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Changes between Initial Version and Version 1 of Ticket #18437

Timestamp:: Aug 15, 2025, 12:22:40 PM (4 months ago)
Author:: Tom Goddard
Comment:: This ChimeraX bug may be fixed in the current ChimeraX 1.10 release. You are using a version prior to the ChimeraX 1.8 release.

Legend:

: Unmodified
: Added
: Removed
: Modified

Ticket #18437
- Property Component Unassigned → Structure Editing
- Property Owner set to Eric Pettersen
- Property Platform → all
- Property Project → ChimeraX
- Property Status new → assigned
- Property Summary ChimeraX bug report submission → Crash in python_instances_of_class after "build join" command

Ticket #18437 – Description

-              initial
+              v1
 > show #1 models
+> hide #1 models
+> show #1 models
+> show #8 models
+> hide #8 models
+> show #!9 models
+> hide #1 models
+> hide #89 models
+> show #!78 models
+> hide #!78 models
+> show #89 models
+> log metadata #89
+The model has no metadata
+> log chains #89
+Chain information for AF-D6YWY5-F1-model_v4.pdb #89
+---
+Chain | Description | UniProt
+A | uncharacterized protein | D6YWY5_WADCW 1-494
+> sequence chain #89/A
+Alignment identifier is 89/A
+> select #89/A:271
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #89/A:271-275
+atoms, 42 bonds, 5 residues, 1 model selected
+> select #89/A:275
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #89/A:88-275
+atoms, 1543 bonds, 188 residues, 1 model selected
+> select #89/A:308-310
+atoms, 17 bonds, 3 residues, 1 model selected
+> select #89/A:308-484
+atoms, 1393 bonds, 177 residues, 1 model selected
+> select #89/A:494
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #89/A:485-494
+atoms, 85 bonds, 10 residues, 1 model selected
+> select #89/A:308
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #89/A:308-494
+atoms, 1479 bonds, 187 residues, 1 model selected
+> select #89/A:88
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #89/A:88-275
+atoms, 1543 bonds, 188 residues, 1 model selected
+> color sel purple
+> select add #89
+atoms, 3974 bonds, 494 residues, 1 model selected
+> select subtract #89
+Nothing selected
+> hide #89 models
+> show #90 models
+> log metadata #90
+The model has no metadata
+> log chains #90
+Chain information for AF-Q9TZA7-F1-model_v4.pdb #90
+---
+Chain | Description | UniProt
+A | BTB domain-containing protein | Q9TZA7_CAEEL 1-213
+> sequence chain #89/A
+Alignment identifier is 89/A
+> log metadata #90
+The model has no metadata
+> log chains #90
+Chain information for AF-Q9TZA7-F1-model_v4.pdb #90
+---
+Chain | Description | UniProt
+A | BTB domain-containing protein | Q9TZA7_CAEEL 1-213
+> sequence chain #90/A
+Alignment identifier is 90/A
+> matchmaker #90 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 6ii0.cropped.06.25.23.pdb, chain B (#1) with
+AF-Q9TZA7-F1-model_v4.pdb, chain A (#90), sequence alignment score = 80.1
+RMSD between 6 pruned atom pairs is 1.018 angstroms; (across all 131 pairs:
+.039)
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #90 models
+> show #101 models
+> matchmaker #101 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 6ii0.cropped.06.25.23.pdb, chain B (#1) with
+WP_231937687.1.ranked_0.pdb, chain A (#101), sequence alignment score = 170.8
+RMSD between 65 pruned atom pairs is 0.876 angstroms; (across all 187 pairs:
+.094)
+> log metadata #101
+The model has no metadata
+> log chains #101
+Chain information for WP_231937687.1.ranked_0.pdb #101
+---
+Chain | Description
+A | No description available
+> sequence chain #101/A
+Alignment identifier is 101/A
+> select #101/A:667
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #101/A:664-667
+atoms, 61 bonds, 4 residues, 1 model selected
+> select #101/A:664
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #101/A:664-666
+atoms, 50 bonds, 3 residues, 1 model selected
+> select #101/A:251
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #101/A:251
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #101/A:666
+atoms, 17 bonds, 1 residue, 1 model selected
+> select #101/A:666-668
+atoms, 49 bonds, 3 residues, 1 model selected
+> sym #9
+ii6 mmCIF Assemblies
+---
+| author_and_software_defined_assembly| 1 copy of chains A,C
+| author_and_software_defined_assembly| 1 copy of chains B,D
+> log metadata #9
+No models had metadata
+> log chains #9
+Chain information for 6ii6 #9
+---
+Chain | Description
+A | Putative RTX-toxin
+> sequence chain #9/A
+Alignment identifier is 9/A
+> select #9/A:3350
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #9/A:3350-3352
+atoms, 24 bonds, 3 residues, 1 model selected
+> select clear
+> select #101/A:561
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #101/A:561-563
+atoms, 53 bonds, 3 residues, 1 model selected
+> select #9/A:3482
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #9/A:3482
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #101/A:524
+atoms, 25 bonds, 1 residue, 1 model selected
+> select #101/A:524-726
+atoms, 3281 bonds, 203 residues, 1 model selected
+> select #101/A:727
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #101/A:727-1744
+atoms, 16303 bonds, 1018 residues, 1 model selected
+> show sel cartoons
+> select #101/A:1744
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #101/A:1744
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #101/A:1285
+atoms, 20 bonds, 1 residue, 1 model selected
+> select #101/A:1285-1295
+atoms, 187 bonds, 11 residues, 1 model selected
+> select #101/A:1296
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #101/A:1296-1397
+atoms, 1602 bonds, 102 residues, 1 model selected
+> select #101/A:1262
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #101/A:1262-1397
+atoms, 2154 bonds, 136 residues, 1 model selected
+> select #101/A:1373
+atoms, 20 bonds, 1 residue, 1 model selected
+> select #101/A:1373-1430
+atoms, 908 bonds, 58 residues, 1 model selected
+> select
+> #101/A:9-11,15-19,45-50,207-211,249-252,334-336,340-345,348-356,635-638,658-662,667-673,676-681,685-689,723-726,761-764,767-770,779-781,803-805,892-899,905-912,917-924,1146-1148,1153-1156,1165-1168,1175-1177,1182-1185,1207-1211,1227-1231,1262-1265,1270-1279,1285-1289,1296-1299,1302-1306,1312-1315,1339-1343,1349-1352,1357-1362,1369-1372,1380-1385,1392-1397,1405-1410,1414-1416,1423-1426,1433-1435,1440-1444,1450-1454,1461-1468,1475-1479,1486-1491,1495-1500,1508-1515,1528-1532,1536-1540,1548-1554,1588-1590,1594-1599,1602-1607,1613-1615,1621-1625,1631-1633,1642-1646,1655-1657,1669-1674,1679-1685,1688-1696,1710-1712,1717-1719,1734-1738
+atoms, 5767 bonds, 344 residues, 1 model selected
+> select #101/A:1296
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #101/A:1296-1695
+atoms, 6380 bonds, 400 residues, 1 model selected
+> select #101/A:1296
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #101/A:1296-1744
+atoms, 7189 bonds, 449 residues, 1 model selected
+> select #101/A:1165
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #101/A:1165-1185
+atoms, 315 bonds, 21 residues, 1 model selected
+> select #101/A:1165
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #101/A:1165-1744
+atoms, 9257 bonds, 580 residues, 1 model selected
+> select #101/A:1146-1196
+atoms, 765 bonds, 51 residues, 1 model selected
+> select #101/A:1146-1744
+atoms, 9540 bonds, 599 residues, 1 model selected
+> color sel light gray
+> lighting flat
+> lighting shadows true intensity 0.5
+> lighting shadows false
+> lighting flat
+> lighting shadows true intensity 0.5
+> graphics silhouettes false
+> graphics silhouettes true
+> lighting shadows false
+> lighting shadows true
+> lighting shadows false
+> lighting shadows true
+> lighting flat
+> lighting shadows true intensity 0.5
+> lighting flat
+> lighting shadows true intensity 0.5
+> lighting flat
+> color sel light gray
+> color sel gray
+> select add #101
+atoms, 28182 bonds, 1744 residues, 1 model selected
+> select subtract #101
+Nothing selected
+> hide #101 models
+> show #!94 models
+> log metadata #94
+No models had metadata
+> log chains #94
+Chain information for GMGC10.017_810_714.ranked_0.pdb #94
+---
+Chain | Description
+A | No description available
+> sequence chain #94/A
+Alignment identifier is 94/A
+> select #94/A:1531
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #94/A:1531-1698
+atoms, 2603 bonds, 168 residues, 1 model selected
+> select #94/A:1521-1522
+atoms, 35 bonds, 2 residues, 1 model selected
+> select #94/A:1521-1737
+atoms, 3376 bonds, 217 residues, 1 model selected
+> select #94/A:1521-1737
+atoms, 3376 bonds, 217 residues, 1 model selected
+> select #94/A:1521-2166
+atoms, 9937 bonds, 646 residues, 1 model selected
+> select #94/A:1489
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #94/A:1489-1494
+atoms, 95 bonds, 6 residues, 1 model selected
+> select #94/A:2167-2168
+atoms, 25 bonds, 2 residues, 1 model selected
+> select #94/A:2167-2223
+atoms, 861 bonds, 57 residues, 1 model selected
+> select #94/A:2166
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #94/A:2153-2166
+atoms, 231 bonds, 14 residues, 1 model selected
+> select #94/A:2166
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #94/A:1672-2166
+atoms, 7652 bonds, 495 residues, 1 model selected
+> select #94/A:1421-2166
+atoms, 11402 bonds, 746 residues, 1 model selected
+> select add #94
+atoms, 34892 bonds, 2223 residues, 2 models selected
+> select subtract #94
+model selected
+> hide #!94 models
+> show #77 models
+> log metadata #77
+The model has no metadata
+> log chains #77
+Chain information for AF-A0A097A1Q2-F1-model_v4.pdb #77
+---
+Chain | Description
+A | putative RTX-toxin
+> sequence chain #77/A
+Alignment identifier is 77/A
+> select
+> #77/A:16-22,31-46,52-68,70-72,75-93,96-98,111-113,117-125,127-129,153-155
+atoms, 609 bonds, 83 residues, 1 model selected
+> save /Users/aho2840/Desktop/1q2 format fasta alignment 77/A
+> select add #77
+atoms, 1295 bonds, 171 residues, 1 model selected
+> select subtract #77
+Nothing selected
+> hide #77 models
+> show #75 models
+> log metadata #75
+The model has no metadata
+> log chains #75
+Chain information for AF-A0A0K0E9U3-F1-model_v4.pdb #75
+---
+Chain | Description
+A | ubiquitinyl hydrolase 1
+> sequence chain #75/A
+Alignment identifier is 75/A
+> select #75/A:204-252
+atoms, 398 bonds, 49 residues, 1 model selected
+> select #75/A
+atoms, 2043 bonds, 252 residues, 1 model selected
+> matchmaker #75 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 6ii0.cropped.06.25.23.pdb, chain B (#1) with
+AF-A0A0K0E9U3-F1-model_v4.pdb, chain A (#75), sequence alignment score = 64.1
+RMSD between 27 pruned atom pairs is 1.251 angstroms; (across all 166 pairs:
+.318)
+> select subtract #75
+Nothing selected
+> select add #75
+atoms, 2043 bonds, 252 residues, 1 model selected
+> select subtract #75
+Nothing selected
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> select #75/A:1
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #75/A:1-26
+atoms, 215 bonds, 26 residues, 1 model selected
+> select #75/A:238
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #75/A:1-238
+atoms, 1932 bonds, 238 residues, 1 model selected
+> select #75/A:240
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #75/A:240
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #75/A:194
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #75/A:171-194
+atoms, 187 bonds, 24 residues, 1 model selected
+> select #75/A:170
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #75/A:1-170
+atoms, 1386 bonds, 170 residues, 1 model selected
+> color sel purple
+> select add #75
+atoms, 2043 bonds, 252 residues, 1 model selected
+> select subtract #75
+Nothing selected
+> select #75/A:252
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #75/A:252
+atoms, 8 bonds, 1 residue, 1 model selected
+> select add #75
+atoms, 2043 bonds, 252 residues, 1 model selected
+> select subtract #75
+Nothing selected
+> hide #75 models
+> show #100 models
+> matchmaker #100 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 6ii0.cropped.06.25.23.pdb, chain B (#1) with
+WP_148121377.1.ranked_0.pdb, chain A (#100), sequence alignment score = 124.8
+RMSD between 57 pruned atom pairs is 1.106 angstroms; (across all 188 pairs:
+.164)
+> hide #!9 models
+> log metadata #100
+The model has no metadata
+> log chains #100
+Chain information for WP_148121377.1.ranked_0.pdb #100
+---
+Chain | Description
+A | No description available
+> sequence chain #100/A
+Alignment identifier is 100/A
+> select #100/A:421
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #100/A:351-421
+atoms, 1234 bonds, 71 residues, 1 model selected
+> select #100/A:422
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #100/A:422-424
+atoms, 41 bonds, 3 residues, 1 model selected
+> select #100/A:421-422
+atoms, 29 bonds, 2 residues, 1 model selected
+> select #100/A:421-437
+atoms, 275 bonds, 17 residues, 1 model selected
+> show #!9 models
+> select #100/A:747
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #100/A:421-747
+atoms, 5372 bonds, 327 residues, 1 model selected
+> select #100/A:1
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #100/A:1-294
+atoms, 4906 bonds, 294 residues, 1 model selected
+> ui tool show Matchmaker
+> matchmaker #100 & sel 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 6ii0.cropped.06.25.23.pdb, chain B (#1) with
+WP_148121377.1.ranked_0.pdb, chain A (#100), sequence alignment score = 129.3
+RMSD between 53 pruned atom pairs is 0.785 angstroms; (across all 180 pairs:
+.140)
+> matchmaker #100 & sel 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 6ii0.cropped.06.25.23.pdb, chain B (#1) with
+WP_148121377.1.ranked_0.pdb, chain A (#100), sequence alignment score = 129.3
+RMSD between 53 pruned atom pairs is 0.785 angstroms; (across all 180 pairs:
+.140)
+> select add #100
+atoms, 31455 bonds, 1953 residues, 1 model selected
+> select subtract #100
+Nothing selected
+> select #100/A:421
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #100/A:421-747
+atoms, 5372 bonds, 327 residues, 1 model selected
+> color sel purple
+> select add #100
+atoms, 31455 bonds, 1953 residues, 1 model selected
+> select subtract #100
+Nothing selected
+> hide #100 models
+> show #93 models
+> log metadata #93
+The model has no metadata
+> log chains #93
+Chain information for C4K5K2.ranked_0.pdb #93
+---
+Chain | Description
+A | No description available
+> sequence chain #93/A
+Alignment identifier is 93/A
+> matchmaker #93 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 6ii0.cropped.06.25.23.pdb, chain B (#1) with C4K5K2.ranked_0.pdb,
+chain A (#93), sequence alignment score = 133.9
+RMSD between 51 pruned atom pairs is 0.709 angstroms; (across all 196 pairs:
+.970)
+> select #93/A:309
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #93/A:1-309
+atoms, 5230 bonds, 309 residues, 1 model selected
+> select #93/A:1
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #93/A:1-294
+atoms, 4952 bonds, 294 residues, 1 model selected
+> color sel purple
+> select #93/A:1243
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #93/A:1243-1300
+atoms, 896 bonds, 58 residues, 1 model selected
+> select #93/A:1243-1901
+atoms, 10326 bonds, 659 residues, 1 model selected
+> color sel #941751ff
+> select add #93
+atoms, 31675 bonds, 1960 residues, 1 model selected
+> select subtract #93
+Nothing selected
+> select #93/A:303
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #93/A:303-1251
+atoms, 15476 bonds, 949 residues, 1 model selected
+> ui tool show Matchmaker
+> matchmaker #93 & sel 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 6ii0.cropped.06.25.23.pdb, chain B (#1) with C4K5K2.ranked_0.pdb,
+chain A (#93), sequence alignment score = 121.2
+RMSD between 51 pruned atom pairs is 1.196 angstroms; (across all 187 pairs:
+.810)
+> matchmaker #93 & sel 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 6ii0.cropped.06.25.23.pdb, chain B (#1) with C4K5K2.ranked_0.pdb,
+chain A (#93), sequence alignment score = 121.2
+RMSD between 51 pruned atom pairs is 1.196 angstroms; (across all 187 pairs:
+.810)
+> select add #93
+atoms, 31675 bonds, 1960 residues, 1 model selected
+> select subtract #93
+Nothing selected
+> ui mousemode right select
+Drag select of 804 residues
+> hide sel cartoons
+Drag select of 606 residues
+> hide sel cartoons
+Drag select of 54 residues
+> hide sel cartoons
+Drag select of 108 residues
+> hide sel cartoons
+Drag select of 12 residues
+> hide sel cartoons
+> ui mousemode right "translate selected models"
+> view matrix models
+> #93,-0.54652,0.1758,0.81879,36.258,-0.76539,0.2919,-0.57355,17.296,-0.33984,-0.94015,-0.024975,11.622
+> undo
+> select add #93
+atoms, 31675 bonds, 1960 residues, 1 model selected
+> select subtract #93
+Nothing selected
+> select #93/A:462
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #93/A:412-462
+atoms, 788 bonds, 51 residues, 1 model selected
+> select #93/A:425
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #93/A:425-450
+atoms, 407 bonds, 26 residues, 1 model selected
+> show sel cartoons
+> select add #93
+atoms, 31675 bonds, 1960 residues, 1 model selected
+> select subtract #93
+Nothing selected
+> select #93/A:424
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #93/A:374-424
+atoms, 835 bonds, 51 residues, 1 model selected
+> show sel cartoons
+> select add #93
+atoms, 31675 bonds, 1960 residues, 1 model selected
+> select subtract #93
+Nothing selected
+> select #93/A:464
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #93/A:464-516
+atoms, 871 bonds, 53 residues, 1 model selected
+> select #93/A:416
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #93/A:416-748
+atoms, 5478 bonds, 333 residues, 1 model selected
+> select #93/A:416
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #93/A:416-742
+atoms, 5373 bonds, 327 residues, 1 model selected
+> select #93/A:1912-1960
+atoms, 759 bonds, 49 residues, 1 model selected
+> select #93/A
+atoms, 31675 bonds, 1960 residues, 1 model selected
+> show sel cartoons
+> select subtract #93
+Nothing selected
+> select add #93
+atoms, 31675 bonds, 1960 residues, 1 model selected
+> select subtract #93
+Nothing selected
+> select #93/A:263
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #93/A:263-364
+atoms, 1800 bonds, 102 residues, 1 model selected
+> select #93/A:86-136
+atoms, 851 bonds, 51 residues, 1 model selected
+> select #93/A:35-136
+atoms, 1716 bonds, 102 residues, 1 model selected
+> select #93/A:295
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #93/A:295-415
+atoms, 2122 bonds, 121 residues, 1 model selected
+> color sel #040e52ff
+> select #93/A:416
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #93/A:416-742
+atoms, 5373 bonds, 327 residues, 1 model selected
+> color sel purple
+> select #93/A:743
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #93/A:743-1242
+atoms, 7989 bonds, 500 residues, 1 model selected
+> color sel #040e52ff
+> select #93/A:1902
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #93/A:1902-1960
+atoms, 908 bonds, 59 residues, 1 model selected
+> color sel #040e52ff
+> select add #93
+atoms, 31675 bonds, 1960 residues, 1 model selected
+> select subtract #93
+Nothing selected
+> hide #93 models
+> show #104 models
+> show #105 models
+> select add #104
+atoms, 30638 bonds, 1999 residues, 1 model selected
+> select subtract #104
+Nothing selected
+> log metadata #105
+The model has no metadata
+> log chains #105
+Chain information for GMGC10.011_528_202.ranked_0.1800.3500.pdb #105
+---
+Chain | Description
+A | No description available
+> sequence chain #105/A
+Alignment identifier is 105/A
+> log metadata #104
+The model has no metadata
+> log chains #104
+Chain information for GMGC10.011_528_202.ranked_0.1.2000.ranked_0.pdb #104
+---
+Chain | Description
+A | No description available
+> sequence chain #104/A
+Alignment identifier is 104/A
+Already setting window visible!
