> color sel red
+> ui mousemode right translate
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+——— End of log from Tue Jun 13 11:14:29 2023 ———
+opened ChimeraX session
+> select #22/A:1-30
+atoms, 519 bonds, 30 residues, 1 model selected
+> select #22/A:1-30
+atoms, 519 bonds, 30 residues, 1 model selected
+> ui mousemode right select
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #22/A:119
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #22/A:121
+atoms, 16 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #22/A:233
+atoms, 14 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #22/A:183
+atoms, 14 bonds, 1 residue, 1 model selected
+> color sel magenta
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #22/A:176
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #22/A:176
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #22/A:176
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #22/A:176
+atoms, 16 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 17 atom styles
+> show sel atoms
+> color sel orange
+> ui mousemode right translate
+> ui mousemode right rotate
+> ui mousemode right select
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #22/A:171
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #22/A:170
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #22/A:171
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #22/A:171
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+Drag select of 5 residues
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #22/A:147
+atoms, 16 bonds, 1 residue, 1 model selected
+> color sel orange
+> style sel stick
+Changed 17 atom styles
+> show sel atoms
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #22/A:147
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #22/A:150
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #22/A:149
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #22/A:150
+atoms, 9 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 10 atom styles
+> show sel atoms
+Drag select of 3 residues, 2 atoms, 4 bonds
+> select #22/A:150
+atoms, 9 bonds, 1 residue, 1 model selected
+> color sel gray
+> ui mousemode right translate
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+——— End of log from Tue Jun 13 12:23:11 2023 ———
+opened ChimeraX session
+> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/Mosso das Pedras virus AlphaFold.pdb"
+Chain information for Mosso das Pedras virus AlphaFold.pdb #23
+---
+Chain | Description
+A | No description available
+> ui tool show Matchmaker
+> matchmaker #2-4,6,9-22#!5,7-8 to #23
+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 Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with 3j2w.pdb,
+chain I (#2), sequence alignment score = 525
+RMSD between 147 pruned atom pairs is 0.747 angstroms; (across all 149 pairs:
+.843)
+Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with 1kxf.pdb,
+chain A (#3), sequence alignment score = 555.1
+RMSD between 150 pruned atom pairs is 0.697 angstroms; (across all 158 pairs:
+.182)
+Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with 7sfu.pdb,
+chain F (#4), sequence alignment score = 774.4
+RMSD between 146 pruned atom pairs is 0.748 angstroms; (across all 162 pairs:
+.048)
+Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with 4agk.pdb,
+chain A (#6), sequence alignment score = 564
+RMSD between 151 pruned atom pairs is 0.736 angstroms; (across all 151 pairs:
+.736)
+Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with 7ko8.pdb,
+chain G (#9), sequence alignment score = 530.6
+RMSD between 138 pruned atom pairs is 1.162 angstroms; (across all 152 pairs:
+.566)
+Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with AlphFold
+Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 796.6
+RMSD between 151 pruned atom pairs is 0.563 angstroms; (across all 261 pairs:
+.344)
+Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with AlphaFold
+Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
+.9
+RMSD between 135 pruned atom pairs is 0.567 angstroms; (across all 263 pairs:
+.641)
+Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with AlphaFold
+Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
+.5
+RMSD between 13 pruned atom pairs is 1.031 angstroms; (across all 272 pairs:
+.100)
+Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Alpha Fold
+Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
+score = 560.8
+RMSD between 25 pruned atom pairs is 0.636 angstroms; (across all 270 pairs:
+.007)
+Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Alpha Fold
+Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
+.8
+RMSD between 164 pruned atom pairs is 0.325 angstroms; (across all 255 pairs:
+.044)
+Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Ndumu
+virus Alphafold.pdb, chain A (#15), sequence alignment score = 808.2
+RMSD between 149 pruned atom pairs is 0.627 angstroms; (across all 267 pairs:
+.210)
+Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Everglades
+virus Alphafold.pdb, chain A (#16), sequence alignment score = 1181.5
+RMSD between 13 pruned atom pairs is 1.030 angstroms; (across all 272 pairs:
+.103)
+Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Bebaru
+virus Alphafold.pdb, chain A (#17), sequence alignment score = 796.3
+RMSD between 147 pruned atom pairs is 0.540 angstroms; (across all 258 pairs:
+.949)
+Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Caaingua
+virus AlphaFold.pdb, chain A (#18), sequence alignment score = 669.3
+RMSD between 143 pruned atom pairs is 0.659 angstroms; (across all 254 pairs:
+.135)
+Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Cabassou
+virus Alphafold.pdb, chain A (#19), sequence alignment score = 1176
+RMSD between 165 pruned atom pairs is 0.262 angstroms; (across all 274 pairs:
+.984)
+Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Eilat
+virus Alphafold.pdb, chain A (#20), sequence alignment score = 704.1
+RMSD between 148 pruned atom pairs is 0.693 angstroms; (across all 253 pairs:
+.728)
+Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Highlands
+J. virus Alphafold.pdb, chain A (#21), sequence alignment score = 962.3
+RMSD between 12 pruned atom pairs is 1.277 angstroms; (across all 255 pairs:
+.902)
+Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Madariaga
+virus Alpha Fold.pdb, chain A (#22), sequence alignment score = 976.4
+RMSD between 163 pruned atom pairs is 0.314 angstroms; (across all 257 pairs:
+.593)
+Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with 6xo4.pdb,
+chain C (#5), sequence alignment score = 680.4
+RMSD between 103 pruned atom pairs is 1.187 angstroms; (across all 151 pairs:
+.065)
+Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with 1vcp.pdb,
+chain C (#7), sequence alignment score = 558.9
+RMSD between 147 pruned atom pairs is 0.584 angstroms; (across all 149 pairs:
+.736)
+Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with 2yew.pdb,
+chain G (#8), sequence alignment score = 499.1
+RMSD between 55 pruned atom pairs is 1.261 angstroms; (across all 170 pairs:
+.233)
+> hide #22 models
+> select add #22
+atoms, 4228 bonds, 261 residues, 1 model selected
+> select subtract #22
+Nothing selected
+> color #23 #aaaa7fff
+> color #23 #999972ff
+> color #23 #94946eff
+> color #23 #9e9e76ff
+> color #23 #a3a379ff
+> color #23 #a5a57bff
+> color #23 #a1a178ff
+> ui mousemode right select
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #23/A:137
+atoms, 11 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+Alignment identifier is 23/A
+> color sel red
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #23/A:139
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> select clear
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #23/A:251
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #23/A:201
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #23/A:201
+atoms, 23 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 24 atom styles
+> show sel atoms
+> color sel blue
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #23/A:201
+atoms, 23 bonds, 1 residue, 1 model selected
+> select clear
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #23/A:194
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #23/A:194
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #23/A:194
+atoms, 21 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+> ui mousemode right select
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #23/A:189
+atoms, 23 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 24 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #23/A:168
+atoms, 9 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 10 atom styles
+> show sel atoms
+> color sel gray
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #23/A:165
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #23/A:168
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #23/A:165
+atoms, 18 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 19 atom styles
+> show sel atoms
+> color sel gray
+> ui mousemode right translate
+[Repeated 1 time(s)]
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+> ui mousemode right select
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #23/A:137
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #23/A:139
+atoms, 21 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right rotate
+> ui mousemode right select
+> select #23/A:251
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #23/A:201
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:183@CA
+atom, 1 residue, 1 model selected
+> select #23/A:194
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #23/A:194
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #23/A:194
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #23/A:189
+atoms, 23 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #23/A:168@CA
+atom, 1 residue, 1 model selected
+> select #23/A:165
+atoms, 18 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+——— End of log from Wed Jun 14 15:40:04 2023 ———
+opened ChimeraX session
+> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/Southern Elephant Seal virus AlphaFold.pdb"
+Chain information for Southern Elephant Seal virus AlphaFold.pdb #24
+---
+Chain | Description
+A | No description available
+> ui tool show Matchmaker
+> matchmaker #2-4,6,9-23#!5,7-8 to #24
+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 Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
+j2w.pdb, chain I (#2), sequence alignment score = 595.1
+RMSD between 149 pruned atom pairs is 0.700 angstroms; (across all 149 pairs:
+.700)
+Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
+kxf.pdb, chain A (#3), sequence alignment score = 543.6
+RMSD between 147 pruned atom pairs is 0.771 angstroms; (across all 157 pairs:
+.959)
+Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
+sfu.pdb, chain I (#4), sequence alignment score = 577.8
+RMSD between 143 pruned atom pairs is 0.786 angstroms; (across all 161 pairs:
+.477)
+Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
+agk.pdb, chain A (#6), sequence alignment score = 575.4
+RMSD between 147 pruned atom pairs is 0.663 angstroms; (across all 150 pairs:
+.772)
+Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
+ko8.pdb, chain D (#9), sequence alignment score = 657.3
+RMSD between 133 pruned atom pairs is 1.065 angstroms; (across all 152 pairs:
+.706)
+Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
+AlphFold Colaboratory Ross River.pdb, chain A (#10), sequence alignment score
+= 914
+RMSD between 154 pruned atom pairs is 0.396 angstroms; (across all 251 pairs:
+.072)
+Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
+AlphaFold Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment
+score = 910.1
+RMSD between 156 pruned atom pairs is 0.463 angstroms; (across all 251 pairs:
+.684)
+Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
+AlphaFold Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment
+score = 745.1
+RMSD between 147 pruned atom pairs is 0.547 angstroms; (across all 258 pairs:
+.865)
+Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
+Alpha Fold Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence
+alignment score = 561.1
+RMSD between 132 pruned atom pairs is 0.772 angstroms; (across all 265 pairs:
+.702)
+Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
+Alpha Fold Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence
+alignment score = 747.2
+RMSD between 150 pruned atom pairs is 0.471 angstroms; (across all 258 pairs:
+.727)
+Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
+Ndumu virus Alphafold.pdb, chain A (#15), sequence alignment score = 876.2
+RMSD between 153 pruned atom pairs is 0.454 angstroms; (across all 260 pairs:
+.995)
+Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
+Everglades virus Alphafold.pdb, chain A (#16), sequence alignment score =
+.1
+RMSD between 147 pruned atom pairs is 0.547 angstroms; (across all 258 pairs:
+.865)
+Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
+Bebaru virus Alphafold.pdb, chain A (#17), sequence alignment score = 885.6
+RMSD between 154 pruned atom pairs is 0.323 angstroms; (across all 250 pairs:
+.775)
+Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
+Caaingua virus AlphaFold.pdb, chain A (#18), sequence alignment score = 686.5
+RMSD between 101 pruned atom pairs is 0.541 angstroms; (across all 257 pairs:
+.122)
+Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
+Cabassou virus Alphafold.pdb, chain A (#19), sequence alignment score = 746.3
+RMSD between 5 pruned atom pairs is 0.781 angstroms; (across all 261 pairs:
+.736)
+Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
+Eilat virus Alphafold.pdb, chain A (#20), sequence alignment score = 688.6
+RMSD between 154 pruned atom pairs is 0.690 angstroms; (across all 238 pairs:
+.995)
+Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
+Highlands J. virus Alphafold.pdb, chain A (#21), sequence alignment score =
+.8
+RMSD between 150 pruned atom pairs is 0.515 angstroms; (across all 252 pairs:
+.621)
+Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
+Madariaga virus Alpha Fold.pdb, chain A (#22), sequence alignment score =
+.9
+RMSD between 150 pruned atom pairs is 0.532 angstroms; (across all 254 pairs:
+.232)
+Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
+Mosso das Pedras virus AlphaFold.pdb, chain A (#23), sequence alignment score
+= 761.8
+RMSD between 150 pruned atom pairs is 0.559 angstroms; (across all 260 pairs:
+.762)
+Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
+xo4.pdb, chain C (#5), sequence alignment score = 496.9