+> select
+> #105/A:10-18,30-42,46-68,70-76,109-128,144-152,159-161,182-190,196-198,201-210,221-229,231-245,259-289,301-303,316-328,334-354,361-379,383-385,394-403,447-458,469-472,487-492,494-505,511-518,530-535,547-555,561-563,568-576,581-597,603-605,624-635,646-670,674-689,695-704,710-726,732-740,743-752,766-775,778-790,793-804,809-821,828-833,836-855,859-869,879-896,915-927,935-958,975-977,984-991,995-1018,1020-1022,1026-1038,1043-1082,1331-1333,1394-1396,1434-1442,1546-1548
+atoms, 10318 bonds, 667 residues, 1 model selected
+> select #105/A:1
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #105/A:1-43
+atoms, 687 bonds, 43 residues, 1 model selected
+> select #105/A:1
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #105/A:1-200
+atoms, 3094 bonds, 200 residues, 1 model selected
+> select #105/A:201
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #105/A:201-209
+atoms, 139 bonds, 9 residues, 1 model selected
+> select add #105
+atoms, 24336 bonds, 1601 residues, 1 model selected
+> select subtract #105
+Nothing selected
+> matchmaker #9 to #104
+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 GMGC10.011_528_202.ranked_0.1.2000.ranked_0.pdb, chain A (#104)
+with 6ii6, chain A (#9), sequence alignment score = 105.4
+RMSD between 4 pruned atom pairs is 0.393 angstroms; (across all 200 pairs:
+.701)
+> undo
+> matchmaker #9 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 6ii0.cropped.06.25.23.pdb, chain B (#1) with 6ii6, chain A (#9),
+sequence alignment score = 1498.3
+RMSD between 212 pruned atom pairs is 0.553 angstroms; (across all 223 pairs:
+.561)
+> hide #!9 models
+> select subtract #105
+Nothing selected
+> hide #105 models
+> show #105 models
+> matchmaker #9 to #105
+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 GMGC10.011_528_202.ranked_0.1800.3500.pdb, chain A (#105) with
+ii6, chain A (#9), sequence alignment score = 270
+RMSD between 108 pruned atom pairs is 1.145 angstroms; (across all 292 pairs:
+.773)
+> show #!9 models
+> select #105/A:300
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #105/A:300-303
+atoms, 61 bonds, 4 residues, 1 model selected
+> select #105/A:299
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #105/A:291-299
+atoms, 141 bonds, 9 residues, 1 model selected
+> toolshed show
+> ui tool show "Renumber Residues"
+> select #105/A:260-310
+atoms, 779 bonds, 51 residues, 1 model selected
+> select #105/A:260-410
+atoms, 2237 bonds, 151 residues, 1 model selected
+> select add #105
+atoms, 24336 bonds, 1601 residues, 1 model selected
+> select subtract #105
+Nothing selected
+> hide #105 models
+> show #105 models
+> select #105/A:1
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #105/A:1
+atoms, 15 bonds, 1 residue, 1 model selected
+> select add #105
+atoms, 24336 bonds, 1601 residues, 1 model selected
+> select subtract #105
+Nothing selected
+> ui tool show "Renumber Residues"
+> renumber #105/A seqStart 1800
+residues renumbered
+> select #105/A:2100
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #105/A:2100-2404
+atoms, 4593 bonds, 305 residues, 1 model selected
+> select #105/A:2100
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #105/A:2100-2111
+atoms, 167 bonds, 12 residues, 1 model selected
+> select #105/A:2099
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #105/A:2077-2099
+atoms, 346 bonds, 23 residues, 1 model selected
+> select
+> #105/A:1809-1817,1829-1841,1845-1867,1869-1875,1908-1927,1943-1951,1958-1960,1981-1989,1995-1997,2000-2009,2020-2028,2030-2044,2058-2088,2100-2102,2115-2127,2133-2153,2160-2178,2182-2184,2193-2202,2246-2257,2268-2271,2286-2291,2293-2304,2310-2317,2329-2334,2346-2354,2360-2362,2367-2375,2380-2396,2402-2404,2423-2434,2445-2469,2473-2488,2494-2503,2509-2525,2531-2539,2542-2551,2565-2574,2577-2589,2592-2603,2608-2620,2627-2632,2635-2654,2658-2668,2678-2695,2714-2726,2734-2757,2774-2776,2783-2790,2794-2817,2819-2821,2825-2837,2842-2881,3130-3132,3193-3195,3233-3241,3345-3347
+atoms, 10318 bonds, 667 residues, 1 model selected
+> select add #105
+atoms, 24336 bonds, 1601 residues, 1 model selected
+> select subtract #105
+Nothing selected
+> select #105/A:2058-2059
+atoms, 16 bonds, 2 residues, 1 model selected
+> select #105/A:2058-2088
+atoms, 475 bonds, 31 residues, 1 model selected
+> select #105/A:2000
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #105/A:2000-2047
+atoms, 762 bonds, 48 residues, 1 model selected
+> select #105/A:2305
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #105/A:2305-2323
+atoms, 280 bonds, 19 residues, 1 model selected
+> color sel #040e52ff
+> select add #105
+atoms, 24336 bonds, 1601 residues, 1 model selected
+> select subtract #105
+Nothing selected
+> select #104/A:210
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #104/A:210-580
+atoms, 5651 bonds, 371 residues, 1 model selected
+> select #104/A:210
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #104/A:210-572
+atoms, 5531 bonds, 363 residues, 1 model selected
+> select #104/A:209
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #104/A:1-209
+atoms, 3238 bonds, 209 residues, 1 model selected
+> color sel #040e52ff
+> select #104/A:573
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #104/A:573-576
+atoms, 54 bonds, 4 residues, 1 model selected
+> select #104/A:573-576
+atoms, 54 bonds, 4 residues, 1 model selected
+> select #104/A:573-918
+atoms, 5272 bonds, 346 residues, 1 model selected
+> select #104/A:573-1221
+atoms, 9977 bonds, 649 residues, 1 model selected
+> color sel #040e52ff
+> select #104/A:1223
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #104/A:1223-1273
+atoms, 736 bonds, 51 residues, 1 model selected
+> select #104/A:1222
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #104/A:1222-1324
+atoms, 1477 bonds, 103 residues, 1 model selected
+> select #104/A:1222-1706
+atoms, 7351 bonds, 485 residues, 1 model selected
+> color sel black
+> select #104/A:1707
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #104/A:1707-1716
+atoms, 152 bonds, 10 residues, 1 model selected
+> show #!45 models
+> hide #!45 models
+> show #!45 models
+> hide #!45 models
+> show #!45 models
+> hide #!45 models
+> select add #104
+atoms, 30638 bonds, 1999 residues, 1 model selected
+> select subtract #104
+Nothing selected
+> hide #105 models
+> hide #104 models
+> show #!45 models
+> hide #!45 models
+> show #!45 models
+> select add #45
+atoms, 1012 bonds, 253 residues, 2 models selected
+> show #!9 cartoons
+> select subtract #45
+Nothing selected
+> select add #45
+atoms, 1012 bonds, 253 residues, 2 models selected
+> select subtract #45
+Nothing selected
+> hide #!45 models
+> hide #!9 models
+> show #!45 models
+> select add #45
+atoms, 1012 bonds, 253 residues, 2 models selected
+> show #45.2 models
+> view matrix models #45,1,0,0,40.708,0,1,0,63.372,0,0,1,-69.846
+> hide #45.2 models
+> hide #!45 models
+> select subtract #45.2
+model selected
+> select add #45
+atoms, 1012 bonds, 253 residues, 2 models selected
+> select subtract #45
+Nothing selected
+> open "/Users/aho2840/Downloads/ranked_0 (4).pdb"
+Chain information for ranked_0 (4).pdb #110
+---
+Chain | Description
+A | No description available
+> open "/Users/aho2840/Downloads/ranked_0 (5).pdb"
+Chain information for ranked_0 (5).pdb #111
+---
+Chain | Description
+A | No description available
+> rename #110 GMGC10.011_528_202.ranked_0.1800.3500.pdb
+> rename #110 GMGC10.011_528_202.ranked_0.3247.3500.pdb
+> rename #110 GMGC10.011_528_202.ranked_0.3247.4160.pdb
+> rename #111 GMGC10.011_528_202.ranked_0.4000.3500.pdb
+> rename #111 GMGC10.011_528_202.ranked_0.4000.5243.pdb
+> matchmaker #110 to #105
+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 GMGC10.011_528_202.ranked_0.1800.3500.pdb, chain A (#105) with
+GMGC10.011_528_202.ranked_0.3247.4160.pdb, chain A (#110), sequence alignment
+score = 1226.3
+RMSD between 129 pruned atom pairs is 0.511 angstroms; (across all 253 pairs:
+.842)
+> matchmaker #111 to #110
+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 GMGC10.011_528_202.ranked_0.3247.4160.pdb, chain A (#110) with
+GMGC10.011_528_202.ranked_0.4000.5243.pdb, chain A (#111), sequence alignment
+score = 708.7
+RMSD between 7 pruned atom pairs is 1.070 angstroms; (across all 161 pairs:
+.247)
+> show #105 models
+> select #105/A:3156
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #105/A:3156-3314
+atoms, 2447 bonds, 159 residues, 1 model selected
+> select #105/A:3250
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #105/A:3250-3400
+atoms, 2384 bonds, 151 residues, 1 model selected
+> ui tool show Matchmaker
+> matchmaker #110 to #105 & sel
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker GMGC10.011_528_202.ranked_0.1800.3500.pdb, chain A (#105) with
+GMGC10.011_528_202.ranked_0.3247.4160.pdb, chain A (#110), sequence alignment
+score = 752.3
+RMSD between 8 pruned atom pairs is 1.302 angstroms; (across all 151 pairs:
+.005)
+> matchmaker #110 to #105 & sel
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker GMGC10.011_528_202.ranked_0.1800.3500.pdb, chain A (#105) with
+GMGC10.011_528_202.ranked_0.3247.4160.pdb, chain A (#110), sequence alignment
+score = 752.3
+RMSD between 8 pruned atom pairs is 1.302 angstroms; (across all 151 pairs:
+.005)
+> select add #105
+atoms, 24336 bonds, 1601 residues, 1 model selected
+> select subtract #105
+Nothing selected
+> select #105/A:3250
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #105/A:3250-3400
+atoms, 2384 bonds, 151 residues, 1 model selected
+> log metadata #110
+The model has no metadata
+> log chains #110
+Chain information for GMGC10.011_528_202.ranked_0.3247.4160.pdb #110
+---
+Chain | Description
+A | No description available
+> sequence chain #110/A
+Alignment identifier is 110/A
+> select #110/A:1
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #110/A:1
+atoms, 15 bonds, 1 residue, 1 model selected
+> ui tool show "Renumber Residues"
+> renumber #110/A seqStart 3247
+residues renumbered
+> renumber #110/A seqStart 3247
+residues renumbered
+> select #110/A:3247
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #110/A:3247-3501
+atoms, 3955 bonds, 255 residues, 1 model selected
+> ui tool show Matchmaker
+> matchmaker #110 & sel to #105 & sel
+No 'to' model specified
+> select #105/A:3250
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #105/A:3250-3400
+atoms, 2384 bonds, 151 residues, 1 model selected
+> ui tool show Matchmaker
+> matchmaker #110 & sel to #105 & sel
+No molecules/chains to match specified
+> select #110/A:3501
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #110/A:3247-3501
+atoms, 3955 bonds, 255 residues, 1 model selected
+> ui tool show Matchmaker
+> matchmaker #105 to #110 & sel
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker GMGC10.011_528_202.ranked_0.3247.4160.pdb, chain A (#110) with
+GMGC10.011_528_202.ranked_0.1800.3500.pdb, chain A (#105), sequence alignment
+score = 1226.3
+RMSD between 129 pruned atom pairs is 0.511 angstroms; (across all 253 pairs:
+.842)
+> matchmaker #105 to #110 & sel
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker GMGC10.011_528_202.ranked_0.3247.4160.pdb, chain A (#110) with
+GMGC10.011_528_202.ranked_0.1800.3500.pdb, chain A (#105), sequence alignment
+score = 1226.3
+RMSD between 129 pruned atom pairs is 0.511 angstroms; (across all 253 pairs:
+.842)
+> select add #110
+atoms, 14133 bonds, 913 residues, 1 model selected
+> select subtract #110
+Nothing selected
+> select #110/A:3247
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #110/A:3247-3499
+atoms, 3931 bonds, 253 residues, 1 model selected
+> view matrix models
+> #110,0.15907,0.871,0.46482,23.648,0.26589,-0.49121,0.82946,67.554,0.95079,-0.0083555,-0.30973,62.328
+> undo
+> hide sel cartoons
+> select #110/A:3500
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #110/A:3500-3579
+atoms, 1241 bonds, 80 residues, 1 model selected
+> view matrix models
+> #110,0.15907,0.871,0.46482,-35.338,0.26589,-0.49121,0.82946,31.014,0.95079,-0.0083555,-0.30973,38.751
+> select #105/A:3393
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #105/A:3393-3400
+atoms, 128 bonds, 8 residues, 1 model selected
+> view matrix models
+> #105,0.070652,0.61953,-0.78179,58.534,-0.84869,0.44916,0.27924,77.982,0.52415,0.64377,0.55752,4.1016
+> undo
+> select add #105
+atoms, 24336 bonds, 1601 residues, 1 model selected
+> select subtract #105
+Nothing selected
+> select #110/A:3247
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #110/A:3247-3263
+atoms, 271 bonds, 17 residues, 1 model selected
+> select #110/A:3247
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #110/A:3247-3510
+atoms, 4102 bonds, 264 residues, 1 model selected
+> select #110/A:3504-3505
+atoms, 38 bonds, 2 residues, 1 model selected
+> select #110/A:3504-3510
+atoms, 115 bonds, 7 residues, 1 model selected
+> select #110/A:3500
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #110/A:3500-3534
+atoms, 590 bonds, 35 residues, 1 model selected
+> view matrix models
+> #110,0.15907,0.871,0.46482,-22.055,0.26589,-0.49121,0.82946,63.614,0.95079,-0.0083555,-0.30973,185.11
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #110,0.47262,-0.25828,0.84257,-25.085,-0.61466,-0.78176,0.10513,73.004,0.63153,-0.56758,-0.52823,188.63
+> view matrix models
+> #110,0.50805,-0.24833,0.82475,-25.704,-0.63892,-0.75081,0.16751,73.694,0.57763,-0.61206,-0.54012,189.36
+> view matrix models
+> #110,0.41155,-0.2799,0.86734,-24.051,-0.56296,-0.82648,0.00040731,71.684,0.71673,-0.48845,-0.49771,187.53
+> view matrix models
+> #110,0.53239,-0.24265,0.81098,-26.137,-0.65303,-0.72733,0.21107,74.134,0.53863,-0.64196,-0.54568,189.91
+> view matrix models
+> #110,0.58365,-0.23401,0.77755,-27.073,-0.6754,-0.67148,0.30488,74.962,0.45077,-0.7031,-0.54996,191.19
+> view matrix models
+> #110,0.50053,-0.26305,0.82479,-25.595,-0.61091,-0.78236,0.12122,73.03,0.6134,-0.56455,-0.55229,188.78
+> view matrix models
+> #110,0.54811,-0.2445,0.79987,-26.43,-0.65256,-0.72323,0.22609,74.204,0.52321,-0.64588,-0.55596,190.09
+> view matrix models
+> #110,0.49249,-0.26667,0.82845,-25.457,-0.60267,-0.79124,0.10358,72.815,0.62789,-0.5503,-0.5504,188.57
+> view matrix models
+> #110,0.56859,-0.23809,0.78741,-26.798,-0.66661,-0.69423,0.27144,74.654,0.48202,-0.67923,-0.55345,190.71
+> view matrix models
+> #110,-0.45753,-0.84636,0.27265,-14.236,-0.8879,0.41828,-0.19153,75.864,0.048064,-0.32971,-0.94286,195.29
+> view matrix models
+> #110,0.16212,-0.729,0.66504,-21.465,-0.98276,-0.17998,0.042289,78.334,0.088865,-0.66043,-0.74561,195.61
+> ui mousemode right "translate selected models"
+> view matrix models
+> #110,0.16212,-0.729,0.66504,13.429,-0.98276,-0.17998,0.042289,14.171,0.088865,-0.66043,-0.74561,150.07
+> ui mousemode right rotate
+> ui mousemode right "translate selected models"
+> view matrix models
+> #110,0.16212,-0.729,0.66504,56.796,-0.98276,-0.17998,0.042289,30.661,0.088865,-0.66043,-0.74561,177.29
+> ui mousemode right "translate selected models"
+> view matrix models
+> #110,0.16212,-0.729,0.66504,62.215,-0.98276,-0.17998,0.042289,36.02,0.088865,-0.66043,-0.74561,170.42
+> view matrix models
+> #110,0.16212,-0.729,0.66504,47.904,-0.98276,-0.17998,0.042289,38.086,0.088865,-0.66043,-0.74561,171.89
+> view matrix models
+> #110,0.16212,-0.729,0.66504,48.471,-0.98276,-0.17998,0.042289,4.313,0.088865,-0.66043,-0.74561,146.61
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #110,0.13868,-0.7211,0.67881,48.894,-0.9903,-0.095156,0.10124,4.7482,-0.0084073,-0.68627,-0.7273,148.15
+> view matrix models
+> #110,0.14058,-0.72184,0.67763,48.86,-0.99007,-0.10231,0.096411,4.7183,-0.00026617,-0.68445,-0.72906,148.02
+> view matrix models
+> #110,0.15864,-0.728,0.66697,48.533,-0.9845,-0.16785,0.05096,4.3863,0.074849,-0.66471,-0.74334,146.83
+> ui mousemode right "translate selected models"
+> view matrix models
+> #110,0.15864,-0.728,0.66697,47.311,-0.9845,-0.16785,0.05096,2.404,0.074849,-0.66471,-0.74334,145.71
+> select add #110
+atoms, 14133 bonds, 913 residues, 1 model selected
+> select subtract #110
+Nothing selected
+> select #110/A:3513
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #110/A:3513-3555
+atoms, 697 bonds, 43 residues, 1 model selected
+> ui mousemode right "translate selected models"
+> view matrix models
+> #110,0.15864,-0.728,0.66697,45.54,-0.9845,-0.16785,0.05096,3.5472,0.074849,-0.66471,-0.74334,148.09
+> view matrix models
+> #110,0.15864,-0.728,0.66697,43.732,-0.9845,-0.16785,0.05096,4.7486,0.074849,-0.66471,-0.74334,147.21
+> view matrix models
+> #110,0.15864,-0.728,0.66697,43.927,-0.9845,-0.16785,0.05096,4.2323,0.074849,-0.66471,-0.74334,146.75
+> view matrix models
+> #110,0.15864,-0.728,0.66697,43.656,-0.9845,-0.16785,0.05096,3.9038,0.074849,-0.66471,-0.74334,146.59
+> select add #110
+atoms, 14133 bonds, 913 residues, 1 model selected
+> select subtract #110
+Nothing selected
+> ui mousemode right "translate selected models"
+> log metadata #111
+The model has no metadata
+> log chains #111
+Chain information for GMGC10.011_528_202.ranked_0.4000.5243.pdb #111
+---
+Chain | Description
+A | No description available
+> sequence chain #111/A
+Alignment identifier is 111/A
+> ui tool show "Renumber Residues"
+> renumber #111/A seqStart 4000
+residues renumbered
+> renumber #111/A seqStart 4000
+residues renumbered
+> matchmaker #111 to #110
+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 GMGC10.011_528_202.ranked_0.3247.4160.pdb, chain A (#110) with
+GMGC10.011_528_202.ranked_0.4000.5243.pdb, chain A (#111), sequence alignment
+score = 708.7
+RMSD between 7 pruned atom pairs is 1.070 angstroms; (across all 161 pairs:
+.247)
+> select #110/A:3297
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #110/A:3297-3303
+atoms, 116 bonds, 7 residues, 1 model selected
+> select #110/A:3297-3298
+atoms, 32 bonds, 2 residues, 1 model selected
+> select #110/A:3298-3499
+atoms, 3130 bonds, 202 residues, 1 model selected
+> select #110/A:3500-3501
+atoms, 23 bonds, 2 residues, 1 model selected
+> select #110/A:3500-3562
+atoms, 983 bonds, 63 residues, 1 model selected
+> select add #110
+atoms, 14133 bonds, 913 residues, 1 model selected
+> select subtract #110
+Nothing selected
+> select #111/A:4158-4159
+atoms, 32 bonds, 2 residues, 1 model selected
+> select #111/A:4000-4159
+atoms, 2448 bonds, 160 residues, 1 model selected
+> hide sel cartoons
+> select #111/A:4160
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #111/A:4160-4184
+atoms, 419 bonds, 25 residues, 1 model selected
+> select #110/A:4152
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #110/A:4152-4159
+atoms, 116 bonds, 8 residues, 1 model selected
+> select #111/A:4160-4161
+atoms, 27 bonds, 2 residues, 1 model selected
+> select #111/A:4160-4181
+atoms, 364 bonds, 22 residues, 1 model selected
+> view matrix models
+> #111,-0.93959,0.29781,0.16873,42.264,-0.33284,-0.67993,-0.65339,-38.87,-0.07986,-0.67008,0.73798,108.14
+> view matrix models
+> #111,-0.93959,0.29781,0.16873,42.797,-0.33284,-0.67993,-0.65339,-42.124,-0.07986,-0.67008,0.73798,107.72
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #111,-0.62713,0.69959,0.34245,41.74,-0.75038,-0.42473,-0.5065,-39.054,-0.20889,-0.57461,0.79132,108.71
+> ui mousemode right "translate selected models"
+> view matrix models
+> #111,-0.62713,0.69959,0.34245,39.779,-0.75038,-0.42473,-0.5065,-28.572,-0.20889,-0.57461,0.79132,111.29
+> view matrix models
+> #111,-0.62713,0.69959,0.34245,41.276,-0.75038,-0.42473,-0.5065,-30.269,-0.20889,-0.57461,0.79132,108.14
+> view matrix models
+> #111,-0.62713,0.69959,0.34245,40.683,-0.75038,-0.42473,-0.5065,-26.478,-0.20889,-0.57461,0.79132,111.91
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #111,-0.97688,0.12135,0.17602,41.593,-0.21316,-0.48928,-0.84568,-29.863,-0.016504,-0.86364,0.50383,110.14
+> ui mousemode right "translate selected models"
+> view matrix models
+> #111,-0.97688,0.12135,0.17602,43.383,-0.21316,-0.48928,-0.84568,-27.172,-0.016504,-0.86364,0.50383,105.83
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #111,-0.99466,0.089736,0.051026,43.43,-0.098489,-0.67688,-0.72947,-28.271,-0.030922,-0.7306,0.6821,106.19
+> ui mousemode right "translate selected models"
+> view matrix models
+> #111,-0.99466,0.089736,0.051026,45.183,-0.098489,-0.67688,-0.72947,-41.19,-0.030922,-0.7306,0.6821,108.26
+> view matrix models
+> #111,-0.99466,0.089736,0.051026,45.845,-0.098489,-0.67688,-0.72947,-42.078,-0.030922,-0.7306,0.6821,107.43
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #111,-0.9879,0.15505,0.0031988,45.944,-0.10909,-0.68007,-0.72499,-42.021,-0.11024,-0.71657,0.68875,107.94
+> ui mousemode right translate
+> ui mousemode right rotate
+> ui mousemode right "translate selected models"
+> view matrix models
+> #111,-0.9879,0.15505,0.0031988,46.032,-0.10909,-0.68007,-0.72499,-38.774,-0.11024,-0.71657,0.68875,110.99
+> view matrix models
+> #111,-0.9879,0.15505,0.0031988,46.099,-0.10909,-0.68007,-0.72499,-38.417,-0.11024,-0.71657,0.68875,111.67
+> view matrix models
+> #111,-0.9879,0.15505,0.0031988,50.478,-0.10909,-0.68007,-0.72499,-37.638,-0.11024,-0.71657,0.68875,114.86
+> view matrix models
+> #111,-0.9879,0.15505,0.0031988,54.429,-0.10909,-0.68007,-0.72499,-39.744,-0.11024,-0.71657,0.68875,112.26
+> view matrix models
+> #111,-0.9879,0.15505,0.0031988,53.684,-0.10909,-0.68007,-0.72499,-39.925,-0.11024,-0.71657,0.68875,111.24
+> view matrix models
+> #111,-0.9879,0.15505,0.0031988,53.467,-0.10909,-0.68007,-0.72499,-39.84,-0.11024,-0.71657,0.68875,111.92
+> select add #111
+atoms, 18537 bonds, 1244 residues, 1 model selected
+> select subtract #111
+Nothing selected
+> select #110/A:4159
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #110/A:3797-4159
+atoms, 5653 bonds, 363 residues, 1 model selected
+> color sel #040e52ff
+> select #111/A:4000-4001
+atoms, 22 bonds, 2 residues, 1 model selected
+> select #111/A
+atoms, 18537 bonds, 1244 residues, 1 model selected
+> color sel #040e52ff
+> select #110/A:3247
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #110/A
+atoms, 14133 bonds, 913 residues, 1 model selected
+> color sel #040e52ff
+> select subtract #110
+Nothing selected
+> show #104 models
+> log metadata #104
+The model has no metadata
+> log chains #104
+Chain information for GMGC10.011_528_202.ranked_0.1.2000.ranked_0.pdb #104
+---
+Chain | Description
+A | No description available
+> sequence chain #104/A
+Alignment identifier is 104/A
+> select #104/A:1-2
+atoms, 29 bonds, 2 residues, 1 model selected
+> select #104/A
+atoms, 30638 bonds, 1999 residues, 1 model selected
+> color sel #040e52ff
+Already setting window visible!
+> select #105/A:3353-3400
+atoms, 777 bonds, 48 residues, 1 model selected
+> select #105/A
+atoms, 24336 bonds, 1601 residues, 1 model selected
+> color sel #040e52ff
+> select subtract #105
+Nothing selected
+> select add #105
+atoms, 24336 bonds, 1601 residues, 1 model selected
+> select subtract #105
+Nothing selected
+> select #105/A:2000
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #105/A:2000-2304
+atoms, 4636 bonds, 305 residues, 1 model selected
+> color sel purple
+> show #!9 models
+> matchmaker #9 to #105
+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 GMGC10.011_528_202.ranked_0.1800.3500.pdb, chain A (#105) with
+ii6, chain A (#9), sequence alignment score = 270
+RMSD between 108 pruned atom pairs is 1.145 angstroms; (across all 292 pairs:
+.773)
+> hide #!9 models
+> select add #105
+atoms, 24336 bonds, 1601 residues, 1 model selected
+> select subtract #105
+Nothing selected
+> show #!9 models
+> select #104/A:208
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #104/A:208-209
+atoms, 23 bonds, 2 residues, 1 model selected
+> select #104/A:210
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #104/A:210-572
+atoms, 5531 bonds, 363 residues, 1 model selected
+> color sel black
+> select #104/A:1222
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #104/A:1222-1226
+atoms, 65 bonds, 5 residues, 1 model selected
+> select #104/A:1222
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #104/A:1222-1706
+atoms, 7351 bonds, 485 residues, 1 model selected
+> color sel black
+> select add #104
+atoms, 30638 bonds, 1999 residues, 1 model selected
+> select subtract #104
+Nothing selected
+> select #111/A:4513
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #111/A:4467-4513
+atoms, 714 bonds, 47 residues, 1 model selected
+> select #111/A:4413
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #111/A:4413
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #111/A:4529
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #111/A:4529-4540
+atoms, 167 bonds, 12 residues, 1 model selected
+> select #111/A:4529
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #111/A:4529-4672
+atoms, 2039 bonds, 144 residues, 1 model selected
+> select #111/A:4394-4672
+atoms, 4092 bonds, 279 residues, 1 model selected
+> select #111/A:4358
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #111/A:4358-4393
+atoms, 557 bonds, 36 residues, 1 model selected
+> select #111/A:4358-4561
+atoms, 3098 bonds, 204 residues, 1 model selected
+> select #111/A:4358-4672
+atoms, 4650 bonds, 315 residues, 1 model selected
+> select #111/A:4358-4832
+atoms, 6945 bonds, 475 residues, 1 model selected
+> view matrix models
+> #111,-0.9879,0.15505,0.0031988,-8.1987,-0.10909,-0.68007,-0.72499,71.437,-0.11024,-0.71657,0.68875,123.17
+> undo
+> select #111/A:4832
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #111/A:4832-4877
+atoms, 721 bonds, 46 residues, 1 model selected
+> select #111/A:4949
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #111/A:4931-4949
+atoms, 286 bonds, 19 residues, 1 model selected
+> select #111/A:4952
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #111/A:4750-4952
+atoms, 3033 bonds, 203 residues, 1 model selected
+> select #111/A:4810
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #111/A:4759-4810
+atoms, 762 bonds, 52 residues, 1 model selected
+> select #111/A:4854
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #111/A:4757-4854
+atoms, 1503 bonds, 98 residues, 1 model selected
+> select #111/A:4761
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #111/A:4761
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #111/A:4759-4760
+atoms, 28 bonds, 2 residues, 1 model selected
+> select #111/A:4759-4762
+atoms, 58 bonds, 4 residues, 1 model selected
+> select #111/A:4769
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #111/A:4769-4774
+atoms, 95 bonds, 6 residues, 1 model selected
+> select #111/A:4826
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #111/A:4826-4832
+atoms, 116 bonds, 7 residues, 1 model selected
+> select #111/A:4931
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #111/A:4931-4938
+atoms, 108 bonds, 8 residues, 1 model selected
+> select #111/A:4891
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #111/A:4884-4891
+atoms, 140 bonds, 8 residues, 1 model selected
+> select #111/A:4854
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #111/A:4851-4854
+atoms, 66 bonds, 4 residues, 1 model selected
+> select #111/A:4804-4854
+atoms, 821 bonds, 51 residues, 1 model selected
+> select #111/A:4358-4854
+atoms, 7330 bonds, 497 residues, 1 model selected
+> color sel #941751ff
+> select add #111
+atoms, 18537 bonds, 1244 residues, 1 model selected
+> select subtract #111
+Nothing selected
+> select #111/A:5065
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #111/A:5065-5122
+atoms, 816 bonds, 58 residues, 1 model selected
+> select #111/A:5065
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #111/A:5065-5212
+atoms, 2163 bonds, 148 residues, 1 model selected
+> view matrix models
+> #111,-0.9879,0.15505,0.0031988,51.419,-0.10909,-0.68007,-0.72499,-38.212,-0.11024,-0.71657,0.68875,109.14
+> undo
+> select #111/A:5035
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #111/A:5035-5243
+atoms, 3048 bonds, 209 residues, 1 model selected
+> color sel #945200ff
+> select add #111
+atoms, 18537 bonds, 1244 residues, 1 model selected
+> select subtract #111
+Nothing selected
+> hide #111 models
+> hide #110 models
+> hide #105 models
+> hide #104 models
+> show #97 models
+> rename #97 A0A2X2DF79.ranked_0.pdb
+> log metadata #97
+The model has no metadata
+> log chains #97
+Chain information for A0A2X2DF79.ranked_0.pdb #97
+---
+Chain | Description
+A | No description available
+> sequence chain #97/A
+Alignment identifier is 97/A
+> matchmaker #97 to #9
+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 6ii6, chain A (#9) with A0A2X2DF79.ranked_0.pdb, chain A (#97),
+sequence alignment score = 398.6
+RMSD between 127 pruned atom pairs is 1.100 angstroms; (across all 305 pairs:
+.055)
+> select #97/A:1306
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #97/A:619-1306
+atoms, 10903 bonds, 688 residues, 1 model selected
+> select #97/A:1960
+atoms, 22 bonds, 1 residue, 1 model selected
+> select #97/A:1960
+atoms, 22 bonds, 1 residue, 1 model selected
+> select add #97
+atoms, 31645 bonds, 1960 residues, 1 model selected
+> select subtract #97
+Nothing selected
+> hide #97 models
+> show #92 models
+> log metadata #92
+The model has no metadata
+> log chains #92
+Chain information for B6XGD1.ranked_0.pdb #92
+---
+Chain | Description
+A | No description available
+> sequence chain #92/A
+Alignment identifier is 92/A
+> select #92/A:419
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #92/A:419-737
+atoms, 5111 bonds, 319 residues, 1 model selected
+> select #92/A:419
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #92/A:419-710
+atoms, 4667 bonds, 292 residues, 1 model selected
+> select #92/A:711
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #92/A:711-714
+atoms, 47 bonds, 4 residues, 1 model selected
+> select #92/A:419
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #92/A:419-710
+atoms, 4667 bonds, 292 residues, 1 model selected
+> select #92/A:418
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #92/A:401-418
+atoms, 271 bonds, 18 residues, 1 model selected
+> select #92/A:419
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #92/A:419-710
+atoms, 4667 bonds, 292 residues, 1 model selected
+> select #92/A:1
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #92/A
+atoms, 33762 bonds, 2103 residues, 1 model selected
+> color sel #040e52ff
+> select #92/A:318-368
+atoms, 880 bonds, 51 residues, 1 model selected
+> select #92/A:267-368
+atoms, 1730 bonds, 102 residues, 1 model selected
+> select #92/A:419
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #92/A:419-710
+atoms, 4667 bonds, 292 residues, 1 model selected
+> color sel purple
+> matchmaker #92 to #9
+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 6ii6, chain A (#9) with B6XGD1.ranked_0.pdb, chain A (#92),
+sequence alignment score = 401.5
+RMSD between 133 pruned atom pairs is 1.062 angstroms; (across all 317 pairs:
+.801)
+> select add #92
+atoms, 33762 bonds, 2103 residues, 1 model selected
+> select subtract #92
+Nothing selected
+> select #92/A:739
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #92/A:739-789
+atoms, 859 bonds, 51 residues, 1 model selected
+> select #92/A:1370-1419
+atoms, 797 bonds, 50 residues, 1 model selected
+> select #92/A:739-1419
+atoms, 10845 bonds, 681 residues, 1 model selected
+> select #92/A:739
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #92/A:739-1419
+atoms, 10845 bonds, 681 residues, 1 model selected
+> color sel cornflower blue
+> select add #92
+atoms, 33762 bonds, 2103 residues, 1 model selected
+> select subtract #92
+Nothing selected
+> hide #92 models
+> show #88 models
+> log metadata #88
+The model has no metadata
+> log chains #88
+Chain information for Mcf2.ranked_0.pdb #88
+---
+Chain | Description
+A | No description available
+> sequence chain #88/A
+Alignment identifier is 88/A
+> select #88/A:1
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #88/A:1-627
+atoms, 9811 bonds, 627 residues, 1 model selected
+> select #88/A:2339-2388
+atoms, 724 bonds, 50 residues, 1 model selected
+> select #88/A
+atoms, 37035 bonds, 2388 residues, 1 model selected
+> select subtract #88
+Nothing selected
+> select add #88
+atoms, 37035 bonds, 2388 residues, 1 model selected
+> select subtract #88
+Nothing selected
+> ui mousemode right select
+Drag select of 384 residues
+> select #88/A:674
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #88/A:674
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #88/A:670
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #88/A:670-971
+atoms, 4665 bonds, 302 residues, 1 model selected
+> select
+> #88/A:5-21,24-39,46-49,59-69,80-94,112-114,117-122,133-138,153-167,202-215,249-267,271-281,294-302,319-326,328-334,340-344,447-450,460-462,520-538,541-544,571-598,608-652,654-656,662-665,676-700,716-725,730-767,776-783,791-822,827-840,844-848,858-867,911-924,927-930,949-954,965-967,972-994,996-1024,1035-1037,1067-1086,1104-1132,1139-1156,1162-1173,1177-1180,1187-1190,1211-1217,1221-1229,1231-1234,1277-1302,1375-1379,1416-1418,1424-1431,1586-1589,1596-1605,1646-1650,1739-1747,1754-1765,1929-1932,1938-1944,2016-2022,2082-2102,2225-2228,2288-2290,2307-2317,2327-2329,2352-2360
+atoms, 12098 bonds, 758 residues, 1 model selected
+> select #88/A:670-971
+atoms, 4665 bonds, 302 residues, 1 model selected
+> select #88/A:612-613
+atoms, 28 bonds, 2 residues, 1 model selected
+> select #88/A:561-613
+atoms, 889 bonds, 53 residues, 1 model selected
+> select #88/A:676-677
+atoms, 22 bonds, 2 residues, 1 model selected
+> select #88/A:676-700
+atoms, 376 bonds, 25 residues, 1 model selected
+> matchmaker #89 to #9
+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 6ii6, chain A (#9) with AF-D6YWY5-F1-model_v4.pdb, chain A (#89),
+sequence alignment score = 111.4
+RMSD between 37 pruned atom pairs is 1.149 angstroms; (across all 266 pairs:
+.856)
+> matchmaker #88 to #9
+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 6ii6, chain A (#9) with Mcf2.ranked_0.pdb, chain A (#88), sequence
+alignment score = 405.2
+RMSD between 128 pruned atom pairs is 0.972 angstroms; (across all 303 pairs:
+.736)
+Drag select of 651 residues
+> select #88/A:973
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #88/A:973-974
+atoms, 27 bonds, 2 residues, 1 model selected
+> select #88/A:967
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #88/A:965-967
+atoms, 44 bonds, 3 residues, 1 model selected
+Drag select of 651 residues
+> select #88/A:973
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #88/A:973-975
+atoms, 43 bonds, 3 residues, 1 model selected
+> select
+> #88/A:5-21,24-39,46-49,59-69,80-94,112-114,117-122,133-138,153-167,202-215,249-267,271-281,294-302,319-326,328-334,340-344,447-450,460-462,520-538,541-544,571-598,608-652,654-656,662-665,676-700,716-725,730-767,776-783,791-822,827-840,844-848,858-867,911-924,927-930,949-954,965-967,972-994,996-1024,1035-1037,1067-1086,1104-1132,1139-1156,1162-1173,1177-1180,1187-1190,1211-1217,1221-1229,1231-1234,1277-1302,1375-1379,1416-1418,1424-1431,1586-1589,1596-1605,1646-1650,1739-1747,1754-1765,1929-1932,1938-1944,2016-2022,2082-2102,2225-2228,2288-2290,2307-2317,2327-2329,2352-2360
+atoms, 12098 bonds, 758 residues, 1 model selected
+> select #88/A:967
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #88/A:965-967
+atoms, 44 bonds, 3 residues, 1 model selected
+> select #88/A:676
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #88/A:676-967
+atoms, 4515 bonds, 292 residues, 1 model selected
+> select #88/A:2339-2388
+atoms, 724 bonds, 50 residues, 1 model selected
+> select #88/A
+atoms, 37035 bonds, 2388 residues, 1 model selected
+> show sel cartoons
+> select #88/A:675-725
+atoms, 816 bonds, 51 residues, 1 model selected
+> select #88/A:675-820
+atoms, 2276 bonds, 146 residues, 1 model selected
+> select #88/A:924
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #88/A:924-974
+atoms, 774 bonds, 51 residues, 1 model selected
+> select #88/A:676
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #88/A:676-967
+atoms, 4515 bonds, 292 residues, 1 model selected
+> color sel purple
+> select add #88
+atoms, 37035 bonds, 2388 residues, 1 model selected
+> select subtract #88
+Nothing selected
+> select #88/A:281
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #88/A:133-281
+atoms, 2293 bonds, 149 residues, 1 model selected
+> select #88/A:125-126
+atoms, 30 bonds, 2 residues, 1 model selected
+> select #88/A:125-281
+atoms, 2433 bonds, 157 residues, 1 model selected
+> select clear
+> select #88/A:125
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #88/A:125-281
+atoms, 2433 bonds, 157 residues, 1 model selected
+> ui mousemode right "translate selected models"
+> color sel yellow
+> select #88/A:996
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #88/A:996-1675
+atoms, 10525 bonds, 680 residues, 1 model selected
+> select add #88
+atoms, 37035 bonds, 2388 residues, 1 model selected
+> select subtract #88
+Nothing selected
+> select #88/A:996
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #88/A:996-1005
+atoms, 156 bonds, 10 residues, 1 model selected
+> select #88/A:1675
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #88/A:1501-1675
+atoms, 2699 bonds, 175 residues, 1 model selected
+> select #88/A:1675
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #88/A:1663-1675
+atoms, 198 bonds, 13 residues, 1 model selected
+> select #88/A:996
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #88/A:996-1096
+atoms, 1644 bonds, 101 residues, 1 model selected
+> select #88/A:1675
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #88/A:1416-1675
+atoms, 4122 bonds, 260 residues, 1 model selected
+> select #88/A:1675
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #88/A:1665-1675
+atoms, 155 bonds, 11 residues, 1 model selected
+> select #88/A:1625-1675
+atoms, 794 bonds, 51 residues, 1 model selected
+> select #88/A:1312-1675
+atoms, 5797 bonds, 364 residues, 1 model selected
+> select #88/A:996
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #88/A:996-1675
+atoms, 10525 bonds, 680 residues, 1 model selected
+> color sel cornflower blue
+> select add #88
+atoms, 37035 bonds, 2388 residues, 1 model selected
+> select subtract #88
+Nothing selected
+> select #88/A:2388
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #88/A:2388
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #88/A:2342-2388
+atoms, 680 bonds, 47 residues, 1 model selected
+> select #88/A
+atoms, 37035 bonds, 2388 residues, 1 model selected
+> color sel #040e52ff
+> select #88/A:705
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #88/A:705-812
+atoms, 1672 bonds, 108 residues, 1 model selected
+> select #88/A:676
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #88/A:676-967
+atoms, 4515 bonds, 292 residues, 1 model selected
+> color sel purple
+> select #88/A:996
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #88/A:996-1094
+atoms, 1605 bonds, 99 residues, 1 model selected
+> select #88/A:996
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #88/A:996-1665
+atoms, 10381 bonds, 670 residues, 1 model selected
+> select #88/A:996-1675
+atoms, 10525 bonds, 680 residues, 1 model selected
+> color sel cornflower blue
+> select #88/A:125
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #88/A:125-281
+atoms, 2433 bonds, 157 residues, 1 model selected
+> color sel yellow
+> select add #88
+atoms, 37035 bonds, 2388 residues, 1 model selected
+> select subtract #88
+Nothing selected
+> hide #88 models
+> show #95 models
+> log metadata #95
+The model has no metadata
+> log chains #95
+Chain information for MGYP000860465678.ranked_0.pdb #95
+---
+Chain | Description
+A | No description available
+> sequence chain #95/A
+Alignment identifier is 95/A
+> select #95/A:1-2
+atoms, 32 bonds, 2 residues, 1 model selected
+> select #95/A
+atoms, 32283 bonds, 1998 residues, 1 model selected
+> select subtract #95
+Nothing selected
+> matchmaker #95 to #9
+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 6ii6, chain A (#9) with MGYP000860465678.ranked_0.pdb, chain A
+(#95), sequence alignment score = 382.4
+RMSD between 134 pruned atom pairs is 1.003 angstroms; (across all 296 pairs:
+.540)
+> select #95/A:730
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #95/A:730-732
+atoms, 40 bonds, 3 residues, 1 model selected
+> select #95/A:980
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #95/A:980-1031
+atoms, 734 bonds, 52 residues, 1 model selected
+> select #95/A:737
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #95/A:737-1397
+atoms, 10612 bonds, 661 residues, 1 model selected
+> select #95/A:721
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #95/A:721-799
+atoms, 1309 bonds, 79 residues, 1 model selected
+> select #95/A:716
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #95/A:563-716
+atoms, 2538 bonds, 154 residues, 1 model selected
+> select #95/A:1646
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #95/A:1629-1646
+atoms, 255 bonds, 18 residues, 1 model selected
+> select #95/A:1397
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #95/A:1391-1397
+atoms, 127 bonds, 7 residues, 1 model selected
+> select #95/A:1397
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #95/A:1395-1397
+atoms, 49 bonds, 3 residues, 1 model selected
+> select #95/A:1398
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #95/A:1398-1998
+atoms, 9624 bonds, 601 residues, 1 model selected
+> color sel #040e52ff
+> select #95/A:1741
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #95/A:1741-1841
+atoms, 1566 bonds, 101 residues, 1 model selected
+> select #95/A:1397
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #95/A:1391-1397
+atoms, 127 bonds, 7 residues, 1 model selected
+> select add #95
+atoms, 32283 bonds, 1998 residues, 1 model selected
+> select subtract #95
+Nothing selected
+> select #95/A:1391
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #95/A:1391-1397
+atoms, 127 bonds, 7 residues, 1 model selected
+> select #95/A:1385-1386
+atoms, 42 bonds, 2 residues, 1 model selected
+> select #95/A:1378-1386
+atoms, 152 bonds, 9 residues, 1 model selected
+> select #95/A:1397
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #95/A:1316-1397
+atoms, 1363 bonds, 82 residues, 1 model selected
+> select #95/A:1397
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #95/A:1397
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #95/A:1397
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #95/A:1392-1397
+atoms, 105 bonds, 6 residues, 1 model selected
+> select #95/A:1395-1396
+atoms, 37 bonds, 2 residues, 1 model selected
+> select #95/A:1389-1396
+atoms, 146 bonds, 8 residues, 1 model selected
+> select #95/A:1397
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #95/A:1292-1397
+atoms, 1730 bonds, 106 residues, 1 model selected
+> select #95/A:1397
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #95/A:721-1397
+atoms, 10869 bonds, 677 residues, 1 model selected
+> select add #95
+atoms, 32283 bonds, 1998 residues, 1 model selected
+> select subtract #95
+Nothing selected
+> hide #95 models
+> show #54 models
+> matchmaker #54 to #9
+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 6ii6, chain A (#9) with AF-A0A2X2DBV1-F1-model_v4.pdb, chain A
+(#54), sequence alignment score = 359.9
+RMSD between 135 pruned atom pairs is 0.987 angstroms; (across all 298 pairs:
+.517)
+> log metadata #54
+The model has no metadata
+> log chains #54
+Chain information for AF-A0A2X2DBV1-F1-model_v4.pdb #54
+---
+Chain | Description
+A | toxin B
+> sequence chain #54/A
+Alignment identifier is 54/A
+> select #54/A:364
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #54/A:364-568
+atoms, 1666 bonds, 205 residues, 1 model selected
+> select #54/A:364
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #54/A:364-658
+atoms, 2401 bonds, 295 residues, 1 model selected
+> select #54/A:361-362
+atoms, 17 bonds, 2 residues, 1 model selected
+> select #54/A:357-362
+atoms, 55 bonds, 6 residues, 1 model selected
+> select #54/A:658
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #54/A:654-658
+atoms, 38 bonds, 5 residues, 1 model selected
+> select #54/A:663
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #54/A:663-1269
+atoms, 4991 bonds, 607 residues, 1 model selected
+> select #54/A:663
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #54/A:663-668
+atoms, 45 bonds, 6 residues, 1 model selected
+> select #54/A:663
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #54/A:663-1269
+atoms, 4991 bonds, 607 residues, 1 model selected
+> select #54/A:612
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #54/A:562-612
+atoms, 440 bonds, 51 residues, 1 model selected
+> select add #54
+atoms, 10482 bonds, 1269 residues, 1 model selected
+> select subtract #54
+Nothing selected
+> hide #54 models
+> show #91 models
+> log metadata #91
+The model has no metadata
+> log chains #91
+Chain information for A0A4P2SNJ1.longerNterm.ranked_0.pdb #91
+---
+Chain | Description
+A | No description available
+> sequence chain #91/A
+Alignment identifier is 91/A
+> select #91/A:254-255
+atoms, 29 bonds, 2 residues, 1 model selected
+> select #91/A:254-259
+atoms, 83 bonds, 6 residues, 1 model selected
+> select #91/A:304-305
+atoms, 36 bonds, 2 residues, 1 model selected
+> select #91/A:304-309
+atoms, 98 bonds, 6 residues, 1 model selected
+> matchmaker #91 to #9
+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 6ii6, chain A (#9) with A0A4P2SNJ1.longerNterm.ranked_0.pdb, chain
+A (#91), sequence alignment score = 180.1
+RMSD between 57 pruned atom pairs is 0.921 angstroms; (across all 231 pairs:
+.738)
+> log metadata #43
+The model has no metadata
+> log chains #43
+Chain information for AF-A0A1Y3API8-F1-model_v4.pdb #43
+---
+Chain | Description
+A | rhodanese domain-containing protein
+> sequence chain #43/A
+Alignment identifier is 43/A
+> open "/Users/aho2840/Desktop/Satchell Lab/MCFHomologs/A0A097A1Q2.1.A
+> Putative RTX-toxin.pdb"
+A0A097A1Q2.1.A Putative RTX-toxin.pdb title:
+SWISS-MODEL SERVER (https://swissmodel.expasy.org) aMCF [more info...]
+Chain information for A0A097A1Q2.1.A Putative RTX-toxin.pdb #112
+---
+Chain | Description
+A | No description available
+> hide #112 models
+> show #112 models
+> log metadata #112
+Metadata for A0A097A1Q2.1.A Putative RTX-toxin.pdb #112
+---
+Title | SWISS-MODEL SERVER (https://swissmodel.expasy.org) aMCF
+Citation | Swiss-model: homology modelling of protein structures andcomplexes PMID: 29788355
+Experimental method | Theoretical model (swiss-model server)
+> log chains #112
+Chain information for A0A097A1Q2.1.A Putative RTX-toxin.pdb #112
+---
+Chain | Description
+A | No description available
+> sequence chain #112/A
+Alignment identifier is 112/A
+> sym #9
+ii6 mmCIF Assemblies
+---
+| author_and_software_defined_assembly| 1 copy of chains A,C
+| author_and_software_defined_assembly| 1 copy of chains B,D
+> log metadata #9
+No models had metadata
+> log chains #9
+Chain information for 6ii6 #9
+---
+Chain | Description
+A | Putative RTX-toxin
+> sequence chain #9/A
+Alignment identifier is 9/A
+> select #9/A:3267
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #9/A:3267-3269
+atoms, 24 bonds, 3 residues, 1 model selected
+> select #9/A:3349
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #9/A:3349-3351
+atoms, 20 bonds, 3 residues, 1 model selected
+> select #9/A:3352
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #9/A:3350-3352
+atoms, 24 bonds, 3 residues, 1 model selected
+> select #9/A:3269
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #9/A:3267-3269
+atoms, 24 bonds, 3 residues, 1 model selected
+> select #9/A:3352