+RMSD between 101 pruned atom pairs is 1.204 angstroms; (across all 150 pairs:
+.038)
+Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
+vcp.pdb, chain C (#7), sequence alignment score = 628.6
+RMSD between 149 pruned atom pairs is 0.536 angstroms; (across all 149 pairs:
+.536)
+Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
+yew.pdb, chain G (#8), sequence alignment score = 628.5
+RMSD between 56 pruned atom pairs is 1.258 angstroms; (across all 171 pairs:
+.304)
+> hide #23 models
+> select add #23
+atoms, 4504 bonds, 279 residues, 1 model selected
+> select subtract #23
+Nothing selected
+> show #23 models
+> hide #23 models
+> color #24 #555500ff
+> color #24 black
+> color #24 #550000ff
+> color #24 #aaaa7fff
+> color #24 #aaaa00ff
+> color #24 #555500ff
+> color #24 #6c6c00ff
+> color #24 #7f7f00ff
+> color #24 #666600ff
+> color #24 #aaaa7fff
+> color #24 #757557ff
+> color #24 #707053ff
+> color #24 #68684dff
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+> ui mousemode right select
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #24/A:127
+atoms, 11 bonds, 1 residue, 1 model selected
+Alignment identifier is 24/A
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+Drag select of 1 residues
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #24/A:129
+atoms, 18 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 19 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #24/A:241
+atoms, 14 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> ui mousemode right select
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #24/A:241
+atoms, 14 bonds, 1 residue, 1 model selected
+> color sel red
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #24/A:191
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> select clear
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #24/A:184
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #24/A:179
+atoms, 23 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 24 atom styles
+> show sel atoms
+> color sel blue
+> set bgColor black
+> set bgColor white
+> ui mousemode right translate
+> ui mousemode right rotate
+> ui mousemode right select
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #24/A:158
+atoms, 21 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right select
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #24/A:155
+atoms, 18 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 19 atom styles
+> show sel atoms
+> color sel gray
+> ui mousemode right translate
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+> ui mousemode right select
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #24/A:129
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #24/A:129
+atoms, 18 bonds, 1 residue, 1 model selected
+> color sel gray
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #24/A:241
+atoms, 14 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #24/A:184
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #24/A:179
+atoms, 23 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #24/A:158
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #24/A:155
+atoms, 18 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+——— End of log from Thu Jun 15 13:33:00 2023 ———
+opened ChimeraX session
+> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/Mucambo virus AlphaFold.pdb"
+Chain information for Mucambo virus AlphaFold.pdb #25
+---
+Chain | Description
+A | No description available
+> ui tool show Matchmaker
+[Repeated 1 time(s)]
+> matchmaker #2-4,6,9-24#!5,7-8 to #25
+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 Mucambo virus AlphaFold.pdb, chain A (#25) with 3j2w.pdb, chain I
+(#2), sequence alignment score = 529.5
+RMSD between 148 pruned atom pairs is 0.719 angstroms; (across all 149 pairs:
+.763)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 1kxf.pdb, chain A
+(#3), sequence alignment score = 561.4
+RMSD between 150 pruned atom pairs is 0.671 angstroms; (across all 158 pairs:
+.955)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 7sfu.pdb, chain F
+(#4), sequence alignment score = 791.4
+RMSD between 148 pruned atom pairs is 0.732 angstroms; (across all 162 pairs:
+.042)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 4agk.pdb, chain A
+(#6), sequence alignment score = 559.3
+RMSD between 150 pruned atom pairs is 0.713 angstroms; (across all 151 pairs:
+.739)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 7ko8.pdb, chain G
+(#9), sequence alignment score = 568.5
+RMSD between 129 pruned atom pairs is 1.055 angstroms; (across all 152 pairs:
+.523)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with AlphFold
+Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 797.8
+RMSD between 148 pruned atom pairs is 0.605 angstroms; (across all 261 pairs:
+.742)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with AlphaFold
+Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
+.8
+RMSD between 151 pruned atom pairs is 0.653 angstroms; (across all 262 pairs:
+.551)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with AlphaFold
+Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
+.9
+RMSD between 152 pruned atom pairs is 0.330 angstroms; (across all 274 pairs:
+.227)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Alpha Fold
+Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
+score = 569.6
+RMSD between 132 pruned atom pairs is 0.920 angstroms; (across all 267 pairs:
+.674)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Alpha Fold
+Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
+.5
+RMSD between 155 pruned atom pairs is 0.353 angstroms; (across all 255 pairs:
+.484)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Ndumu virus
+Alphafold.pdb, chain A (#15), sequence alignment score = 830.2
+RMSD between 137 pruned atom pairs is 0.550 angstroms; (across all 267 pairs:
+.448)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Everglades virus
+Alphafold.pdb, chain A (#16), sequence alignment score = 1240.9
+RMSD between 152 pruned atom pairs is 0.330 angstroms; (across all 274 pairs:
+.231)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Bebaru virus
+Alphafold.pdb, chain A (#17), sequence alignment score = 795.9
+RMSD between 146 pruned atom pairs is 0.593 angstroms; (across all 258 pairs:
+.444)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Caaingua virus
+AlphaFold.pdb, chain A (#18), sequence alignment score = 680.9
+RMSD between 130 pruned atom pairs is 0.713 angstroms; (across all 261 pairs:
+.031)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Cabassou virus
+Alphafold.pdb, chain A (#19), sequence alignment score = 1287
+RMSD between 13 pruned atom pairs is 0.146 angstroms; (across all 274 pairs:
+.862)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Eilat virus
+Alphafold.pdb, chain A (#20), sequence alignment score = 686.9
+RMSD between 11 pruned atom pairs is 1.306 angstroms; (across all 254 pairs:
+.777)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Highlands J. virus
+Alphafold.pdb, chain A (#21), sequence alignment score = 984.3
+RMSD between 156 pruned atom pairs is 0.293 angstroms; (across all 255 pairs:
+.661)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Madariaga virus
+Alpha Fold.pdb, chain A (#22), sequence alignment score = 988.9
+RMSD between 135 pruned atom pairs is 0.294 angstroms; (across all 257 pairs:
+.924)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Mosso das Pedras
+virus AlphaFold.pdb, chain A (#23), sequence alignment score = 1167.1
+RMSD between 20 pruned atom pairs is 1.361 angstroms; (across all 274 pairs:
+.794)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Southern Elephant
+Seal virus AlphaFold.pdb, chain A (#24), sequence alignment score = 764.6
+RMSD between 147 pruned atom pairs is 0.552 angstroms; (across all 262 pairs:
+.695)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 6xo4.pdb, chain C
+(#5), sequence alignment score = 701.7
+RMSD between 104 pruned atom pairs is 1.212 angstroms; (across all 151 pairs:
+.018)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 1vcp.pdb, chain C
+(#7), sequence alignment score = 563.4
+RMSD between 147 pruned atom pairs is 0.576 angstroms; (across all 149 pairs:
+.688)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 2yew.pdb, chain G
+(#8), sequence alignment score = 508.8
+RMSD between 54 pruned atom pairs is 1.257 angstroms; (across all 171 pairs:
+.382)
+> hide #24 models
+> color #25 #ff557fff
+> color #25 #f4517aff
+> color #25 #e64d73ff
+> color #25 #da496dff
+> color #25 #e34c72ff
+> color #25 #f8537cff
+> color #25 #ff007fff
+> color #25 #ff557fff
+> color #25 #be3f5fff
+> color #25 #e14b71ff
+> color #25 #ef5078ff
+> color #25 #ffaaffff
+> color #25 #ff557fff
+> color #25 #ff679cff
+> color #25 #ff82baff
+> color #25 #ff97dbff
+> color #25 #ff86c7ff
+> color #25 #ff81d9ff
+> color #25 #ff7bcaff
+> ui mousemode right select
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #25/A:133
+atoms, 11 bonds, 1 residue, 1 model selected
+Alignment identifier is 25/A
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+Alignment identifier is 2/I
+> select #25/A:133
+atoms, 11 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #25/A:135
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #25/A:135
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #25/A:247
+atoms, 14 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> style sel stick
+Changed 15 atom styles
+> ui mousemode right rotate
+> ui mousemode right select
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #25/A:197
+atoms, 16 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 17 atom styles
+> show sel atoms
+> color sel orange
+> ui mousemode right translate
+> ui mousemode right select
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #25/A:190
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #25/A:185
+atoms, 23 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 24 atom styles
+> show sel atoms
+> color sel blue
+> select #25/A:190
+atoms, 21 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #25/A:164
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #25/A:164
+atoms, 10 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 11 atom styles
+> hide sel atoms
+> show sel atoms
+> style sel stick
+Changed 11 atom styles
+> color sel orange
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #25/A:161
+atoms, 13 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 14 atom styles
+> show sel atoms
+> color sel orange
+> ui mousemode right translate
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+——— End of log from Fri Jun 16 15:07:56 2023 ———
+opened ChimeraX session
+> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/Onyong-nyong virus AlphaFold.pdb"
+Chain information for Onyong-nyong virus AlphaFold.pdb #26
+---
+Chain | Description
+A | No description available
+> select add #25
+atoms, 4479 bonds, 275 residues, 1 model selected
+> hide #25 models
+> select subtract #25
+Nothing selected
+> ui tool show Matchmaker
+> matchmaker #2-4,6,9-25#!5,7-8 to #26
+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 Onyong-nyong virus AlphaFold.pdb, chain A (#26) with 3j2w.pdb,
+chain I (#2), sequence alignment score = 693.1
+RMSD between 145 pruned atom pairs is 0.692 angstroms; (across all 149 pairs:
+.928)
+Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with 1kxf.pdb,
+chain A (#3), sequence alignment score = 550.8
+RMSD between 145 pruned atom pairs is 0.764 angstroms; (across all 157 pairs:
+.974)
+Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with 7sfu.pdb,
+chain I (#4), sequence alignment score = 571.5
+RMSD between 141 pruned atom pairs is 0.808 angstroms; (across all 161 pairs:
+.633)
+Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with 4agk.pdb,
+chain A (#6), sequence alignment score = 554.2
+RMSD between 145 pruned atom pairs is 0.645 angstroms; (across all 150 pairs:
+.967)
+Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with 7ko8.pdb,
+chain D (#9), sequence alignment score = 789.3
+RMSD between 135 pruned atom pairs is 1.096 angstroms; (across all 152 pairs:
+.761)
+Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with AlphFold
+Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 1011.1
+RMSD between 161 pruned atom pairs is 0.532 angstroms; (across all 259 pairs:
+.498)
+Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with AlphaFold
+Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
+.1
+RMSD between 166 pruned atom pairs is 0.493 angstroms; (across all 260 pairs:
+.774)
+Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with AlphaFold
+Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
+.5
+RMSD between 148 pruned atom pairs is 0.549 angstroms; (across all 253 pairs:
+.234)
+Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Alpha Fold
+Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
+score = 521
+RMSD between 129 pruned atom pairs is 0.751 angstroms; (across all 253 pairs:
+.504)
+Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Alpha Fold
+Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
+.6
+RMSD between 148 pruned atom pairs is 0.466 angstroms; (across all 257 pairs:
+.771)
+Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Ndumu virus
+Alphafold.pdb, chain A (#15), sequence alignment score = 883
+RMSD between 153 pruned atom pairs is 0.307 angstroms; (across all 255 pairs:
+.508)
+Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Everglades
+virus Alphafold.pdb, chain A (#16), sequence alignment score = 745.5
+RMSD between 148 pruned atom pairs is 0.549 angstroms; (across all 253 pairs:
+.235)
+Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Bebaru virus
+Alphafold.pdb, chain A (#17), sequence alignment score = 1010.1
+RMSD between 168 pruned atom pairs is 0.393 angstroms; (across all 256 pairs:
+.447)
+Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Caaingua virus
+AlphaFold.pdb, chain A (#18), sequence alignment score = 714.7
+RMSD between 131 pruned atom pairs is 0.592 angstroms; (across all 248 pairs:
+.461)
+Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Cabassou virus
+Alphafold.pdb, chain A (#19), sequence alignment score = 737.3
+RMSD between 12 pruned atom pairs is 0.503 angstroms; (across all 255 pairs:
+.820)
+Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Eilat virus
+Alphafold.pdb, chain A (#20), sequence alignment score = 665.2
+RMSD between 146 pruned atom pairs is 0.659 angstroms; (across all 248 pairs:
+.950)
+Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Highlands J.
+virus Alphafold.pdb, chain A (#21), sequence alignment score = 778.5
+RMSD between 148 pruned atom pairs is 0.516 angstroms; (across all 257 pairs:
+.355)
+Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Madariaga
+virus Alpha Fold.pdb, chain A (#22), sequence alignment score = 752.9
+RMSD between 148 pruned atom pairs is 0.535 angstroms; (across all 255 pairs:
+.725)
+Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Mosso das
+Pedras virus AlphaFold.pdb, chain A (#23), sequence alignment score = 734.5
+RMSD between 148 pruned atom pairs is 0.559 angstroms; (across all 255 pairs:
+.406)
+Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Southern
+Elephant Seal virus AlphaFold.pdb, chain A (#24), sequence alignment score =
+.1
+RMSD between 151 pruned atom pairs is 0.324 angstroms; (across all 248 pairs:
+.757)
+Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Mucambo virus
+AlphaFold.pdb, chain A (#25), sequence alignment score = 737.4
+RMSD between 147 pruned atom pairs is 0.545 angstroms; (across all 256 pairs:
+.618)
+Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with 6xo4.pdb,
+chain C (#5), sequence alignment score = 495.9
+RMSD between 99 pruned atom pairs is 1.202 angstroms; (across all 150 pairs:
+.096)
+Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with 1vcp.pdb,
+chain C (#7), sequence alignment score = 720.3
+RMSD between 145 pruned atom pairs is 0.504 angstroms; (across all 149 pairs:
+.805)
+Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with 2yew.pdb,
+chain G (#8), sequence alignment score = 682.7
+RMSD between 54 pruned atom pairs is 1.188 angstroms; (across all 171 pairs:
+.494)
+> color #26 #55557fff
+> color #26 #67679aff
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+——— End of log from Sat Jun 17 16:13:53 2023 ———
+opened ChimeraX session
+> ui mousemode right select
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #26/A:119
+atoms, 14 bonds, 1 residue, 1 model selected
+Alignment identifier is 26/A
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select clear
+> select #26/A:119
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #26/A:119
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #26/A:121
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #26/A:233
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #26/A:183
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right translate
+> ui mousemode right rotate
+> ui mousemode right select
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #26/A:176
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> select #2/I:183@CA
+atom, 1 residue, 1 model selected
+> select #26/A:176
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #26/A:176
+atoms, 21 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #26/A:171
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #26/A:171
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #26/A:171
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #26/A:150
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #26/A:150
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #26/A:147
+atoms, 11 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+Drag select of 9 residues
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:237
+atoms, 3 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/Pixuna virus AlphaFold.pdb"
+Chain information for Pixuna virus AlphaFold.pdb #27
+---
+Chain | Description
+A | No description available
+> ui tool show Matchmaker
+> matchmaker #2-4,6,9-26#!5,7-8 to #27
+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 Pixuna virus AlphaFold.pdb, chain A (#27) with 3j2w.pdb, chain I
+(#2), sequence alignment score = 521
+RMSD between 147 pruned atom pairs is 0.730 angstroms; (across all 149 pairs:
+.820)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 1kxf.pdb, chain A
+(#3), sequence alignment score = 570.9
+RMSD between 149 pruned atom pairs is 0.684 angstroms; (across all 158 pairs:
+.897)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 7sfu.pdb, chain F
+(#4), sequence alignment score = 784.4
+RMSD between 148 pruned atom pairs is 0.745 angstroms; (across all 162 pairs:
+.028)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 4agk.pdb, chain A
+(#6), sequence alignment score = 557.4
+RMSD between 149 pruned atom pairs is 0.706 angstroms; (across all 151 pairs:
+.770)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 7ko8.pdb, chain G
+(#9), sequence alignment score = 555.5
+RMSD between 135 pruned atom pairs is 1.130 angstroms; (across all 152 pairs:
+.573)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphFold
+Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 768.3
+RMSD between 150 pruned atom pairs is 0.552 angstroms; (across all 258 pairs:
+.415)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphaFold
+Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
+.5
+RMSD between 140 pruned atom pairs is 0.581 angstroms; (across all 263 pairs:
+.104)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphaFold
+Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
+.1
+RMSD between 24 pruned atom pairs is 0.507 angstroms; (across all 273 pairs:
+.005)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Alpha Fold
+Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
+score = 600.2
+RMSD between 92 pruned atom pairs is 0.792 angstroms; (across all 268 pairs:
+.726)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Alpha Fold
+Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
+.2
+RMSD between 153 pruned atom pairs is 0.312 angstroms; (across all 255 pairs:
+.821)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Ndumu virus
+Alphafold.pdb, chain A (#15), sequence alignment score = 849.5
+RMSD between 148 pruned atom pairs is 0.597 angstroms; (across all 266 pairs:
+.320)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Everglades virus
+Alphafold.pdb, chain A (#16), sequence alignment score = 1176.1
+RMSD between 24 pruned atom pairs is 0.507 angstroms; (across all 273 pairs:
+.005)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Bebaru virus
+Alphafold.pdb, chain A (#17), sequence alignment score = 755.1
+RMSD between 140 pruned atom pairs is 0.521 angstroms; (across all 258 pairs:
+.677)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Caaingua virus
+AlphaFold.pdb, chain A (#18), sequence alignment score = 629.3
+RMSD between 10 pruned atom pairs is 0.489 angstroms; (across all 258 pairs:
+.729)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Cabassou virus
+Alphafold.pdb, chain A (#19), sequence alignment score = 1205.6
+RMSD between 149 pruned atom pairs is 0.247 angstroms; (across all 274 pairs:
+.936)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Eilat virus
+Alphafold.pdb, chain A (#20), sequence alignment score = 645.7
+RMSD between 152 pruned atom pairs is 0.709 angstroms; (across all 247 pairs:
+.031)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Highlands J. virus
+Alphafold.pdb, chain A (#21), sequence alignment score = 931.4
+RMSD between 139 pruned atom pairs is 0.323 angstroms; (across all 254 pairs:
+.964)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Madariaga virus
+Alpha Fold.pdb, chain A (#22), sequence alignment score = 930.4
+RMSD between 155 pruned atom pairs is 0.321 angstroms; (across all 256 pairs:
+.809)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Mosso das Pedras
+virus AlphaFold.pdb, chain A (#23), sequence alignment score = 1156
+RMSD between 144 pruned atom pairs is 0.209 angstroms; (across all 275 pairs:
+.847)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Southern Elephant
+Seal virus AlphaFold.pdb, chain A (#24), sequence alignment score = 743.4
+RMSD between 148 pruned atom pairs is 0.534 angstroms; (across all 265 pairs:
+.355)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Mucambo virus
+AlphaFold.pdb, chain A (#25), sequence alignment score = 1188.8
+RMSD between 41 pruned atom pairs is 0.760 angstroms; (across all 274 pairs:
+.851)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Onyong-nyong virus
+AlphaFold.pdb, chain A (#26), sequence alignment score = 689.8
+RMSD between 144 pruned atom pairs is 0.546 angstroms; (across all 255 pairs:
+.486)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 6xo4.pdb, chain C
+(#5), sequence alignment score = 676.1
+RMSD between 104 pruned atom pairs is 1.210 angstroms; (across all 151 pairs:
+.057)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 1vcp.pdb, chain C
+(#7), sequence alignment score = 554.2
+RMSD between 147 pruned atom pairs is 0.608 angstroms; (across all 149 pairs:
+.747)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 2yew.pdb, chain G
+(#8), sequence alignment score = 518.2
+RMSD between 51 pruned atom pairs is 1.245 angstroms; (across all 171 pairs:
+.032)
+> hide #26 models
+> color #27 #ff5500ff
+> color #27 #aa007fff
+> color #27 #a7007dff
+> color #27 #a10079ff
+> ui mousemode right select
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #27/A:133
+atoms, 14 bonds, 1 residue, 1 model selected
+Alignment identifier is 27/A
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #27/A:135
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #27/A:135
+atoms, 23 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 24 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:240@CA
+atom, 1 residue, 1 model selected
+> select #27/A:247
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #2/I:240@CA
+atom, 1 residue, 1 model selected
+> select #27/A:247
+atoms, 14 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> style sel stick
+Changed 15 atom styles
+> show sel cartoons
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #27/A:197
+atoms, 16 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 17 atom styles
+> show sel atoms
+> color sel orange
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:183@CA
+atom, 1 residue, 1 model selected
+> select #27/A:190
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #27/A:185
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #27/A:185
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #27/A:185
+atoms, 23 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 24 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #27/A:164
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #27/A:164
+atoms, 9 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 10 atom styles
+> show sel atoms
+> color sel gray
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #27/A:161
+atoms, 9 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 10 atom styles
+> show sel atoms
+> ui mousemode right translate
+> color sel gray
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+——— End of log from Mon Jun 19 14:50:40 2023 ———
+opened ChimeraX session
+> hide #27 models
+> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/RioNegro virus AlphaFold.pdb"
+Chain information for RioNegro virus AlphaFold.pdb #28
+---
+Chain | Description
+A | No description available
+> ui tool show Matchmaker
+> matchmaker #2-4,6,9-27#!5,7-8 to #28
+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 RioNegro virus AlphaFold.pdb, chain A (#28) with 3j2w.pdb, chain I
+(#2), sequence alignment score = 527.8
+RMSD between 147 pruned atom pairs is 0.698 angstroms; (across all 149 pairs:
+.789)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 1kxf.pdb, chain A
+(#3), sequence alignment score = 566.3
+RMSD between 150 pruned atom pairs is 0.681 angstroms; (across all 158 pairs:
+.969)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 7sfu.pdb, chain F
+(#4), sequence alignment score = 787.7
+RMSD between 147 pruned atom pairs is 0.760 angstroms; (across all 162 pairs:
+.092)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 4agk.pdb, chain A
+(#6), sequence alignment score = 560.5
+RMSD between 150 pruned atom pairs is 0.690 angstroms; (across all 151 pairs:
+.725)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 7ko8.pdb, chain G
+(#9), sequence alignment score = 543.1
+RMSD between 136 pruned atom pairs is 1.140 angstroms; (across all 152 pairs:
+.558)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with AlphFold
+Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 810.7
+RMSD between 149 pruned atom pairs is 0.612 angstroms; (across all 260 pairs:
+.607)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with AlphaFold
+Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
+.9
+RMSD between 150 pruned atom pairs is 0.655 angstroms; (across all 262 pairs:
+.991)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with AlphaFold
+Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
+.9
+RMSD between 153 pruned atom pairs is 0.275 angstroms; (across all 273 pairs:
+.699)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Alpha Fold
+Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
+score = 570
+RMSD between 129 pruned atom pairs is 0.916 angstroms; (across all 274 pairs:
+.045)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Alpha Fold
+Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
+.5
+RMSD between 153 pruned atom pairs is 0.346 angstroms; (across all 255 pairs:
+.468)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Ndumu virus
+Alphafold.pdb, chain A (#15), sequence alignment score = 805.7
+RMSD between 110 pruned atom pairs is 0.481 angstroms; (across all 266 pairs:
+.937)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Everglades virus
+Alphafold.pdb, chain A (#16), sequence alignment score = 1186.9
+RMSD between 153 pruned atom pairs is 0.275 angstroms; (across all 273 pairs:
+.702)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Bebaru virus
+Alphafold.pdb, chain A (#17), sequence alignment score = 803.1
+RMSD between 150 pruned atom pairs is 0.602 angstroms; (across all 255 pairs:
+.125)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Caaingua virus
+AlphaFold.pdb, chain A (#18), sequence alignment score = 690.7
+RMSD between 142 pruned atom pairs is 0.666 angstroms; (across all 260 pairs:
+.522)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Cabassou virus
+Alphafold.pdb, chain A (#19), sequence alignment score = 1172
+RMSD between 14 pruned atom pairs is 1.444 angstroms; (across all 275 pairs:
+.262)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Eilat virus
+Alphafold.pdb, chain A (#20), sequence alignment score = 686
+RMSD between 13 pruned atom pairs is 1.555 angstroms; (across all 251 pairs:
+.745)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Highlands J. virus
+Alphafold.pdb, chain A (#21), sequence alignment score = 974.3
+RMSD between 154 pruned atom pairs is 0.271 angstroms; (across all 255 pairs:
+.224)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Madariaga virus
+Alpha Fold.pdb, chain A (#22), sequence alignment score = 972.7
+RMSD between 133 pruned atom pairs is 0.245 angstroms; (across all 257 pairs:
+.677)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Mosso das Pedras
+virus AlphaFold.pdb, chain A (#23), sequence alignment score = 1260.3
+RMSD between 23 pruned atom pairs is 1.168 angstroms; (across all 278 pairs:
+.771)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Southern Elephant
+Seal virus AlphaFold.pdb, chain A (#24), sequence alignment score = 777
+RMSD between 148 pruned atom pairs is 0.570 angstroms; (across all 265 pairs:
+.463)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Mucambo virus
+AlphaFold.pdb, chain A (#25), sequence alignment score = 1175.9
+RMSD between 159 pruned atom pairs is 0.307 angstroms; (across all 274 pairs:
+.018)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Onyong-nyong virus
+AlphaFold.pdb, chain A (#26), sequence alignment score = 731.4
+RMSD between 148 pruned atom pairs is 0.584 angstroms; (across all 255 pairs:
+.382)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Pixuna virus
+AlphaFold.pdb, chain A (#27), sequence alignment score = 1160.6
+RMSD between 44 pruned atom pairs is 1.121 angstroms; (across all 275 pairs:
+.129)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 6xo4.pdb, chain C
+(#5), sequence alignment score = 670.2
+RMSD between 100 pruned atom pairs is 1.164 angstroms; (across all 151 pairs:
+.092)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 1vcp.pdb, chain C
+(#7), sequence alignment score = 561.7
+RMSD between 146 pruned atom pairs is 0.547 angstroms; (across all 149 pairs:
+.720)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 2yew.pdb, chain G
+(#8), sequence alignment score = 489.8
+RMSD between 57 pruned atom pairs is 1.297 angstroms; (across all 171 pairs:
+.267)
+> color #28 #55557fff
+> color #28 #55007fff
+> color #28 black
+> color #28 #545454ff
+> color #28 #868686ff
+> color #28 #212121ff
+> color #28 #414141ff
+> color #28 #4c4c4cff
+> color #28 #55557fff
+> color #28 #4e4e75ff
+> color #28 #414161ff
+> color #28 black
+> color #28 #2c2c2cff
+> color #28 #474747ff
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+——— End of log from Tue Jun 20 13:21:24 2023 ———
+opened ChimeraX session
+Alignment identifier is 27/A
+> select add #27
+atoms, 4485 bonds, 275 residues, 1 model selected
+> select subtract #27
+Nothing selected
+> select add #28
+atoms, 4477 bonds, 278 residues, 1 model selected
+Alignment identifier is 28/A
+> select subtract #28
+Nothing selected
+> ui mousemode right rotate
+> ui mousemode right select
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #28/A:136
+atoms, 11 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 12 atom styles
+> hide sel atoms
+> show sel atoms
+> color sel red
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #28/A:138
+atoms, 23 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 24 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #28/A:250
+atoms, 14 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right select
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #28/A:200
+atoms, 16 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 17 atom styles
+> show sel atoms
+> color sel orange
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+> ui mousemode right select
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #28/A:193
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #28/A:193
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #28/A:188
+atoms, 23 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 24 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #28/A:167
+atoms, 13 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 14 atom styles
+> show sel atoms
+> color sel orange
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #28/A:164
+atoms, 15 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 16 atom styles
+> show sel atoms
+> color sel gray
+> ui mousemode right translate
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+> hide #28 models
+> show #28 models
+> hide #28 models
+> show #27 models
+> select add #28
+atoms, 4477 bonds, 278 residues, 1 model selected
+> select subtract #28
+Nothing selected
+> show #26 models
+> hide #26 models
+> hide #27 models
+> show #27 models
+> ui tool show Matchmaker
+> matchmaker #2-4,6,9-26,28#!5,7-8 to #27
+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 Pixuna virus AlphaFold.pdb, chain A (#27) with 3j2w.pdb, chain I
+(#2), sequence alignment score = 521
+RMSD between 147 pruned atom pairs is 0.730 angstroms; (across all 149 pairs:
+.820)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 1kxf.pdb, chain A
+(#3), sequence alignment score = 570.9
+RMSD between 149 pruned atom pairs is 0.684 angstroms; (across all 158 pairs:
+.897)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 7sfu.pdb, chain F
+(#4), sequence alignment score = 784.4
+RMSD between 148 pruned atom pairs is 0.745 angstroms; (across all 162 pairs:
+.028)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 4agk.pdb, chain A
+(#6), sequence alignment score = 557.4
+RMSD between 149 pruned atom pairs is 0.706 angstroms; (across all 151 pairs:
+.770)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 7ko8.pdb, chain G
+(#9), sequence alignment score = 555.5
+RMSD between 135 pruned atom pairs is 1.130 angstroms; (across all 152 pairs:
+.573)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphFold
+Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 768.3
+RMSD between 150 pruned atom pairs is 0.552 angstroms; (across all 258 pairs:
+.415)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphaFold
+Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
+.5
+RMSD between 140 pruned atom pairs is 0.581 angstroms; (across all 263 pairs:
+.104)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphaFold
+Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
+.1
+RMSD between 24 pruned atom pairs is 0.507 angstroms; (across all 273 pairs:
+.005)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Alpha Fold
+Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
+score = 600.2
+RMSD between 92 pruned atom pairs is 0.792 angstroms; (across all 268 pairs:
+.726)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Alpha Fold
+Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
+.2
+RMSD between 153 pruned atom pairs is 0.312 angstroms; (across all 255 pairs:
+.821)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Ndumu virus
+Alphafold.pdb, chain A (#15), sequence alignment score = 849.5
+RMSD between 148 pruned atom pairs is 0.597 angstroms; (across all 266 pairs:
+.320)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Everglades virus
+Alphafold.pdb, chain A (#16), sequence alignment score = 1176.1
+RMSD between 24 pruned atom pairs is 0.507 angstroms; (across all 273 pairs:
+.005)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Bebaru virus
+Alphafold.pdb, chain A (#17), sequence alignment score = 755.1
+RMSD between 140 pruned atom pairs is 0.521 angstroms; (across all 258 pairs:
+.677)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Caaingua virus
+AlphaFold.pdb, chain A (#18), sequence alignment score = 629.3
+RMSD between 10 pruned atom pairs is 0.489 angstroms; (across all 258 pairs:
+.729)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Cabassou virus
+Alphafold.pdb, chain A (#19), sequence alignment score = 1205.6
+RMSD between 149 pruned atom pairs is 0.247 angstroms; (across all 274 pairs:
+.936)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Eilat virus
+Alphafold.pdb, chain A (#20), sequence alignment score = 645.7
+RMSD between 152 pruned atom pairs is 0.709 angstroms; (across all 247 pairs:
+.031)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Highlands J. virus
+Alphafold.pdb, chain A (#21), sequence alignment score = 931.4
+RMSD between 139 pruned atom pairs is 0.323 angstroms; (across all 254 pairs:
+.964)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Madariaga virus
+Alpha Fold.pdb, chain A (#22), sequence alignment score = 930.4
+RMSD between 155 pruned atom pairs is 0.321 angstroms; (across all 256 pairs:
+.809)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Mosso das Pedras
+virus AlphaFold.pdb, chain A (#23), sequence alignment score = 1156
+RMSD between 144 pruned atom pairs is 0.209 angstroms; (across all 275 pairs:
+.847)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Southern Elephant
+Seal virus AlphaFold.pdb, chain A (#24), sequence alignment score = 743.4
+RMSD between 148 pruned atom pairs is 0.534 angstroms; (across all 265 pairs:
+.355)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Mucambo virus
+AlphaFold.pdb, chain A (#25), sequence alignment score = 1188.8
+RMSD between 41 pruned atom pairs is 0.760 angstroms; (across all 274 pairs:
+.851)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Onyong-nyong virus
+AlphaFold.pdb, chain A (#26), sequence alignment score = 689.8
+RMSD between 144 pruned atom pairs is 0.546 angstroms; (across all 255 pairs:
+.486)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with RioNegro virus
+AlphaFold.pdb, chain A (#28), sequence alignment score = 1160.6
+RMSD between 44 pruned atom pairs is 1.121 angstroms; (across all 275 pairs:
+.129)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 6xo4.pdb, chain C
+(#5), sequence alignment score = 676.1
+RMSD between 104 pruned atom pairs is 1.210 angstroms; (across all 151 pairs:
+.057)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 1vcp.pdb, chain C
+(#7), sequence alignment score = 554.2
+RMSD between 147 pruned atom pairs is 0.608 angstroms; (across all 149 pairs:
+.747)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 2yew.pdb, chain G
+(#8), sequence alignment score = 518.2
+RMSD between 51 pruned atom pairs is 1.245 angstroms; (across all 171 pairs:
+.032)
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+——— End of log from Tue Jun 20 13:33:55 2023 ———
+opened ChimeraX session
+> hide #27 models
+> show #28 models
+> show #26 models
+> hide #26 models
+> ui tool show Matchmaker
+> matchmaker #2-4,6,9-27#!5,7-8 to #28
+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 RioNegro virus AlphaFold.pdb, chain A (#28) with 3j2w.pdb, chain I
+(#2), sequence alignment score = 527.8
+RMSD between 147 pruned atom pairs is 0.698 angstroms; (across all 149 pairs:
+.789)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 1kxf.pdb, chain A
+(#3), sequence alignment score = 566.3
+RMSD between 150 pruned atom pairs is 0.681 angstroms; (across all 158 pairs:
+.969)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 7sfu.pdb, chain F
+(#4), sequence alignment score = 787.7
+RMSD between 147 pruned atom pairs is 0.760 angstroms; (across all 162 pairs:
+.092)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 4agk.pdb, chain A
+(#6), sequence alignment score = 560.5
+RMSD between 150 pruned atom pairs is 0.690 angstroms; (across all 151 pairs:
+.725)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 7ko8.pdb, chain G
+(#9), sequence alignment score = 543.1
+RMSD between 136 pruned atom pairs is 1.140 angstroms; (across all 152 pairs:
+.558)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with AlphFold
+Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 810.7
+RMSD between 149 pruned atom pairs is 0.612 angstroms; (across all 260 pairs:
+.607)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with AlphaFold
+Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
+.9
+RMSD between 150 pruned atom pairs is 0.655 angstroms; (across all 262 pairs:
+.991)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with AlphaFold
+Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
+.9
+RMSD between 153 pruned atom pairs is 0.275 angstroms; (across all 273 pairs:
+.699)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Alpha Fold
+Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
+score = 570
+RMSD between 129 pruned atom pairs is 0.916 angstroms; (across all 274 pairs:
+.045)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Alpha Fold
+Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
+.5
+RMSD between 153 pruned atom pairs is 0.346 angstroms; (across all 255 pairs:
+.468)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Ndumu virus
+Alphafold.pdb, chain A (#15), sequence alignment score = 805.7
+RMSD between 110 pruned atom pairs is 0.481 angstroms; (across all 266 pairs:
+.937)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Everglades virus
+Alphafold.pdb, chain A (#16), sequence alignment score = 1186.9
+RMSD between 153 pruned atom pairs is 0.275 angstroms; (across all 273 pairs:
+.702)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Bebaru virus
+Alphafold.pdb, chain A (#17), sequence alignment score = 803.1
+RMSD between 150 pruned atom pairs is 0.602 angstroms; (across all 255 pairs:
+.125)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Caaingua virus
+AlphaFold.pdb, chain A (#18), sequence alignment score = 690.7
+RMSD between 142 pruned atom pairs is 0.666 angstroms; (across all 260 pairs:
+.522)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Cabassou virus
+Alphafold.pdb, chain A (#19), sequence alignment score = 1172
+RMSD between 14 pruned atom pairs is 1.444 angstroms; (across all 275 pairs:
+.262)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Eilat virus
+Alphafold.pdb, chain A (#20), sequence alignment score = 686
+RMSD between 13 pruned atom pairs is 1.555 angstroms; (across all 251 pairs:
+.745)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Highlands J. virus
+Alphafold.pdb, chain A (#21), sequence alignment score = 974.3
+RMSD between 154 pruned atom pairs is 0.271 angstroms; (across all 255 pairs:
+.224)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Madariaga virus
+Alpha Fold.pdb, chain A (#22), sequence alignment score = 972.7
+RMSD between 133 pruned atom pairs is 0.245 angstroms; (across all 257 pairs:
+.677)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Mosso das Pedras
+virus AlphaFold.pdb, chain A (#23), sequence alignment score = 1260.3
+RMSD between 23 pruned atom pairs is 1.168 angstroms; (across all 278 pairs:
+.771)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Southern Elephant
+Seal virus AlphaFold.pdb, chain A (#24), sequence alignment score = 777
+RMSD between 148 pruned atom pairs is 0.570 angstroms; (across all 265 pairs:
+.463)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Mucambo virus
+AlphaFold.pdb, chain A (#25), sequence alignment score = 1175.9
+RMSD between 159 pruned atom pairs is 0.307 angstroms; (across all 274 pairs:
+.018)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Onyong-nyong virus
+AlphaFold.pdb, chain A (#26), sequence alignment score = 731.4
+RMSD between 148 pruned atom pairs is 0.584 angstroms; (across all 255 pairs:
+.382)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Pixuna virus
+AlphaFold.pdb, chain A (#27), sequence alignment score = 1160.6
+RMSD between 44 pruned atom pairs is 1.121 angstroms; (across all 275 pairs:
+.129)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 6xo4.pdb, chain C
+(#5), sequence alignment score = 670.2
+RMSD between 100 pruned atom pairs is 1.164 angstroms; (across all 151 pairs:
+.092)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 1vcp.pdb, chain C
+(#7), sequence alignment score = 561.7
+RMSD between 146 pruned atom pairs is 0.547 angstroms; (across all 149 pairs:
+.720)
+Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 2yew.pdb, chain G
+(#8), sequence alignment score = 489.8
+RMSD between 57 pruned atom pairs is 1.297 angstroms; (across all 171 pairs:
+.267)
+> show #26 models
+> hide #26 models
+> hide #28 models
+> show #27 models
+> ui tool show Matchmaker
+> matchmaker #2-4,6,9-26,28#!5,7-8 to #27
+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 Pixuna virus AlphaFold.pdb, chain A (#27) with 3j2w.pdb, chain I
+(#2), sequence alignment score = 521
+RMSD between 147 pruned atom pairs is 0.730 angstroms; (across all 149 pairs:
+.820)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 1kxf.pdb, chain A
+(#3), sequence alignment score = 570.9
+RMSD between 149 pruned atom pairs is 0.684 angstroms; (across all 158 pairs:
+.897)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 7sfu.pdb, chain F
+(#4), sequence alignment score = 784.4
+RMSD between 148 pruned atom pairs is 0.745 angstroms; (across all 162 pairs:
+.028)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 4agk.pdb, chain A
+(#6), sequence alignment score = 557.4
+RMSD between 149 pruned atom pairs is 0.706 angstroms; (across all 151 pairs:
+.770)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 7ko8.pdb, chain G
+(#9), sequence alignment score = 555.5