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #9/A:3350-3352
+atoms, 24 bonds, 3 residues, 1 model selected
+> show #109 models
+> hide #112 models
+> hide #109 models
+> show #72 models
+> log metadata #72
+The model has no metadata
+> log chains #72
+Chain information for AF-Q327I5-F1-model_v4.pdb #72
+---
+Chain | Description | UniProt
+A | OSPD2 | Q327I5_SHIDS 1-572
+> sequence chain #72/A
+Alignment identifier is 72/A
+> select #72/A:1
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #72/A:1-106
+atoms, 860 bonds, 106 residues, 1 model selected
+> select #72/A:1
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #72/A:1-250
+atoms, 2085 bonds, 250 residues, 1 model selected
+> hide #91 models
+> matchmaker #72 to #9
+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 6ii6, chain A (#9) with AF-Q327I5-F1-model_v4.pdb, chain A (#72),
+sequence alignment score = 126.1
+RMSD between 10 pruned atom pairs is 1.365 angstroms; (across all 189 pairs:
+.434)
+> ui tool show Matchmaker
+> matchmaker #72 & sel to #9
+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 6ii6, chain A (#9) with AF-Q327I5-F1-model_v4.pdb, chain A (#72),
+sequence alignment score = 34.4
+RMSD between 23 pruned atom pairs is 1.153 angstroms; (across all 229 pairs:
+.731)
+> matchmaker #72 & sel to #9
+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 6ii6, chain A (#9) with AF-Q327I5-F1-model_v4.pdb, chain A (#72),
+sequence alignment score = 34.4
+RMSD between 23 pruned atom pairs is 1.153 angstroms; (across all 229 pairs:
+.731)
+> select add #72
+atoms, 4687 bonds, 572 residues, 1 model selected
+> select subtract #72
+Nothing selected
+> hide #72 models
+> show #99 models
+> log metadata #99
+The model has no metadata
+> log chains #99
+Chain information for WP_095034189.1.ranked_0.pdb #99
+---
+Chain | Description
+A | No description available
+> sequence chain #99/A
+Alignment identifier is 99/A
+> select #99/A:324
+atoms, 20 bonds, 1 residue, 1 model selected
+> select #99/A:322-324
+atoms, 45 bonds, 3 residues, 1 model selected
+> select #99/A:343
+atoms, 20 bonds, 1 residue, 1 model selected
+> select #99/A:1-343
+atoms, 5652 bonds, 343 residues, 1 model selected
+> view matrix models
+> #99,-0.24018,-0.60835,-0.75645,11.198,0.83562,0.26701,-0.48005,61.266,0.49402,-0.7474,0.44422,112.71
+> undo
+> select #99/A:349
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #99/A:349-499
+atoms, 2466 bonds, 151 residues, 1 model selected
+> view matrix models
+> #99,-0.24018,-0.60835,-0.75645,5.0569,0.83562,0.26701,-0.48005,32.943,0.49402,-0.7474,0.44422,41.557
+> select #99/A:349-499,501-502
+atoms, 2495 bonds, 153 residues, 1 model selected
+> select #99/A:349-502
+atoms, 2510 bonds, 154 residues, 1 model selected
+> select add #99
+atoms, 8876 bonds, 543 residues, 1 model selected
+> select subtract #99
+Nothing selected
+> hide #99 models
+> show #100 models
+> log metadata #100
+The model has no metadata
+> log chains #100
+Chain information for WP_148121377.1.ranked_0.pdb #100
+---
+Chain | Description
+A | No description available
+> sequence chain #100/A
+Alignment identifier is 100/A
+> select #100/A:1386
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #100/A:1386
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #100/A:1386-1422
+atoms, 564 bonds, 37 residues, 1 model selected
+> select #100/A:1428
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #100/A:1386-1428
+atoms, 623 bonds, 43 residues, 1 model selected
+> view matrix models
+> #100,-0.75361,-0.61809,-0.2237,28.604,-0.07069,0.41455,-0.90728,101.69,0.65351,-0.66792,-0.3561,72.831
+> select #100/A:1367
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #100/A:1367-1953
+atoms, 9226 bonds, 587 residues, 1 model selected
+> select add #100
+atoms, 31455 bonds, 1953 residues, 1 model selected
+> select subtract #100
+Nothing selected
+> hide #100 models
+> show #93 models
+> log metadata #93
+The model has no metadata
+> log chains #93
+Chain information for C4K5K2.ranked_0.pdb #93
+---
+Chain | Description
+A | No description available
+> sequence chain #93/A
+Alignment identifier is 93/A
+> select #93/A:1751
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #93/A:1751-1880
+atoms, 1915 bonds, 130 residues, 1 model selected
+> select #93/A:1863
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #93/A:1751-1863
+atoms, 1623 bonds, 113 residues, 1 model selected
+> select #93/A:1862
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #93/A:1860-1862
+atoms, 27 bonds, 3 residues, 1 model selected
+> select #93/A:1863
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #93/A:1751-1863
+atoms, 1623 bonds, 113 residues, 1 model selected
+> select #93/A:1751
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #93/A:1751-1753
+atoms, 37 bonds, 3 residues, 1 model selected
+> select #93/A:1396
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #93/A:1396-1413
+atoms, 273 bonds, 18 residues, 1 model selected
+> select #93/A:1435-1437
+atoms, 43 bonds, 3 residues, 1 model selected
+> select #93/A:1396-1435
+atoms, 555 bonds, 40 residues, 1 model selected
+> select add #93
+atoms, 31675 bonds, 1960 residues, 1 model selected
+> select subtract #93
+Nothing selected
+> hide #93 models
+> show #35 models
+> log metadata #35
+The model has no metadata
+> log chains #35
+Chain information for AF-A0A7U6JX76-F1-model_v4.pdb #35
+---
+Chain | Description
+A | EFA1/lifa-like protein, N-terminal part
+> sequence chain #35/A
+Alignment identifier is 35/A
+> select #35/A:165
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #35/A:165-229
+atoms, 533 bonds, 65 residues, 1 model selected
+> select #35/A:161
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #35/A:161-164
+atoms, 30 bonds, 4 residues, 1 model selected
+> select #35/A:210
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #35/A:209-210
+atoms, 16 bonds, 2 residues, 1 model selected
+> select #35/A:161
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #35/A:161-229
+atoms, 564 bonds, 69 residues, 1 model selected
+> select #35/A:152
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #35/A:152-229
+atoms, 639 bonds, 78 residues, 1 model selected
+> select #35/A:261
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #35/A:261-363
+atoms, 847 bonds, 103 residues, 1 model selected
+> select #35/A:164-166
+atoms, 23 bonds, 3 residues, 1 model selected
+> select #35/A:166-253
+atoms, 712 bonds, 88 residues, 1 model selected
+> select #35/A:754
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #35/A:754-805
+atoms, 426 bonds, 52 residues, 1 model selected
+> select #35/A:253
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #35/A:167-253
+atoms, 703 bonds, 87 residues, 1 model selected
+> select #35/A:165-253
+atoms, 719 bonds, 89 residues, 1 model selected
+> view matrix models
+> #35,0.22503,-0.93827,0.26272,7.1151,0.23315,0.31365,0.92047,40.856,-0.94605,-0.14588,0.28934,83.248
+> select add #35
+atoms, 10180 bonds, 1238 residues, 1 model selected
+> hide #35 models
+> select subtract #35
+Nothing selected
+> show #38 models
+> matchmaker #38 to #9
+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 6ii6, chain A (#9) with AF-A0A0K3YVA7-F1-model_v4.pdb, chain A
+(#38), sequence alignment score = 929.6
+RMSD between 298 pruned atom pairs is 0.887 angstroms; (across all 338 pairs:
+.776)
+> log metadata #38
+The model has no metadata
+> log chains #38
+Chain information for AF-A0A0K3YVA7-F1-model_v4.pdb #38
+---
+Chain | Description
+A | EFA1/lifa-like protein
+> sequence chain #38/A
+Alignment identifier is 38/A
+> select #38/A:151
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #38/A:151-490
+atoms, 2788 bonds, 340 residues, 1 model selected
+> select #38/A:144-145
+atoms, 14 bonds, 2 residues, 1 model selected
+> select #38/A:1-145
+atoms, 1117 bonds, 145 residues, 1 model selected
+> select add #38
+atoms, 3947 bonds, 490 residues, 1 model selected
+> select subtract #38
+Nothing selected
+> hide #38 models
+> show #43 models
+> log metadata #43
+The model has no metadata
+> log chains #43
+Chain information for AF-A0A1Y3API8-F1-model_v4.pdb #43
+---
+Chain | Description
+A | rhodanese domain-containing protein
+> sequence chain #43/A
+Alignment identifier is 43/A
+> select #43/A:115-116
+atoms, 15 bonds, 2 residues, 1 model selected
+> select #43/A:1-116
+atoms, 889 bonds, 116 residues, 1 model selected
+> select #43/A:132
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #43/A:1-132
+atoms, 1026 bonds, 132 residues, 1 model selected
+> show #84 models
+> select add #43
+atoms, 6504 bonds, 812 residues, 1 model selected
+> select subtract #43
+Nothing selected
+> hide #43 models
+> hide #!9 models
+> hide #84 models
+> show #43 models
+> select #43/A:1
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #43/A:1-132
+atoms, 1026 bonds, 132 residues, 1 model selected
+> color sel red
+> select add #43
+atoms, 6504 bonds, 812 residues, 1 model selected
+> select subtract #43
+Nothing selected
+> hide #43 models
+> show #111 models
+> show #104 models
+> show #105 models
+> show #110 models
+> log metadata #111
+The model has no metadata
+> log chains #111
+Chain information for GMGC10.011_528_202.ranked_0.4000.5243.pdb #111
+---
+Chain | Description
+A | No description available
+> sequence chain #111/A
+Alignment identifier is 111/A
+> select #111/A:4583
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #111/A:4583-4816
+atoms, 3269 bonds, 234 residues, 1 model selected
+> select #111/A:4583-4832
+atoms, 3501 bonds, 250 residues, 1 model selected
+> select #111/A:4583-4854
+atoms, 3886 bonds, 272 residues, 1 model selected
+> select #111/A:4573
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #111/A:4573-4816
+atoms, 3449 bonds, 244 residues, 1 model selected
+> view matrix models
+> #111,-0.9879,0.15505,0.0031988,27.034,-0.10909,-0.68007,-0.72499,-18.027,-0.11024,-0.71657,0.68875,102.91
+> undo
+> select #111/A:4621-4671
+atoms, 663 bonds, 51 residues, 1 model selected
+> select #111/A:4621-4671
+atoms, 663 bonds, 51 residues, 1 model selected
+> select #111/A:4583
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #111/A:4583-4816
+atoms, 3269 bonds, 234 residues, 1 model selected
+> select #111/A:4583-4817
+atoms, 3276 bonds, 235 residues, 1 model selected
+> select add #111
+atoms, 18537 bonds, 1244 residues, 1 model selected
+> select subtract #111
+Nothing selected
+> hide #111 models
+> hide #110 models
+> hide #105 models
+> hide #104 models
+> show #96 models
+> log metadata #96
+The model has no metadata
+> log chains #96
+Chain information for MGYP003605169772.ranked_0.pdb #96
+---
+Chain | Description
+A | No description available
+> sequence chain #96/A
+Alignment identifier is 96/A
+> select #96/A:942
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #96/A:942-1234
+atoms, 4471 bonds, 293 residues, 1 model selected
+> select #96/A:941
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #96/A:1-941
+atoms, 14805 bonds, 941 residues, 1 model selected
+> color sel #040e52ff
+> select #96/A:1062
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #96/A:1061-1062
+atoms, 23 bonds, 2 residues, 1 model selected
+> select #96/A:819
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #96/A:819-936
+atoms, 1740 bonds, 118 residues, 1 model selected
+> select #96/A:815-816
+atoms, 27 bonds, 2 residues, 1 model selected
+> select #96/A:765-816
+atoms, 771 bonds, 52 residues, 1 model selected
+> select #96/A:907-908
+atoms, 30 bonds, 2 residues, 1 model selected
+> select #96/A:819-907
+atoms, 1336 bonds, 89 residues, 1 model selected
+> view matrix models
+> #96,0.61612,0.18057,0.76667,-0.57975,-0.38691,-0.77845,0.49428,21.519,0.68607,-0.60117,-0.40975,90.045
+> select add #96
+atoms, 19277 bonds, 1234 residues, 1 model selected
+> select subtract #96
+Nothing selected
+> hide #96 models
+> show #112 models
+> log metadata #112
+Metadata for A0A097A1Q2.1.A Putative RTX-toxin.pdb #112
+---
+Title | SWISS-MODEL SERVER (https://swissmodel.expasy.org) aMCF
+Citation | Swiss-model: homology modelling of protein structures andcomplexes PMID: 29788355
+Experimental method | Theoretical model (swiss-model server)
+> log chains #112
+Chain information for A0A097A1Q2.1.A Putative RTX-toxin.pdb #112
+---
+Chain | Description
+A | No description available
+> sequence chain #112/A
+Alignment identifier is 112/A
+> show #!78 models
+> log metadata #78
+No models had metadata
+> log chains #78
+Chain information for 8adb #78
+---
+Chain | Description | UniProt
+A | Wc-VDT1 | D6YWY5_WADCW 279-493
+> sequence chain #78/A
+Alignment identifier is 78/A
+> hide #!78 models
+> show #19 models
+> log metadata #19
+The model has no metadata
+> log chains #19
+Chain information for AF-D6YWY5-F1-model_v4.pdb #19
+---
+Chain | Description | UniProt
+A | uncharacterized protein | D6YWY5_WADCW 1-494
+> sequence chain #19/A
+Alignment identifier is 19/A
+> show #!9 models
+> matchmaker #19 to #9
+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 6ii6, chain A (#9) with AF-D6YWY5-F1-model_v4.pdb, chain A (#19),
+sequence alignment score = 111.4
+RMSD between 37 pruned atom pairs is 1.149 angstroms; (across all 266 pairs:
+.856)
+> hide #112 models
+> select #19/A:494
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #19/A
+atoms, 3974 bonds, 494 residues, 1 model selected
+> color sel #040e52ff
+> select #19/A:72-121
+atoms, 400 bonds, 50 residues, 1 model selected
+> select #19/A:72-120
+atoms, 392 bonds, 49 residues, 1 model selected
+> select #19/A:472
+atoms, 12 bonds, 1 residue, 1 model selected
+> select #19/A:472
+atoms, 12 bonds, 1 residue, 1 model selected
+> select #19/A:86-88
+atoms, 23 bonds, 3 residues, 1 model selected
+> select #19/A:88-275
+atoms, 1543 bonds, 188 residues, 1 model selected
+> color sel purple
+> select #19/A:308
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #19/A:308-494
+atoms, 1479 bonds, 187 residues, 1 model selected
+> color sel purple
+> select #19/A:25
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #19/A:25-80
+atoms, 423 bonds, 56 residues, 1 model selected
+> select #19/A:25
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #19/A:25-80
+atoms, 423 bonds, 56 residues, 1 model selected
+> color sel #929000ff
+> select add #19
+atoms, 3974 bonds, 494 residues, 1 model selected
+> select subtract #19
+Nothing selected
+> hide #19 models
+> show #109 models
+> matchmaker #109 to #9
+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 6ii6, chain A (#9) with C7BKP9.ranked_0.pdb, chain A (#109),
+sequence alignment score = 292.3
+RMSD between 75 pruned atom pairs is 1.064 angstroms; (across all 284 pairs:
+.403)
+> log metadata #109
+The model has no metadata
+> log chains #109
+Chain information for C7BKP9.ranked_0.pdb #109
+---
+Chain | Description
+A | No description available
+> sequence chain #109/A
+Alignment identifier is 109/A
+> select #109/A:527
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #109/A:527-712
+atoms, 3017 bonds, 186 residues, 1 model selected
+> select #109/A:712
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #109/A:706-712
+atoms, 112 bonds, 7 residues, 1 model selected
+> select #109/A:526
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #109/A:1-526
+atoms, 8568 bonds, 526 residues, 1 model selected
+> color sel #040e52ff
+> select #109/A:526-527
+atoms, 33 bonds, 2 residues, 1 model selected
+> select #109/A:527-712
+atoms, 3017 bonds, 186 residues, 1 model selected
+> color sel #945200ff
+> select add #109
+atoms, 47629 bonds, 2957 residues, 1 model selected
+> select subtract #109
+Nothing selected
+> select #109/A:713
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #109/A:713-1745
+atoms, 16831 bonds, 1033 residues, 1 model selected
+> color sel #040e52ff
+> select #109/A:1746
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #109/A:1746-2031
+atoms, 4530 bonds, 286 residues, 1 model selected
+> select #109/A:2054-2055
+atoms, 25 bonds, 2 residues, 1 model selected
+> select #109/A:2032-2054
+atoms, 353 bonds, 23 residues, 1 model selected
+> color sel #040e52ff
+> select #109/A:2055-2056
+atoms, 40 bonds, 2 residues, 1 model selected
+> select #109/A:2055-2394
+atoms, 5528 bonds, 340 residues, 1 model selected
+> select #109/A:2055
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #109/A:2055-2382
+atoms, 5340 bonds, 328 residues, 1 model selected
+> select #109/A:2053
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #109/A:2052-2053
+atoms, 35 bonds, 2 residues, 1 model selected
+> select #109/A:2382
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #109/A:2055-2382
+atoms, 5340 bonds, 328 residues, 1 model selected
+> color sel blue
+> select #109/A:2383-2533
+atoms, 2333 bonds, 151 residues, 1 model selected
+> select #109/A:2383-2675
+atoms, 4610 bonds, 293 residues, 1 model selected
+> select #109/A:2632
+atoms, 20 bonds, 1 residue, 1 model selected
+> select #109/A:2632-2732
+atoms, 1592 bonds, 101 residues, 1 model selected
+> select #109/A:2055
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #109/A:2055-2274
+atoms, 3634 bonds, 220 residues, 1 model selected
+> select #109/A:2055
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #109/A:2055-2296
+atoms, 3971 bonds, 242 residues, 1 model selected
+> select #109/A:2055
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #109/A:2055-2288
+atoms, 3850 bonds, 234 residues, 1 model selected
+> select #109/A:2055
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #109/A:2055-2279
+atoms, 3711 bonds, 225 residues, 1 model selected
+> select #109/A:2055
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #109/A:2055-2274
+atoms, 3634 bonds, 220 residues, 1 model selected
+> select #109/A:2057-2107
+atoms, 849 bonds, 51 residues, 1 model selected
+> select #109/A:2057-2112
+atoms, 930 bonds, 56 residues, 1 model selected
+> select #109/A:2055
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #109/A:2055-2059
+atoms, 95 bonds, 5 residues, 1 model selected
+> select #109/A:2382
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #109/A:2055-2382
+atoms, 5340 bonds, 328 residues, 1 model selected
+> select #109/A:2484
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #109/A:2383-2484
+atoms, 1551 bonds, 102 residues, 1 model selected
+> select #109/A:2383
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #109/A:2383-2484
+atoms, 1551 bonds, 102 residues, 1 model selected
+> color sel #040e52ff
+> select #109/A:2485
+atoms, 9 bonds, 1 residue, 1 model selected
+> select #109/A:2485-2486
+atoms, 23 bonds, 2 residues, 1 model selected
+> select #109/A:2646
+atoms, 17 bonds, 1 residue, 1 model selected
+> select #109/A:2485-2646
+atoms, 2628 bonds, 162 residues, 1 model selected
+> select #109/A:2647
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #109/A:2647-2957
+atoms, 4803 bonds, 311 residues, 1 model selected
+> color sel #040e52ff
+> select add #109
+atoms, 47629 bonds, 2957 residues, 1 model selected
+> select subtract #109
+Nothing selected
+> show #!94 models
+> hide #109 models
+> hide #!94 models
+> show #112 models
+> hide #112 models
+> show #112 models
+> matchmaker #112 to #9
+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 6ii6, chain A (#9) with A0A097A1Q2.1.A Putative RTX-toxin.pdb,
+chain A (#112), sequence alignment score = 835.5
+RMSD between 171 pruned atom pairs is 0.264 angstroms; (across all 171 pairs:
+.264)
+> hide #112 models
+> show #!94 models
+> matchmaker #94 to #9
+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 6ii6, chain A (#9) with GMGC10.017_810_714.ranked_0.pdb, chain A
+(#94), sequence alignment score = 196.4
+RMSD between 49 pruned atom pairs is 0.960 angstroms; (across all 284 pairs:
+.428)
+> log metadata #94
+No models had metadata
+> log chains #94
+Chain information for GMGC10.017_810_714.ranked_0.pdb #94
+---
+Chain | Description
+A | No description available
+> sequence chain #94/A
+Alignment identifier is 94/A
+> select #94/A:1531
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #94/A:1531-1638
+atoms, 1616 bonds, 108 residues, 1 model selected
+> select #94/A:1531-1532
+atoms, 32 bonds, 2 residues, 1 model selected
+> select #94/A:1531-1689
+atoms, 2454 bonds, 159 residues, 1 model selected
+> select #94/A:1531
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #94/A:1531-1683
+atoms, 2348 bonds, 153 residues, 1 model selected
+> view matrix models
+> #94,-0.35268,0.092262,0.93118,19.032,-0.8443,0.39768,-0.35918,87.956,-0.40345,-0.91288,-0.062356,83.392
+> select #94/A:1737
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #94/A:1531-1737
+atoms, 3248 bonds, 207 residues, 1 model selected
+> select #94/A:1521
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #94/A:1521-1683
+atoms, 2476 bonds, 163 residues, 1 model selected
+> select #94/A:1421
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #94/A:1421-1683
+atoms, 3941 bonds, 263 residues, 1 model selected
+> select #94/A:1421
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #94/A:1421-1422
+atoms, 35 bonds, 2 residues, 1 model selected
+> select #94/A:1421
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #94/A:1421-1429
+atoms, 136 bonds, 9 residues, 1 model selected
+> select #94/A:1420
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #94/A:1418-1420
+atoms, 59 bonds, 3 residues, 1 model selected
+> select #94/A:1420
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #94/A:1401-1420
+atoms, 347 bonds, 20 residues, 1 model selected
+> select #94/A:1420
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #94/A:1398-1420
+atoms, 402 bonds, 23 residues, 1 model selected
+> select #94/A:1397
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #94/A:1376-1397
+atoms, 364 bonds, 22 residues, 1 model selected
+> select #94/A:1421
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #94/A:1421-1448
+atoms, 408 bonds, 28 residues, 1 model selected
+> select #94/A:1418-1419
+atoms, 37 bonds, 2 residues, 1 model selected
+> select #94/A:1416-1419
+atoms, 67 bonds, 4 residues, 1 model selected
+> select #94/A:1683
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #94/A:1660-1683
+atoms, 375 bonds, 24 residues, 1 model selected
+> select #94/A:1684
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #94/A:1684-1700
+atoms, 286 bonds, 17 residues, 1 model selected
+> select #94/A:1737
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #94/A:1421-1737
+atoms, 4841 bonds, 317 residues, 1 model selected
+> color (#!94 & sel) #73fdffff
+> color (#!94 & sel) #76d6ffff
+> color (#!94 & sel) #55bef0ff
+> color (#!94 & sel) #b3d7ffff
+> select #94/A:1781
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #94/A:1780-1781
+atoms, 17 bonds, 2 residues, 1 model selected
+> select #94/A:405-406
+atoms, 18 bonds, 2 residues, 1 model selected
+> select #94/A:1-406
+atoms, 6461 bonds, 406 residues, 1 model selected
+> select #94/A:513-562
+atoms, 817 bonds, 50 residues, 1 model selected
+> select #94/A:513-559
+atoms, 767 bonds, 47 residues, 1 model selected
+> select #94/A:354-405
+atoms, 821 bonds, 52 residues, 1 model selected
+> select #94/A:1-405
+atoms, 6449 bonds, 405 residues, 1 model selected
+> select #94/A:550
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #94/A:550-859
+atoms, 4943 bonds, 310 residues, 1 model selected
+> select #94/A:417-418
+atoms, 38 bonds, 2 residues, 1 model selected
+> select #94/A:314-418
+atoms, 1672 bonds, 105 residues, 1 model selected
+> select #94/A:859
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #94/A:550-859
+atoms, 4943 bonds, 310 residues, 1 model selected
+> color (#!94 & sel) purple
+> select #94/A:549
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #94/A:406-549
+atoms, 2350 bonds, 144 residues, 1 model selected
+> select #94/A:1420
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #94/A:860-1420
+atoms, 8882 bonds, 561 residues, 1 model selected
+> select #94/A:1421-1471
+atoms, 740 bonds, 51 residues, 1 model selected
+> select #94/A:1421-1737
+atoms, 4841 bonds, 317 residues, 1 model selected
+> select #94/A:1998
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #94/A:1738-1998
+atoms, 4048 bonds, 261 residues, 1 model selected
+> select #94/A:1999
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #94/A:1999-2147
+atoms, 2188 bonds, 149 residues, 1 model selected
+> select #94/A:2148
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #94/A:2148-2223
+atoms, 1184 bonds, 76 residues, 1 model selected
+> select add #94
+atoms, 34892 bonds, 2223 residues, 2 models selected
+> select subtract #94
+model selected
+> hide #!94 models
+> show #72 models
+> matchmaker #72 to #9
+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 6ii6, chain A (#9) with AF-Q327I5-F1-model_v4.pdb, chain A (#72),
+sequence alignment score = 126.1
+RMSD between 10 pruned atom pairs is 1.365 angstroms; (across all 189 pairs:
+.434)
+> show #72 models
+> log metadata #72
+The model has no metadata
+> log chains #72
+Chain information for AF-Q327I5-F1-model_v4.pdb #72
+---
+Chain | Description | UniProt