+RMSD between 135 pruned atom pairs is 1.130 angstroms; (across all 152 pairs:
+.573)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphFold
+Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 768.3
+RMSD between 150 pruned atom pairs is 0.552 angstroms; (across all 258 pairs:
+.415)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphaFold
+Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
+.5
+RMSD between 140 pruned atom pairs is 0.581 angstroms; (across all 263 pairs:
+.104)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphaFold
+Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
+.1
+RMSD between 24 pruned atom pairs is 0.507 angstroms; (across all 273 pairs:
+.005)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Alpha Fold
+Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
+score = 600.2
+RMSD between 92 pruned atom pairs is 0.792 angstroms; (across all 268 pairs:
+.726)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Alpha Fold
+Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
+.2
+RMSD between 153 pruned atom pairs is 0.312 angstroms; (across all 255 pairs:
+.821)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Ndumu virus
+Alphafold.pdb, chain A (#15), sequence alignment score = 849.5
+RMSD between 148 pruned atom pairs is 0.597 angstroms; (across all 266 pairs:
+.320)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Everglades virus
+Alphafold.pdb, chain A (#16), sequence alignment score = 1176.1
+RMSD between 24 pruned atom pairs is 0.507 angstroms; (across all 273 pairs:
+.005)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Bebaru virus
+Alphafold.pdb, chain A (#17), sequence alignment score = 755.1
+RMSD between 140 pruned atom pairs is 0.521 angstroms; (across all 258 pairs:
+.677)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Caaingua virus
+AlphaFold.pdb, chain A (#18), sequence alignment score = 629.3
+RMSD between 10 pruned atom pairs is 0.489 angstroms; (across all 258 pairs:
+.729)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Cabassou virus
+Alphafold.pdb, chain A (#19), sequence alignment score = 1205.6
+RMSD between 149 pruned atom pairs is 0.247 angstroms; (across all 274 pairs:
+.936)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Eilat virus
+Alphafold.pdb, chain A (#20), sequence alignment score = 645.7
+RMSD between 152 pruned atom pairs is 0.709 angstroms; (across all 247 pairs:
+.031)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Highlands J. virus
+Alphafold.pdb, chain A (#21), sequence alignment score = 931.4
+RMSD between 139 pruned atom pairs is 0.323 angstroms; (across all 254 pairs:
+.964)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Madariaga virus
+Alpha Fold.pdb, chain A (#22), sequence alignment score = 930.4
+RMSD between 155 pruned atom pairs is 0.321 angstroms; (across all 256 pairs:
+.809)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Mosso das Pedras
+virus AlphaFold.pdb, chain A (#23), sequence alignment score = 1156
+RMSD between 144 pruned atom pairs is 0.209 angstroms; (across all 275 pairs:
+.847)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Southern Elephant
+Seal virus AlphaFold.pdb, chain A (#24), sequence alignment score = 743.4
+RMSD between 148 pruned atom pairs is 0.534 angstroms; (across all 265 pairs:
+.355)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Mucambo virus
+AlphaFold.pdb, chain A (#25), sequence alignment score = 1188.8
+RMSD between 41 pruned atom pairs is 0.760 angstroms; (across all 274 pairs:
+.851)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Onyong-nyong virus
+AlphaFold.pdb, chain A (#26), sequence alignment score = 689.8
+RMSD between 144 pruned atom pairs is 0.546 angstroms; (across all 255 pairs:
+.486)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with RioNegro virus
+AlphaFold.pdb, chain A (#28), sequence alignment score = 1160.6
+RMSD between 44 pruned atom pairs is 1.121 angstroms; (across all 275 pairs:
+.129)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 6xo4.pdb, chain C
+(#5), sequence alignment score = 676.1
+RMSD between 104 pruned atom pairs is 1.210 angstroms; (across all 151 pairs:
+.057)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 1vcp.pdb, chain C
+(#7), sequence alignment score = 554.2
+RMSD between 147 pruned atom pairs is 0.608 angstroms; (across all 149 pairs:
+.747)
+Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 2yew.pdb, chain G
+(#8), sequence alignment score = 518.2
+RMSD between 51 pruned atom pairs is 1.245 angstroms; (across all 171 pairs:
+.032)
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+> hide #27 models
+> show #26 models
+> hide #26 models
+> show #26 models
+> hide #26 models
+> show #25 models
+> show #24 models
+> hide #24 models
+> show #23 models
+> hide #23 models
+> ui tool show Matchmaker
+> matchmaker #2-4,6,9-24,26-28#!5,7-8 to #25
+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 Mucambo virus AlphaFold.pdb, chain A (#25) with 3j2w.pdb, chain I
+(#2), sequence alignment score = 529.5
+RMSD between 148 pruned atom pairs is 0.719 angstroms; (across all 149 pairs:
+.763)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 1kxf.pdb, chain A
+(#3), sequence alignment score = 561.4
+RMSD between 150 pruned atom pairs is 0.671 angstroms; (across all 158 pairs:
+.955)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 7sfu.pdb, chain F
+(#4), sequence alignment score = 791.4
+RMSD between 148 pruned atom pairs is 0.732 angstroms; (across all 162 pairs:
+.042)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 4agk.pdb, chain A
+(#6), sequence alignment score = 559.3
+RMSD between 150 pruned atom pairs is 0.713 angstroms; (across all 151 pairs:
+.739)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 7ko8.pdb, chain G
+(#9), sequence alignment score = 568.5
+RMSD between 129 pruned atom pairs is 1.055 angstroms; (across all 152 pairs:
+.523)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with AlphFold
+Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 797.8
+RMSD between 148 pruned atom pairs is 0.605 angstroms; (across all 261 pairs:
+.742)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with AlphaFold
+Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
+.8
+RMSD between 151 pruned atom pairs is 0.653 angstroms; (across all 262 pairs:
+.551)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with AlphaFold
+Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
+.9
+RMSD between 152 pruned atom pairs is 0.330 angstroms; (across all 274 pairs:
+.227)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Alpha Fold
+Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
+score = 569.6
+RMSD between 132 pruned atom pairs is 0.920 angstroms; (across all 267 pairs:
+.674)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Alpha Fold
+Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
+.5
+RMSD between 155 pruned atom pairs is 0.353 angstroms; (across all 255 pairs:
+.484)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Ndumu virus
+Alphafold.pdb, chain A (#15), sequence alignment score = 830.2
+RMSD between 137 pruned atom pairs is 0.550 angstroms; (across all 267 pairs:
+.448)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Everglades virus
+Alphafold.pdb, chain A (#16), sequence alignment score = 1240.9
+RMSD between 152 pruned atom pairs is 0.330 angstroms; (across all 274 pairs:
+.231)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Bebaru virus
+Alphafold.pdb, chain A (#17), sequence alignment score = 795.9
+RMSD between 146 pruned atom pairs is 0.593 angstroms; (across all 258 pairs:
+.444)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Caaingua virus
+AlphaFold.pdb, chain A (#18), sequence alignment score = 680.9
+RMSD between 130 pruned atom pairs is 0.713 angstroms; (across all 261 pairs:
+.031)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Cabassou virus
+Alphafold.pdb, chain A (#19), sequence alignment score = 1287
+RMSD between 13 pruned atom pairs is 0.146 angstroms; (across all 274 pairs:
+.862)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Eilat virus
+Alphafold.pdb, chain A (#20), sequence alignment score = 686.9
+RMSD between 11 pruned atom pairs is 1.306 angstroms; (across all 254 pairs:
+.777)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Highlands J. virus
+Alphafold.pdb, chain A (#21), sequence alignment score = 984.3
+RMSD between 156 pruned atom pairs is 0.293 angstroms; (across all 255 pairs:
+.661)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Madariaga virus
+Alpha Fold.pdb, chain A (#22), sequence alignment score = 988.9
+RMSD between 135 pruned atom pairs is 0.294 angstroms; (across all 257 pairs:
+.924)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Mosso das Pedras
+virus AlphaFold.pdb, chain A (#23), sequence alignment score = 1167.1
+RMSD between 20 pruned atom pairs is 1.361 angstroms; (across all 274 pairs:
+.794)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Southern Elephant
+Seal virus AlphaFold.pdb, chain A (#24), sequence alignment score = 764.6
+RMSD between 147 pruned atom pairs is 0.552 angstroms; (across all 262 pairs:
+.695)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Onyong-nyong virus
+AlphaFold.pdb, chain A (#26), sequence alignment score = 737.4
+RMSD between 147 pruned atom pairs is 0.545 angstroms; (across all 256 pairs:
+.618)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Pixuna virus
+AlphaFold.pdb, chain A (#27), sequence alignment score = 1188.8
+RMSD between 41 pruned atom pairs is 0.760 angstroms; (across all 274 pairs:
+.851)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with RioNegro virus
+AlphaFold.pdb, chain A (#28), sequence alignment score = 1175.9
+RMSD between 159 pruned atom pairs is 0.307 angstroms; (across all 274 pairs:
+.018)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 6xo4.pdb, chain C
+(#5), sequence alignment score = 701.7
+RMSD between 104 pruned atom pairs is 1.212 angstroms; (across all 151 pairs:
+.018)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 1vcp.pdb, chain C
+(#7), sequence alignment score = 563.4
+RMSD between 147 pruned atom pairs is 0.576 angstroms; (across all 149 pairs:
+.688)
+Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 2yew.pdb, chain G
+(#8), sequence alignment score = 508.8
+RMSD between 54 pruned atom pairs is 1.257 angstroms; (across all 171 pairs:
+.382)
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+——— End of log from Tue Jun 20 13:41:59 2023 ———
+opened ChimeraX session
+> hide #25 models
+> show #28 models
+> hide #28 models
+> show #28 models
+> hide #28 models
+> show #27 models
+> show #26 models
+> hide #26 models
+> show #25 models
+> hide #25 models
+> hide #27 models
+> show #28 models
+> show #26 models
+> hide #26 models
+> show #27 models
+> hide #28 models
+> ui tool show Matchmaker
+> matchmaker #27 to #2
+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 3j2w.pdb, chain I (#2) with Pixuna virus AlphaFold.pdb, chain A
+(#27), sequence alignment score = 521
+RMSD between 147 pruned atom pairs is 0.730 angstroms; (across all 149 pairs:
+.820)
+> show #28 models
+> hide #28 models
+> show #28 models
+> hide #28 models
+> show #28 models
+> show #26 models
+> hide #28 models
+> hide #26 models
+> show #26 models
+> hide #27 models
+> show #25 models
+> hide #26 models
+> show #24 models
+> hide #25 models
+> show #13 models
+> hide #24 models
+> show #25 models
+> show #26 models
+> hide #26 models
+> hide #25 models
+> show #27 models
+> show #28 models
+> hide #28 models
+> show #28 models
+> hide #28 models
+> hide #27 models
+> hide #13 models
+> show #28 models
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+——— End of log from Tue Jun 20 13:59:27 2023 ———
+opened ChimeraX session
+> show #27 models
+> hide #27 models
+> hide #28 models
+> show #28 models
+> hide #28 models
+> show #27 models
+> hide #27 models
+> show #28 models
+> show #26 models
+> show #25 models
+> hide #25 models
+> hide #26 models
+> hide #28 models
+> show #28 models
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+——— End of log from Tue Jun 20 14:01:06 2023 ———
+opened ChimeraX session
+> show #27 models
+> hide #27 models
+> show #26 models
+> hide #26 models
+> show #25 models
+> hide #25 models
+> hide #28 models
+> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/Tonate virus AlphaFold.pdb"
+Chain information for Tonate virus AlphaFold.pdb #29
+---
+Chain | Description
+A | No description available
+> ui tool show Matchmaker
+> matchmaker #29 to #2
+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 3j2w.pdb, chain I (#2) with Tonate virus AlphaFold.pdb, chain A
+(#29), sequence alignment score = 516.2
+RMSD between 147 pruned atom pairs is 0.812 angstroms; (across all 149 pairs:
+.929)
+> color #29 #555500ff
+> color #29 #550000ff
+> color #29 #0055ffff
+> color #29 #0042c7ff
+> color #29 #00007fff
+> color #29 #0000a6ff
+> color #29 #0000ecff
+> color #29 #00007cff
+> color #29 #200e7cff
+> color #29 #27167cff
+> color #29 #2e1e7cff
+> color #29 #36287cff
+> color #29 #40237cff
+> color #29 #3b2e7cff
+> color #29 #5240adff
+> color #29 #3638adff
+> color #29 #585cadff
+> color #29 #4b54adff
+> color #29 #333a76ff
+> color #29 #404894ff
+> color #29 #616ee1ff
+> color #29 #434c9cff
+> color #29 #3d458dff
+> color #29 #394084ff
+> color #29 #363d7dff
+> ui mousemode right select
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #29/A:133
+atoms, 11 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+Alignment identifier is 29/A
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #29/A:133
+atoms, 11 bonds, 1 residue, 1 model selected
+> color sel red
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #29/A:135
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:240@CA
+atom, 1 residue, 1 model selected
+> select #29/A:247
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #29/A:197
+atoms, 16 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 17 atom styles
+> show sel atoms
+> color sel orange
+> ui mousemode right zoom
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #29/A:190
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #29/A:190
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #29/A:185
+atoms, 23 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 24 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #29/A:164
+atoms, 9 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #29/A:163
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #29/A:164
+atoms, 9 bonds, 1 residue, 1 model selected
+> select clear
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #29/A:161
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #29/A:164
+atoms, 9 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 10 atom styles
+> show sel atoms
+> color sel gray
+> select #29/A:161
+atoms, 13 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 14 atom styles
+> show sel atoms
+> color sel orange
+> ui mousemode right translate
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+> show #27 models
+> hide #2 models
+> show #2 models
+> hide #27 models
+> select add #29
+atoms, 4487 bonds, 275 residues, 1 model selected
+> select subtract #29
+Nothing selected
+> hide #29 models
+> show #17 models
+> ui tool show Matchmaker
+> matchmaker #17 to #2
+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 3j2w.pdb, chain I (#2) with Bebaru virus Alphafold.pdb, chain A
+(#17), sequence alignment score = 675.4
+RMSD between 148 pruned atom pairs is 0.764 angstroms; (across all 149 pairs:
+.786)
+> show #29 models
+> hide #29 models
+> show #14 models
+> hide #17 models
+> hide #14 models
+> show #29 models
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+——— End of log from Wed Jun 21 13:00:17 2023 ———