+A | OSPD2 | Q327I5_SHIDS 1-572
+> log metadata #72
+The model has no metadata
+> log chains #72
+Chain information for AF-Q327I5-F1-model_v4.pdb #72
+---
+Chain | Description | UniProt
+A | OSPD2 | Q327I5_SHIDS 1-572
+> sequence chain #72/A
+Alignment identifier is 72/A
+> select #72/A:1
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #72/A:1-250
+atoms, 2085 bonds, 250 residues, 1 model selected
+> ui tool show Matchmaker
+> matchmaker #72 & sel to #9
+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 6ii6, chain A (#9) with AF-Q327I5-F1-model_v4.pdb, chain A (#72),
+sequence alignment score = 34.4
+RMSD between 23 pruned atom pairs is 1.153 angstroms; (across all 229 pairs:
+.731)
+> matchmaker #72 & sel to #9
+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 6ii6, chain A (#9) with AF-Q327I5-F1-model_v4.pdb, chain A (#72),
+sequence alignment score = 34.4
+RMSD between 23 pruned atom pairs is 1.153 angstroms; (across all 229 pairs:
+.731)
+> select #72/A:258
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #72/A:258-261
+atoms, 31 bonds, 4 residues, 1 model selected
+> select add #72
+atoms, 4687 bonds, 572 residues, 1 model selected
+> select subtract #72
+Nothing selected
+> hide #72 models
+> show #46 models
+> sym #46
+gqj mmCIF Assemblies
+---
+| author_defined_assembly| 1 copy of chain A
+| software_defined_assembly| 2 copies of chain A
+> log metadata #46
+The model has no metadata
+> log chains #46
+Chain information for 3gqj #46
+---
+Chain | Description | UniProt
+A | Cell Inhibiting Factor (Cif) | Q7N439_PHOLL 48-308
+> sequence chain #46/A
+Alignment identifier is 46/A
+> hide #46 models
+> show #103 models
+> matchmaker #103 to #9
+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 6ii6, chain A (#9) with AF-Q7N439-F1-model_v4.pdb, chain A (#103),
+sequence alignment score = 91.8
+RMSD between 9 pruned atom pairs is 1.075 angstroms; (across all 201 pairs:
+.871)
+> hide #103 models
+> show #103 models
+> hide #!9 models
+> show #46 models
+> matchmaker #46 to #9
+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 6ii6, chain A (#9) with 3gqj, chain A (#46), sequence alignment
+score = 81.1
+RMSD between 13 pruned atom pairs is 1.488 angstroms; (across all 192 pairs:
+.974)
+> hide #46 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> log metadata #103
+The model has no metadata
+> log chains #103
+Chain information for AF-Q7N439-F1-model_v4.pdb #103
+---
+Chain | Description | UniProt
+A | protein-glutamine deamidase cif | CIF_PHOLL 1-313
+> sequence chain #103/A
+Alignment identifier is 103/A
+> select #103/A:58-59
+atoms, 14 bonds, 2 residues, 1 model selected
+> select #103/A:58-313
+atoms, 2078 bonds, 256 residues, 1 model selected
+> select #103/A:57
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #103/A:1-57
+atoms, 439 bonds, 57 residues, 1 model selected
+> select add #103
+atoms, 2518 bonds, 313 residues, 1 model selected
+> select subtract #103
+Nothing selected
+> hide #103 models
+> show #101 models
+> matchmaker #101 to #9
+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 6ii6, chain A (#9) with WP_231937687.1.ranked_0.pdb, chain A
+(#101), sequence alignment score = 205.8
+RMSD between 73 pruned atom pairs is 0.941 angstroms; (across all 296 pairs:
+.392)
+> log metadata #101
+The model has no metadata
+> log chains #101
+Chain information for WP_231937687.1.ranked_0.pdb #101
+---
+Chain | Description
+A | No description available
+> sequence chain #101/A
+Alignment identifier is 101/A
+> select #101/A:524
+atoms, 25 bonds, 1 residue, 1 model selected
+> select #101/A:524-726
+atoms, 3281 bonds, 203 residues, 1 model selected
+> select #101/A:1146
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #101/A:1146-1148
+atoms, 49 bonds, 3 residues, 1 model selected
+> select #101/A:1146
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #101/A:1146-1744
+atoms, 9540 bonds, 599 residues, 1 model selected
+> select add #101
+atoms, 28182 bonds, 1744 residues, 1 model selected
+> select subtract #101
+Nothing selected
+> hide #101 models
+> show #52 models
+> log metadata #52
+The model has no metadata
+> log chains #52
+Chain information for MGYP000706081912.pdb #52
+---
+Chain | Description
+A | No description available
+> sequence chain #52/A
+Alignment identifier is 52/A
+> select #52/A:360
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #52/A:1-360
+atoms, 3015 bonds, 360 residues, 1 model selected
+> matchmaker #52 to #9
+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 6ii6, chain A (#9) with MGYP000706081912.pdb, chain A (#52),
+sequence alignment score = 226.2
+RMSD between 57 pruned atom pairs is 0.989 angstroms; (across all 293 pairs:
+.191)
+> select #52/A:361-362
+atoms, 16 bonds, 2 residues, 1 model selected
+> select #52/A:361-482
+atoms, 1024 bonds, 122 residues, 1 model selected
+> select add #52
+atoms, 4040 bonds, 482 residues, 1 model selected
+> select subtract #52
+Nothing selected
+> hide #52 models
+> show #75 models
+> matchmaker #75 to #9
+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 6ii6, chain A (#9) with AF-A0A0K0E9U3-F1-model_v4.pdb, chain A
+(#75), sequence alignment score = 79
+RMSD between 27 pruned atom pairs is 1.278 angstroms; (across all 165 pairs:
+.308)
+> log metadata #75
+The model has no metadata
+> log chains #75
+Chain information for AF-A0A0K0E9U3-F1-model_v4.pdb #75
+---
+Chain | Description
+A | ubiquitinyl hydrolase 1
+> sequence chain #75/A
+Alignment identifier is 75/A
+> select #75/A:171-172
+atoms, 17 bonds, 2 residues, 1 model selected
+> select #75/A:171-252
+atoms, 656 bonds, 82 residues, 1 model selected
+> color sel #040e52ff
+> select add #75
+atoms, 2043 bonds, 252 residues, 1 model selected
+> select subtract #75
+Nothing selected
+> select #75/A:163
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #75/A:1-163
+atoms, 1335 bonds, 163 residues, 1 model selected
+> select add #75
+atoms, 2043 bonds, 252 residues, 1 model selected
+> select subtract #75
+Nothing selected
+> hide #75 models
+> show #71 models
+> log metadata #71
+The model has no metadata
+> log chains #71
+Chain information for AF-Q327D9-F1-model_v4.pdb #71
+---
+Chain | Description | UniProt
+A | OSPD3 | Q327D9_SHIDS 1-549
+> sequence chain #71/A
+Alignment identifier is 71/A
+> select #71/A:214-216
+atoms, 26 bonds, 3 residues, 1 model selected
+> select #71/A:1-216
+atoms, 1796 bonds, 216 residues, 1 model selected
+> ui tool show Matchmaker
+> matchmaker #71 & sel to #9
+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 6ii6, chain A (#9) with AF-Q327D9-F1-model_v4.pdb, chain A (#71),
+sequence alignment score = 95.1
+RMSD between 27 pruned atom pairs is 1.084 angstroms; (across all 175 pairs:
+.329)
+> matchmaker #71 & sel to #9
+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 6ii6, chain A (#9) with AF-Q327D9-F1-model_v4.pdb, chain A (#71),
+sequence alignment score = 95.1
+RMSD between 27 pruned atom pairs is 1.084 angstroms; (across all 175 pairs:
+.329)
+> select add #71
+atoms, 4400 bonds, 549 residues, 1 model selected
+> select subtract #71
+Nothing selected
+> hide #71 models
+> show #!94 models
+> log metadata #94
+No models had metadata
+> log chains #94
+Chain information for GMGC10.017_810_714.ranked_0.pdb #94
+---
+Chain | Description
+A | No description available
+> matchmaker #94 to #9
+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 6ii6, chain A (#9) with GMGC10.017_810_714.ranked_0.pdb, chain A
+(#94), sequence alignment score = 196.4
+RMSD between 49 pruned atom pairs is 0.960 angstroms; (across all 284 pairs:
+.428)
+> sequence chain #94/A
+Alignment identifier is 94/A
+> select #94/A:404-405
+atoms, 21 bonds, 2 residues, 1 model selected
+> select #94/A:1-405
+atoms, 6449 bonds, 405 residues, 1 model selected
+> hide #!9 models
+> select #94/A:550
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #94/A:406-550
+atoms, 2369 bonds, 145 residues, 1 model selected
+> select #94/A:520
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #94/A:520
+atoms, 15 bonds, 1 residue, 1 model selected
+> select
+> #94/A:13-33,38-45,49-62,66-82,92-144,154-164,166-168,172-182,188-200,209-222,242-270,281-290,299-308,353-365,380-382,388-393,415-420,423-433,486-506,516-518,537-539,545-547,550-565,576-585,595-602,605-624,628-630,633-660,679-699,702-721,726-742,809-824,831-833,852-859,866-873,885-890,902-907,911-914,919-927,934-947,963-977,988-1000,1002-1008,1018-1034,1041-1056,1058-1060,1068-1081,1089-1102,1113-1129,1133-1160,1169-1197,1202-1215,1220-1247,1275-1297,1306-1314,1317-1319,1330-1336,1343-1354,1361-1369,1400-1405,1410-1412,1417-1419,1510-1515,1655-1657,1739-1742,1838-1840,1853-1860,1863-1865,1868-1879,1917-1919,2122-2124,2150-2152,2155-2161,2173-2184
+atoms, 13930 bonds, 857 residues, 1 model selected
+> select #94/A:549
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #94/A:434-549
+atoms, 1888 bonds, 116 residues, 1 model selected
+> select #94/A:406-549
+atoms, 2350 bonds, 144 residues, 1 model selected
+> select #94/A:859
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #94/A:550-859
+atoms, 4943 bonds, 310 residues, 1 model selected
+> select #94/A:1420
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #94/A:860-1420
+atoms, 8882 bonds, 561 residues, 1 model selected
+> select #94/A:1737
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #94/A:1421-1737
+atoms, 4841 bonds, 317 residues, 1 model selected
+> select #94/A:1998
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #94/A:1738-1998
+atoms, 4048 bonds, 261 residues, 1 model selected
+> select #94/A:1999-2000
+atoms, 32 bonds, 2 residues, 1 model selected
+> select #94/A:1999-2223
+atoms, 3373 bonds, 225 residues, 1 model selected
+> select #94/A:1999
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #94/A:1999-2147
+atoms, 2188 bonds, 149 residues, 1 model selected
+> select #94/A:2148
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #94/A:2148-2223
+atoms, 1184 bonds, 76 residues, 1 model selected
+> select add #94
+atoms, 34892 bonds, 2223 residues, 2 models selected
+> select subtract #94
+model selected
+> hide #!94 models
+> show #8 models
+> log metadata #8
+The model has no metadata
+> log chains #8
+Chain information for AF-Q60XN1-F1-model_v4.pdb #8
+---
+Chain | Description | UniProt
+A | ataxin-3 homolog | ATX3_CAEBR 1-319
+> sequence chain #8/A
+Alignment identifier is 8/A
+> show #!9 models
+> matchmaker #8 to #9
+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 6ii6, chain A (#9) with AF-Q60XN1-F1-model_v4.pdb, chain A (#8),
+sequence alignment score = 85.4
+RMSD between 5 pruned atom pairs is 1.161 angstroms; (across all 217 pairs:
+.528)
+> hide #8 models
+> show #8 models
+> matchmaker #1 to #9
+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 6ii6, chain A (#9) with 6ii0.cropped.06.25.23.pdb, chain B (#1),
+sequence alignment score = 1498.3
+RMSD between 212 pruned atom pairs is 0.553 angstroms; (across all 223 pairs:
+.561)
+> matchmaker #8 to #1
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 6ii0.cropped.06.25.23.pdb, chain B (#1) with
+AF-Q60XN1-F1-model_v4.pdb, chain A (#8), sequence alignment score = 63.8
+RMSD between 13 pruned atom pairs is 0.566 angstroms; (across all 192 pairs:
+.787)
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> select #8/A:179
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #8/A:1-179
+atoms, 1477 bonds, 179 residues, 1 model selected
+> select #8/A:188
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #8/A:188-190
+atoms, 27 bonds, 3 residues, 1 model selected
+> select #8/A:188
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #8/A:188-208
+atoms, 182 bonds, 21 residues, 1 model selected
+> select #8/A:205-206
+atoms, 14 bonds, 2 residues, 1 model selected
+> select #8/A:205-207
+atoms, 25 bonds, 3 residues, 1 model selected
+> select #8/A:207
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #8/A:196-207
+atoms, 103 bonds, 12 residues, 1 model selected
+> select #8/A:243
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #8/A:243-254
+atoms, 91 bonds, 12 residues, 1 model selected
+> select #8/A:231
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #8/A:223-231
+atoms, 60 bonds, 9 residues, 1 model selected
+> select #8/A:221
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #8/A:221
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #8/A:221
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #8/A:221-232
+atoms, 88 bonds, 12 residues, 1 model selected
+> select #8/A:293
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #8/A:293-316
+atoms, 207 bonds, 24 residues, 1 model selected
+> select #8/A:89-92,110-114,119-125,128-132,140-142,160-165
+atoms, 271 bonds, 30 residues, 1 model selected
+> select #8/A:1
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #8/A:1-179
+atoms, 1477 bonds, 179 residues, 1 model selected
+> ui tool show Matchmaker
+> matchmaker #8 & sel to #9
+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 6ii6, chain A (#9) with AF-Q60XN1-F1-model_v4.pdb, chain A (#8),
+sequence alignment score = 61.9
+RMSD between 6 pruned atom pairs is 0.950 angstroms; (across all 153 pairs:
+.130)
+> matchmaker #8 & sel to #9
+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 6ii6, chain A (#9) with AF-Q60XN1-F1-model_v4.pdb, chain A (#8),
+sequence alignment score = 61.9
+RMSD between 6 pruned atom pairs is 0.950 angstroms; (across all 153 pairs:
+.130)
+> select add #8
+atoms, 2565 bonds, 319 residues, 1 model selected
+> select subtract #8
+Nothing selected
+> hide #!9 models
+> show #1 models
+> hide #8 models
+> show #!9 models
+> hide #!9 models
+> show #8 models
+> hide #8 models
+> show #8 models
+> hide #8 models
+> show #8 models
+> hide #8 models
+> show #8 models
+> hide #1 models
+> show #1 models
+> hide #8 models
+> show #8 models
+> hide #1 models
+> show #1 models
+> select add #8
+atoms, 2565 bonds, 319 residues, 1 model selected
+> view matrix models
+> #8,-0.25102,-0.52287,-0.81461,-3.9588,-0.96789,0.12376,0.21882,73.446,-0.0136,0.84338,-0.53714,71.947
+> view matrix models
+> #8,-0.25102,-0.52287,-0.81461,4.6156,-0.96789,0.12376,0.21882,49.504,-0.0136,0.84338,-0.53714,62.421
+> view matrix models
+> #8,-0.25102,-0.52287,-0.81461,40.206,-0.96789,0.12376,0.21882,92.988,-0.0136,0.84338,-0.53714,75.666
+> view matrix models
+> #8,-0.25102,-0.52287,-0.81461,41.642,-0.96789,0.12376,0.21882,94.077,-0.0136,0.84338,-0.53714,76.323
+> ui mousemode right rotate
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #8,0.99821,0.034809,-0.048623,66.586,0.035089,0.31745,0.94762,117.22,0.048421,-0.94763,0.31566,99.863
+> view matrix models
+> #8,0.99339,-0.09014,0.07114,68.419,-0.046511,0.25058,0.96698,116.31,-0.10499,-0.96389,0.24473,96.45
+> view matrix models
+> #8,0.99542,0.010348,0.09507,67.658,-0.095363,0.18192,0.97868,116.04,-0.007168,-0.98326,0.18207,98.234
+> view matrix models
+> #8,-0.64407,-0.65726,-0.39139,37.553,-0.71229,0.70186,-0.0064905,92.403,0.27897,0.2746,-0.9202,85.272
+> view matrix models
+> #8,-0.60155,-0.29358,-0.74293,32.782,-0.42497,0.90511,-0.013568,96.286,0.67642,0.30756,-0.66923,94.621
+> view matrix models
+> #8,0.48565,-0.73646,0.47092,66.693,-0.62741,0.081455,0.77442,104.88,-0.60869,-0.67156,-0.4225,79.259
+> view matrix models
+> #8,-0.60353,-0.59059,-0.53568,36.847,-0.68804,0.72526,-0.024424,92.563,0.40293,0.35383,-0.84407,87.522
+> view matrix models
+> #8,0.74809,-0.45538,0.48269,69.45,-0.54575,-0.0083843,0.83791,107.79,-0.37752,-0.89026,-0.25479,87.084
+> view matrix models
+> #8,0.97723,0.10994,0.18147,66.885,-0.19053,0.078401,0.97855,115.08,0.093351,-0.99084,0.097562,99.825
+> ui mousemode right "translate selected models"
+> view matrix models
+> #8,0.97723,0.10994,0.18147,12.749,-0.19053,0.078401,0.97855,82.546,0.093351,-0.99084,0.097562,72.849
+> view matrix models
+> #8,0.97723,0.10994,0.18147,12.847,-0.19053,0.078401,0.97855,83.249,0.093351,-0.99084,0.097562,72.686
+> view matrix models
+> #8,0.97723,0.10994,0.18147,2.0631,-0.19053,0.078401,0.97855,88.77,0.093351,-0.99084,0.097562,86.819
+> select subtract #8
+Nothing selected
+> hide #8 models
+> show #8 models
+> hide #8 models
+> show #69 models
+> matchmaker #69to #9
+Missing or invalid "matchAtoms" argument: only initial part "#69" of atom
+specifier valid
+> matchmaker #69 to #9
+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 6ii6, chain A (#9) with AF-Q9F3T4-F1-model_v4.pdb, chain A (#69),
+sequence alignment score = 99.5
+RMSD between 15 pruned atom pairs is 1.383 angstroms; (across all 244 pairs:
+.018)
+> log metadata #69
+The model has no metadata
+> log chains #69
+Chain information for AF-Q9F3T4-F1-model_v4.pdb #69
+---
+Chain | Description | UniProt
+A | probable cysteine protease avirulence protein AVRPPIC2 | AVRP2_PSESJ 1-269
+> sequence chain #69/A
+Alignment identifier is 69/A
+> hide #69 models
+> show #24 models
+> log metadata #24
+The model has no metadata
+> log chains #24
+Chain information for AF-C4K468-F1-model_v4.pdb #24
+---
+Chain | Description | UniProt
+A | putative autotransporter adhesin | C4K468_HAMD5 1-818
+> sequence chain #24/A
+Alignment identifier is 24/A
+> matchmaker #24 to #9
+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 6ii6, chain A (#9) with AF-C4K468-F1-model_v4.pdb, chain A (#24),
+sequence alignment score = 183.8
+RMSD between 56 pruned atom pairs is 1.189 angstroms; (across all 304 pairs:
+.130)
+> ui mousemode right select
+Drag select of 486 residues
+> select add #24
+atoms, 6889 bonds, 1034 residues, 2 models selected
+> select subtract #24
+atoms, 216 residues, 1 model selected
+> select add #1
+atoms, 1716 bonds, 587 residues, 1 model selected
+> select subtract #1
+Nothing selected
+> hide #1 models
+> show #!9 models
+> hide #!9 models
+> select #24/A:688
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #24/A:688-800
+atoms, 922 bonds, 113 residues, 1 model selected
+> select #24/A:687
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #24/A:359-687
+atoms, 2792 bonds, 329 residues, 1 model selected
+> select clear
+> ui mousemode right "translate selected models"
+> select #24/A:359
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #24/A:359-687
+atoms, 2792 bonds, 329 residues, 1 model selected
+> color sel purple
+> select add #24
+atoms, 6889 bonds, 818 residues, 1 model selected
+> select subtract #24
+Nothing selected
+> select #24/A:1
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #24/A:1-246
+atoms, 2073 bonds, 246 residues, 1 model selected
+> ui tool show Matchmaker
+> matchmaker #24 & sel to #9
+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 6ii6, chain A (#9) with AF-C4K468-F1-model_v4.pdb, chain A (#24),
+sequence alignment score = 189.7
+RMSD between 56 pruned atom pairs is 1.042 angstroms; (across all 223 pairs:
+.806)
+> select add #24
+atoms, 6889 bonds, 818 residues, 1 model selected
+> show #!9 models
+> select subtract #24
+Nothing selected
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #1 models
+> hide #1 models
+> show #1 models
+> hide #1 models
+> show #1 models
+> hide #1 models
+> show #1 models
+> hide #1 models
+> show #1 models
+> hide #1 models
+> show #!9 models
+> select #24/A:242-297
+atoms, 464 bonds, 56 residues, 1 model selected
+> select #24/A:242-297
+atoms, 464 bonds, 56 residues, 1 model selected
+> select #24/A:17
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #24/A:17-19
+atoms, 18 bonds, 3 residues, 1 model selected
+> sym #9
+ii6 mmCIF Assemblies
+---
+| author_and_software_defined_assembly| 1 copy of chains A,C
+| author_and_software_defined_assembly| 1 copy of chains B,D
+> log metadata #9
+No models had metadata
+> log chains #9
+Chain information for 6ii6 #9
+---
+Chain | Description
+A | Putative RTX-toxin
+> sequence chain #9/A
+Alignment identifier is 9/A
+> select #9/A:3482
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #9/A:3482
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #9
+atoms, 2729 bonds, 917 residues, 1 model selected
+> select subtract #9
+Nothing selected
+> matchmaker #24 to #9
+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 6ii6, chain A (#9) with AF-C4K468-F1-model_v4.pdb, chain A (#24),
+sequence alignment score = 183.8
+RMSD between 56 pruned atom pairs is 1.189 angstroms; (across all 304 pairs:
+.130)
+> select #24/A:515
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #24/A:515-517
+atoms, 25 bonds, 3 residues, 1 model selected
+> select #24/A:502
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #24/A:502-504
+atoms, 18 bonds, 3 residues, 1 model selected
+> select #24/A:500
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #24/A:500-502
+atoms, 20 bonds, 3 residues, 1 model selected
+> select #24/A:497
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #24/A:497-499
+atoms, 25 bonds, 3 residues, 1 model selected
+> select #24/A:499
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #24/A:499-501
+atoms, 21 bonds, 3 residues, 1 model selected
+> select #9/A:3482
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #9/A:3482
+atoms, 7 bonds, 1 residue, 1 model selected
+> color sel yellow
+> select clear
+> hide #24 models
+> show #21 models
+> log metadata #21
+The model has no metadata
+> log chains #21
+Chain information for AF-A0A4V0NNU7-F1-model_v4.pdb #21
+---
+Chain | Description
+A | peptidase_C58 domain-containing protein
+> sequence chain #21/A
+Alignment identifier is 21/A
+> matchmaker #21 to #9
+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 6ii6, chain A (#9) with AF-A0A4V0NNU7-F1-model_v4.pdb, chain A
+(#21), sequence alignment score = 208.3
+RMSD between 54 pruned atom pairs is 0.914 angstroms; (across all 285 pairs:
+.672)
+> hide #21 models
+> show #20 models
+> matchmaker #20 to #9
+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 6ii6, chain A (#9) with AF-A0A4V0NNP3-F1-model_v4.pdb, chain A
+(#20), sequence alignment score = 167.5
+RMSD between 54 pruned atom pairs is 0.979 angstroms; (across all 290 pairs:
+.128)
+> show #98 models
+> hide #20 models
+> matchmaker #98 to #9
+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 6ii6, chain A (#9) with WP_095034161.1.ranked_0.pdb, chain A (#98),
+sequence alignment score = 189.7
+RMSD between 60 pruned atom pairs is 1.387 angstroms; (across all 312 pairs:
+.944)
+> log metadata #98
+The model has no metadata
+> log chains #98
+Chain information for WP_095034161.1.ranked_0.pdb #98
+---
+Chain | Description
+A | No description available
+> sequence chain #98/A
+Alignment identifier is 98/A
+> select #98/A:555
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #98/A:555-557
+atoms, 45 bonds, 3 residues, 1 model selected
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> select #98/A:417
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #98/A:417-774
+atoms, 5888 bonds, 358 residues, 1 model selected
+> show #!9 models
+> color sel purple
+> select #98/A:416
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #98/A:1-416
+atoms, 7030 bonds, 416 residues, 1 model selected
+> ui tool show Matchmaker
+> matchmaker #98 & sel to #9
+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 6ii6, chain A (#9) with WP_095034161.1.ranked_0.pdb, chain A (#98),
+sequence alignment score = 157.2
+RMSD between 52 pruned atom pairs is 0.820 angstroms; (across all 263 pairs:
+.967)
+> matchmaker #98 & sel to #9
+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 6ii6, chain A (#9) with WP_095034161.1.ranked_0.pdb, chain A (#98),
+sequence alignment score = 157.2
+RMSD between 52 pruned atom pairs is 0.820 angstroms; (across all 263 pairs:
+.967)
+> select add #98
+atoms, 12919 bonds, 774 residues, 1 model selected
+> select subtract #98
+Nothing selected
+> hide #98 models
+> show #18 models
+> log metadata #18
+The model has no metadata
+> log chains #18
+Chain information for AF-A0A4P2SM79-F1-model_v4.pdb #18
+---
+Chain | Description
+A | peptidase_C58 domain-containing protein
+> sequence chain #18/A
+Alignment identifier is 18/A
+> matchmaker #18 to #9
+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 6ii6, chain A (#9) with AF-A0A4P2SM79-F1-model_v4.pdb, chain A
+(#18), sequence alignment score = 204.4
+RMSD between 54 pruned atom pairs is 1.295 angstroms; (across all 314 pairs:
+.398)
+> select #18/A:415-416
+atoms, 14 bonds, 2 residues, 1 model selected
+> select #18/A:1-416
+atoms, 3581 bonds, 416 residues, 1 model selected
+> ui tool show Matchmaker
+> matchmaker #18 & sel to #9
+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 6ii6, chain A (#9) with AF-A0A4P2SM79-F1-model_v4.pdb, chain A
+(#18), sequence alignment score = 175
+RMSD between 51 pruned atom pairs is 0.849 angstroms; (across all 283 pairs:
+.132)
+> matchmaker #18 & sel to #9
+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 6ii6, chain A (#9) with AF-A0A4P2SM79-F1-model_v4.pdb, chain A
+(#18), sequence alignment score = 175
+RMSD between 51 pruned atom pairs is 0.849 angstroms; (across all 283 pairs:
+.132)
+> select add #18
+atoms, 6589 bonds, 774 residues, 1 model selected
+> select subtract #18
+Nothing selected
+> hide #18 models
+> show #100 models
+> log metadata #100
+The model has no metadata
+> log chains #100
+Chain information for WP_148121377.1.ranked_0.pdb #100
+---
+Chain | Description
+A | No description available
+> sequence chain #100/A
+Alignment identifier is 100/A
+> matchmaker #100 to #9
+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 6ii6, chain A (#9) with WP_148121377.1.ranked_0.pdb, chain A
+(#100), sequence alignment score = 196.6
+RMSD between 63 pruned atom pairs is 1.204 angstroms; (across all 298 pairs:
+.062)
+> select #100/A:1367-1422
+atoms, 872 bonds, 56 residues, 1 model selected
+> select #100/A:1367-1953
+atoms, 9226 bonds, 587 residues, 1 model selected
+> select add #100
+atoms, 31455 bonds, 1953 residues, 1 model selected
+> select subtract #100
+Nothing selected
+> hide #100 models
+> show #93 models
+> matchmaker #93 to #9
+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 6ii6, chain A (#9) with C4K5K2.ranked_0.pdb, chain A (#93),
+sequence alignment score = 190.5
+RMSD between 59 pruned atom pairs is 1.280 angstroms; (across all 299 pairs:
+.592)
+> log metadata #93
+The model has no metadata
+> log chains #93
+Chain information for C4K5K2.ranked_0.pdb #93
+---
+Chain | Description
+A | No description available
+> sequence chain #93/A
+Alignment identifier is 93/A
+> select #93/A:294
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #93/A:1-294
+atoms, 4952 bonds, 294 residues, 1 model selected
+> select #93/A:742
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #93/A:416-742
+atoms, 5373 bonds, 327 residues, 1 model selected
+> select #93/A:1243
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #93/A:1243-1917
+atoms, 10583 bonds, 675 residues, 1 model selected
+> select #93/A:1243
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #93/A:1243-1910
+atoms, 10453 bonds, 668 residues, 1 model selected
+> select #93/A:1243
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #93/A:1243-1901
+atoms, 10326 bonds, 659 residues, 1 model selected
+> select add #93
+atoms, 31675 bonds, 1960 residues, 1 model selected
+> select subtract #93
+Nothing selected
+> hide #93 models
+> show #23 models
+> log metadata #23
+The model has no metadata
+> log chains #23
+Chain information for AF-C4K3P9-F1-model_v4.pdb #23
+---
+Chain | Description | UniProt
+A | putative RTX-family protein-1 | C4K3P9_HAMD5 1-1196
+> sequence chain #23/A
+Alignment identifier is 23/A
+> matchmaker #23 to #9
+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 6ii6, chain A (#9) with AF-C4K3P9-F1-model_v4.pdb, chain A (#23),
+sequence alignment score = 183.4
+RMSD between 61 pruned atom pairs is 1.222 angstroms; (across all 303 pairs:
+.576)
+> hide #23 models
+> show #100 models
+> hide #100 models
+> show #93 models
+> hide #93 models
+> show #23 models
+> hide #!9 models
+> ui mousemode right select
+Drag select of 362 residues
+> select #23/A:478-479
+atoms, 21 bonds, 2 residues, 1 model selected
+> select #23/A:478-812
+atoms, 2827 bonds, 335 residues, 1 model selected
+> select #23/A:478
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #23/A:478-485
+atoms, 63 bonds, 8 residues, 1 model selected
+> show #!9 models
+> select #23/A:767
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #23/A:431-767
+atoms, 2843 bonds, 337 residues, 1 model selected
+> color sel purple
+> select #23/A:307-308
+atoms, 12 bonds, 2 residues, 1 model selected
+> select #23/A:1-308
+atoms, 2635 bonds, 308 residues, 1 model selected
+> ui tool show Matchmaker
+> matchmaker #23 & sel to #9
+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 6ii6, chain A (#9) with AF-C4K3P9-F1-model_v4.pdb, chain A (#23),
+sequence alignment score = 163.6
+RMSD between 53 pruned atom pairs is 0.972 angstroms; (across all 257 pairs:
+.421)
+> hide #!9 models
+> select add #23
+atoms, 10025 bonds, 1196 residues, 1 model selected
+> select subtract #23
+Nothing selected
+> log metadata #24
+The model has no metadata
+> log chains #24
+Chain information for AF-C4K468-F1-model_v4.pdb #24
+---
+Chain | Description | UniProt
+A | putative autotransporter adhesin | C4K468_HAMD5 1-818
+> sequence chain #24/A
+Alignment identifier is 24/A
+> log metadata #98
+The model has no metadata
+> log chains #98
+Chain information for WP_095034161.1.ranked_0.pdb #98
+---
+Chain | Description
+A | No description available
+> sequence chain #98/A
+Alignment identifier is 98/A
+> show #!9 models
+> hide #23 models
+> show #106 models
+> show #107 models
+> hide #107 models
+> hide #106 models
+> show #106 models
+> hide #106 models
+> show #107 models
+> hide #107 models
+> show #108 models
+> hide #108 models
+> show #106 models
+> hide #106 models
+> show #108 models
+> hide #108 models
+> show #106 models
+> show #107 models
+> show #108 models
+> hide #106 models
+> hide #107 models
+> hide #108 models
+> show #106 models
+> show #107 models
+> hide #107 models
+> hide #106 models
+> show #106 models
+> hide #106 models
+> show #107 models
+> hide #107 models
+> show #108 models
+> hide #108 models
+> show #91 models
+> log metadata #91
+The model has no metadata
+> log chains #91
+Chain information for A0A4P2SNJ1.longerNterm.ranked_0.pdb #91
+---
+Chain | Description
+A | No description available
+> sequence chain #91/A
+Alignment identifier is 91/A
+> hide #91 models
+> show #91 models
+> hide #91 models
+> show #17 models
+> log metadata #17
+The model has no metadata
+> log chains #17
+Chain information for AF-A0A2D3T3R8-F1-model_v4.pdb #17
+---
+Chain | Description
+A | uncharacterized protein
+> sequence chain #17/A
+Alignment identifier is 17/A
+> matchmaker #17 to #9
+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 6ii6, chain A (#9) with AF-A0A2D3T3R8-F1-model_v4.pdb, chain A
+(#17), sequence alignment score = 161.4
+RMSD between 53 pruned atom pairs is 0.936 angstroms; (across all 297 pairs:
+.092)
+> hide #17 models
+> show #25 models
+> log metadata #25
+The model has no metadata
+> log chains #25
+Chain information for AF-C4K5L0-F1-model_v4.pdb #25
+---
+Chain | Description | UniProt
+A | putative RTX-family protein-15 | C4K5L0_HAMD5 1-555
+> matchmaker #25 to #9
+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 6ii6, chain A (#9) with AF-C4K5L0-F1-model_v4.pdb, chain A (#25),
+sequence alignment score = 202.4
+RMSD between 71 pruned atom pairs is 0.846 angstroms; (across all 300 pairs:
+.095)
+> log metadata #25
+The model has no metadata
+> log chains #25
+Chain information for AF-C4K5L0-F1-model_v4.pdb #25
+---
+Chain | Description | UniProt
+A | putative RTX-family protein-15 | C4K5L0_HAMD5 1-555
+> sequence chain #25/A
+Alignment identifier is 25/A
+> hide #25 models
+> show #99 models
+> log metadata #99
+The model has no metadata
+> log chains #99
+Chain information for WP_095034189.1.ranked_0.pdb #99
+---
+Chain | Description
+A | No description available
+> sequence chain #99/A
+Alignment identifier is 99/A
+> matchmaker #99 to #9
+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 6ii6, chain A (#9) with WP_095034189.1.ranked_0.pdb, chain A (#99),
+sequence alignment score = 201
+RMSD between 46 pruned atom pairs is 0.814 angstroms; (across all 293 pairs:
+.670)
+> select #99/A:348-349
+atoms, 26 bonds, 2 residues, 1 model selected
+> select #99/A:349-502
+atoms, 2510 bonds, 154 residues, 1 model selected
+> color sel #73fa79ff
+> color sel #7bf78bff
+> color sel #b3f7acff
+> color sel #b4f78fff
+> color sel #d1f7b1ff
+> color sel #c6f78dff
+> color sel #abf789ff
+> color sel #bff7b8ff
+> color sel #b1f798ff
+> color sel #aef77eff
+> color sel #5bf7abff
+> color sel #c9f7cfff
+> color sel #dcf4f7ff
+> color sel #cbf7e2ff
+> color sel #a1f7cbff
+> color sel #93f7a8ff
+> color sel #92f7a7ff
+> color sel #b2f7c9ff
+> color sel #aaf7a6ff
+> color sel #dcf79fff
+> color sel #d0f7b0ff
+> color sel #b8db9cff
+> color sel #c2e6a4ff
+> select add #99
+atoms, 8876 bonds, 543 residues, 1 model selected
+> select subtract #99
+Nothing selected
+> select #99/A:349
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #99/A:349-502
+atoms, 2510 bonds, 154 residues, 1 model selected
+> color sel #c1e6a4ff
+> color sel #c0e4a3ff
+> color sel #bee1a1ff
+> color sel #bbde9eff
+> color sel #badd9eff
+> select add #99
+atoms, 8876 bonds, 543 residues, 1 model selected
+> select subtract #99
+Nothing selected
+> hide #99 models
+> show #!78 models
+> hide #!78 models
+> show #89 models
+> matchmaker #89 to #9
+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 6ii6, chain A (#9) with AF-D6YWY5-F1-model_v4.pdb, chain A (#89),
+sequence alignment score = 111.4
+RMSD between 37 pruned atom pairs is 1.149 angstroms; (across all 266 pairs:
+.856)
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> log metadata #89
+The model has no metadata
+> log chains #89
+Chain information for AF-D6YWY5-F1-model_v4.pdb #89
+---
+Chain | Description | UniProt
+A | uncharacterized protein | D6YWY5_WADCW 1-494
+> sequence chain #89/A
+Alignment identifier is 89/A
+> select #89/A:111
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #89/A:111-116
+atoms, 37 bonds, 6 residues, 1 model selected
+> select add #89
+atoms, 3974 bonds, 494 residues, 1 model selected
+> select subtract #89
+Nothing selected
+> ui mousemode right select
+Drag select of 201 residues
+> select #89/A:282
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #89/A:282-494
+atoms, 1691 bonds, 213 residues, 1 model selected
+> ui tool show Matchmaker
+> matchmaker #89 & sel to #9
+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 6ii6, chain A (#9) with AF-D6YWY5-F1-model_v4.pdb, chain A (#89),
+sequence alignment score = 119.4
+RMSD between 32 pruned atom pairs is 1.387 angstroms; (across all 165 pairs:
+.925)
+> matchmaker #89 & sel to #9
+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 6ii6, chain A (#9) with AF-D6YWY5-F1-model_v4.pdb, chain A (#89),
+sequence alignment score = 119.4
+RMSD between 32 pruned atom pairs is 1.387 angstroms; (across all 165 pairs:
+.925)
+> select add #89
+atoms, 3974 bonds, 494 residues, 1 model selected
+> select subtract #89
+Nothing selected
+> select #89/A:171
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #89/A:116-171
+atoms, 468 bonds, 56 residues, 1 model selected
+> select add #89
+atoms, 3974 bonds, 494 residues, 1 model selected
+> select subtract #89
+Nothing selected
+> hide #89 models
+> show #89 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+Drag select of 178 residues
+> matchmaker #89 to #9
+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 6ii6, chain A (#9) with AF-D6YWY5-F1-model_v4.pdb, chain A (#89),
+sequence alignment score = 111.4
+RMSD between 37 pruned atom pairs is 1.149 angstroms; (across all 266 pairs:
+.856)
+> show #!9 models
+> select add #89
+atoms, 3974 bonds, 494 residues, 1 model selected
+> select subtract #89
+Nothing selected
+> hide #89 models
+> show #89 models
+> hide #!9 models
+> select clear
+> ui mousemode right "translate selected models"
+> ui mousemode right select
+Drag select of 189 residues
+> select #89/A:28
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #89/A:28
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #89/A:88
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #89/A:88-275
+atoms, 1543 bonds, 188 residues, 1 model selected
+> select #89/A:276-277
+atoms, 15 bonds, 2 residues, 1 model selected
+> select #89/A:276-494
+atoms, 1740 bonds, 219 residues, 1 model selected
+> color sel #040e52ff
+> select #89/A:25-27
+atoms, 31 bonds, 3 residues, 1 model selected
+> select #89/A:25-90
+atoms, 502 bonds, 66 residues, 1 model selected
+> select #89/A:25
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #89/A:25-80
+atoms, 423 bonds, 56 residues, 1 model selected
+> color sel #445215ff
+> color sel #4b5b17ff
+> color sel #4c5c18ff
+> color sel #4d5e18ff
+> color sel #596c1cff
+> color sel #6d8422ff
+> color sel #7d9827ff
+> color sel #8aa82bff
+> color sel #8caa2cff
+> color sel #8cab2cff
+> color sel #8ba92cff
+> color sel #85a22aff
+> color sel #809c28ff
+> color sel #7e9928ff
+> color sel #7e9a28ff
+> color sel #849a10ff
+> color sel #7e9a05ff
+> color sel #7f9a05ff
+> color sel #7f9b06ff
+> color sel #819d06ff
+> color sel #829f06ff
+> color sel #84a006ff
+> color sel #85a206ff
+> color sel #86a306ff
+> color sel #89a706ff
+> color sel #8baa06ff
+> color sel #8ead06ff
+> color sel #90af06ff
+> color sel #91b006ff
+> color sel #92b206ff
+> color sel #93b206ff
+> color sel #90b203ff
+> color sel #91b203ff
+> color sel #92b204ff
+> color sel #92b203ff
+> color sel #93b203ff
+> color sel #94b203ff
+> color sel #95b203ff
+> color sel #96b203ff
+> color sel #98b204ff
+> color sel #9ab204ff
+> color sel #9bb204ff
+> color sel #a3b202ff
+> color sel #a7b200ff
+> color sel #a6b201ff
+> color sel #a2b209ff
+> color sel #a1b20bff
+> color sel #a1b20dff
+> color sel #a0b20eff
+> color sel #a0b20fff
+> color sel #a0b210ff
+> color sel #a6b21aff
+> color sel #a7b21cff
+> color sel #a7b21dff
+> color sel #a8b21eff
+> color sel #a8b21dff
+> color sel #a9b21dff
+> color sel #aab21dff
+> color sel #abb21dff
+> color sel #adb21eff
+> color sel #adb21dff
+> color sel #afb21eff
+> color sel #b2b21fff
+> color sel #b2b11fff
+> color sel #b2b01fff
+> color sel #b2ab20ff
+> color sel #b2a820ff
+> color sel #b2a71fff
+> color sel #b2a81eff
+> color sel #b2a81dff
+> color sel #b0a61dff
+> color sel #afa51cff
+> color sel #ada31cff
+> color sel #aca21cff
+> color sel #aba11cff
+> color sel #aaa11cff
+> color sel #a99f1bff
+> color sel #a89e1bff
+> color sel #a79e1bff
+> color sel #a69d1bff
+> color sel #a59c1bff
+> color sel #a49b1bff
+> select add #92
+atoms, 34185 bonds, 2159 residues, 2 models selected
+> select subtract #92
+atoms, 423 bonds, 56 residues, 1 model selected
+> select add #89
+atoms, 3974 bonds, 494 residues, 1 model selected
+> select subtract #89
+Nothing selected
+> hide #89 models
+> show #110 models
+> show #111 models
+> select clear
+> ui mousemode right "translate selected models"
+> show #104 models
+> show #105 models
+> hide #104 models
+> hide #105 models
+> hide #110 models
+> hide #111 models
+> show #67 models
+> log metadata #67
+The model has no metadata
+> log chains #67
+Chain information for 1ukf #67
+---
+Chain | Description | UniProt
+A | Avirulence protein AVRPPH3 | AVRP3_PSESH 81-267
+> sequence chain #67/A
+Alignment identifier is 67/A
+> sequence chain #67/A
+Alignment identifier is 67/A
+> show #112 models
+> hide #112 models
+> show #112 models
+> hide #112 models
+> show #102 models
+> log metadata #102
+The model has no metadata
+> log chains #102
+Chain information for AF-Q52430-F1-model_v4.pdb #102
+---
+Chain | Description | UniProt
+A | cysteine protease avirulence protein avrpphb | AVRP3_PSESH 1-267
+> sequence chain #102/A
+Alignment identifier is 102/A
+> matchmaker #102 to #9
+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 6ii6, chain A (#9) with AF-Q52430-F1-model_v4.pdb, chain A (#102),
+sequence alignment score = 75
+RMSD between 16 pruned atom pairs is 0.930 angstroms; (across all 200 pairs:
+.752)
+> hide #67 models
+> show #!9 models
+> select #102/A:80-81
+atoms, 12 bonds, 2 residues, 1 model selected
+> select #102/A:1-81
+atoms, 611 bonds, 81 residues, 1 model selected
+> select #102/A:136-137
+atoms, 15 bonds, 2 residues, 1 model selected
+> select #102/A:136-138
+atoms, 28 bonds, 3 residues, 1 model selected
+> select #102/A:81
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #102/A:81-82
+atoms, 13 bonds, 2 residues, 1 model selected
+> select #102/A:79-80
+atoms, 15 bonds, 2 residues, 1 model selected
+> select #102/A:79-80
+atoms, 15 bonds, 2 residues, 1 model selected
+> select #102/A:81-82
+atoms, 13 bonds, 2 residues, 1 model selected
+> select #102/A:81-82
+atoms, 13 bonds, 2 residues, 1 model selected
+> select #102/A:81
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #102/A:81
+atoms, 5 bonds, 1 residue, 1 model selected
+> color sel #040e52ff
+> select #102/A:82-85,98-107,114-121,126-148,153-164,181-193,237-239,241-254
+atoms, 671 bonds, 87 residues, 1 model selected
+> select add #102
+atoms, 2057 bonds, 267 residues, 1 model selected
+> select subtract #102
+Nothing selected
+> hide #102 models
+> show #86 models
+> matchmaker #86 to #9
+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 6ii6, chain A (#9) with AF-Q9AMW4-F1-model_v4.pdb, chain A (#86),
+sequence alignment score = 87.8
+RMSD between 30 pruned atom pairs is 0.803 angstroms; (across all 234 pairs:
+.197)
+> log metadata #86
+The model has no metadata
+> log chains #86
+Chain information for AF-Q9AMW4-F1-model_v4.pdb #86
+---
+Chain | Description | UniProt
+A | putative cysteine protease yopt-like BLR2058 | Y2058_BRADU 1-298
+> sequence chain #86/A
+Alignment identifier is 86/A
+> hide #86 models
+> show #85 models
+> log metadata #85
+The model has no metadata
+> log chains #85
+Chain information for AF-Q89T99-F1-model_v4.pdb #85
+---
+Chain | Description | UniProt
+A | putative cysteine protease yopt-like BLR2140 | Y2140_BRADU 1-271
+> sequence chain #85/A
+Alignment identifier is 85/A
+> matchmaker #85 to #9
+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 6ii6, chain A (#9) with AF-Q89T99-F1-model_v4.pdb, chain A (#85),
+sequence alignment score = 83.5
+RMSD between 30 pruned atom pairs is 0.963 angstroms; (across all 195 pairs:
+.092)
+> hide #85 models
+> show #73 models
+> log metadata #73
+The model has no metadata
+> log chains #73
+Chain information for AF-P55730-F1-model_v4.pdb #73
+---
+Chain | Description | UniProt
+A | putative cysteine protease yopt-like Y4ZC | Y4ZC_SINFN 1-261
+> sequence chain #73/A
+Alignment identifier is 73/A
+> matchmaker #73 to #9
+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 6ii6, chain A (#9) with AF-P55730-F1-model_v4.pdb, chain A (#73),
+sequence alignment score = 72.4
+RMSD between 25 pruned atom pairs is 0.955 angstroms; (across all 190 pairs:
+.079)
+> hide #73 models
+> show #43 models
+> log metadata #43
+The model has no metadata
+> log chains #43
+Chain information for AF-A0A1Y3API8-F1-model_v4.pdb #43
+---
+Chain | Description
+A | rhodanese domain-containing protein
+> sequence chain #43/A
+Alignment identifier is 43/A
+> matchmaker #43 to #9
+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 6ii6, chain A (#9) with AF-A0A1Y3API8-F1-model_v4.pdb, chain A
+(#43), sequence alignment score = 317.2
+RMSD between 75 pruned atom pairs is 0.980 angstroms; (across all 295 pairs:
+.271)
+> hide #43 models
+> show #84 models
+> matchmaker #84 to #9
+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 6ii6, chain A (#9) with AF-C4ULG3-F1-model_v4.pdb, chain A (#84),
+sequence alignment score = 321.7
+RMSD between 101 pruned atom pairs is 1.004 angstroms; (across all 280 pairs:
+.316)
+> show #43 models
+> hide #43 models
+> hide #84 models
+> show #109 models
+> hide #109 models
+> show #110 models
+> hide #110 models
+> show #111 models
+> show #109 models
+> hide #111 models
+> log metadata #109
+The model has no metadata
+> log chains #109
+Chain information for C7BKP9.ranked_0.pdb #109
+---
+Chain | Description
+A | No description available
+> sequence chain #109/A
+Alignment identifier is 109/A
+> select #109/A:527-528
+atoms, 29 bonds, 2 residues, 1 model selected
+> select #109/A:527-756
+atoms, 3719 bonds, 230 residues, 1 model selected
+> select #109/A:527
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #109/A:527-712
+atoms, 3017 bonds, 186 residues, 1 model selected
+> select #109/A:527-528
+atoms, 29 bonds, 2 residues, 1 model selected
+> select #109/A:527-713
+atoms, 3031 bonds, 187 residues, 1 model selected
+> color sel #945200ff
+> color sel #8b551cff
+> color sel #8d571cff
+> color sel #9e6120ff
+> color sel #a66621ff
+> color sel #ac6a22ff
+> color sel #b06c23ff
+> color sel #bd7326ff
+> color sel #bd7426ff
+> color sel #c17627ff
+> color sel #c1802aff
+> color sel #c17e29ff
+> color sel #c17b20ff
+> color sel #c1791aff
+> color sel #c17715ff
+> color sel #c17511ff
+> color sel #c17510ff
+> color sel #c1760eff
+> color sel #c1760dff
+> color sel #c1770dff
+> color sel #c1770cff
+> color sel #c1780cff
+> color sel #c1790aff
+> color sel #c17b08ff
+> color sel #c17c07ff
+> color sel #c17d06ff
+> color sel #c17e06ff
+> color sel #c27e06ff
+> color sel #c88206ff
+> color sel #ca8306ff
+> color sel #ca8406ff
+> color sel #cb8406ff
+> color sel #cd8506ff
+> color sel #d08706ff
+> color sel #cf8706ff
+> color sel #c98306ff
+> color sel #c37f06ff
+> color sel #c27e06ff
+> select add #109
+atoms, 47629 bonds, 2957 residues, 1 model selected
+> select subtract #109
+Nothing selected
+> select #109/A:527
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #109/A:527-713
+atoms, 3031 bonds, 187 residues, 1 model selected
+> color sel #945200ff
+> color sel #8b551cff
+> color sel #8f581dff
+> color sel #9c601fff
+> color sel #9e6120ff
+> color sel #a06220ff
+> color sel #a46521ff
+> color sel #a56521ff
+> color sel #a86722ff
+> color sel #a96822ff
+> color sel #aa6822ff
+> color sel #ab6922ff
+> color sel #b06c23ff
+> color sel #b26d24ff
+> color sel #b46e24ff
+> select add #109
+atoms, 47629 bonds, 2957 residues, 1 model selected
+> select subtract #109
+Nothing selected
+> show #111 models
+> hide #111 models
+> hide #109 models
+> show #109 models
+> hide #109 models
+> show #74 models
+> matchmaker #74 to #9
+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 6ii6, chain A (#9) with MGYP001564015939.pdb, chain A (#74),
+sequence alignment score = 205.5
+RMSD between 86 pruned atom pairs is 1.408 angstroms; (across all 190 pairs:
+.441)
+> hide #74 models
+> show #81 models
+> matchmaker #81 to #9
+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 6ii6, chain A (#9) with AF-A1JU65-F1-model_v4.pdb, chain A (#81),
+sequence alignment score = 167
+RMSD between 24 pruned atom pairs is 1.316 angstroms; (across all 252 pairs:
+.802)
+> hide #81 models
+> show #83 models
+> matchmaker #83 to #9
+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 6ii6, chain A (#9) with AF-Q93RN4-F1-model_v4.pdb, chain A (#83),
+sequence alignment score = 154.3
+RMSD between 61 pruned atom pairs is 1.078 angstroms; (across all 253 pairs:
+.858)
+> hide #83 models
+> show #46 models
+> sym #46
+gqj mmCIF Assemblies
+---
+| author_defined_assembly| 1 copy of chain A
+| software_defined_assembly| 2 copies of chain A
+> log metadata #46
+The model has no metadata
+> log chains #46
+Chain information for 3gqj #46
+---
+Chain | Description | UniProt
+A | Cell Inhibiting Factor (Cif) | Q7N439_PHOLL 48-308
+> sequence chain #46/A
+Alignment identifier is 46/A
+> log metadata #36
+The model has no metadata
+> log chains #36
+Chain information for pdb3efy.ent #36
+---
+Chain | Description | UniProt
+A B | cif (cell cycle inhibiting factor) | Q7WRZ5_ECOLX 100-282
+> sequence chain #36/A#36/B
+Alignment identifier is 1
+> log metadata #6
+The model has no metadata
+> log chains #6
+Chain information for 2ffg.pdb #6
+---
+Chain | Description | UniProt
+A B | YKUJ | O34588_BACSU 1-79
+> hide #46 models
+> log metadata #47
+No models had metadata
+> log chains #47
+Chain information for 8p52 #47
+---
+Chain | Description | UniProt
+A | Toxin protein | Q8KT65_PHOLU 1-2929
+> show #82 models
+> log metadata #82
+The model has no metadata
+> log chains #82
+Chain information for AF-O68703-F1-model_v4.pdb #82
+---
+Chain | Description | UniProt
+A | cysteine protease yopt | YOPT_YERPE 1-322
+> sequence chain #82/A
+Alignment identifier is 82/A
+> matchmaker #82 to #9
+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 6ii6, chain A (#9) with AF-O68703-F1-model_v4.pdb, chain A (#82),
+sequence alignment score = 155.7
+RMSD between 60 pruned atom pairs is 1.095 angstroms; (across all 245 pairs:
+.853)
+> show #38 models
+> log metadata #38
+The model has no metadata
+> log chains #38
+Chain information for AF-A0A0K3YVA7-F1-model_v4.pdb #38
+---
+Chain | Description
+A | EFA1/lifa-like protein
+> sequence chain #38/A
+Alignment identifier is 38/A
+> select #38/A:145
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #38/A:1-145
+atoms, 1117 bonds, 145 residues, 1 model selected
+> select #38/A:150
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #38/A:1-150
+atoms, 1158 bonds, 150 residues, 1 model selected
+> color sel #040e52ff
+> select #38/A:1
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #38/A:1-145
+atoms, 1117 bonds, 145 residues, 1 model selected
+> color sel #030d52ff
+> color sel #040e52ff
+> color sel #050f52ff
+> color sel #0a1452ff
+> color sel #0d1652ff
+> color sel #0f1852ff
+> color sel #121a52ff
+> color sel #151d52ff
+> color sel #181f52ff
+> color sel #1a2152ff
+> color sel #1b2152ff
+> color sel #1c2152ff
+> color sel #1d2252ff
+> color sel #1e2252ff
+> color sel #1e2152ff
+> color sel #212252ff
+> color sel #2b2852ff
+> color sel #2e2a52ff
+> color sel #302c52ff
+> color sel #312d52ff
+> color sel #322e52ff
+> color sel #322f52ff
+> color sel #323052ff
+> color sel #413e6bff