+opened ChimeraX session
+> ui tool show Registration
+> hide #29 models
+> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/Trocara virus AlphaFold.pdb"
+Chain information for Trocara virus AlphaFold.pdb #30
+---
+Chain | Description
+A | No description available
+> ui tool show Matchmaker
+> matchmaker #30 to #2
+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 3j2w.pdb, chain I (#2) with Trocara virus AlphaFold.pdb, chain A
+(#30), sequence alignment score = 500.7
+RMSD between 144 pruned atom pairs is 0.680 angstroms; (across all 149 pairs:
+.933)
+> color #30 #550000ff
+> color #30 #670000ff
+> color #30 #740000ff
+> color #30 #940000ff
+> color #30 #750000ff
+> color #30 #750b0bff
+> color #30 #752616ff
+> color #30 #752620ff
+> color #30 #751414ff
+> color #30 #750b0bff
+> color #30 #b51212ff
+> color #30 #620a0aff
+> color #30 #810d0dff
+> color #30 #8f0e0eff
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #30/A:121
+atoms, 14 bonds, 1 residue, 1 model selected
+Alignment identifier is 30/A
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+Drag select of 1 bonds
+> select #30/A:121
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #30/A:121
+atoms, 14 bonds, 1 residue, 1 model selected
+> select clear
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #30/A:124
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #30/A:124
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:240@CA
+atom, 1 residue, 1 model selected
+> select #30/A:236
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #30/A:236
+atoms, 16 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 17 atom styles
+> show sel atoms
+> color sel orange
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:190@CA
+atom, 1 residue, 1 model selected
+> select #30/A:186
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #30/A:179
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #30/A:179
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #30/A:174
+atoms, 23 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 24 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #30/A:174
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #30/A:153
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #30/A:153
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #30/A:150
+atoms, 9 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 10 atom styles
+> show sel atoms
+> color sel gray
+> ui mousemode right translate
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+> show #28 models
+> hide #28 models
+> show #28 models
+> show #27 models
+> hide #27 models
+> hide #28 models
+> select add #30
+atoms, 4243 bonds, 264 residues, 1 model selected
+> select subtract #30
+Nothing selected
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+——— End of log from Thu Jun 22 13:48:19 2023 ———
+opened ChimeraX session
+> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/Una virus AlphaFold.pdb"
+Chain information for Una virus AlphaFold.pdb #31
+---
+Chain | Description
+A | No description available
+> hide #30 models
+> ui tool show Matchmaker
+> matchmaker #31 to #2
+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 3j2w.pdb, chain I (#2) with Una virus AlphaFold.pdb, chain A (#31),
+sequence alignment score = 668.1
+RMSD between 144 pruned atom pairs is 0.726 angstroms; (across all 149 pairs:
+.900)
+> color #31 #ff557fff
+> color #31 #ff007fff
+> color #31 #55557fff
+> color #31 #ff557fff
+> color #31 #ff5580ff
+> color #31 #ffaaffff
+> color #31 #ff557fff
+> color #31 #ff5a99ff
+> color #31 #ff5ea4ff
+> color #31 #ff67abff
+> color #31 #ff69a2ff
+> color #31 #ff5496ff
+> color #31 #ff557fff
+> color #31 #ff5892ff
+> color #31 #ff4f8dff
+> color #31 #ff52a6ff
+> color #31 #ff54a1ff
+> ui mousemode right select
+Drag select of 2 atoms, 1 bonds
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #31/A:122
+atoms, 11 bonds, 1 residue, 1 model selected
+Alignment identifier is 31/A
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> select clear
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #31/A:124
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #31/A:236
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> select clear
+> ui mousemode right rotate
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #31/A:186
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #31/A:179
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+Drag select of 6 residues
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+Drag select of 1 residues
+> style sel stick
+Changed 24 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #31/A:153
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+Drag select of 19 residues
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #31/A:150
+atoms, 11 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+> show #30 models
+> hide #31 models
+> ui mousemode right select
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #30/A:153
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #30/A:150
+atoms, 9 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #30/A:236
+atoms, 16 bonds, 1 residue, 1 model selected
+> hide #30 models
+> show #31 models
+> ui mousemode right translate
+> show #30 models
+> show #29 models
+> hide #29 models
+> hide #30 models
+> hide #31 models
+> show #31 models
+> select add #30
+atoms, 4243 bonds, 264 residues, 1 model selected
+> select subtract #30
+Nothing selected
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+——— End of log from Fri Jun 23 14:27:32 2023 ———
+opened ChimeraX session
+> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/Whataroa virus AlphaFold.pdb"
+Chain information for Whataroa virus AlphaFold.pdb #32
+---
+Chain | Description
+A | No description available
+> ui tool show Matchmaker
+> matchmaker #32 to #2
+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 3j2w.pdb, chain I (#2) with Whataroa virus AlphaFold.pdb, chain A
+(#32), sequence alignment score = 516.5
+RMSD between 146 pruned atom pairs is 0.667 angstroms; (across all 149 pairs:
+.786)
+> hide #31 models
+> color #32 #ffaa7fff
+> color #32 #ffaa00ff
+> color #32 #ffff7fff
+> color #32 yellow
+> color #32 #ffcb0eff
+> color #32 #ffcd07ff
+> color #32 #ffca0cff
+> color #32 #ffd711ff
+> ui mousemode right select
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #32/A:123
+atoms, 14 bonds, 1 residue, 1 model selected
+Alignment identifier is 32/A
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #32/A:126
+atoms, 11 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #32/A:238
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right translate
+> ui mousemode right rotate
+> ui mousemode right select
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #32/A:188
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+Drag select of 2 atoms, 2 residues, 3 bonds
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #32/A:181
+atoms, 13 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> style sel stick
+Changed 14 atom styles
+> show sel atoms
+> color sel orange
+> color #32 #ffec20ff
+> color #32 #ffd70cff
+> color #32 #ffff7fff
+> color #32 #ffaa00ff
+> color #32 #ffff7fff
+> color #32 #ffff5cff
+> color #32 #fcff4aff
+> color #32 #ddff43ff
+> color #32 #ffff38ff
+> color #32 #ff9cd9ff
+> color #32 #ffa7d2ff
+> color #32 #ffa4d3ff
+> color #32 #fcff39ff
+> color #32 #ffef3aff
+> style sel stick
+Changed 14 atom styles
+> hide sel atoms
+> show sel atoms
+> color sel orange
+> ui mousemode right select
+> select #32/A:123
+atoms, 14 bonds, 1 residue, 1 model selected
+> color sel red
+> select #32/A:126
+atoms, 11 bonds, 1 residue, 1 model selected
+> color sel red
+> select #32/A:123
+atoms, 14 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #32/A:238
+atoms, 14 bonds, 1 residue, 1 model selected
+> color sel red
+> ui mousemode right translate
+> ui mousemode right select
+> select #32/A:188
+atoms, 14 bonds, 1 residue, 1 model selected
+> color sel red
+> ui mousemode right translate
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+> ui mousemode right rotate
+> ui mousemode right select
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #32/A:176
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> select clear
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #32/A:152
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #32/A:152
+atoms, 15 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 16 atom styles
+> hide sel atoms
+> show sel atoms
+> color sel gray
+> select #32/A:155
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #32/A:155
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right translate
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/AguaSalud alphavirus AlphaFold.pdb"
+Chain information for AguaSalud alphavirus AlphaFold.pdb #33
+---
+Chain | Description
+A | No description available
+> ui tool show Matchmaker
+> matchmaker #33 to #2
+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 3j2w.pdb, chain I (#2) with AguaSalud alphavirus AlphaFold.pdb,
+chain A (#33), sequence alignment score = 497.5
+RMSD between 147 pruned atom pairs is 0.696 angstroms; (across all 149 pairs:
+.798)
+> hide #32 models
+> select add #32
+atoms, 4273 bonds, 266 residues, 1 model selected
+> select subtract #32
+Nothing selected
+> color #33 #56344dff
+> color #33 #4e3256ff
+> color #33 #562651ff
+> color #33 #561b3cff
+> color #33 #ffaaffff
+> color #33 #f78affff
+> color #33 #ff66f0ff
+> color #33 #f352ffff
+> color #33 #55ffffff
+> color #33 #ffaaffff
+> color #33 #ffb3feff
+> color #33 #fcb0ffff
+> color #33 #ffa1efff
+> color #33 #ffb9e9ff
+> color #33 #ffb2e7ff
+> color #33 #ffaed8ff
+> ui mousemode right select
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #33/A:123
+atoms, 10 bonds, 1 residue, 1 model selected
+Alignment identifier is 33/A
+> select #33/A:124
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #33/A:123
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #33/A:124
+atoms, 11 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> set bgColor black
+[Repeated 1 time(s)]
+> set bgColor white
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #33/A:126
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #33/A:127
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #33/A:126
+atoms, 16 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> style sel stick
+Changed 17 atom styles
+> show sel atoms
+> color sel orange
+> ui mousemode right select
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #33/A:238
+atoms, 14 bonds, 1 residue, 1 model selected
+> show #32 models
+> select #32/A:238
+atoms, 14 bonds, 1 residue, 1 model selected
+> hide #32 models
+> select add #32
+atoms, 4273 bonds, 266 residues, 1 model selected
+> select subtract #32
+Nothing selected
+> select #33/A:238
+atoms, 14 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right select
+> select #2/I:190@CA
+atom, 1 residue, 1 model selected
+> select #33/A:188
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+Drag select of 2 residues
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #33/A:181
+atoms, 23 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> style sel stick
+Changed 24 atom styles
+> hide sel cartoons
+> show sel cartoons
+> style sel stick
+Changed 24 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #33/A:176
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #33/A:176
+atoms, 21 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #33/A:155
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #33/A:152
+atoms, 18 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 19 atom styles
+> show sel atoms
+> color sel gray
+> ui mousemode right translate
+> show #32 models
+> hide #33 models
+> show #33 models
+> hide #32 models
+> select add #33
+atoms, 4258 bonds, 266 residues, 1 model selected
+> select subtract #33
+Nothing selected
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+[Repeated 1 time(s)]
+——— End of log from Mon Jun 26 10:11:19 2023 ———
+opened ChimeraX session
+> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/Comber alphavirus AlphaFold.pdb"
+Chain information for Comber alphavirus AlphaFold.pdb #34
+---
+Chain | Description
+A | No description available
+> hide #33 models
+> ui tool show Matchmaker
+> matchmaker #34 to #2
+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 3j2w.pdb, chain I (#2) with Comber alphavirus AlphaFold.pdb, chain
+A (#34), sequence alignment score = 336.5
+RMSD between 118 pruned atom pairs is 0.991 angstroms; (across all 144 pairs:
+.924)
+> color #34 #cd7248ff
+> color #34 #cd4a33ff
+> color #34 #cd5647ff
+> color #34 #cd7d44ff
+> color #34 #bd733fff
+> color #34 #b36d3cff
+> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/Harbor porpoise alphavirus AlphaFold.pdb"
+Chain information for Harbor porpoise alphavirus AlphaFold.pdb #35
+---
+Chain | Description
+A | No description available
+> ui tool show Matchmaker
+> matchmaker #35 to #2
+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 3j2w.pdb, chain I (#2) with Harbor porpoise alphavirus
+AlphaFold.pdb, chain A (#35), sequence alignment score = 612.2
+RMSD between 146 pruned atom pairs is 0.708 angstroms; (across all 149 pairs:
+.922)
+> hide #34 models
+> color #35 #ff557fff
+> color #35 #ffff7fff
+> color #35 yellow
+> color #35 #ffff7fff
+> color #35 #fff049ff
+> color #35 #f6ff42ff
+> color #35 #e0ff6eff
+> color #35 #d3ff73ff
+> color #35 #ddff61ff
+> color #35 #cbea59ff
+> color #35 #bcd953ff
+> color #35 #bad94aff
+> color #35 #c9d93cff
+> color #35 #bdd92fff
+> color #35 #c0d941ff
+> color #35 #cad946ff
+> color #35 #d1d93cff
+> color #35 #bad931ff
+> color #35 #d9d93fff
+> color #35 #bfd93cff
+> color #35 #d1d93cff
+> color #35 #b7d93cff
+> color #35 #bfd93cff
+> color #35 #bed938ff
+> color #35 #cae63cff
+> color #35 #c2e640ff
+> color #35 #cae63eff
+> color #35 #c9e53eff
+> show #34 models
+> hide #35 models
+> ui mousemode right select
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #34/A:161
+atoms, 14 bonds, 1 residue, 1 model selected
+Alignment identifier is 34/A
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #34/A:163
+atoms, 13 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 14 atom styles
+> show sel atoms
+> color sel blue
+> color sel orange
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select clear
+> select #34/A:274
+atoms, 10 bonds, 1 residue, 1 model selected
+Drag select of 1 atoms, 2 residues
+> ui mousemode right translate
+> ui mousemode right select
+> select #34/A:274
+atoms, 10 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 11 atom styles
+> show sel atoms
+> color sel orange
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #34/A:225
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #34/A:224
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #34/A:225
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #34/A:224
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #34/A:225
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #34/A:224
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #34/A:225
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #34/A:225
+atoms, 6 bonds, 1 residue, 1 model selected
+> select clear
+> select #34/A:225
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #34/A:224
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #34/A:225
+atoms, 6 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 7 atom styles
+> show sel atoms
+[Repeated 1 time(s)]
+> hide sel atoms
+> style sel stick
+Changed 7 atom styles
+> hide sel atoms
+> show sel atoms
+> select #34/A:225
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #2/I:190@CA
+atom, 1 residue, 1 model selected
+> select #34/A:225
+atoms, 6 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 7 atom styles