+> color sel #494578ff
+> color sel #4a4679ff
+> color sel #4b477bff
+> color sel #4d497eff
+> color sel #4e4980ff
+> color sel #4d4a80ff
+> color sel #4d4880ff
+> color sel #4d4680ff
+> color sel #4c4280ff
+> color sel #4c3f80ff
+> color sel #4c3e80ff
+> color sel #4c3d80ff
+> color sel #4c3c80ff
+> color sel #4d3c80ff
+> color sel #4d3980ff
+> color sel #4d3680ff
+> color sel #4d3580ff
+> color sel #4c3480ff
+> color sel #4f3980ff
+> color sel #513b80ff
+> color sel #513c80ff
+> color sel #533e80ff
+> color sel #564280ff
+> color sel #594480ff
+> color sel #5a4680ff
+> color sel #5b4680ff
+> color sel #5b4780ff
+> color sel #5b4680ff
+> color sel #593c80ff
+> color sel #542b80ff
+> color sel #501b80ff
+> color sel #4f1980ff
+> color sel #4f1880ff
+> color sel #4d1680ff
+> color sel #441080ff
+> color sel #3d0c80ff
+> color sel #3b0a80ff
+> color sel #3a0a80ff
+> color sel #390a80ff
+> color sel #380980ff
+> color sel #360880ff
+> color sel #350880ff
+> color sel #350780ff
+> color sel #340780ff
+> color sel #300580ff
+> color sel #2e0480ff
+> color sel #2d0480ff
+> color sel #2d047fff
+> color sel #2d047dff
+> color sel #2c047dff
+> color sel #2c047bff
+> color sel #2b047aff
+> color sel #2b0479ff
+> color sel #2a0477ff
+> color sel #2a0476ff
+> color sel #2a0475ff
+> color sel #290474ff
+> color sel #2b0674ff
+> color sel #2c0774ff
+> color sel #2f0b74ff
+> color sel #341074ff
+> color sel #381574ff
+> color sel #3c1b74ff
+> color sel #3e1d74ff
+> color sel #3f1e74ff
+> color sel #3f1f74ff
+> color sel #3f1e74ff
+> color sel #3e1e72ff
+> color sel #3d1e71ff
+> color sel #3c1d6fff
+> color sel #3b1d6dff
+> color sel #3b1c6cff
+> color sel #391c6aff
+> color sel #381b68ff
+> color sel #371b66ff
+> color sel #371b65ff
+> select add #38
+atoms, 3947 bonds, 490 residues, 1 model selected
+> select subtract #38
+Nothing selected
+> hide #38 models
+> show #41 models
+> log metadata #41
+The model has no metadata
+> log chains #41
+Chain information for AF-A0A3W5Y7A7-F1-model_v4.pdb #41
+---
+Chain | Description
+A | uncharacterized protein
+> sequence chain #41/A
+Alignment identifier is 41/A
+> matchmaker #41 to #9
+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 6ii6, chain A (#9) with AF-A0A3W5Y7A7-F1-model_v4.pdb, chain A
+(#41), sequence alignment score = 930.7
+RMSD between 280 pruned atom pairs is 0.685 angstroms; (across all 298 pairs:
+.326)
+> hide #41 models
+> show #39 models
+> log metadata #39
+The model has no metadata
+> log chains #39
+Chain information for AF-A0A2X3JAL5-F1-model_v4.pdb #39
+---
+Chain | Description
+A | EFA1/lifa-like protein
+> sequence chain #39/A
+Alignment identifier is 39/A
+> hide #39 models
+> hide #82 models
+> show #39 models
+> matchmaker #39 to #9
+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 6ii6, chain A (#9) with AF-A0A2X3JAL5-F1-model_v4.pdb, chain A
+(#39), sequence alignment score = 1054.4
+RMSD between 315 pruned atom pairs is 0.673 angstroms; (across all 343 pairs:
+.660)
+> hide #39 models
+> show #35 models
+> matchmaker #35 to #9
+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 6ii6, chain A (#9) with AF-A0A7U6JX76-F1-model_v4.pdb, chain A
+(#35), sequence alignment score = 1035.8
+RMSD between 314 pruned atom pairs is 0.728 angstroms; (across all 343 pairs:
+.052)
+> log metadata #35
+The model has no metadata
+> log chains #35
+Chain information for AF-A0A7U6JX76-F1-model_v4.pdb #35
+---
+Chain | Description
+A | EFA1/lifa-like protein, N-terminal part
+> sequence chain #35/A
+Alignment identifier is 35/A
+> hide #35 models
+> show #40 models
+> log metadata #40
+The model has no metadata
+> log chains #40
+Chain information for AF-A0A376U9H5-F1-model_v4.pdb #40
+---
+Chain | Description
+A | EFA1/lifa-like protein
+> sequence chain #40/A
+Alignment identifier is 40/A
+> matchmaker #40 to #9
+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 6ii6, chain A (#9) with AF-A0A376U9H5-F1-model_v4.pdb, chain A
+(#40), sequence alignment score = 1050.8
+RMSD between 316 pruned atom pairs is 0.697 angstroms; (across all 343 pairs:
+.132)
+> hide #40 models
+> show #65 models
+> log metadata #65
+The model has no metadata
+> log chains #65
+Chain information for AF-A0A2T4FGD4-F1-model_v4.pdb #65
+---
+Chain | Description
+A | uncharacterized protein
+> sequence chain #65/A
+Alignment identifier is 65/A
+> matchmaker #65 to #9
+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 6ii6, chain A (#9) with AF-A0A2T4FGD4-F1-model_v4.pdb, chain A
+(#65), sequence alignment score = 328.4
+RMSD between 116 pruned atom pairs is 0.971 angstroms; (across all 291 pairs:
+.697)
+> hide #65 models
+> show #61 models
+> matchmaker #61 to #9
+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 6ii6, chain A (#9) with MGYP003613210660.pdb, chain A (#61),
+sequence alignment score = 251.9
+RMSD between 96 pruned atom pairs is 1.039 angstroms; (across all 196 pairs:
+.185)
+> hide #61 models
+> show #63 models
+> matchmaker #63 to #9
+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 6ii6, chain A (#9) with AF-A0A7Z6MWD8-F1-model_v4.pdb, chain A
+(#63), sequence alignment score = 318.1
+RMSD between 109 pruned atom pairs is 1.021 angstroms; (across all 290 pairs:
+.681)
+> log metadata #63
+The model has no metadata
+> log chains #63
+Chain information for AF-A0A7Z6MWD8-F1-model_v4.pdb #63
+---
+Chain | Description
+A | uncharacterized protein
+> sequence chain #63/A
+Alignment identifier is 63/A
+> show #60 models
+> hide #63 models
+> matchmaker #60 to #9
+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 6ii6, chain A (#9) with MGYP003607098654.pdb, chain A (#60),
+sequence alignment score = 252.9
+RMSD between 84 pruned atom pairs is 0.881 angstroms; (across all 209 pairs:
+.498)
+> hide #60 models
+> show #64 models
+> log metadata #64
+The model has no metadata
+> log chains #64
+Chain information for AF-A0A656YJH9-F1-model_v4 (1).pdb #64
+---
+Chain | Description
+A | uncharacterized protein
+> sequence chain #64/A
+Alignment identifier is 64/A
+> matchmaker #64 to #9
+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 6ii6, chain A (#9) with AF-A0A656YJH9-F1-model_v4 (1).pdb, chain A
+(#64), sequence alignment score = 367.2
+RMSD between 108 pruned atom pairs is 1.011 angstroms; (across all 303 pairs:
+.242)
+> hide #64 models
+> show #62 models
+> log metadata #62
+The model has no metadata
+> log chains #62
+Chain information for AF-A0A7X1AT80-F1-model_v4.pdb #62
+---
+Chain | Description
+A | uncharacterized protein
+> sequence chain #62/A
+Alignment identifier is 62/A
+> matchmaker #62 to #9
+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 6ii6, chain A (#9) with AF-A0A7X1AT80-F1-model_v4.pdb, chain A
+(#62), sequence alignment score = 362.8
+RMSD between 133 pruned atom pairs is 1.005 angstroms; (across all 278 pairs:
+.096)
+> hide #62 models
+> show #55 models
+> log metadata #55
+The model has no metadata
+> log chains #55
+Chain information for MGYP003605169772.pdb #55
+---
+Chain | Description
+A | No description available
+> sequence chain #55/A
+Alignment identifier is 55/A
+> show #96 models
+> hide #55 models
+> matchmaker #96 to #9
+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 6ii6, chain A (#9) with MGYP003605169772.ranked_0.pdb, chain A
+(#96), sequence alignment score = 378.7
+RMSD between 133 pruned atom pairs is 1.066 angstroms; (across all 289 pairs:
+.432)
+> log metadata #96
+The model has no metadata
+> log chains #96
+Chain information for MGYP003605169772.ranked_0.pdb #96
+---
+Chain | Description
+A | No description available
+> sequence chain #96/A
+Alignment identifier is 96/A
+> select #96/A:818-819
+atoms, 40 bonds, 2 residues, 1 model selected
+> select #96/A:819-907
+atoms, 1336 bonds, 89 residues, 1 model selected
+> color sel #ff7e79ff
+> color sel #ef8d85ff
+> color sel #ef8d86ff
+> color sel #ef908cff
+> color sel #ef9495ff
+> color sel #ef969dff
+> color sel #ef98aaff
+> color sel #ef9ab4ff
+> color sel #ef9bb9ff
+> color sel #ef9bbbff
+> color sel #ef9cbdff
+> color sel #ef9cbfff
+> color sel #ef9cc1ff
+> color sel #ef9cc2ff
+> color sel #ef9bc1ff
+> color sel #ef97bfff
+> color sel #ef93bcff
+> color sel #ef8bb5ff
+> color sel #ef86b0ff
+> color sel #ef85afff
+> color sel #ef82acff
+> color sel #ef7ca6ff
+> color sel #ef79a3ff
+> color sel #ef80a8ff
+> color sel #ef7fa8ff
+> color sel #ef80a3ff
+> color sel #ef7f9fff
+> color sel #ef809eff
+> color sel #ef809dff
+> color sel #ef819aff
+> color sel #ef8095ff
+> color sel #ef7f94ff
+> color sel #ef7e93ff
+> color sel #ef7c91ff
+> color sel #ef798eff
+> color sel #ef768bff
+> color sel #ef7489ff
+> color sel #ef7287ff
+> color sel #ef6c80ff
+> color sel #ef6b80ff
+> color sel #ef6b7fff
+> color sel #ef6c7dff
+> color sel #ef717fff
+> color sel #ef717eff
+> color sel #ef717dff
+> color sel #ef717cff
+> color sel #ef7079ff
+> color sel #ef7078ff
+> color sel #ef7077ff
+> color sel #ef6f76ff
+> color sel #ef6e76ff
+> color sel #ef6975ff
+> color sel #ef6976ff
+> color sel #ef6a72ff
+> color sel #ef6b73ff
+> color sel #ef6b75ff
+> color sel #ef6b79ff
+> color sel #ef6c7eff
+> color sel #ef6d82ff
+> color sel #ef6d85ff
+> color sel #ef6e86ff
+> color sel #ef6e89ff
+> color sel #ee6e89ff
+> color sel #ec6d88ff
+> color sel #ea6c86ff
+> color sel #e76b85ff
+> color sel #e56a83ff
+> select add #96
+atoms, 19277 bonds, 1234 residues, 1 model selected
+> select subtract #96
+Nothing selected
+> hide #96 models
+> show #66 models
+> log metadata #66
+The model has no metadata
+> log chains #66
+Chain information for AF-A0A7Y1H706-F1-model_v4.pdb #66
+---
+Chain | Description
+A | uncharacterized protein
+> sequence chain #66/A
+Alignment identifier is 66/A
+> matchmaker #66 to #9
+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 6ii6, chain A (#9) with AF-A0A7Y1H706-F1-model_v4.pdb, chain A
+(#66), sequence alignment score = 356.6
+RMSD between 101 pruned atom pairs is 1.011 angstroms; (across all 289 pairs:
+.691)
+> hide #66 models
+> show #70 models
+> log metadata #70
+The model has no metadata
+> log chains #70
+Chain information for MGYP000967698752.pdb #70
+---
+Chain | Description
+A | No description available
+> sequence chain #70/A
+Alignment identifier is 70/A
+> matchmaker #70 to #9
+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 6ii6, chain A (#9) with MGYP000967698752.pdb, chain A (#70),
+sequence alignment score = 390.3
+RMSD between 87 pruned atom pairs is 0.959 angstroms; (across all 261 pairs:
+.937)
+> hide #70 models
+> show #59 models
+> matchmaker #59 to #9
+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 6ii6, chain A (#9) with MGYP003580314631.pdb, chain A (#59),
+sequence alignment score = 308.2
+RMSD between 92 pruned atom pairs is 1.075 angstroms; (across all 214 pairs:
+.876)
+> hide #59 models
+> show #51 models
+> log metadata #51
+The model has no metadata
+> log chains #51
+Chain information for MGYP003392964057.pdb #51
+---
+Chain | Description
+A | No description available
+> matchmaker #51 to #9
+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 6ii6, chain A (#9) with MGYP003392964057.pdb, chain A (#51),
+sequence alignment score = 173.6
+RMSD between 63 pruned atom pairs is 1.174 angstroms; (across all 170 pairs:
+.258)
+> hide #51 models
+> show #49 models
+> matchmaker #49 to #9
+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 6ii6, chain A (#9) with MGYP003443402579.pdb, chain A (#49),
+sequence alignment score = 259.8
+RMSD between 93 pruned atom pairs is 1.207 angstroms; (across all 252 pairs:
+.060)
+> show #48 models
+> hide #49 models
+> matchmaker #48 to #9
+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 6ii6, chain A (#9) with MGYP003405926657.pdb, chain A (#48),
+sequence alignment score = 252.6
+RMSD between 94 pruned atom pairs is 0.977 angstroms; (across all 232 pairs:
+.888)
+> show #68 models
+> log metadata #68
+The model has no metadata
+> log chains #68
+Chain information for AF-A0A2R7TF17-F1-model_v4.pdb #68
+---
+Chain | Description
+A | uncharacterized protein
+> sequence chain #68/A
+Alignment identifier is 68/A
+> matchmaker #68 to #9
+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 6ii6, chain A (#9) with AF-A0A2R7TF17-F1-model_v4.pdb, chain A
+(#68), sequence alignment score = 322.1
+RMSD between 115 pruned atom pairs is 1.131 angstroms; (across all 311 pairs:
+.935)
+> hide #68 models
+> show #58 models
+> log metadata #58
+The model has no metadata
+> log chains #58
+Chain information for MGYP003469346235.pdb #58
+---
+Chain | Description
+A | No description available
+> matchmaker #58 to #9
+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 6ii6, chain A (#9) with MGYP003469346235.pdb, chain A (#58),
+sequence alignment score = 260
+RMSD between 112 pruned atom pairs is 0.911 angstroms; (across all 214 pairs:
+.268)
+> hide #48 models
+> hide #58 models
+> show #57 models
+> matchmaker #57 to #9
+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 6ii6, chain A (#9) with MGYP001106352814.pdb, chain A (#57),
+sequence alignment score = 257.4
+RMSD between 108 pruned atom pairs is 0.961 angstroms; (across all 204 pairs:
+.932)
+> hide #57 models
+> show #56 models
+> matchmaker #56 to #9
+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 6ii6, chain A (#9) with MGYP001094995491.pdb, chain A (#56),
+sequence alignment score = 219.4
+RMSD between 81 pruned atom pairs is 0.883 angstroms; (across all 176 pairs:
+.421)
+> show #76 models
+> hide #56 models
+> matchmaker #76 to #9
+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 6ii6, chain A (#9) with MGYP001011426704.pdb, chain A (#76),
+sequence alignment score = 250.7
+RMSD between 136 pruned atom pairs is 1.144 angstroms; (across all 235 pairs:
+.027)
+> log metadata #76
+The model has no metadata
+> log chains #76
+Chain information for MGYP001011426704.pdb #76
+---
+Chain | Description
+A | No description available
+> sequence chain #76/A
+Alignment identifier is 76/A
+> select #76/A:279
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #76/A
+atoms, 2185 bonds, 279 residues, 1 model selected
+> color sel purple
+> select subtract #76
+Nothing selected
+> hide #76 models
+> show #44 models
+> matchmaker #44 to #9
+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 6ii6, chain A (#9) with AF-A0A3A3FFL6-F1-model_v4.pdb, chain A
+(#44), sequence alignment score = 336.7
+RMSD between 120 pruned atom pairs is 1.136 angstroms; (across all 290 pairs:
+.449)
+> log metadata #44
+The model has no metadata
+> log chains #44
+Chain information for AF-A0A3A3FFL6-F1-model_v4.pdb #44
+---
+Chain | Description
+A | peptidase_C58 domain-containing protein
+> sequence chain #44/A
+Alignment identifier is 44/A
+> hide #44 models
+> show #92 models
+> log metadata #92
+The model has no metadata
+> log chains #92
+Chain information for B6XGD1.ranked_0.pdb #92
+---
+Chain | Description
+A | No description available
+> sequence chain #92/A
+Alignment identifier is 92/A
+> hide #92 models
+> show #97 models
+> log metadata #97
+The model has no metadata
+> log chains #97
+Chain information for A0A2X2DF79.ranked_0.pdb #97
+---
+Chain | Description
+A | No description available
+> sequence chain #97/A
+Alignment identifier is 97/A
+> hide #97 models
+> show #88 models
+> log metadata #88
+The model has no metadata
+> log chains #88
+Chain information for Mcf2.ranked_0.pdb #88
+---
+Chain | Description
+A | No description available
+> sequence chain #88/A
+Alignment identifier is 88/A
+> hide #88 models
+> show #!47 models
+> log metadata #47
+No models had metadata
+> log chains #47
+Chain information for 8p52 #47
+---
+Chain | Description | UniProt
+A | Toxin protein | Q8KT65_PHOLU 1-2929
+> matchmaker #47 to #9
+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 6ii6, chain A (#9) with 8p52, chain A (#47), sequence alignment
+score = 363.5
+RMSD between 115 pruned atom pairs is 1.082 angstroms; (across all 307 pairs:
+.407)
+> log metadata #47
+No models had metadata
+> log chains #47
+Chain information for 8p52 #47
+---
+Chain | Description | UniProt
+A | Toxin protein | Q8KT65_PHOLU 1-2929
+> sequence chain #47/A
+Alignment identifier is 47/A
+> select #47/A:968
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #47/A:968-970
+atoms, 19 bonds, 3 residues, 1 model selected
+> select #47/A:996
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #47/A:968-996
+atoms, 227 bonds, 29 residues, 1 model selected
+> view matrix models
+> #47,-0.74537,0.41033,-0.52541,120.04,-0.45766,0.25812,0.85084,-18.258,0.48474,0.87464,-0.0046032,-50.831
+> view matrix models
+> #47,-0.74537,0.41033,-0.52541,98.946,-0.45766,0.25812,0.85084,0.71671,0.48474,0.87464,-0.0046032,-115.16
+> select #47/A:1576-1577
+atoms, 16 bonds, 2 residues, 1 model selected
+> select #47/A:1576-1666
+atoms, 760 bonds, 91 residues, 1 model selected
+> select #47/A:1576
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #47/A:1575-1576
+atoms, 17 bonds, 2 residues, 1 model selected
+> select #47/A:1576-1603
+atoms, 224 bonds, 28 residues, 1 model selected
+> select #47/A:1599-1600
+atoms, 16 bonds, 2 residues, 1 model selected
+> select #47/A:1576-1600
+atoms, 199 bonds, 25 residues, 1 model selected
+> color sel #040e52ff
+> select #47/A:1909
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #47/A:1810-1909
+atoms, 692 bonds, 100 residues, 1 model selected
+> select #47/A:1809
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #47/A:1809-1909
+atoms, 696 bonds, 101 residues, 1 model selected
+> select #47/A:1810
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #47/A:1810-1907
+atoms, 680 bonds, 98 residues, 1 model selected
+> select #47/A:1810
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #47/A:1810-1908
+atoms, 684 bonds, 99 residues, 1 model selected
+> view matrix models
+> #47,-0.74537,0.41033,-0.52541,105.06,-0.45766,0.25812,0.85084,-12.022,0.48474,0.87464,-0.0046032,-149.14
+> color sel #040e52ff
+> select add #47
+atoms, 23225 bonds, 1 pseudobond, 2914 residues, 2 models selected
+> select subtract #47
+Nothing selected
+> select #47/A:2188-2189
+atoms, 14 bonds, 2 residues, 1 model selected
+> select #47/A:2188-2217
+atoms, 248 bonds, 30 residues, 1 model selected
+> select #47/A:2188-2189
+atoms, 14 bonds, 2 residues, 1 model selected
+> select #47/A:2188-2213
+atoms, 214 bonds, 26 residues, 1 model selected
+> select #47/A:2188-2189
+atoms, 14 bonds, 2 residues, 1 model selected
+> select #47/A:2188-2212
+atoms, 205 bonds, 25 residues, 1 model selected
+> color sel #040e52ff
+> select add #47
+atoms, 23225 bonds, 1 pseudobond, 2914 residues, 2 models selected
+> select subtract #47
+Nothing selected
+> matchmaker #47 to #9
+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 6ii6, chain A (#9) with 8p52, chain A (#47), sequence alignment
+score = 363.5
+RMSD between 115 pruned atom pairs is 1.082 angstroms; (across all 307 pairs:
+.407)
+> hide #!47 models
+> show #54 models
+> log metadata #54
+The model has no metadata
+> log chains #54
+Chain information for AF-A0A2X2DBV1-F1-model_v4.pdb #54
+---
+Chain | Description
+A | toxin B
+> sequence chain #54/A
+Alignment identifier is 54/A
+> matchmaker #54 to #9
+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 6ii6, chain A (#9) with AF-A0A2X2DBV1-F1-model_v4.pdb, chain A
+(#54), sequence alignment score = 359.9
+RMSD between 135 pruned atom pairs is 0.987 angstroms; (across all 298 pairs:
+.517)
+> hide #54 models
+> show #50 models
+> show #95 models
+> hide #50 models
+> log metadata #95
+The model has no metadata
+> log chains #95
+Chain information for MGYP000860465678.ranked_0.pdb #95
+---
+Chain | Description
+A | No description available
+> sequence chain #95/A
+Alignment identifier is 95/A
+> hide #95 models
+> show #53 models
+> log metadata #53
+The model has no metadata
+> log chains #53
+Chain information for AF-B6XGD5-F1-model_v4.pdb #53
+---
+Chain | Description | UniProt
+A | cysteine protease domain, yopt-type | B6XGD5_9GAMM 1-966
+> sequence chain #53/A
+Alignment identifier is 53/A
+> matchmaker #53 to #9
+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 6ii6, chain A (#9) with AF-B6XGD5-F1-model_v4.pdb, chain A (#53),
+sequence alignment score = 383.9
+RMSD between 114 pruned atom pairs is 0.934 angstroms; (across all 277 pairs:
+.206)
+> save "/Users/aho2840/Desktop/Satchell
+> Lab/MCFHomologs/MCF:Homolog.paper/Homologs.08.11.25.cxs"
+> hide #53 models
+> show #103 models
+> matchmaker #103 to #9
+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 6ii6, chain A (#9) with AF-Q7N439-F1-model_v4.pdb, chain A (#103),
+sequence alignment score = 91.8
+RMSD between 9 pruned atom pairs is 1.075 angstroms; (across all 201 pairs:
+.871)
+> hide #103 models
+> select add #53
+atoms, 7983 bonds, 966 residues, 1 model selected
+> select subtract #53
+Nothing selected
+> select add #9
+atoms, 2729 bonds, 917 residues, 1 model selected
+> color sel gray
+> color sel light gray
+> color sel dark gray
+> select subtract #9
+Nothing selected
+> color #9 #040e5200
+> color #9 #040e52cc
+> color #9 #c0c0c0ff
+> show #10 models
+> hide #10 models
+> show #32 models
+> hide #32 models
+> show #53 models
+> hide #53 models
+> show #103 models
+> lighting flat
+> graphics silhouettes false
+> graphics silhouettes true
+> lighting shadows true intensity 0.5
+> lighting shadows false
+> lighting shadows true
+> lighting shadows false
+> lighting flat
+> lighting shadows true intensity 0.5
+> lighting shadows false
+> lighting shadows true
+> lighting flat
+> graphics silhouettes false
+> graphics silhouettes true
+> lighting flat
+> lighting shadows true intensity 0.5
+> lighting shadows false
+> lighting shadows true
+> lighting flat
+> hide #103 models
+> show #103 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!7 models
+> hide #!7 models
+> show #6 models
+> hide #6 models
+> show #!9 models
+> undo
+> hide #!7 models
+> show #!9 models
+> hide #103 models
+> show #103 models
+> hide #103 models
+> show #103 models
+> hide #103 models
+> show #103 models
+> hide #103 models
+> show #103 models
+> hide #103 models
+> show #103 models
+> matchmaker #103 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 6ii0.cropped.06.25.23.pdb, chain B (#1) with
+AF-Q7N439-F1-model_v4.pdb, chain A (#103), sequence alignment score = 58.6
+RMSD between 24 pruned atom pairs is 1.518 angstroms; (across all 208 pairs:
+.755)
+> matchmaker #1 to #9
+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 6ii6, chain A (#9) with 6ii0.cropped.06.25.23.pdb, chain B (#1),
+sequence alignment score = 1498.3
+RMSD between 212 pruned atom pairs is 0.553 angstroms; (across all 223 pairs:
+.561)
+> matchmaker #103 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 6ii0.cropped.06.25.23.pdb, chain B (#1) with
+AF-Q7N439-F1-model_v4.pdb, chain A (#103), sequence alignment score = 58.6
+RMSD between 24 pruned atom pairs is 1.518 angstroms; (across all 208 pairs:
+.755)
+> hide #!9 models
+> show #!9 models
+> hide #103 models
+> show #103 models
+> hide #103 models
+> show #103 models
+> hide #103 models
+> hide #!9 models
+> show #1 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #1 models
+> show #103 models
+> hide #103 models
+> show #103 models
+> select add #9
+atoms, 2729 bonds, 917 residues, 1 model selected
+> color sel #c0c0c0ff
+> color sel #c0c0c0fb
+> color sel #c0c0c0f8
+> color sel #c0c0c0f6
+> color sel #c0c0c0f4
+> color sel #c0c0c0f3
+> color sel #c0c0c0eb
+> color sel #c0c0c0ea
+> color sel #c0c0c0e3
+> color sel #c0c0c0df
+> color sel #c0c0c0dc
+> color sel #c0c0c0db
+> color sel #c0c0c0d7
+> color sel #c0c0c0d4
+> color sel #c0c0c0d1
+> color sel #c0c0c0d0
+> color sel #c0c0c0ce
+> color sel #c0c0c0c6
+> color sel #c0c0c0be
+> color sel #c0c0c0cc
+> color sel #c0c0c0db
+> color sel #c0c0c0da
+> color sel #c0c0c0d7
+> color sel #c0c0c0d4
+> color sel #c0c0c0d2
+> color sel #c0c0c0d1
+> color sel #c0c0c0cf
+> color sel #c0c0c0cd
+> color sel #c0c0c0cc
+> select subtract #9
+Nothing selected
+> select add #9
+atoms, 2729 bonds, 917 residues, 1 model selected
+> color sel #c0c0c0cb
+> color sel #c0c0c0b5
+> color sel #c0c0c0a8
+> color sel #c0c0c0a7
+> color sel #c0c0c0a6
+> color sel #c0c0c0a3
+> color sel #c0c0c0a4
+> color sel #c0c0c0a5
+> color sel #c0c0c0a6
+> select subtract #9
+Nothing selected
+> select add #9
+atoms, 2729 bonds, 917 residues, 1 model selected
+> color sel #c0c0c0a5
+> color sel #c0c0c090
+> color sel #c0c0c08e
+> color sel #c0c0c089
+> color sel #c0c0c087
+> color sel #c0c0c086
+> color sel #c0c0c084
+> color sel #c0c0c083
+> color sel #c0c0c082
+> color sel #c0c0c081
+> color sel #c0c0c080
+> select subtract #9
+Nothing selected
+> select add #9
+atoms, 2729 bonds, 917 residues, 1 model selected
+> color sel #c0c0c07f
+> color sel #c0c0c06d
+> color sel #c0c0c066
+> color sel #c0c0c064
+> color sel #c0c0c062
+> color sel #c0c0c05f
+> color sel #c0c0c05e
+> color sel #c0c0c05b
+> color sel #c0c0c05a
+> color sel #c0c0c056
+> color sel #c0c0c052
+> color sel #c0c0c04a
+> color sel #c0c0c03b
+> color sel #c0c0c03e
+> color sel #c0c0c043
+> color sel #c0c0c048
+> color sel #c0c0c04b
+> color sel #c0c0c04e
+> color sel #c0c0c050
+> color sel #c0c0c051
+> color sel #c0c0c052
+> color sel #c0c0c053
+> color sel #c0c0c052
+> color sel #c0c0c050
+> color sel #c0c0c04f
+> color sel #c0c0c04e
+> color sel #c0c0c04c
+> color sel #c0c0c04d
+> select subtract #9
+Nothing selected
+> select add #103
+atoms, 2518 bonds, 313 residues, 1 model selected
+> hide #!9 models
+> select subtract #103
+Nothing selected
+> select add #103
+atoms, 2518 bonds, 313 residues, 1 model selected
+> select subtract #103
+Nothing selected
+> hide #103 models
+> show #!9 models
+> color #9 #c0c0c04c
+> color #9 #c0c0c04a
+> color #9 #c0c0c044
+> color #9 #c0c0c03d
+> color #9 #c0c0c03a
+> color #9 #c0c0c032
+> color #9 #c0c0c02e
+> color #9 #c0c0c02c
+> color #9 #c0c0c02a
+> color #9 #c0c0c026
+> color #9 #c0c0c023
+> color #9 #c0c0c022
+> color #9 #c0c0c021
+> color #9 #c0c0c022
+> color #9 #c0c0c024
+> color #9 #c0c0c026
+> show #103 models
+> hide #103 models
+> hide #!9 models
+> show #!9 models
+> select add #9
+atoms, 2729 bonds, 917 residues, 1 model selected
+> show sel surfaces
+> hide sel surfaces
+> select subtract #9
+model selected
+> show #103 models
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #103 models
+> select add #9
+atoms, 2729 bonds, 917 residues, 1 model selected
+> color (#!9 & sel) #c0c0c027
+> color (#!9 & sel) #c0c0c029
+> color (#!9 & sel) #c0c0c02e
+> color (#!9 & sel) #c0c0c034
+> color (#!9 & sel) #c0c0c038
+> color (#!9 & sel) #c0c0c03c
+> color (#!9 & sel) #c0c0c04c
+> color (#!9 & sel) #c0c0c055
+> color (#!9 & sel) #c0c0c058
+> color (#!9 & sel) #c0c0c05a
+> color (#!9 & sel) #c0c0c063
+> color (#!9 & sel) #c0c0c067
+> color (#!9 & sel) #c0c0c074
+> color (#!9 & sel) #c0c0c07d
+> color (#!9 & sel) #c0c0c07f
+> color (#!9 & sel) #c0c0c080
+> color (#!9 & sel) #c0c0c081
+> color (#!9 & sel) #c0c0c084
+> color (#!9 & sel) #c0c0c086
+> color (#!9 & sel) #c0c0c085
+> color (#!9 & sel) #c0c0c080
+> select subtract #9
+model selected
+> show #103 models
+> save /Users/aho2840/Desktop/image2.png supersample 3
+> hide #103 models
+> show #89 models
+> save /Users/aho2840/Desktop/image2.png supersample 3
+> hide #89 models
+> show #77 models
+> hide #77 models
+> show #75 models
+> save /Users/aho2840/Desktop/image2.png supersample 3
+> hide #75 models
+> show #38 models
+> save /Users/aho2840/Desktop/image2.png supersample 3
+> hide #38 models
+> show #43 models
+> save /Users/aho2840/Desktop/image2.png supersample 3
+> hide #43 models
+> show #17 models
+> save /Users/aho2840/Desktop/image2.png supersample 3
+> hide #17 models
+> show #68 models
+> save /Users/aho2840/Desktop/image2.png supersample 3
+> hide #68 models
+> show #65 models
+> save /Users/aho2840/Desktop/image2.png supersample 3
+> matchmaker #65 to #9
+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 6ii6, chain A (#9) with AF-A0A2T4FGD4-F1-model_v4.pdb, chain A
+(#65), sequence alignment score = 328.4
+RMSD between 116 pruned atom pairs is 0.971 angstroms; (across all 291 pairs:
+.697)
+> turn x 180
+> turn y 180
+> save /Users/aho2840/Desktop/image2.png supersample 3
+> turn y 180
+> hide #65 models
+> show #54 models
+> matchmaker #54 to #9
+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 6ii6, chain A (#9) with AF-A0A2X2DBV1-F1-model_v4.pdb, chain A
+(#54), sequence alignment score = 359.9
+RMSD between 135 pruned atom pairs is 0.987 angstroms; (across all 298 pairs:
+.517)
+> save /Users/aho2840/Desktop/image2.png supersample 3
+> hide #54 models
+> show #97 models
+> matchmaker #97 to #9
+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 6ii6, chain A (#9) with A0A2X2DF79.ranked_0.pdb, chain A (#97),
+sequence alignment score = 398.6
+RMSD between 127 pruned atom pairs is 1.100 angstroms; (across all 305 pairs:
+.055)
+> save /Users/aho2840/Desktop/image2.png supersample 3
+> hide #97 models
+> show #39 models
+> matchmaker #39 to #9
+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 6ii6, chain A (#9) with AF-A0A2X3JAL5-F1-model_v4.pdb, chain A
+(#39), sequence alignment score = 1054.4
+RMSD between 315 pruned atom pairs is 0.673 angstroms; (across all 343 pairs:
+.660)
+> save /Users/aho2840/Desktop/image2.png supersample 3
+> hide #39 models
+> show #40 models
+> matchmaker #40 to #9
+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 6ii6, chain A (#9) with AF-A0A376U9H5-F1-model_v4.pdb, chain A
+(#40), sequence alignment score = 1050.8
+RMSD between 316 pruned atom pairs is 0.697 angstroms; (across all 343 pairs:
+.132)
+> save /Users/aho2840/Desktop/image2.png supersample 3
+> hide #40 models
+> show #44 models
+> matchmaker #404to #9
+Missing or invalid "matchAtoms" argument: only initial part "#404" of atom
+specifier valid
+> matchmaker #44to #9
+Missing or invalid "matchAtoms" argument: only initial part "#44" of atom
+specifier valid
+> save /Users/aho2840/Desktop/image2.png supersample 3
+> hide #44 models
+> show #41 models
+> matchmaker #41 to #9
+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 6ii6, chain A (#9) with AF-A0A3W5Y7A7-F1-model_v4.pdb, chain A
+(#41), sequence alignment score = 930.7
+RMSD between 280 pruned atom pairs is 0.685 angstroms; (across all 298 pairs:
+.326)
+> save /Users/aho2840/Desktop/image2.png supersample 3
+> hide #41 models
+> show #18 models
+> matchmaker #18 to #9
+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 6ii6, chain A (#9) with AF-A0A4P2SM79-F1-model_v4.pdb, chain A
+(#18), sequence alignment score = 204.4
+RMSD between 54 pruned atom pairs is 1.295 angstroms; (across all 314 pairs:
+.398)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> log metadata #18
+The model has no metadata
+> log chains #18
+Chain information for AF-A0A4P2SM79-F1-model_v4.pdb #18
+---
+Chain | Description
+A | peptidase_C58 domain-containing protein
+> sequence chain #18/A
+Alignment identifier is 18/A
+> ui mousemode right select
+Drag select of 589 residues
+> select #18/A:407-463
+atoms, 449 bonds, 57 residues, 1 model selected
+> select #18/A:1-463
+atoms, 3958 bonds, 463 residues, 1 model selected
+> ui tool show Matchmaker
+> matchmaker #18 & sel to #9
+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 6ii6, chain A (#9) with AF-A0A4P2SM79-F1-model_v4.pdb, chain A
+(#18), sequence alignment score = 175
+RMSD between 51 pruned atom pairs is 0.849 angstroms; (across all 283 pairs:
+.132)
+> select add #18
+atoms, 6589 bonds, 774 residues, 1 model selected
+> select subtract #18
+Nothing selected
+> select clear
+> ui mousemode right "translate selected models"
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #18 models
+> show #91 models
+> matchmaker #91 to #9
+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 6ii6, chain A (#9) with A0A4P2SNJ1.longerNterm.ranked_0.pdb, chain
+A (#91), sequence alignment score = 180.1
+RMSD between 57 pruned atom pairs is 0.921 angstroms; (across all 231 pairs:
+.738)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #91 models
+> show #20 models
+> matchmaker #20 to #9
+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 6ii6, chain A (#9) with AF-A0A4V0NNP3-F1-model_v4.pdb, chain A
+(#20), sequence alignment score = 167.5
+RMSD between 54 pruned atom pairs is 0.979 angstroms; (across all 290 pairs:
+.128)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #20 models
+> show #21 models
+> matchmaker #21 to #9
+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 6ii6, chain A (#9) with AF-A0A4V0NNU7-F1-model_v4.pdb, chain A
+(#21), sequence alignment score = 208.3
+RMSD between 54 pruned atom pairs is 0.914 angstroms; (across all 285 pairs:
+.672)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #21 models
+> show #64 models
+> matchmaker #64 to #9
+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 6ii6, chain A (#9) with AF-A0A656YJH9-F1-model_v4 (1).pdb, chain A
+(#64), sequence alignment score = 367.2
+RMSD between 108 pruned atom pairs is 1.011 angstroms; (across all 303 pairs:
+.242)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> matchmaker #35 to #9
+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 6ii6, chain A (#9) with AF-A0A7U6JX76-F1-model_v4.pdb, chain A
+(#35), sequence alignment score = 1035.8
+RMSD between 314 pruned atom pairs is 0.728 angstroms; (across all 343 pairs:
+.052)
+> hide #64 models
+> show #35 models
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #35 models
+> show #62 models
+> matchmaker #62 to #9
+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 6ii6, chain A (#9) with AF-A0A7X1AT80-F1-model_v4.pdb, chain A
+(#62), sequence alignment score = 362.8
+RMSD between 133 pruned atom pairs is 1.005 angstroms; (across all 278 pairs:
+.096)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> turn y 180
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #62 models
+> show #66 models
+> turn y 180
+> matchmaker #66 to #9
+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 6ii6, chain A (#9) with AF-A0A7Y1H706-F1-model_v4.pdb, chain A
+(#66), sequence alignment score = 356.6
+RMSD between 101 pruned atom pairs is 1.011 angstroms; (across all 289 pairs:
+.691)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #66 models
+> show #63 models
+> matchmaker #63 to #9
+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 6ii6, chain A (#9) with AF-A0A7Z6MWD8-F1-model_v4.pdb, chain A
+(#63), sequence alignment score = 318.1
+RMSD between 109 pruned atom pairs is 1.021 angstroms; (across all 290 pairs:
+.681)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> turn y 180
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> turn y 180
+> hide #63 models
+> show #81 models
+> matchmaker #81 to #9
+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 6ii6, chain A (#9) with AF-A1JU65-F1-model_v4.pdb, chain A (#81),
+sequence alignment score = 167
+RMSD between 24 pruned atom pairs is 1.316 angstroms; (across all 252 pairs:
+.802)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #81 models
+> show #84 models
+> matchmaker #84 to #9
+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 6ii6, chain A (#9) with AF-C4ULG3-F1-model_v4.pdb, chain A (#84),
+sequence alignment score = 321.7
+RMSD between 101 pruned atom pairs is 1.004 angstroms; (across all 280 pairs:
+.316)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #84 models
+> show #102 models
+> matchmaker #102 to #9
+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 6ii6, chain A (#9) with AF-Q52430-F1-model_v4.pdb, chain A (#102),
+sequence alignment score = 75
+RMSD between 16 pruned atom pairs is 0.930 angstroms; (across all 200 pairs:
+.752)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #102 models
+> show #92 models
+> matchmaker #92 to #9
+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 6ii6, chain A (#9) with B6XGD1.ranked_0.pdb, chain A (#92),
+sequence alignment score = 401.5
+RMSD between 133 pruned atom pairs is 1.062 angstroms; (across all 317 pairs:
+.801)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #92 models
+> show #53 models
+> matchmaker #53 to #9
+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 6ii6, chain A (#9) with AF-B6XGD5-F1-model_v4.pdb, chain A (#53),
+sequence alignment score = 383.9
+RMSD between 114 pruned atom pairs is 0.934 angstroms; (across all 277 pairs:
+.206)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #53 models
+> show #23 models
+> matchmaker #23 to #9
+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 6ii6, chain A (#9) with AF-C4K3P9-F1-model_v4.pdb, chain A (#23),
+sequence alignment score = 183.4
+RMSD between 61 pruned atom pairs is 1.222 angstroms; (across all 303 pairs:
+.576)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> ui mousemode right select
+Drag select of 351 residues
+> ui tool show Matchmaker
+> matchmaker #23 & sel to #9
+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 6ii6, chain A (#9) with AF-C4K3P9-F1-model_v4.pdb, chain A (#23),
+sequence alignment score = 165.1
+RMSD between 53 pruned atom pairs is 0.972 angstroms; (across all 279 pairs:
+.183)
+> matchmaker #23 & sel to #9
+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 6ii6, chain A (#9) with AF-C4K3P9-F1-model_v4.pdb, chain A (#23),
+sequence alignment score = 165.1
+RMSD between 53 pruned atom pairs is 0.972 angstroms; (across all 279 pairs:
+.183)
+> select add #23
+atoms, 10025 bonds, 1196 residues, 1 model selected
+> select subtract #23
+Nothing selected
+> select clear
+> ui mousemode right "translate selected models"
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #23 models
+> show #24 models
+> matchmaker #24 to #9
+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 6ii6, chain A (#9) with AF-C4K468-F1-model_v4.pdb, chain A (#24),
+sequence alignment score = 183.8
+RMSD between 56 pruned atom pairs is 1.189 angstroms; (across all 304 pairs:
+.130)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> ui mousemode right select
+Drag select of 271 residues
+> ui tool show Matchmaker
+> matchmaker #24 & sel to #9
+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 6ii6, chain A (#9) with AF-C4K468-F1-model_v4.pdb, chain A (#24),
+sequence alignment score = 171.6
+RMSD between 45 pruned atom pairs is 1.057 angstroms; (across all 234 pairs:
+.465)
+> matchmaker #24 & sel to #9
+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 6ii6, chain A (#9) with AF-C4K468-F1-model_v4.pdb, chain A (#24),
+sequence alignment score = 171.6
+RMSD between 45 pruned atom pairs is 1.057 angstroms; (across all 234 pairs:
+.465)
+> select add #24
+atoms, 6889 bonds, 818 residues, 1 model selected
+> select subtract #24
+Nothing selected
+> select clear
+> ui mousemode right "translate selected models"
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #24 models
+> show #93 models
+> matchmaker #93 to #9
+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 6ii6, chain A (#9) with C4K5K2.ranked_0.pdb, chain A (#93),
+sequence alignment score = 190.5
+RMSD between 59 pruned atom pairs is 1.280 angstroms; (across all 299 pairs:
+.592)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> ui mousemode right select
+Drag select of 333 residues
+> ui tool show Matchmaker
+> matchmaker #93 & sel to #9
+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 6ii6, chain A (#9) with C4K5K2.ranked_0.pdb, chain A (#93),
+sequence alignment score = 186.6
+RMSD between 49 pruned atom pairs is 0.723 angstroms; (across all 252 pairs:
+.651)
+> matchmaker #93 & sel to #9
+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 6ii6, chain A (#9) with C4K5K2.ranked_0.pdb, chain A (#93),
+sequence alignment score = 186.6
+RMSD between 49 pruned atom pairs is 0.723 angstroms; (across all 252 pairs:
+.651)
+> select add #93
+atoms, 31675 bonds, 1960 residues, 1 model selected
+> select subtract #93
+Nothing selected
+> select clear
+> ui mousemode right "translate selected models"
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #93 models
+> show #25 models
+> matchmaker #25 to #9
+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 6ii6, chain A (#9) with AF-C4K5L0-F1-model_v4.pdb, chain A (#25),
+sequence alignment score = 202.4
+RMSD between 71 pruned atom pairs is 0.846 angstroms; (across all 300 pairs:
+.095)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #25 models
+> show #!94 models
+> matchmaker #94 to #9
+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 6ii6, chain A (#9) with GMGC10.017_810_714.ranked_0.pdb, chain A
+(#94), sequence alignment score = 196.4
+RMSD between 49 pruned atom pairs is 0.960 angstroms; (across all 284 pairs:
+.428)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> ui mousemode right select
+Drag select of 609 residues
+> ui tool show Matchmaker
+> matchmaker #!94 & sel to #9
+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 6ii6, chain A (#9) with GMGC10.017_810_714.ranked_0.pdb, chain A
+(#94), sequence alignment score = 167.3
+RMSD between 47 pruned atom pairs is 1.286 angstroms; (across all 245 pairs:
+.473)
+> select add #94
+atoms, 34892 bonds, 2223 residues, 2 models selected
+> select subtract #94
+model selected
+> select clear
+> ui mousemode right "translate selected models"
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> turn y 180
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> turn y 180
+> hide #!94 models
+> show #!47 models
+> matchmaker #47 to #9
+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 6ii6, chain A (#9) with 8p52, chain A (#47), sequence alignment
+score = 363.5
+RMSD between 115 pruned atom pairs is 1.082 angstroms; (across all 307 pairs:
+.407)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #!47 models
+> show #88 models
+> matchmaker #88 to #9
+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 6ii6, chain A (#9) with Mcf2.ranked_0.pdb, chain A (#88), sequence
+alignment score = 405.2
+RMSD between 128 pruned atom pairs is 0.972 angstroms; (across all 303 pairs:
+.736)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #88 models
+> show #52 models
+> matchmaker #52 to #9
+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 6ii6, chain A (#9) with MGYP000706081912.pdb, chain A (#52),
+sequence alignment score = 226.2
+RMSD between 57 pruned atom pairs is 0.989 angstroms; (across all 293 pairs:
+.191)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #52 models
+> show #95 models
+> matchmaker #95 to #9
+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 6ii6, chain A (#9) with MGYP000860465678.ranked_0.pdb, chain A
+(#95), sequence alignment score = 382.4
+RMSD between 134 pruned atom pairs is 1.003 angstroms; (across all 296 pairs:
+.540)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #95 models
+> show #70 models
+> matchmaker #70 to #9
+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 6ii6, chain A (#9) with MGYP000967698752.pdb, chain A (#70),
+sequence alignment score = 390.3
+RMSD between 87 pruned atom pairs is 0.959 angstroms; (across all 261 pairs:
+.937)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #70 models
+> show #76 models
+> matchmaker #76 to #9
+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 6ii6, chain A (#9) with MGYP001011426704.pdb, chain A (#76),
+sequence alignment score = 250.7
+RMSD between 136 pruned atom pairs is 1.144 angstroms; (across all 235 pairs:
+.027)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #76 models
+> show #56 models
+> matchmaker #56 to #9
+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 6ii6, chain A (#9) with MGYP001094995491.pdb, chain A (#56),
+sequence alignment score = 219.4
+RMSD between 81 pruned atom pairs is 0.883 angstroms; (across all 176 pairs:
+.421)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #56 models
+> show #57 models
+> matchmaker #57 to #9
+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 6ii6, chain A (#9) with MGYP001106352814.pdb, chain A (#57),
+sequence alignment score = 257.4
+RMSD between 108 pruned atom pairs is 0.961 angstroms; (across all 204 pairs:
+.932)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #57 models
+> show #74 models
+> matchmaker #74 to #9
+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 6ii6, chain A (#9) with MGYP001564015939.pdb, chain A (#74),
+sequence alignment score = 205.5
+RMSD between 86 pruned atom pairs is 1.408 angstroms; (across all 190 pairs:
+.441)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #74 models
+> show #51 models
+> matchmaker #51 to #9
+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 6ii6, chain A (#9) with MGYP003392964057.pdb, chain A (#51),
+sequence alignment score = 173.6
+RMSD between 63 pruned atom pairs is 1.174 angstroms; (across all 170 pairs:
+.258)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #51 models
+> show #48 models
+> matchmaker #48 to #9
+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 6ii6, chain A (#9) with MGYP003405926657.pdb, chain A (#48),
+sequence alignment score = 252.6
+RMSD between 94 pruned atom pairs is 0.977 angstroms; (across all 232 pairs:
+.888)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #48 models
+> show #49 models
+> matchmaker #49 to #9
+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 6ii6, chain A (#9) with MGYP003443402579.pdb, chain A (#49),
+sequence alignment score = 259.8
+RMSD between 93 pruned atom pairs is 1.207 angstroms; (across all 252 pairs:
+.060)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #49 models
+> show #58 models
+> matchmaker #58 to #9
+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 6ii6, chain A (#9) with MGYP003469346235.pdb, chain A (#58),
+sequence alignment score = 260
+RMSD between 112 pruned atom pairs is 0.911 angstroms; (across all 214 pairs:
+.268)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #58 models
+> show #59 models
+> matchmaker #59 to #9
+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 6ii6, chain A (#9) with MGYP003580314631.pdb, chain A (#59),
+sequence alignment score = 308.2
+RMSD between 92 pruned atom pairs is 1.075 angstroms; (across all 214 pairs:
+.876)
+> hide #59 models
+> show #58 models
+> hide #58 models
+> show #59 models
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #59 models
+> show #96 models
+> matchmaker #96 to #9
+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 6ii6, chain A (#9) with MGYP003605169772.ranked_0.pdb, chain A
+(#96), sequence alignment score = 378.7
+RMSD between 133 pruned atom pairs is 1.066 angstroms; (across all 289 pairs:
+.432)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> turn y 180
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #96 models
+> show #60 models
+> matchmaker #60 to #9
+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 6ii6, chain A (#9) with MGYP003607098654.pdb, chain A (#60),
+sequence alignment score = 252.9
+RMSD between 84 pruned atom pairs is 0.881 angstroms; (across all 209 pairs:
+.498)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #60 models
+> show #61 models
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> matchmaker #61 to #9
+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 6ii6, chain A (#9) with MGYP003613210660.pdb, chain A (#61),
+sequence alignment score = 251.9
+RMSD between 96 pruned atom pairs is 1.039 angstroms; (across all 196 pairs:
+.185)
+> save /Users/aho2840/Desktop/image2.png supersample 3
+> hide #61 models
+> show #73 models
+> matchmaker #73 to #9
+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 6ii6, chain A (#9) with AF-P55730-F1-model_v4.pdb, chain A (#73),
+sequence alignment score = 72.4
+RMSD between 25 pruned atom pairs is 0.955 angstroms; (across all 190 pairs:
+.079)
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #73 models
+> show #109 models
+> matchmaker #109 to #9
+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 6ii6, chain A (#9) with C7BKP9.ranked_0.pdb, chain A (#109),
+sequence alignment score = 292.3
+RMSD between 75 pruned atom pairs is 1.064 angstroms; (across all 284 pairs:
+.403)
+> turn y 180
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #109 models
+> show #71 models
+> matchmaker #71 to #9
+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 6ii6, chain A (#9) with AF-Q327D9-F1-model_v4.pdb, chain A (#71),
+sequence alignment score = 132.8
+RMSD between 7 pruned atom pairs is 0.829 angstroms; (across all 185 pairs:
+.982)
+> ui mousemode right select
+Drag select of 210 residues
+> ui tool show Matchmaker
+> matchmaker #71 & sel to #9
+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 6ii6, chain A (#9) with AF-Q327D9-F1-model_v4.pdb, chain A (#71),
+sequence alignment score = 89.5
+RMSD between 26 pruned atom pairs is 1.053 angstroms; (across all 175 pairs:
+.568)
+> select add #71
+atoms, 4400 bonds, 549 residues, 1 model selected
+> select subtract #71
+Nothing selected
+> select clear
+> ui mousemode right zoom
+> ui mousemode right "translate selected models"
+> save /Users/aho2840/Desktop/image1.png supersample 3
+> hide #71 models
+> show #72 models
+> matchmaker #72 to #9
+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 6ii6, chain A (#9) with AF-Q327I5-F1-model_v4.pdb, chain A (#72),
+sequence alignment score = 126.1
+RMSD between 10 pruned atom pairs is 1.365 angstroms; (across all 189 pairs:
+.434)
+> ui mousemode right select
+Drag select of 377 residues
+> ui tool show Matchmaker
+> matchmaker #72 & sel to #9
+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 6ii6, chain A (#9) with AF-Q327I5-F1-model_v4.pdb, chain A (#72),
+sequence alignment score = 49.7
+RMSD between 5 pruned atom pairs is 1.045 angstroms; (across all 46 pairs:
+.497)
+Drag select of 193 residues
+> ui tool show Matchmaker
+> matchmaker #72 & sel to #9
+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 6ii6, chain A (#9) with AF-Q327I5-F1-model_v4.pdb, chain A (#72),
+sequence alignment score = 44.7
+RMSD between 15 pruned atom pairs is 1.296 angstroms; (across all 168 pairs:
+.337)
+*** Deleted thousands of lines to make the description small enough for Trac. TomG
 > matchmaker #72 & sel to #9