+> show sel atoms
+> hide sel atoms
+> hide sel cartoons
+[Repeated 1 time(s)]
+> show sel cartoons
+> show sel atoms
+> hide sel atoms
+[Repeated 1 time(s)]
+> show sel atoms
+> hide sel cartoons
+> show sel cartoons
+> show sel atoms
+> color sel magenta
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #34/A:218
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right translate
+> ui mousemode right select
+> select #34/A:225
+atoms, 6 bonds, 1 residue, 1 model selected
+> show sel atoms
+> hide sel atoms
+> show sel cartoons
+> hide sel cartoons
+> show sel cartoons
+> show sel atoms
+> style sel stick
+Changed 7 atom styles
+> show sel atoms
+> ui mousemode right zoom
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #34/A:213
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> select clear
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:157@CA
+atom, 1 residue, 1 model selected
+> select #34/A:192
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #34/A:192
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #34/A:189
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right translate
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+——— End of log from Tue Jun 27 12:45:33 2023 ———
+opened ChimeraX session
+> ui mousemode right select
+> select #34/A:225
+atoms, 6 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 7 atom styles
+> show sel atoms
+> hide sel atoms
+> show sel atoms
+> hide #34 models
+> select add #34
+atoms, 4847 bonds, 303 residues, 1 model selected
+> select subtract #34
+Nothing selected
+> show #35 models
+> ui mousemode right rotate
+> ui mousemode right translate
+> ui mousemode right select
+> select #35/A:95
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #35/A:95
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #35/A:95
+atoms, 11 bonds, 1 residue, 1 model selected
+> interfaces select & ~solvent
+Missing or invalid "atoms" argument: invalid atoms specifier
+Alignment identifier is 35/A
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #35/A:97
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #35/A:209
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #35/A:159
+atoms, 11 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select clear
+> select #35/A:152
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> hide sel atoms
+> show sel atoms
+> color sel blue
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #35/A:147
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> select clear
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #35/A:126
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+Drag select of 1 residues
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #35/A:123
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #35/A:123
+atoms, 15 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> show sel cartoons
+> style sel stick
+Changed 16 atom styles
+> show sel atoms
+> color sel gray
+> ui mousemode right translate
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+——— End of log from Tue Jun 27 13:05:48 2023 ———
+opened ChimeraX session
+> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/Mwinilunga alphavirus AlphaFold.pdb"
+Chain information for Mwinilunga alphavirus AlphaFold.pdb #36
+---
+Chain | Description
+A | No description available
+> hide #35 models
+> select add #35
+atoms, 3815 bonds, 236 residues, 1 model selected
+> select subtract #35
+Nothing selected
+> color #36 #cd4e7aff
+> color #36 #cd4355ff
+> color #36 #8d81cdff
+> color #36 #7867cdff
+> color #36 #574fcdff
+> color #36 #7272cdff
+> color #36 #8383ebff
+> color #36 #888debff
+> ui tool show Angles/Torsions
+> ui tool show Matchmaker
+> matchmaker #36 to #2
+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 3j2w.pdb, chain I (#2) with Mwinilunga alphavirus AlphaFold.pdb,
+chain A (#36), sequence alignment score = 461.6
+RMSD between 143 pruned atom pairs is 0.699 angstroms; (across all 149 pairs:
+.975)
+> color #36 #8086dcff
+> ui mousemode right select
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #36/A:113
+atoms, 11 bonds, 1 residue, 1 model selected
+Alignment identifier is 36/A
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #36/A:113
+atoms, 11 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> select clear
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #36/A:116
+atoms, 9 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 10 atom styles
+> show sel atoms
+> color sel gray
+> ui mousemode right translate
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+> ui mousemode right select
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #36/A:228
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right translate
+> ui mousemode right select
+> select #36/A:178
+atoms, 11 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #36/A:171
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #36/A:172
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #36/A:171
+atoms, 13 bonds, 1 residue, 1 model selected
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+——— End of log from Wed Jun 28 16:04:54 2023 ———
+opened ChimeraX session
+> ui mousemode right select
+> select #36/A:178
+atoms, 11 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #36/A:171
+atoms, 13 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 14 atom styles
+> show sel atoms
+> ui mousemode right translate
+> color sel orange
+> ui mousemode right select
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #36/A:166
+atoms, 23 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 24 atom styles
+> style sel stick
+Changed 24 atom styles
+> ui mousemode right translate
+> show sel atoms
+> color sel blue
+> ui mousemode right select
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #36/A:145
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #36/A:145
+atoms, 13 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 14 atom styles
+> show sel atoms
+> color sel orange
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #36/A:142
+atoms, 18 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 19 atom styles
+> show sel atoms
+> color sel gray
+> set bgColor white
+> ui mousemode right translate
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/selected_prediction Pirahy virus.pdb"
+Chain information for selected_prediction Pirahy virus.pdb #37
+---
+Chain | Description
+A | No description available
+> hide #36 models
+> select add #36
+atoms, 4027 bonds, 256 residues, 1 model selected
+> select subtract #36
+Nothing selected
+> ui tool show Matchmaker
+> matchmaker #37 to #2
+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 3j2w.pdb, chain I (#2) with selected_prediction Pirahy virus.pdb,
+chain A (#37), sequence alignment score = 544.4
+RMSD between 147 pruned atom pairs is 0.769 angstroms; (across all 149 pairs:
+.873)
+> color #37 #55557fff
+> color #37 #550000ff
+> color #37 #0055ffff
+> color #37 #aaff7fff
+> color #37 #55ff00ff
+> color #37 #4ade00ff
+> color #37 #4cde0dff
+> color #37 #47de1dff
+> color #37 #65de39ff
+> color #37 #6bde41ff
+> ui mousemode right select
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #37/A:134
+atoms, 11 bonds, 1 residue, 1 model selected
+> interfaces select & ~solvent
+Missing or invalid "atoms" argument: invalid atoms specifier
+Alignment identifier is 37/A
+> ui mousemode right translate
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right select
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #37/A:136
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #37/A:136
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right zoom
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #37/A:248
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #37/A:248
+atoms, 14 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right select
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #37/A:198
+atoms, 16 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> style sel stick
+Changed 17 atom styles
+> show sel atoms
+> color sel orange
+[Repeated 1 time(s)]
+> ui mousemode right select
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select clear
+> select #37/A:191
+atoms, 21 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #37/A:186
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #37/A:185
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #37/A:186
+atoms, 23 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 24 atom styles
+> show sel atoms
+> color sel blue
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #37/A:186
+atoms, 23 bonds, 1 residue, 1 model selected
+> ui mousemode right rotate
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #37/A:165
+atoms, 10 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> style sel stick
+Changed 11 atom styles
+> show sel atoms
+> color sel orange
+> ui mousemode right select
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #37/A:162
+atoms, 13 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 14 atom styles
+> show sel atoms
+> color sel orange
+> ui mousemode right translate
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+> hide #37 models
+> select add #37
+atoms, 4459 bonds, 276 residues, 1 model selected
+> show #37 models
+> select subtract #37
+Nothing selected
+> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/selected_prediction tai forest alphavirus
+> .pdb"
+Chain information for selected_prediction tai forest alphavirus .pdb #38
+---
+Chain | Description
+A | No description available
+> ui tool show Matchmaker
+> matchmaker #38 to #2
+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 3j2w.pdb, chain I (#2) with selected_prediction tai forest
+alphavirus .pdb, chain A (#38), sequence alignment score = 454.7
+RMSD between 140 pruned atom pairs is 0.831 angstroms; (across all 149 pairs:
+.170)
+> hide #37 models
+> color #38 #348d22ff
+> color #38 #aaaa00ff
+> color #38 #aaaa7fff
+> color #38 #93936eff
+> color #38 #939362ff
+> color #38 #939360ff
+> color #38 #938f54ff
+> color #38 #93934bff
+> color #38 #a6a655ff
+> ui mousemode right select
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #38/A:115
+atoms, 16 bonds, 1 residue, 1 model selected
+Alignment identifier is 38/A
+> select #38/A:114
+atoms, 11 bonds, 1 residue, 1 model selected
+Drag select of 12 residues
+> select clear
+> select #38/A:114
+atoms, 11 bonds, 1 residue, 1 model selected
+Destroying pre-existing alignment with identifier 38/A
+Alignment identifier is 38/A
+> ui mousemode right zoom
+> ui mousemode right translate
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right select
+> select clear
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #38/A:117
+atoms, 15 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 16 atom styles
+> show sel atoms
+> ui mousemode right translate
+> color sel gray
+> ui mousemode right select
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #38/A:229
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #38/A:179
+atoms, 11 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right select
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #38/A:172
+atoms, 10 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> style sel stick
+Changed 11 atom styles
+> show sel atoms
+> color sel orange
+> ui mousemode right rotate
+> ui mousemode right select
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #38/A:167
+atoms, 23 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 24 atom styles
+> show sel atoms
+> color sel blue
+> select clear
+> ui mousemode right translate
+> ui mousemode right rotate
+> ui mousemode right select
+Drag select of 1 atoms, 6 residues
+> select clear
+> select #38/A:146
+atoms, 10 bonds, 1 residue, 1 model selected
+> style sel sphere
+Changed 11 atom styles
+> style sel stick
+Changed 11 atom styles
+> show sel atoms
+> color sel orange
+> select #38/A:147
+atoms, 18 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #38/A:143
+atoms, 18 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 19 atom styles
+> show sel atoms
+> color sel gray
+> ui mousemode right translate
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+——— End of log from Wed Jun 28 17:55:43 2023 ———
+opened ChimeraX session
+> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/selected_prediction Weglinng hagfish
+> alphavirus consensus.pdb"
+Chain information for selected_prediction Weglinng hagfish alphavirus
+consensus.pdb #39
+---
+Chain | Description
+A | No description available
+> hide #38 models
+> select add #38
+atoms, 4055 bonds, 257 residues, 1 model selected
+> select subtract #38
+Nothing selected
+> color #39 #550000ff
+> color #39 #aa5500ff
+> color #39 #550000ff
+> color #39 #6b0000ff
+> color #39 #810000ff
+> color #39 #814a3dff
+> ui tool show Matchmaker
+> matchmaker #39 to #2
+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 3j2w.pdb, chain I (#2) with selected_prediction Weglinng hagfish
+alphavirus consensus.pdb, chain A (#39), sequence alignment score = 364.7
+RMSD between 66 pruned atom pairs is 0.877 angstroms; (across all 134 pairs:
+.771)
+> set bgColor white
+> ui mousemode right select
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #39/A:186
+atoms, 14 bonds, 1 residue, 1 model selected
+Alignment identifier is 39/A
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> select #39/A:188
+atoms, 6 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 7 atom styles
+> show sel atoms
+> color sel magenta
+> show sel atoms
+[Repeated 1 time(s)]
+> ui mousemode right translate
+> ui mousemode right select
+> select #39/A:300
+atoms, 6 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #39/A:299
+atoms, 11 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right select
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #39/A:249
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #39/A:250
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #39/A:249
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #39/A:263
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #39/A:249
+atoms, 11 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #39/A:249
+atoms, 11 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #39/A:299
+atoms, 11 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:183@CA
+atom, 1 residue, 1 model selected
+> select #39/A:243
+atoms, 21 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right select
+> select #39/A:238
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #39/A:238
+atoms, 23 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> style sel stick
+Changed 24 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right select
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #39/A:217
+atoms, 13 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 14 atom styles
+> show sel atoms
+> color sel orange
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #39/A:214
+atoms, 11 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right translate
+> color #39 #965647ff
+> color #39 #ba6a58ff
+> color #39 #7f483cff
+> color #39 #8f5043ff
+> color #39 #8c4e42ff
+> color #39 #8c5444ff
+> color #39 #8c4545ff
+> color #39 #8c4b49ff
+> color #39 #9d5452ff
+> color #39 #96514eff
+> ui mousemode right select
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #39/A:186
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> color sel red
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #39/A:188
+atoms, 6 bonds, 1 residue, 1 model selected
+> color sel magenta
+> ui mousemode right translate
+> ui mousemode right select
+> select #39/A:300
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #39/A:299
+atoms, 11 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> show sel atoms
+> color sel red
+> ui mousemode right translate
+> ui mousemode right select
+> select #39/A:249
+atoms, 11 bonds, 1 residue, 1 model selected
+> color sel red
+> set bgColor black
+> set bgColor white
+> ui mousemode right translate
+> ui mousemode right select
+> select clear
+> select #39/A:243
+atoms, 21 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> color sel blue
+> ui mousemode right select
+> select #39/A:238
+atoms, 23 bonds, 1 residue, 1 model selected
+> color sel blue
+Drag select of 4 residues
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #39/A:214
+atoms, 11 bonds, 1 residue, 1 model selected
+> ui mousemode right rotate
+> ui mousemode right translate
+> color sel red
+> ui mousemode right select
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #39/A:217
+atoms, 13 bonds, 1 residue, 1 model selected
+> color sel orange
+[Repeated 1 time(s)]
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+Drag select of 44 residues
+> select #39/A:187
+atoms, 6 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+——— End of log from Wed Jun 28 18:20:41 2023 ———
+opened ChimeraX session
+> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/Norwegian salmonid alphavirus AlphaFold.pdb"
+Chain information for Norwegian salmonid alphavirus AlphaFold.pdb #40
+---
+Chain | Description
+A | No description available
+> ui tool show Matchmaker
+> matchmaker #40 to #2
+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 3j2w.pdb, chain I (#2) with Norwegian salmonid alphavirus
+AlphaFold.pdb, chain A (#40), sequence alignment score = 379.7
+RMSD between 128 pruned atom pairs is 0.984 angstroms; (across all 148 pairs:
+.791)
+> hide #39 models
+> select add #39
+atoms, 4999 bonds, 312 residues, 1 model selected
+> select subtract #39
+Nothing selected
+> color #40 #cd8444ff
+> color #40 #cd6c58ff
+> color #40 #cd8b4aff
+> color #40 #966636ff
+> color #40 #ba7f43ff
+> color #40 #b57b41ff
+> color #40 #b58a34ff
+> color #40 #9e782dff
+> color #40 #ba8e35ff
+> color #40 #b08632ff
+> ui mousemode right select
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #40/A:141
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #40/A:140
+atoms, 11 bonds, 1 residue, 1 model selected
+Alignment identifier is 40/A
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #40/A:142
+atoms, 9 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 10 atom styles
+> show sel atoms
+> color sel gray
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #40/A:253
+atoms, 11 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #40/A:204
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #40/A:203
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #40/A:204
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #40/A:203
+atoms, 11 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> set bgColor white
+> ui mousemode right select
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #40/A:197
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #40/A:197
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #40/A:192
+atoms, 23 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 24 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right translate
+> ui mousemode right select
+> select #40/A:140
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #40/A:142
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #40/A:253
+atoms, 11 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #40/A:203
+atoms, 11 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #40/A:197
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #40/A:192
+atoms, 23 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #40/A:171
+atoms, 11 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #40/A:167
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #40/A:168
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #40/A:168
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> select #40/A:171
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #40/A:167
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #40/A:168
+atoms, 14 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #40/A:203
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #40/A:197
+atoms, 14 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #40/A:192
+atoms, 23 bonds, 1 residue, 1 model selected
+> color sel blue
+> ui mousemode right translate
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/selected_prediction Wenling fish
+> alphavirus.pdb"
+Chain information for selected_prediction Wenling fish alphavirus.pdb #41
+---
+Chain | Description
+A | No description available
+> ui tool show Matchmaker
+> matchmaker #41 to #2
+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 3j2w.pdb, chain I (#2) with selected_prediction Wenling fish
+alphavirus.pdb, chain A (#41), sequence alignment score = 320.8
+RMSD between 130 pruned atom pairs is 0.918 angstroms; (across all 148 pairs:
+.592)
+> hide #40 models
+> select add #40
+atoms, 4461 bonds, 281 residues, 1 model selected
+> select subtract #40
+Nothing selected
+> color #41 #286b1aff
+> ui mousemode right select
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #41/A:156
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #41/A:155
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #41/A:156
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #41/A:155
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #41/A:156
+atoms, 21 bonds, 1 residue, 1 model selected
+Alignment identifier is 41/A
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #41/A:158
+atoms, 13 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> hide #41 models
+> select add #41
+atoms, 4801 bonds, 296 residues, 1 model selected
+> select subtract #41
+Nothing selected
+> show #26 models
+> hide #26 models
+> show #39 models
+> show #40 models
+> hide #39 models
+> show #38 models
+> hide #40 models
+> hide #38 models
+> show #41 models
+> ui mousemode right select
+> select #41/A:158
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #41/A:158
+atoms, 13 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 14 atom styles
+> show sel atoms
+> color sel orange
+> ui mousemode right translate
+> ui mousemode right select
+> select clear
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #41/A:269
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+Drag select of 1 residues
+> ui mousemode right translate
+> ui mousemode right rotate
+> ui mousemode right select
+> select #41/A:219
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #41/A:219
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+——— End of log from Thu Jun 29 15:37:27 2023 ———
+opened ChimeraX session
+> ui mousemode right select
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #41/A:138
+atoms, 18 bonds, 1 residue, 1 model selected
+> select clear
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #41/A:213
+atoms, 9 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> style sel stick
+Changed 10 atom styles
+> show sel atoms
+> color sel gray
+> ui mousemode right select
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #41/A:208
+atoms, 17 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> style sel stick
+Changed 17 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right select
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #41/A:187
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #41/A:187
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel sphere
+Changed 15 atom styles
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+Drag select of 3 atoms, 6 residues, 2 bonds
+> select clear
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #41/A:184
+atoms, 18 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> style sel stick
+Changed 19 atom styles
+> show sel atoms
+> color sel gray
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/Yada yada virus AlphaFold.pdb"
+Chain information for Yada yada virus AlphaFold.pdb #42
+---
+Chain | Description
+A | No description available
+> color #42 #5555ffff
+> color #42 #5500ffff
+> color #42 #ff007fff
+> color #42 #ca0065ff
+> color #42 #5dcac6ff
+> color #42 #6647caff
+> color #42 #ca6d89ff
+> color #42 #ca758cff
+> color #42 #ca7585ff
+> color #42 #77ca53ff
+> color #42 #ca78c3ff
+> color #42 #ca7894ff
+> color #42 #ca6d83ff
+> color #42 magenta
+> color #42 #ff2ad8ff
+> color #42 #ff1ebbff
+> color #42 #b623ffff
+> color #42 #da23ffff
+> color #42 #e837ffff
+> color #42 #ff4c91ff
+> color #42 #ff3acaff
+> color #42 #ff2fd2ff
+> color #42 #ff11b4ff
+> color #42 #c30d89ff
+> color #42 #c340abff
+> color #42 #5d6fc3ff
+> color #42 #7a73c3ff
+> color #42 #c35344ff
+> color #42 #a8473bff
+> color #42 #a84e37ff
+> color #42 #a8412fff
+> color #42 #a83931ff
+> color #42 #b63d35ff
+> color #42 #b6877bff
+> color #42 #b67d6fff
+> color #42 #b65b5bff
+> color #42 #a65353ff
+> color #42 #b15959ff
+> color #42 #b13e3aff
+> color #42 #b13227ff
+> color #42 #89b19eff
+> ui tool show Matchmaker
+> matchmaker #42 to #2
+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 3j2w.pdb, chain I (#2) with Yada yada virus AlphaFold.pdb, chain A
+(#42), sequence alignment score = 480
+RMSD between 140 pruned atom pairs is 0.706 angstroms; (across all 149 pairs:
+.975)
+> hide #41 models
+> select add #41
+atoms, 4801 bonds, 296 residues, 1 model selected
+> select subtract #41
+Nothing selected
+> ui mousemode right select
+> select #2/I:126
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #42/A:125
+atoms, 14 bonds, 1 residue, 1 model selected
+Alignment identifier is 42/A
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #42/A:128
+atoms, 23 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> style sel stick
+Changed 24 atom styles
+> show sel atoms
+> color sel blue
+> ui mousemode right select
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #42/A:240
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> select clear
+Drag select of 1 atoms, 1 bonds
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #42/A:190
+atoms, 11 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right select
+> ui mousemode right translate
+> ui mousemode right select
+> select clear
+> select #2/I:183
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #42/A:183
+atoms, 9 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> style sel stick
+Changed 10 atom styles
+> show sel atoms
+> color sel gray
+> color #42 #a5d6beff
+> color #42 #9eccb6ff
+> color sel gray
+> ui mousemode right select
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #42/A:178
+atoms, 23 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 24 atom styles
+> show sel atoms
+> color sel red
+> color sel blue
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #42/A:178
+atoms, 23 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #42/A:128
+atoms, 23 bonds, 1 residue, 1 model selected
+> select clear
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #42/A:125
+atoms, 14 bonds, 1 residue, 1 model selected
+> color sel red
+> select #42/A:128
+atoms, 23 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> color sel blue
+> ui mousemode right select
+> select #42/A:240
+atoms, 14 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> color sel red
+> ui mousemode right select
+> select #42/A:190
+atoms, 11 bonds, 1 residue, 1 model selected
+> color sel red
+> select #42/A:240
+atoms, 14 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:157
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #42/A:157
+atoms, 10 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 11 atom styles
+> show sel atoms
+> color sel orange
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #42/A:154
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #2/I:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #42/A:154
+atoms, 13 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> style sel stick
+Changed 14 atom styles
+> show sel atoms
+> color sel orange
+> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
+——— End of log from Thu Jun 29 18:48:25 2023 ———
+opened ChimeraX session
+> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
+> UASLP/Lab Virología/AlphaFold/Aura virus AlphaFold.pdb"
+Chain information for Aura virus AlphaFold.pdb #43
+---
+Chain | Description
+A | No description available
+> ui tool show Matchmaker
+> matchmaker #43 to #2
+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 3j2w.pdb, chain I (#2) with Aura virus AlphaFold.pdb, chain A
+(#43), sequence alignment score = 493.2
+RMSD between 143 pruned atom pairs is 0.738 angstroms; (across all 149 pairs:
+.063)
+> color #43 #55007fff
+> color #43 #8d00d3ff
+> hide #42 models
+> select add #42
+atoms, 4199 bonds, 268 residues, 1 model selected
+> select subtract #42
+Nothing selected
+> ui mousemode right select
+> select #43/A:124
+atoms, 14 bonds, 1 residue, 1 model selected
+Alignment identifier is 43/A
+> select #43/A:125
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #43/A:124
+atoms, 14 bonds, 1 residue, 1 model selected
+Drag select of 15 residues
+> select clear
+Drag select of 31 residues
+> ui mousemode right translate
+> ui mousemode right select
+> select #43/A:125
+atoms, 11 bonds, 1 residue, 1 model selected
+> ui mousemode right rotate
+> ui mousemode right translate
+> style sel stick
+Changed 12 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right select
+> select #43/A:127
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #2/I:128
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #43/A:127
+atoms, 21 bonds, 1 residue, 1 model selected
+> ui mousemode right rotate
+> ui mousemode right select
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel light sea green
+> color sel blue
+> ui mousemode right translate
+> ui mousemode right select
+> select clear
+> select #2/I:240
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #43/A:239
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right translate
+> ui mousemode right select
+> select #43/A:189
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #2/I:190
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #43/A:189
+atoms, 14 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 15 atom styles
+> show sel atoms
+> color sel red
+> ui mousemode right translate
+> ui mousemode right select
+> select #43/A:182
+atoms, 6 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 7 atom styles
+> show sel atoms
+> color sel magenta
+> style sel stick
+Changed 7 atom styles
+> show sel atoms
+> hide sel atoms
+[Repeated 1 time(s)]
+> hide sel cartoons
+[Repeated 1 time(s)]
+> show sel cartoons
+> show sel atoms
+[Repeated 3 time(s)]
+> hide sel atoms
+> show sel atoms
+> style sel stick
+Changed 7 atom styles
+> show sel atoms
+> color sel magenta
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/I:178
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #43/A:177
+atoms, 21 bonds, 1 residue, 1 model selected
+> ui mousemode right translate
+> style sel stick
+Changed 22 atom styles
+> show sel atoms
+> color sel blue
+> color #43 #ff55ffff
+> color #43 #aaaaffff
+> color #43 #8d8dd3ff
+> color #43 #9696e1ff
+> color #43 #a391e1ff
+> color #43 #b58ae1ff
+> color #43 #bb8ee8ff
+> color sel blue
+> ui mousemode right select
+> select #43/A:182
+atoms, 6 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 7 atom styles
+> hide sel atoms
+> show sel atoms
+[Repeated 1 time(s)]
+> style sel stick
+Changed 7 atom styles
+> show sel atoms
+> color sel magenta
+> ui mousemode right translate
+> color #43 #c797f7ff
+> color sel magenta
+> color sel blue
+> color sel magenta
+> ui mousemode right select
+> select #43/A:177
+atoms, 21 bonds, 1 residue, 1 model selected
+> color sel blue
+> ui mousemode right translate
+[deleted to fit within ticket limits]
 > ui mousemode right select